BLM helicase facilitates telomere replication during leading strand synthesis of telomeres

Abstract: Based on its in vitro unwinding activity on G-quadruplex (G4) DNA, the Bloom syndrome-associated helicase BLM is proposed to participate in telomere replication by aiding fork progression through G-rich telomeric DNA.

Abstract: Single molecule analysis of replicated DNA (SMARD) was used to determine the contribution of BLM helicase to telomere replication.

Abstract: In BLM-deficient cells, replication forks initiating from origins within the telomere, which copy the G-rich strand by leading strand synthesis, moved slower through the telomere compared with the adjacent subtelomere.

Abstract: Fork progression through the telomere was further slowed in the presence of a G4 stabilizer.

Abstract: Using a G4-specific antibody, we found that deficiency of BLM, or another G4-unwinding helicase, the Werner syndrome-associated helicase WRN, resulted in increased G4 structures in cells.

Abstract: Importantly, deficiency of either helicase led to greater increases in G4 DNA detected in the telomere compared with G4 seen genome-wide.

Abstract: Collectively, our findings are consistent with BLM helicase facilitating telomere replication by resolving G4 structures formed during copying of the G-rich strand by leading strand synthesis.


Reflecting on 25 years with MYC

Abstract: Just over 25 years ago, MYC, the human homologue of a retroviral oncogene, was identified.

Abstract: Since that time, MYC research has been intense and the advances impressive.

Abstract: On reflection, it is astonishing how each incremental insight into MYC regulation and function has also had an impact on numerous biological disciplines, including our understanding of molecular oncogenesis in general.

Abstract: Here we chronicle the major advances in our understanding of MYC biology, and peer into the future of MYC research.


Protective effects of exercise and phosphoinositide 3-kinase(p110alpha) signaling in dilated and hypertrophic cardiomyopathy.

Abstract: Physical activity protects against cardiovascular disease, and physiological cardiac hypertrophy associated with regular exercise is usually beneficial, in marked contrast to pathological hypertrophy associated with disease.

Abstract: The p110alpha isoform of phosphoinositide 3-kinase (PI3K) plays a critical role in the induction of exercise-induced hypertrophy.

Abstract: Whether it or other genes activated in the athlete's heart might have an impact on cardiac function and survival in a setting of heart failure is unknown.

Abstract: To examine whether progressive exercise training and PI3K(p110alpha) activity affect survival and/or cardiac function in two models of heart disease, we subjected a transgenic mouse model of dilated cardiomyopathy (DCM) to swim training, genetically crossed cardiac-specific transgenic mice with increased or decreased PI3K(p110alpha) activity to the DCM model, and subjected PI3K(p110alpha) transgenics to acute pressure overload (ascending aortic constriction).

Abstract: Life-span, cardiac function, and molecular markers of pathological hypertrophy were examined.

Abstract: Exercise training and increased cardiac PI3K(p110alpha) activity prolonged survival in the DCM model by 15-20%.

Abstract: In contrast, reduced PI3K(p110alpha) activity drastically shortened lifespan by approximately 50%.

Abstract: Increased PI3K(p110alpha) activity had a favorable effect on cardiac function and fibrosis in the pressure-overload model and attenuated pathological growth.

Abstract: PI3K(p110alpha) signaling negatively regulated G protein-coupled receptor stimulated extracellular responsive kinase and Akt (via PI3K, p110gamma) activation in isolated cardiomyocytes.

Abstract: These findings suggest that exercise and enhanced PI3K(p110alpha) activity delay or prevent progression of heart disease, and that supraphysiologic activity can be beneficial.

Abstract: Identification of genes important for hypertrophy in the athlete's heart could offer new strategies for treating heart failure.


The effect of cigarette smoking, alcohol consumption and fruit and vegetable consumption on IVF outcomes: a review and presentation of original data

Abstract: BACKGROUND Lifestyle factors including cigarette smoking, alcohol consumption and nutritional habits impact on health, wellness, and the risk of chronic diseases.

Abstract: In the areas of in-vitro fertilization (IVF) and pregnancy, lifestyle factors influence oocyte production, fertilization rates, pregnancy and pregnancy loss, while chronic, low-grade oxidative stress may underlie poor outcomes for some IVF cases.

Abstract: METHODS Here, we review the current literature and present some original, previously unpublished data, obtained from couples attending the PIVET Medical Centre in Western Australia.

Abstract: RESULTS During the study, 80 % of females and 70 % of male partners completed a 1-week diary documenting their smoking, alcohol and fruit and vegetable intake.

Abstract: The subsequent clinical outcomes of their IVF treatment such as quantity of oocytes collected, fertilization rates, pregnancy and pregnancy loss were submitted to multiple regression analysis, in order to investigate the relationship between patients, treatment and the recorded lifestyle factors.

Abstract: Of significance, it was found that male smoking caused an increased risk of pregnancy loss (p = 0.029), while female smoking caused an adverse effect on ovarian reserve.

Abstract: Both alcohol consumption (β = 0.074, p < 0.001) and fruit and vegetable consumption (β = 0.034, p < 0.001) had positive effects on fertilization.

Abstract: CONCLUSION Based on our results and the current literature, there is an important impact of lifestyle factors on IVF clinical outcomes.

Abstract: Currently, there are conflicting results regarding other lifestyle factors such as nutritional habits and alcohol consumption, but it is apparent that chronic oxidative stress induced by lifestyle factors and poor nutritional habits associate with a lower rate of IVF success.


Efficient Mitochondrial Genome Editing by CRISPR/Cas9

Abstract: The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has been widely used for nuclear DNA editing to generate mutations or correct specific disease alleles.

Abstract: Despite its flexible application, it has not been determined if CRISPR/Cas9, originally identified as a bacterial defense system against virus, can be targeted to mitochondria for mtDNA editing.

Abstract: Here, we show that regular FLAG-Cas9 can localize to mitochondria to edit mitochondrial DNA with sgRNAs targeting specific loci of the mitochondrial genome.

Abstract: Expression of FLAG-Cas9 together with gRNA targeting Cox1 and Cox3 leads to cleavage of the specific mtDNA loci.

Abstract: In addition, we observed disruption of mitochondrial protein homeostasis following mtDNA truncation or cleavage by CRISPR/Cas9.

Abstract: To overcome nonspecific distribution of FLAG-Cas9, we also created a mitochondria-targeted Cas9 (mitoCas9).

Abstract: This new version of Cas9 localizes only to mitochondria; together with expression of gRNA targeting mtDNA, there is specific cleavage of mtDNA.

Abstract: MitoCas9-induced reduction of mtDNA and its transcription leads to mitochondrial membrane potential disruption and cell growth inhibition.

Abstract: This mitoCas9 could be applied to edit mtDNA together with gRNA expression vectors without affecting genomic DNA.

Abstract: In this brief study, we demonstrate that mtDNA editing is possible using CRISPR/Cas9.

Abstract: Moreover, our development of mitoCas9 with specific localization to the mitochondria should facilitate its application for mitochondrial genome editing.


Histone Variant H2A.Z Marks the 5′ Ends of Both Active and Inactive Genes in Euchromatin

Abstract: In S. cerevisiae, histone variant H2A.Z is deposited in euchromatin at the flanks of silent heterochromatin to prevent its ectopic spread.

Abstract: We show that H2A.Z nucleosomes are found at promoter regions of nearly all genes in euchromatin.

Abstract: They generally occur as two positioned nucleosomes that flank a nucleosome-free region (NFR) that contains the transcription start site.

Abstract: Astonishingly, enrichment at 5' ends is observed not only at actively transcribed genes but also at inactive loci.

Abstract: Mutagenesis of a typical promoter revealed a 22 bp segment of DNA sufficient to program formation of a NFR flanked by two H2A.Z nucleosomes.

Abstract: This segment contains a binding site of the Myb-related protein Reb1 and an adjacent dT:dA tract.

Abstract: Efficient deposition of H2A.Z is further promoted by a specific pattern of histone H3 and H4 tail acetylation and the bromodomain protein Bdf1, a component of the Swr1 remodeling complex that deposits H2A.Z.


Exercise and respiratory training improve exercise capacity and quality of life in patients with severe chronic pulmonary hypertension.

Abstract: BACKGROUND Pulmonary hypertension (PH) is associated with restricted physical capacity, limited quality of life, and a poor prognosis because of right heart failure.

Abstract: The present study is the first prospective randomized study to evaluate the effects of exercise and respiratory training in patients with severe symptomatic PH.

Abstract: METHODS AND RESULTS Thirty patients with PH (21 women; mean age, 50+/-13 years; mean pulmonary artery pressure, 50+/-15 mm Hg; mean World Health Organization [WHO] class, 2.9+/-0.5; pulmonary arterial hypertension, n=23; chronic thromboembolic PH, n=7) on stable disease-targeted medication were randomly assigned to a control (n=15) and a primary training (n=15) group.

Abstract: Medication remained unchanged during the study period.

Abstract: Primary end points were the changes from baseline to week 15 in the distance walked in 6 minutes and in scores of the Short Form Health Survey quality-of-life questionnaire.

Abstract: Changes in WHO functional class, Borg scale, and parameters of echocardiography and gas exchange also were assessed.

Abstract: At week 15, patients in the primary and secondary training groups had an improved 6-minute walking distance; the mean difference between the control and the primary training group was 111 m (95% confidence interval, 65 to 139 m; P<0.001).

Abstract: Exercise training was well tolerated and improved scores of quality of life, WHO functional class, peak oxygen consumption, oxygen consumption at the anaerobic threshold, and achieved workload.

Abstract: Systolic pulmonary artery pressure values at rest did not change significantly after 15 weeks of exercise and respiratory training (from 61+/-18 to 54+/-18 mm Hg) within the training group.

Abstract: CONCLUSIONS This study indicates that respiratory and physical training could be a promising adjunct to medical treatment in severe PH.

Abstract: The effects add to the beneficial results of modern medical treatment.


HIV-1 regulation of latency in the monocyte-macrophage lineage and in CD4+ T lymphocytes.

Abstract: The introduction in 1996 of the HAART raised hopes for the eradication of HIV-1.

Abstract: Unfortunately, the discovery of latent HIV-1 reservoirs in CD4+ T cells and in the monocyte-macrophage lineage proved the optimism to be premature.

Abstract: The long-lived HIV-1 reservoirs constitute a major obstacle to the eradication of HIV-1.

Abstract: In this review, we focus on the establishment and maintenance of HIV-1 latency in the two major targets for HIV-1: the CD4+ T cells and the monocyte-macrophage lineage.

Abstract: Understanding the cell-type molecular mechanisms of establishment, maintenance, and reactivation of HIV-1 latency in these reservoirs is crucial for efficient therapeutic intervention.

Abstract: A complete viral eradication, the holy graal for clinicians, might be achieved by strategic interventions targeting latently and productively infected cells.

Abstract: We suggest that new approaches, such as the combination of different kinds of proviral activators, may help to reduce dramatically the size of latent HIV-1 reservoirs in patients on HAART.


Effects of Electro-Acupuncture Therapy on Post-Stroke Depression in Patients with Different Degrees of Motor Function Impairments: a Pilot Study

Abstract: [Purpose] The present study examined whether electro-acupuncture therapy reduces post-stroke depression (PSD) and whether motor function impairments interact with the effects of the therapy.

Abstract: [Subjects] Twenty-eight PSD patients were assessed and assigned to either a good or poor motor function group depending on their motor grade.

Abstract: [Methods] The Beck Depression Inventory (BDI), Hamilton Depression Rating Scale (HDRS) and Manual Muscle Test (MMT) were administered at the screening and initial phases of the study, and at the 4th, 8th, 12th and 16th week of the daily electro-acupuncture treatment.

Abstract: [Results] The electro-acupuncture treatment reduced PSD (as assessed by BDI and HDRS) of the patients.

Abstract: In particular, the depression of the good motor function group was significantly more reduced than that of the poor motor function group.

Abstract: The degree of motor function impairment did not change throughout the study in either group.

Abstract: [Conclusion] The results of the present study demonstrate that electro-acupuncture therapy can improve PSD, and that the treatment effect varies depending on the degree of motor function impairment.


T cell receptor ligation induces the formation of dynamically regulated signaling assemblies

Abstract: Tcell antigen receptor (TCR) ligation initiates tyrosine kinase activation, signaling complex assembly, and immune synapse formation.

Abstract: Here, we studied the kinetics and mechanics of signaling complex formation in live Jurkat leukemic T cells using signaling proteins fluorescently tagged with variants of enhanced GFP (EGFP).

Abstract: Within seconds of contacting coverslips coated with stimulatory antibodies, T cells developed small, dynamically regulated clusters which were enriched in the TCR, phosphotyrosine, ZAP-70, LAT, Grb2, Gads, and SLP-76, excluded the lipid raft marker enhanced yellow fluorescent protein–GPI, and were competent to induce calcium elevations.

Abstract: LAT, Grb2, and Gads were transiently associated with the TCR.

Abstract: Although ZAP-70–containing clusters persisted for more than 20 min, photobleaching studies revealed that ZAP-70 continuously dissociated from and returned to these complexes.

Abstract: Strikingly, SLP-76 translocated to a perinuclear structure after clustering with the TCR.

Abstract: Our results emphasize the dynamically changing composition of signaling complexes and indicate that these complexes can form within seconds of TCR engagement, in the absence of either lipid raft aggregation or the formation of a central TCR-rich cluster.


Developmental heterogeneity of cardiac fibroblasts does not predict pathological proliferation and activation.

Abstract: RATIONALE Fibrosis is mediated partly by extracellular matrix-depositing fibroblasts in the heart.

Abstract: Although these mesenchymal cells are reported to have multiple embryonic origins, the functional consequence of this heterogeneity is unknown.

Abstract: OBJECTIVE We sought to validate a panel of surface markers to prospectively identify cardiac fibroblasts.

Abstract: We elucidated the developmental origins of cardiac fibroblasts and characterized their corresponding phenotypes.

Abstract: We also determined proliferation rates of each developmental subset of fibroblasts after pressure overload injury.

Abstract: METHODS AND RESULTS We showed that Thy1(+)CD45(-)CD31(-)CD11b(-)Ter119(-) cells constitute the majority of cardiac fibroblasts.

Abstract: We characterized these cells using flow cytometry, epifluorescence and confocal microscopy, and transcriptional profiling (using reverse transcription polymerase chain reaction and RNA-seq).

Abstract: We used lineage tracing, transplantation studies, and parabiosis to show that most adult cardiac fibroblasts derive from the epicardium, a minority arises from endothelial cells, and a small fraction from Pax3-expressing cells.

Abstract: We did not detect generation of cardiac fibroblasts by bone marrow or circulating cells.

Abstract: Interestingly, proliferation rates of fibroblast subsets on injury were identical, and the relative abundance of each lineage remained the same after injury.

Abstract: The anatomic distribution of fibroblast lineages also remained unchanged after pressure overload.

Abstract: Furthermore, RNA-seq analysis demonstrated that Tie2-derived and Tbx18-derived fibroblasts within each operation group exhibit similar gene expression profiles.

Abstract: CONCLUSIONS The cellular expansion of cardiac fibroblasts after transaortic constriction surgery was not restricted to any single developmental subset.

Abstract: The parallel proliferation and activation of a heterogeneous population of fibroblasts on pressure overload could suggest that common signaling mechanisms stimulate their pathological response.


Pre-eclampsia: connecting angiogenic and metabolic pathways.

Abstract: Pre-eclampsia is a hypertensive disease of pregnancy with a worldwide incidence of 5-8%.

Abstract: This review focuses on recent developments in pre-eclampsia research related to angiogenesis and metabolism.

Abstract: We first address the 'angiogenic imbalance' theory, which hypothesizes that pre-eclampsia results from an imbalance of factors that promote or antagonize angiogenesis, such as soluble fms-like tyrosine kinase (sFlt1), 2-methoxyestradiol (2-ME) and catechol-O-methyltransferase (COMT).

Abstract: Next, we analyze the association between pre-eclampsia and dysfunctional metabolism of both homocysteine and placental glycogen.

Abstract: We hope that illuminating some of the various connections existing between angiogenesis and metabolism in pre-eclampsia will facilitate the update or reconsideration of old models of pathogenesis.


Protein Lysine Acetylated/Deacetylated Enzymes and the Metabolism-Related Diseases

Abstract: Lysine acetylation is a reversible posttranslational modifcation, an epigenetic phenomenon, referred to as transfer of an acetyl group from acetyl CoA to lysine e- amino group of targeted protein, which is modulated by acetyltransferases (histone/ lysine (K) acetyltransferases, HATs/KATs) and deacetylases (histone/lysine (K) deacetylases, HDACs/KDACs).

Abstract: Lysine acetylation regulates various metabolic processes, such as fatty acid oxidation, Krebs cycle, oxidative phosphorylation, angiogenesis and so on.

Abstract: Thus disorders of lysine acetylation may be correlated with obesity, diabetes and cardiovascular disease, which are termed as the metabolic complication.

Abstract: With accumulating studies on proteomic acetylation, lysine acetylation also involves in cell immune status and degenerative diseases, for example, Alzheimer’s disease and Huntington’s disease.

Abstract: This review primarily summarizes the current studies of lysine acetylation in metabolism modulation and in metabolism-related diseases, such as cardiovascular disease and fat metabolism disorder.


Differential Specificity of Endocrine FGF19 and FGF21 to FGFR1 and FGFR4 in Complex with KLB

Abstract: BACKGROUND Recent studies suggest that betaKlotho (KLB) and endocrine FGF19 and FGF21 redirect FGFR signaling to regulation of metabolic homeostasis and suppression of obesity and diabetes.

Abstract: However, the identity of the predominant metabolic tissue in which a major FGFR-KLB resides that critically mediates the differential actions and metabolism effects of FGF19 and FGF21 remain unclear.

Abstract: METHODOLOGY/PRINCIPAL FINDINGS We determined the receptor and tissue specificity of FGF21 in comparison to FGF19 by using direct, sensitive and quantitative binding kinetics, and downstream signal transduction and expression of early response gene upon administration of FGF19 and FGF21 in mice.

Abstract: We found that FGF21 binds FGFR1 with much higher affinity than FGFR4 in presence of KLB; while FGF19 binds both FGFR1 and FGFR4 in presence of KLB with comparable affinity.

Abstract: The interaction of FGF21 with FGFR4-KLB is very weak even at high concentration and could be negligible at physiological concentration.

Abstract: Both FGF19 and FGF21 but not FGF1 exhibit binding affinity to KLB.

Abstract: The binding of FGF1 is dependent on where FGFRs are present.

Abstract: Both FGF19 and FGF21 are unable to displace the FGF1 binding, and conversely FGF1 cannot displace FGF19 and FGF21 binding.

Abstract: These results indicate that KLB is an indispensable mediator for the binding of FGF19 and FGF21 to FGFRs that is not required for FGF1.

Abstract: Although FGF19 can predominantly activate the responses of the liver and to a less extent the adipose tissue, FGF21 can do so significantly only in the adipose tissue and adipocytes.

Abstract: Among several metabolic and endocrine tissues, the response of adipose tissue to FGF21 is predominant, and can be blunted by the ablation of KLB or FGFR1.

Abstract: CONCLUSIONS Our results indicate that unlike FGF19, FGF21 is unable to bind FGFR4-KLB complex with affinity comparable to FGFR1-KLB, and therefore, at physiological concentration less likely to directly and significantly target the liver where FGFR4-KLB predominantly resides.

Abstract: However, both FGF21 and FGF19 have the potential to activate responses of primarily the adipose tissue where FGFR1-KLB resides.


Therapeutic efficacy of a multi-epitope vaccine against Helicobacter pylori infection in BALB/c mice model.

Abstract: Epitope vaccine is a promising option for therapeutic vaccination against Helicobacter pylori (H. pylori) infection.

Abstract: In this study, we constructed a multi-epitope vaccine with five epitopes and mucosal adjuvant E. coli heat-labile enterotoxin B subunit (LTB) named HUepi-LTB and evaluated its therapeutic effect against H. pylori infection in BALB/c mice model.

Abstract: HUepi-LTB containing three Th epitopes from UreB and two B cell epitopes from UreB and HpaA was constructed and expressed in E. coli.

Abstract: Oral therapeutic immunization with HUepi-LTB significantly decreased H. pylori colonization compared with oral immunization with PBS, and the protection was correlated with antigen-specific CD4+ T cells and IgG and mucosal IgA antibody responses.

Abstract: This multi-epitope vaccine may be a promising vaccine candidate that may help to control H. pylori infection.


DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells.

Abstract: Increased levels of DNA fragments have frequently been found in the blood plasma of cancer patients.

Abstract: Published data suggest that only a fraction of the DNA in blood plasma is derived from cancer cells.

Abstract: However, it is not known how much of the circulating DNA is from cancer or from noncancer cells.

Abstract: By quantitative methylation-specific PCR of the promoter region of the CDKN2A tumor suppressor gene, we were able to quantify the fraction of plasma DNA derived from tumor cells.

Abstract: In the plasma samples of 30 unselected cancer patients, we detected quantities of tumor DNA from only 3% to as much as 93% of total circulating DNA.

Abstract: We investigated possible origins of nontumor DNA in the plasma and demonstrate here a contribution of T-cell DNA in a few cases only.

Abstract: To investigate the possibility that plasma DNA originates from apoptotic or necrotic cells, we performed studies with apoptotic (staurosporine) and necrotic (staurosporine plus oligomycin) cells in vitro and with mice after induction of apoptotic (anti-CD95) or necrotic (acetaminophen) liver injury.

Abstract: Increasing amounts of DNA were found to be released in the supernatants of cells and in the blood plasma samples of treated animals.

Abstract: A clear discrimination of apoptotic and necrotic plasma DNA was possible by gel electrophoresis.

Abstract: The same characteristic patterns of DNA fragments could be identified in plasma derived from different cancer patients.

Abstract: The data are consistent with the possibility that apoptotic and necrotic cells are a major source for plasma DNA in cancer patients.


Pharmacodynamics and pharmacokinetics of eptifibatide in patients with acute coronary syndromes: prospective analysis from PURSUIT.

Abstract: BACKGROUND Platelet deposition and aggregation are central to the pathogenesis of ischemic complications of acute coronary syndromes (ACS).

Abstract: Pharmacodynamic effects of the platelet glycoprotein IIb/IIIa antagonist eptifibatide have been delineated in healthy subjects but not in patients with ACS.

Abstract: We assessed effects of eptifibatide on ex vivo platelet aggregation in patients enrolled in the Platelet glycoprotein IIb/IIIa in Unstable angina: Receptor Suppression Using Integrilin (eptifibatide) Therapy (PURSUIT) trial of ACS.

Abstract: METHODS AND RESULTS Patients were randomly assigned to an intravenous bolus (180 microgram/kg) and 72-hour infusion of eptifibatide (2.0 microgram/kg per minute, n=48) or placebo (n=50).

Abstract: We assessed correlations of plasma eptifibatide levels with receptor occupancy and inhibition of ex vivo platelet aggregation at 5 minutes and 1, 4, 24, 48, and 72 hours during treatment and 4 and 8 hours after termination of infusion.

Abstract: Blood was collected in buffered citrate and D-phenylalanyl-L-prolyl-L-arginine chloromethylketone anticoagulants.

Abstract: Although eptifibatide produced profound, prolonged inhibition of platelet aggregation during therapy, aggregation appeared to recover partially by 4 hours after the bolus.

Abstract: The aggregation response was greater with thrombin receptor agonist peptide versus ADP stimulation; inhibition of platelet aggregation was greater in blood samples anticoagulated with citrate versus D-phenylalanyl-L-prolyl-L-arginine chloromethylketone (PPACK).

Abstract: Plasma eptifibatide levels correlated significantly with receptor occupancy but not with inhibition of platelet aggregation.

Abstract: CONCLUSIONS A bolus and infusion of eptifibatide inhibits platelet aggregation profoundly in patients with ACS and is followed by brief, partial recovery.

Abstract: These results enhance our understanding of the relation between pharmacodynamic and clinical effects of eptifibatide in such patients and may have important implications for its use in percutaneous interventions.


Proinflammatory cytokines underlying the inflammation of Crohn's disease.

Abstract: PURPOSE OF REVIEW To encapsulate our current understanding of the proinflammatory cytokines responsible for the inflammation underlying Crohn's disease and the prospect of using this information to devise therapy for this condition based on inhibition of these cytokines.

Abstract: RECENT FINDINGS Current research is shedding new light on the role of both T helper cell (Th)1 and Th17 responses in the pathogenesis of Crohn's disease.

Abstract: Initial studies conducted a decade ago highlighted the view that Crohn's disease inflammation is caused by an interleukin-12-driven Th1 response, which resulted in the generation of interferon-gamma, which then served as the main inflammatory mediator.

Abstract: In recent years, however, this view has been largely eclipsed by studies, conducted mainly in murine models, showing that a Th17 response is the main cause of Crohn's disease inflammation through the production of interleukin-17.

Abstract: Now, a somewhat more balanced view is emerging, which holds that interferon-gamma is still a major proinflammatory cytokine in Crohn's disease, although it may arise from both the Th1 and Th17-mediated responses at different phases of the inflammatory process.

Abstract: SUMMARY The new findings continue to support the idea that anti-interleukin-12p40, an antibody that inhibits both the Th1 and Th17 response, is logically the most potent anticytokine for the treatment of Crohn's disease.


STATISTICAL METHODS FOR ASSESSING AGREEMENT BETWEEN TWO METHODS OF CLINICAL MEASUREMENT

Abstract: In clinical measurement comparison of a new measurement technique with an established one is often needed to see whether they agree sufficiently for the new to replace the old.

Abstract: Such investigations are often analysed inappropriately, notably by using correlation coefficients.

Abstract: The use of correlation is misleading.

Abstract: An alternative approach, based on graphical techniques and simple calculations, is described, together with the relation between this analysis and the assessment of repeatability.


The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism

Abstract: Expression of particular drug transporters in response to antibiotic pressure is a critical element in the development of bacterial multidrug resistance, and represents a serious concern for human health.

Abstract: To obtain a better understanding of underlying regulatory mechanisms, we have dissected the transcriptional activation of the ATP-binding cassette (ABC) transporter BmrC/BmrD of the Gram-positive model bacterium Bacillus subtilis.

Abstract: By using promoter-GFP fusions and live cell array technology, we demonstrate a temporally controlled transcriptional activation of the bmrCD genes in response to antibiotics that target protein synthesis.

Abstract: Intriguingly, bmrCD expression only occurs during the late-exponential and stationary growth stages, irrespective of the timing of the antibiotic challenge.

Abstract: We show that this is due to tight transcriptional control by the transition state regulator AbrB. Moreover, our results show that the bmrCD genes are co-transcribed with bmrB (yheJ), a small open reading frame immediately upstream of bmrC that harbors three alternative stem-loop structures.

Abstract: These stem-loops are apparently crucial for antibiotic-induced bmrCD transcription.

Abstract: Importantly, the antibiotic-induced bmrCD expression requires translation of bmrB, which implies that BmrB serves as a regulatory leader peptide.

Abstract: Altogether, we demonstrate for the first time that a ribosome-mediated transcriptional attenuation mechanism can control the expression of a multidrug ABC transporter.


The neural crest is a source of mesenchymal stem cells with specialized hematopoietic stem cell niche function

Abstract: Mesenchymal stem cells (MSCs) and osteolineage cells contribute to the hematopoietic stem cell (HSC) niche in the bone marrow of long bones.

Abstract: However, their developmental relationships remain unclear.

Abstract: In this study, we demonstrate that different MSC populations in the developing marrow of long bones have distinct functions.

Abstract: Proliferative mesoderm-derived nestin(-) MSCs participate in fetal skeletogenesis and lose MSC activity soon after birth.

Abstract: In contrast, quiescent neural crest-derived nestin(+) cells preserve MSC activity, but do not generate fetal chondrocytes.

Abstract: Instead, they differentiate into HSC niche-forming MSCs, helping to establish the HSC niche by secreting Cxcl12.

Abstract: Perineural migration of these cells to the bone marrow requires the ErbB3 receptor.

Abstract: The neonatal Nestin-GFP(+) Pdgfrα(-) cell population also contains Schwann cell precursors, but does not comprise mature Schwann cells.

Abstract: Thus, in the developing bone marrow HSC niche-forming MSCs share a common origin with sympathetic peripheral neurons and glial cells, and ontogenically distinct MSCs have non-overlapping functions in endochondrogenesis and HSC niche formation.


Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

Abstract: Induced pluripotent stem cells (iPSCs) offer immense potential for regenerative medicine and studies of disease and development.

Abstract: Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells.

Abstract: However, it remains unknown how complete the reestablishment of ES-cell-like DNA methylation patterns is throughout the genome.

Abstract: Here we report the first whole-genome profiles of DNA methylation at single-base resolution in five human iPSC lines, along with methylomes of ES cells, somatic cells, and differentiated iPSCs and ES cells.

Abstract: iPSCs show significant reprogramming variability, including somatic memory and aberrant reprogramming of DNA methylation.

Abstract: iPSCs share megabase-scale differentially methylated regions proximal to centromeres and telomeres that display incomplete reprogramming of non-CG methylation, and differences in CG methylation and histone modifications.

Abstract: Lastly, differentiation of iPSCs into trophoblast cells revealed that errors in reprogramming CG methylation are transmitted at a high frequency, providing an iPSC reprogramming signature that is maintained after differentiation.


Inheritance of coronary artery disease in men: an analysis of the role of the Y chromosome

Abstract: BACKGROUND A sexual dimorphism exists in the incidence and prevalence of coronary artery disease--men are more commonly affected than are age-matched women.

Abstract: We explored the role of the Y chromosome in coronary artery disease in the context of this sexual inequity.

Abstract: METHODS We genotyped 11 markers of the male-specific region of the Y chromosome in 3233 biologically unrelated British men from three cohorts: the British Heart Foundation Family Heart Study (BHF-FHS), West of Scotland Coronary Prevention Study (WOSCOPS), and Cardiogenics Study.

Abstract: On the basis of this information, each Y chromosome was tracked back into one of 13 ancient lineages defined as haplogroups.

Abstract: We then examined associations between common Y chromosome haplogroups and the risk of coronary artery disease in cross-sectional BHF-FHS and prospective WOSCOPS.

Abstract: Finally, we undertook functional analysis of Y chromosome effects on monocyte and macrophage transcriptome in British men from the Cardiogenics Study.

Abstract: FINDINGS Of nine haplogroups identified, two (R1b1b2 and I) accounted for roughly 90% of the Y chromosome variants among British men.

Abstract: Carriers of haplogroup I had about a 50% higher age-adjusted risk of coronary artery disease than did men with other Y chromosome lineages in BHF-FHS (odds ratio 1·75, 95% CI 1·20-2·54, p=0·004), WOSCOPS (1·45, 1·08-1·95, p=0·012), and joint analysis of both populations (1·56, 1·24-1·97, p=0·0002).

Abstract: The association between haplogroup I and increased risk of coronary artery disease was independent of traditional cardiovascular and socioeconomic risk factors.

Abstract: Analysis of macrophage transcriptome in the Cardiogenics Study revealed that 19 molecular pathways showing strong differential expression between men with haplogroup I and other lineages of the Y chromosome were interconnected by common genes related to inflammation and immunity, and that some of them have a strong relevance to atherosclerosis.

Abstract: INTERPRETATION The human Y chromosome is associated with risk of coronary artery disease in men of European ancestry, possibly through interactions of immunity and inflammation.

Abstract: FUNDING British Heart Foundation; UK National Institute for Health Research; LEW Carty Charitable Fund; National Health and Medical Research Council of Australia; European Union 6th Framework Programme; Wellcome Trust.


Cytoscape 2.8: new features for data integration and network visualization

Abstract: UNLABELLED Cytoscape is a popular bioinformatics package for biological network visualization and data integration.

Abstract: Version 2.8 introduces two powerful new features--Custom Node Graphics and Attribute Equations--which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities.

Abstract: Custom Node Graphics allow an image to be projected onto a node, including images generated dynamically or at remote locations.

Abstract: Attribute Equations provide Cytoscape with spreadsheet-like functionality in which the value of an attribute is computed dynamically as a function of other attributes and network properties.

Abstract: AVAILABILITY AND IMPLEMENTATION Cytoscape is a desktop Java application released under the Library Gnu Public License (LGPL).

Abstract: Binary install bundles and source code for Cytoscape 2.8 are available for download from http://cytoscape.org.


Detection of Histone Modifications at Specific Gene Loci in Single Cells in Histological Sections

Abstract: Chromatin immunoprecipitation assays have contributed greatly to our understanding of the role of histone modifications in gene regulation.

Abstract: However, they do not permit analysis with single-cell resolution, thus confounding analyses of heterogeneous cell populations.

Abstract: Here we present a method that permits visualization of histone modifications of single genomic loci with single-cell resolution in formaldehyde-fixed paraffin-embedded tissue sections based on combined use of in situ hybridization and proximity ligation assays.

Abstract: We show that dimethylation of lysine 4 of histone H3 (H3K4me2) at the MYH11 locus is restricted to the smooth muscle cell (SMC) lineage in human and mouse tissue sections and that the mark persists even in phenotypically modulated SMC in atherosclerotic lesions that show no detectable expression of SMC marker genes.

Abstract: This methodology has promise for broad applications in the study of epigenetic mechanisms in complex multicellular tissues in development and disease.


Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions

Abstract: The wobble modification in tRNAs, 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U), is required for the proper decoding of NNR codons in eukaryotes.

Abstract: The 2-thio group confers conformational rigidity of mcm(5)s(2)U by largely fixing the C3'-endo ribose puckering, ensuring stable and accurate codon-anticodon pairing.

Abstract: We have identified five genes in Saccharomyces cerevisiae, YIL008w (URM1), YHR111w (UBA4), YOR251c (TUM1), YNL119w (NCS2) and YGL211w (NCS6), that are required for 2-thiolation of mcm(5)s(2)U. An in vitro sulfur transfer experiment revealed that Tum1p stimulated the cysteine desulfurase of Nfs1p, and accepted persulfide sulfurs from Nfs1p.

Abstract: URM1 is a ubiquitin-related modifier, and UBA4 is an E1-like enzyme involved in protein urmylation.

Abstract: The carboxy-terminus of Urm1p was activated as an acyl-adenylate (-COAMP), then thiocarboxylated (-COSH) by Uba4p.

Abstract: The activated thiocarboxylate can be utilized in the subsequent reactions for 2-thiouridine formation, mediated by Ncs2p/Ncs6p.

Abstract: We could successfully reconstitute the 2-thiouridine formation in vitro using recombinant proteins.

Abstract: This study revealed that 2-thiouridine formation shares a pathway and chemical reactions with protein urmylation.

Abstract: The sulfur-flow of eukaryotic 2-thiouridine formation is distinct mechanism from the bacterial sulfur-relay system which is based on the persulfide chemistry.


High prevalence of asthma in cross country skiers.

Abstract: OBJECTIVES To study the prevalence of asthma (asthma symptoms and bronchial hyperresponsiveness) in Swedish cross country skiers compared with non-skiers and monitor changes in symptoms and bronchial hyperresponsiveness during the year.

Abstract: DESIGN Cross sectional study during the winter ski season and in the summer.

Abstract: SETTING Six ski clubs for élite skiers (total 47) in two different areas of Sweden.

Abstract: SUBJECTS 42 élite cross country skiers and 29 non-skiing referents.

Abstract: MAIN OUTCOME MEASURES Bronchial responsiveness, asthma symptoms, and lung function.

Abstract: RESULTS Bronchial responsiveness was significantly greater and asthma symptoms more prevalent in the skiers than in the referents.

Abstract: There was no difference in bronchial responsiveness within either group between winter and summer.

Abstract: 15 of the 42 skiers used antiasthmatic drugs regularly and 23 had a combination of asthma symptoms and hyperresponsive airways or physician diagnosed asthma, or both.

Abstract: Altogether 33 skiers had symptoms of asthma or bronchial hyperresponsiveness.

Abstract: One of the referents had symptoms of asthma and bronchial hyperresponsiveness, and none used antiasthmatic drugs regularly.

Abstract: CONCLUSIONS Asthma, asthma-like symptoms, and bronchial hyperresponsiveness are much more common in cross country skiers than in the general population and non-skiers.

Abstract: Strenuous exercise at low temperatures entailing breathing large volumes of cold air is the most probable explanation of persistent asthma in skiers.


Characterization of biochemical properties of Bacillus subtilis RecQ helicase.

Abstract: RecQ family helicases function as safeguards of the genome.

Abstract: Unlike Escherichia coli, the Gram-positive Bacillus subtilis bacterium possesses two RecQ-like homologues, RecQ[Bs] and RecS, which are required for the repair of DNA double-strand breaks.

Abstract: RecQ[Bs] also binds to the forked DNA to ensure a smooth progression of the cell cycle.

Abstract: Here we present the first biochemical analysis of recombinant RecQ[Bs].

Abstract: RecQ[Bs] binds weakly to single-stranded DNA (ssDNA) and blunt-ended double-stranded DNA (dsDNA) but strongly to forked dsDNA.

Abstract: The protein exhibits a DNA-stimulated ATPase activity and ATP- and Mg(2+)-dependent DNA helicase activity with a 3' → 5' polarity.

Abstract: Molecular modeling shows that RecQ[Bs] shares high sequence and structure similarity with E. coli RecQ. Surprisingly, RecQ[Bs] resembles the truncated Saccharomyces cerevisiae Sgs1 and human RecQ helicases more than RecQ[Ec] with regard to its enzymatic activities.

Abstract: Specifically, RecQ[Bs] unwinds forked dsDNA and DNA duplexes with a 3'-overhang but is inactive on blunt-ended dsDNA and 5'-overhung duplexes.

Abstract: Interestingly, RecQ[Bs] unwinds blunt-ended DNA with structural features, including nicks, gaps, 5'-flaps, Kappa joints, synthetic replication forks, and Holliday junctions.

Abstract: We discuss these findings in the context of RecQ[Bs]'s possible functions in preserving genomic stability.


SOD1 Integrates Signals from Oxygen and Glucose to Repress Respiration

Abstract: Cu/Zn superoxide dismutase (SOD1) is an abundant enzyme that has been best studied as a regulator of antioxidant defense.

Abstract: Using the yeast Saccharomyces cerevisiae, we report that SOD1 transmits signals from oxygen and glucose to repress respiration.

Abstract: The mechanism involves SOD1-mediated stabilization of two casein kinase 1-gamma (CK1γ) homologs, Yck1p and Yck2p, required for respiratory repression.

Abstract: SOD1 binds a C-terminal degron we identified in Yck1p/Yck2p and promotes kinase stability by catalyzing superoxide conversion to peroxide.

Abstract: The effects of SOD1 on CK1γ stability are also observed with mammalian SOD1 and CK1γ and in a human cell line.

Abstract: Therefore, in a single circuit, oxygen, glucose, and reactive oxygen can repress respiration through SOD1/CK1γ signaling.

Abstract: Our data therefore may provide mechanistic insight into how rapidly proliferating cells and many cancers accomplish glucose-mediated repression of respiration in favor of aerobic glycolysis.


The prognostic impact of the platelet distribution width-to-platelet count ratio in patients with breast cancer

Abstract: Activated platelets promote tumor cell growth, angiogenesis, and invasion.

Abstract: Platelet activity can be inferred by platelet volume indices (PVIs), which include platelet distribution width (PDW), mean platelet volume (MPV), platelet distribution width-to-platelet count ratio (PDW/P), and mean platelet volume-to-platelet count ratio.

Abstract: Platelets and platelet-related markers, such as the platelet-to-lymphocyte ratio, have been found to be significant prognostic factors in patients with breast cancer.

Abstract: However, the role of PVIs for predicting survival in breast cancer remains unknown; hence, we performed this retrospective analysis of 275 patients with breast cancer.

Abstract: PVIs were compared with clinicopathological variables, and were assessed to identify independent indicators associated with disease-free survival (DFS) using the Cox proportional hazards model.

Abstract: An elevated PDW/P significantly correlated with age and HER2 status.

Abstract: Univariate analysis revealed that elevated PDW, MPV, and PDW/P as well as tumor size, nuclear grade, and lymph node involvement were significantly associated with inferior DFS rates (tumor size: p<0.01; nuclear grade, lymph node involvement, PDW, MPV, and PDW/P: p<0.05).

Abstract: On multivariate analysis, a large tumor size and elevated PDW/P were significant prognostic factors for DFS, with hazard ratios of 3.24 (95% confidence interval [CI]: 1.24-8.47) and 2.99 (95% CI: 1.18-7.57), respectively (p<0.05).

Abstract: Our study is the first to reveal that an elevated PDW/P significantly reduces DFS in patients with breast carcinoma.

Abstract: Measuring the PDW/P is simple, relatively inexpensive, and almost universally available using routine blood counts; this makes it an attractive biomarker for improved risk assessment.


Persistent LCMV infection is controlled by blockade of type I interferon signaling.

Abstract: During persistent viral infections, chronic immune activation, negative immune regulator expression, an elevated interferon signature, and lymphoid tissue destruction correlate with disease progression.

Abstract: We demonstrated that blockade of type I interferon (IFN-I) signaling using an IFN-I receptor neutralizing antibody reduced immune system activation, decreased expression of negative immune regulatory molecules, and restored lymphoid architecture in mice persistently infected with lymphocytic choriomeningitis virus.

Abstract: IFN-I blockade before and after establishment of persistent virus infection resulted in enhanced virus clearance and was CD4 T cell-dependent.

Abstract: Hence, we demonstrate a direct causal link between IFN-I signaling, immune activation, negative immune regulator expression, lymphoid tissue disorganization, and virus persistence.

Abstract: Our results suggest that therapies targeting IFN-I may help control persistent virus infections.


Lam6 Regulates the Extent of Contacts between Organelles

Abstract: Communication between organelles is crucial for eukaryotic cells to function as one coherent unit.

Abstract: An important means of communication is through membrane contact sites, where two organelles come into close proximity allowing the transport of lipids and small solutes between them.

Abstract: Contact sites are dynamic in size and can change in response to environmental or cellular stimuli; however, how this is regulated has been unclear.

Abstract: Here, we show that Saccharomyces cerevisiae Lam6 resides in several central contact sites: ERMES (ER/mitochondria encounter structure), vCLAMP (vacuole and mitochondria patch), and NVJ (nuclear vacuolar junction).

Abstract: We show that Lam6 is sufficient for expansion of contact sites under physiological conditions and necessary for coordination of contact site size.

Abstract: Given that Lam6 is part of a large protein family and is conserved in vertebrates, our work opens avenues for investigating the underlying principles of organelle communication.


Endocrine regulation of human fetal growth: the role of the mother, placenta, and fetus.

Abstract: The environment in which the fetus develops is critical for its survival and long-term health.

Abstract: The regulation of normal human fetal growth involves many multidirectional interactions between the mother, placenta, and fetus.

Abstract: The mother supplies nutrients and oxygen to the fetus via the placenta.

Abstract: The fetus influences the provision of maternal nutrients via the placental production of hormones that regulate maternal metabolism.

Abstract: The placenta is the site of exchange between mother and fetus and regulates fetal growth via the production and metabolism of growth-regulating hormones such as IGFs and glucocorticoids.

Abstract: Adequate trophoblast invasion in early pregnancy and increased uteroplacental blood flow ensure sufficient growth of the uterus, placenta, and fetus.

Abstract: The placenta may respond to fetal endocrine signals to increase transport of maternal nutrients by growth of the placenta, by activation of transport systems, and by production of placental hormones to influence maternal physiology and even behavior.

Abstract: There are consequences of poor fetal growth both in the short term and long term, in the form of increased mortality and morbidity.

Abstract: Endocrine regulation of fetal growth involves interactions between the mother, placenta, and fetus, and these effects may program long-term physiology.


Endothelial-to-mesenchymal transition contributes to cardiac fibrosis

Abstract: Cardiac fibrosis, associated with a decreased extent of microvasculature and with disruption of normal myocardial structures, results from excessive deposition of extracellular matrix, which is mediated by the recruitment of fibroblasts.

Abstract: The source of these fibroblasts is unclear and specific anti-fibrotic therapies are not currently available.

Abstract: Here we show that cardiac fibrosis is associated with the emergence of fibroblasts originating from endothelial cells, suggesting an endothelial-mesenchymal transition (EndMT) similar to events that occur during formation of the atrioventricular cushion in the embryonic heart.

Abstract: Transforming growth factor-β1 (TGF-β1) induced endothelial cells to undergo EndMT, whereas bone morphogenic protein 7 (BMP-7) preserved the endothelial phenotype.

Abstract: The systemic administration of recombinant human BMP-7 (rhBMP-7) significantly inhibited EndMT and the progression of cardiac fibrosis in mouse models of pressure overload and chronic allograft rejection.

Abstract: Our findings show that EndMT contributes to the progression of cardiac fibrosis and that rhBMP-7 can be used to inhibit EndMT and to intervene in the progression of chronic heart disease associated with fibrosis.


Coupled local translation and degradation regulate growth cone collapse

Abstract: Local translation mediates axonal responses to Semaphorin3A (Sema3A) and other guidance cues.

Abstract: However, only a subset of the axonal proteome is locally synthesized, whereas most proteins are trafficked from the soma.

Abstract: The reason why only specific proteins are locally synthesized is unknown.

Abstract: Here we show that local protein synthesis and degradation are linked events in growth cones.

Abstract: We find that growth cones exhibit high levels of ubiquitination and that local signalling pathways trigger the ubiquitination and degradation of RhoA, a mediator of Sema3A-induced growth cone collapse.

Abstract: Inhibition of RhoA degradation is sufficient to remove the protein-synthesis requirement for Sema3A-induced growth cone collapse.

Abstract: In addition to RhoA, we find that locally translated proteins are the main targets of the ubiquitin-proteasome system in growth cones.

Abstract: Thus, local protein degradation is a major feature of growth cones and creates a requirement for local translation to replenish proteins needed to maintain growth cone responses.


Cdk11 is a RanGTP-dependent microtubule stabilization factor that regulates spindle assembly rate

Abstract: Production of Ran-guanosine triphosphate (GTP) around chromosomes induces local nucleation and plus end stabilization of microtubules (MTs).

Abstract: The nuclear protein TPX2 is required for RanGTP-dependent MT nucleation.

Abstract: To find the MT stabilizer, we affinity purify nuclear localization signal (NLS)-containing proteins from Xenopus laevis egg extracts.

Abstract: This NLS protein fraction contains the MT stabilization activity.

Abstract: After further purification, we used mass spectrometry to identify proteins in active fractions, including cyclin-dependent kinase 11 (Cdk11).

Abstract: Cdk11 localizes on spindle poles and MTs in Xenopus culture cells and egg extracts.

Abstract: Recombinant Cdk11 demonstrates RanGTP-dependent MT stabilization activity, whereas a kinase-dead mutant does not.

Abstract: Inactivation of Cdk11 in egg extracts blocks RanGTP-dependent MT stabilization and dramatically decreases the spindle assembly rate.

Abstract: Simultaneous depletion of TPX2 completely inhibits centrosome-dependent spindle assembly.

Abstract: Our results indicate that Cdk11 is responsible for RanGTP-dependent MT stabilization around chromosomes and that this local stabilization is essential for normal rates of spindle assembly and spindle function.


Population dynamics of a pathogen: the conundrum of vivax malaria

Abstract: Building a mathematical model of population dynamics of pathogens within their host involves considerations of factors similar to those in ecology, as pathogens can prey on cells in the host.

Abstract: But within the multicellular host, attacked cell types are integrated with other cellular systems, which in turn intervene in the infection.

Abstract: For example, immune responses attempt to sense and then eliminate or contain pathogens, and homeostatic mechanisms try to compensate for cell loss.

Abstract: This review focuses on modeling applied to malarias, diseases caused by single-cell eukaryote parasites that infect red blood cells, with special concern given to vivax malaria, a disease often thought to be benign (if sometimes incapacitating) because the parasite only attacks a small proportion of red blood cells, the very youngest ones.

Abstract: However, I will use mathematical modeling to argue that depletion of this pool of red blood cells can be disastrous to the host if growth of the parasite is not vigorously check by host immune responses.

Abstract: Also, modeling can elucidate aspects of new field observations that indicate that vivax malaria is more dangerous than previously thought.

Abstract: ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12551-010-0034-3) contains supplementary material, which is available to authorized users.


Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes

Abstract: RNases P and MRP are ribonucleoprotein complexes involved in tRNA and rRNA processing, respectively.

Abstract: The RNA subunits of these two enzymes are structurally related to each other and play an essential role in the enzymatic reaction.

Abstract: Both of the RNAs have a highly conserved helical region, P4, which is important in the catalytic reaction.

Abstract: We have used a bioinformatics approach based on conserved elements to computationally analyze available genomic sequences of eukaryotic organisms and have identified a large number of novel nuclear RNase P and MRP RNA genes.

Abstract: For MRP RNA for instance, this investigation increases the number of known sequences by a factor of three.

Abstract: We present secondary structure models of many of the predicted RNAs.

Abstract: Although all sequences are able to fold into the consensus secondary structure of P and MRP RNAs, a striking variation in size is observed, ranging from a Nosema locustae MRP RNA of 160 nt to much larger RNAs, e.g. a Plasmodium knowlesi P RNA of 696 nt.

Abstract: The P and MRP RNA genes appear in tandem in some protists, further emphasizing the close evolutionary relationship of these RNAs.


Calcium absorption varies within the reference range for serum 25-hydroxyvitamin D.

Abstract: BACKGROUND Calcium absorption is generally considered to be impaired under conditions of vitamin D deficiency, but the vitamin D status that fully normalizes absorption is not known for humans.

Abstract: OBJECTIVE To quantify calcium absorption at two levels of vitamin D repletion, using pharmacokinetic methods and commercially marketed calcium supplements.

Abstract: DESIGN Two experiments performed in the spring of the year, one year apart.

Abstract: In the first, in which participants were pretreated with 25-hydroxyvitamin D (25OHD), mean serum 25OHD concentration was 86.5 nmol/L; and in the other, with no pretreatment, mean serum concentration was 50.2 nmol/L. Participants received 500 mg oral calcium loads as a part of a standard low calcium breakfast.

Abstract: A low calcium lunch was provided at mid-day.

Abstract: Blood was obtained fasting and at frequent intervals for 10 to 12 hours thereafter.

Abstract: METHODS Relative calcium absorption at the two 25OHD concentrations was estimated from the area under the curve (AUC) for the load-induced increment in serum total calcium.

Abstract: RESULTS AUC(9) (+/-

Abstract: SEM), was 3.63 mg hr/dL +/-

Abstract: 0.234 in participants pretreated with 25OHD and 2.20 +/-

Abstract: 0.240 in those not pretreated (P < 0.001).

Abstract: In brief, absorption was 65% higher at serum 25OHD levels averaging 86.5 nmol/L than at levels averaging 50 nmol/L (both values within the nominal reference range for this analyte).

Abstract: CONCLUSIONS Despite the fact that the mean serum 25OHD level in the experiment without supplementation was within the current reference ranges, calcium absorptive performance at 50 nmol/L was significantly reduced relative to that at a mean 25OHD level of 86 nmol/L. Thus, individuals with serum 25-hydroxyvitamin D levels at the low end of the current reference ranges may not be getting the full benefit from their calcium intake.

Abstract: We conclude that the lower end of the current reference range is set too low.


Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control

Abstract: Standard virulence evolution theory assumes that virulence factors are maintained because they aid parasitic exploitation, increasing growth within and/or transmission between hosts.

Abstract: An increasing number of studies now demonstrate that many opportunistic pathogens (OPs) do not conform to these assumptions, with virulence factors maintained instead because of advantages in non-parasitic contexts.

Abstract: Here we review virulence evolution theory in the context of OPs and highlight the importance of incorporating environments outside a focal virulence site.

Abstract: We illustrate that virulence selection is constrained by correlations between these external and focal settings and pinpoint drivers of key environmental correlations, with a focus on generalist strategies and phenotypic plasticity.

Abstract: We end with a summary of key theoretical and empirical challenges to be met for a fuller understanding of OPs.


Genome-Wide Profiling of H3K56 Acetylation and Transcription Factor Binding Sites in Human Adipocytes

Abstract: The growing epidemic of obesity and metabolic diseases calls for a better understanding of adipocyte biology.

Abstract: The regulation of transcription in adipocytes is particularly important, as it is a target for several therapeutic approaches.

Abstract: Transcriptional outcomes are influenced by both histone modifications and transcription factor binding.

Abstract: Although the epigenetic states and binding sites of several important transcription factors have been profiled in the mouse 3T3-L1 cell line, such data are lacking in human adipocytes.

Abstract: In this study, we identified H3K56 acetylation sites in human adipocytes derived from mesenchymal stem cells.

Abstract: H3K56 is acetylated by CBP and p300, and deacetylated by SIRT1, all are proteins with important roles in diabetes and insulin signaling.

Abstract: We found that while almost half of the genome shows signs of H3K56 acetylation, the highest level of H3K56 acetylation is associated with transcription factors and proteins in the adipokine signaling and Type II Diabetes pathways.

Abstract: In order to discover the transcription factors that recruit acetyltransferases and deacetylases to sites of H3K56 acetylation, we analyzed DNA sequences near H3K56 acetylated regions and found that the E2F recognition sequence was enriched.

Abstract: Using chromatin immunoprecipitation followed by high-throughput sequencing, we confirmed that genes bound by E2F4, as well as those by HSF-1 and C/EBPα, have higher than expected levels of H3K56 acetylation, and that the transcription factor binding sites and acetylation sites are often adjacent but rarely overlap.

Abstract: We also discovered a significant difference between bound targets of C/EBPα in 3T3-L1 and human adipocytes, highlighting the need to construct species-specific epigenetic and transcription factor binding site maps.

Abstract: This is the first genome-wide profile of H3K56 acetylation, E2F4, C/EBPα and HSF-1 binding in human adipocytes, and will serve as an important resource for better understanding adipocyte transcriptional regulation.


Detecting and characterizing circular RNAs

Abstract: Circular RNA transcripts were first identified in the early 1990s but knowledge of these species has remained limited, as their study through traditional methods of RNA analysis has been difficult.

Abstract: Now, novel bioinformatic approaches coupled with biochemical enrichment strategies and deep sequencing have allowed comprehensive studies of circular RNA species.

Abstract: Recent studies have revealed thousands of endogenous circular RNAs in mammalian cells, some of which are highly abundant and evolutionarily conserved.

Abstract: Evidence is emerging that some circRNAs might regulate microRNA (miRNA) function, and roles in transcriptional control have also been suggested.

Abstract: Therefore, study of this class of noncoding RNAs has potential implications for therapeutic and research applications.

Abstract: We believe the key future challenge for the field will be to understand the regulation and function of these unusual molecules.


A classification of unstable angina revisited.

Abstract: Unstable angina is a critical phase of coronary heart disease with widely variable symptoms and prognosis.

Abstract: A decade ago, a classification of unstable angina based on clinical symptoms was introduced.

Abstract: This system was then validated by prospective clinical studies to correlate with the prognosis and was linked to angiographic and histological findings.

Abstract: It has been used to categorize patients in many large clinical trials.

Abstract: In recent years, the pathophysiological roles of platelet activation and inflammation in unstable angina have been elucidated.

Abstract: Subsequently, improved markers of myocardial injury, acute-phase proteins, and hemostatic markers that may be associated with clinical outcomes have been identified.

Abstract: Particularly, cardiac-specific troponin T and troponin I have been shown to represent the best predictors of early risk in patients with angina at rest.

Abstract: Accordingly, it is suggested that the original classification be extended by subclassifying one large group of unstable angina patients, ie, those with angina at rest within the past 48 hours (class IIIB), into troponin-positive (T(pos)) and troponin-negative (T(neg)) patients.

Abstract: The 30-days risk for death and myocardial infarction is considered to be up to 20% in class IIIB-T(pos) but <2% in class IIIB-T(neg) patients.

Abstract: Initial results suggest that troponins may function as surrogate markers for thrombus formation and can effectively guide therapy with glycoprotein IIb/IIIa antagonists or low-molecular-weight heparins.

Abstract: These observations provide additional impetus for adding the measurement of these markers to the clinical classification and represent a novel concept of treating these high-risk patients.


Alcohol Intake and Blood Pressure: A Systematic Review Implementing a Mendelian Randomization Approach

Abstract: BACKGROUND Alcohol has been reported to be a common and modifiable risk factor for hypertension.

Abstract: However, observational studies are subject to confounding by other behavioural and sociodemographic factors, while clinical trials are difficult to implement and have limited follow-up time.

Abstract: Mendelian randomization can provide robust evidence on the nature of this association by use of a common polymorphism in aldehyde dehydrogenase 2 (ALDH2) as a surrogate for measuring alcohol consumption.

Abstract: ALDH2 encodes a major enzyme involved in alcohol metabolism.

Abstract: Individuals homozygous for the null variant (*2*2) experience adverse symptoms when drinking alcohol and consequently drink considerably less alcohol than wild-type homozygotes (*1*1) or heterozygotes.

Abstract: We hypothesise that this polymorphism may influence the risk of hypertension by affecting alcohol drinking behaviour.

Abstract: METHODS AND FINDINGS We carried out fixed effect meta-analyses of the ALDH2 genotype with blood pressure (five studies, n = 7,658) and hypertension (three studies, n = 4,219) using studies identified via systematic review.

Abstract: In males, we obtained an overall odds ratio of 2.42 (95% confidence interval [CI] 1.66-3.55, p = 4.8 x 10(-6)) for hypertension comparing *1*1 with *2*2 homozygotes and an odds ratio of 1.72 (95% CI 1.17-2.52, p = 0.006) comparing heterozygotes (surrogate for moderate drinkers) with *2*2 homozygotes.

Abstract: Systolic blood pressure was 7.44 mmHg (95% CI 5.39-9.49, p = 1.1 x 10(-12)) greater among *1*1 than among *2*2 homozygotes, and 4.24 mmHg (95% CI 2.18-6.31, p = 0.00005) greater among heterozygotes than among *2*2 homozygotes.

Abstract: CONCLUSIONS These findings support the hypothesis that alcohol intake has a marked effect on blood pressure and the risk of hypertension.


Rapid and Sensitive RT-QuIC Detection of Human Creutzfeldt-Jakob Disease Using Cerebrospinal Fluid

Abstract: UNLABELLED Fast, definitive diagnosis of Creutzfeldt-Jakob disease (CJD) is important in assessing patient care options and transmission risks.

Abstract: Real-time quaking-induced conversion (RT-QuIC) assays of cerebrospinal fluid (CSF) and nasal-brushing specimens are valuable in distinguishing CJD from non-CJD conditions but have required 2.5 to 5 days.

Abstract: Here, an improved RT-QuIC assay is described which identified positive CSF samples within 4 to 14 h with better analytical sensitivity.

Abstract: Moreover, analysis of 11 CJD patients demonstrated that while 7 were RT-QuIC positive using the previous conditions, 10 were positive using the new assay.

Abstract: In these and further analyses, a total of 46 of 48 CSF samples from sporadic CJD patients were positive, while all 39 non-CJD patients were negative, giving 95.8% diagnostic sensitivity and 100% specificity.

Abstract: This second-generation RT-QuIC assay markedly improved the speed and sensitivity of detecting prion seeds in CSF specimens from CJD patients.

Abstract: This should enhance prospects for rapid and accurate ante mortem CJD diagnosis.

Abstract: IMPORTANCE A long-standing problem in dealing with various neurodegenerative protein misfolding diseases is early and accurate diagnosis.

Abstract: This issue is particularly important with human prion diseases, such as CJD, because prions are deadly, transmissible, and unusually resistant to decontamination.

Abstract: The recently developed RT-QuIC test allows for highly sensitive and specific detection of CJD in human cerebrospinal fluid and is being broadly implemented as a key diagnostic tool.

Abstract: However, as currently applied, RT-QuIC takes 2.5 to 5 days and misses 11 to 23% of CJD cases.

Abstract: Now, we have markedly improved RT-QuIC analysis of human CSF such that CJD and non-CJD patients can be discriminated in a matter of hours rather than days with enhanced sensitivity.

Abstract: These improvements should allow for much faster, more accurate, and practical testing for CJD.

Abstract: In broader terms, our study provides a prototype for tests for misfolded protein aggregates that cause many important amyloid diseases, such as Alzheimer's, Parkinson's, and tauopathies.


Wortmannin, a phosphoinositide 3-kinase inhibitor, selectively enhances cytotoxicity of receptor-directed-toxin chimeras in vitro and in vivo.

Abstract: BACKGROUND Generalized resistance of some neoplastic cell lines to treatment with ligand-toxin chimeras has been attributed to an increased rate of lysosomal uptake and degradation following endocytosis of the chimera-receptor complex.

Abstract: Because phosphoinositide 3-kinase (Pl 3-kinase) activity is known to play a role in intracellular trafficking, particularly from endosomes to lysosomes, we hypothesized that co-exposing cells to the Pl 3-kinase inhibitor, wortmannin, might enhance cytotoxicity of ligand-toxin chimeras.

Abstract: METHODS In vitro, cytotoxicity of five receptor directed-toxin chimeras (bFGF-SAP, bFGF-PE, aFGF-PE, HBEGF-SAP, bFGF-gelonin) and an immunotoxin (11A8-SAP) was examined in the presence or absence of this Pl 3-kinase inhibitor against a panel of human neoplastic cell lines: SK-MEL-5 (melanoma), PA-1 (ovarian teratocarcinoma), DU145 (prostatic carcinoma) and MCF-7 (breast carcinoma).

Abstract: In vivo, antitumor activity of a treatment regimen combining wortmannin (1 or 2 mg/kg i.p.) and bFGF-SAP (10 micrograms/kg i.v.) once a week for 4 weeks was evaluated compared to administration of each agent alone in C3H/HeN mice implanted with the FSallC murine fibrosarcoma.

Abstract: RESULTS At concentrations greater than the reported Ki for Pl 3-kinase inhibition (1-10 microM), wortmannin enhanced cytotoxicity when combined with saporin or gelonin chimeras, but produced subadditive cytotoxicity when combined with Pseudomonas exotoxin chimeras.

Abstract: When low nanomolar concentrations selective for Pl 3-kinase inhibition (5-100 nM) were examined for effects on one receptor directed-toxin chimera, wortmannin dramatically enhanced bFGF-SAP cytotoxicity in three of the four cell lines.

Abstract: A different Pl 3-kinase inhibitor, LY294002 (Ki approximately 1 microM), however, failed to potentiate bFGF-SAP.

Abstract: When administered to mice, wortmannin combined with bFGF-SAP resulted in a significant decrease in tumor volumes compared to vehicle-treated controls that was not observed in mice treated with either agent alone.

Abstract: CONCLUSIONS Taken together, these results suggest that although wortmannin increases the cytotoxic efficacy of some receptor-directed chimeras, potentiation may occur through an alternative pathway not involving Pl 3-kinase inhibition.


Chronic stress, glucocorticoid receptor resistance, inflammation, and disease risk.

Abstract: We propose a model wherein chronic stress results in glucocorticoid receptor resistance (GCR) that, in turn, results in failure to down-regulate inflammatory response.

Abstract: Here we test the model in two viral-challenge studies.

Abstract: In study 1, we assessed stressful life events, GCR, and control variables including baseline antibody to the challenge virus, age, body mass index (BMI), season, race, sex, education, and virus type in 276 healthy adult volunteers.

Abstract: The volunteers were subsequently quarantined, exposed to one of two rhinoviruses, and followed for 5 d with nasal washes for viral isolation and assessment of signs/symptoms of a common cold.

Abstract: In study 2, we assessed the same control variables and GCR in 79 subjects who were subsequently exposed to a rhinovirus and monitored at baseline and for 5 d after viral challenge for the production of local (in nasal secretions) proinflammatory cytokines (IL-1β, TNF-α, and IL-6).

Abstract: Study 1: After covarying the control variables, those with recent exposure to a long-term threatening stressful experience demonstrated GCR; and those with GCR were at higher risk of subsequently developing a cold.

Abstract: Study 2: With the same controls used in study 1, greater GCR predicted the production of more local proinflammatory cytokines among infected subjects.

Abstract: These data provide support for a model suggesting that prolonged stressors result in GCR, which, in turn, interferes with appropriate regulation of inflammation.

Abstract: Because inflammation plays an important role in the onset and progression of a wide range of diseases, this model may have broad implications for understanding the role of stress in health.


Pituitary Adenylate Cyclase-Activating Polypeptide (PACAP), a Neuron-Derived Peptide Regulating Glial Glutamate Transport and Metabolism

Abstract: In the brain, glutamatergic neurotransmission is terminated predominantly by the rapid uptake of synaptically released glutamate into astrocytes through the Na(+)-dependent glutamate transporters GLT-1 and GLAST and its subsequent conversion into glutamine by the enzyme glutamine synthetase (GS).

Abstract: To date, several factors have been identified that rapidly alter glial glutamate uptake by post-translational modification of glutamate transporters.

Abstract: The only condition known to affect the expression of glial glutamate transporters and GS is the coculturing of glia with neurons.

Abstract: We now demonstrate that neurons regulate glial glutamate turnover via pituitary adenylate cyclase-activating polypeptide (PACAP).

Abstract: In the cerebral cortex PACAP is synthesized by neurons and acts on the subpopulation of astroglia involved in glutamate turnover.

Abstract: Exposure of astroglia to PACAP increased the maximal velocity of [(3)H]glutamate uptake by promoting the expression of GLT-1, GLAST, and GS.

Abstract: Moreover, the stimulatory effects of neuron-conditioned medium on glial glutamate transporter expression were attenuated in the presence of PACAP-inactivating antibodies or the PACAP receptor antagonist PACAP 6-38.

Abstract: In contrast to PACAP, vasoactive intestinal peptide promoted glutamate transporter expression only at distinctly higher concentrations, suggesting that PACAP exerts its effects on glial glutamate turnover via PAC1 receptors.

Abstract: Although PAC1 receptor-dependent activation of protein kinase A (PKA) was sufficient to promote the expression of GLAST, the activation of both PKA and protein kinase C (PKC) was required to promote GLT-1 expression optimally.

Abstract: Given the existence of various PAC1 receptor isoforms that activate PKA and PKC to different levels, these findings point to a complex mechanism by which PACAP regulates glial glutamate transport and metabolism.

Abstract: Disturbances of these regulatory mechanisms could represent a major cause for glutamate-associated neurological and psychiatric disorders.


Factors influencing B lymphopoiesis after allogeneic hematopoietic cell transplantation.

Abstract: In 93 allograft recipients, the numbers of marrow B-cell precursors on days 80 and 365 correlated with the counts of circulating B cells, suggesting that the posttransplantation B-cell deficiency is at least in part due to insufficient B lymphopoiesis.

Abstract: Factors that could affect B lymphopoiesis were evaluated.

Abstract: The number of marrow B-cell precursors on days 30 and 80 was at least 4-fold lower in patients with grade 2 to 4 acute graft-versus-host disease (GVHD) compared with patients with grade 0 to 1 acute GVHD.

Abstract: The number of B-cell precursors on day 365 was 18-fold lower in patients with extensive chronic GVHD compared with patients with no or limited chronic GVHD.

Abstract: The number of B-cell precursors was not related to CD34 cell dose, type of transplant (marrow versus blood stem cells), donor age, or patient age.

Abstract: It was concluded that posttransplantation B-cell deficiency results in part from inhibition of B lymphopoiesis by GVHD and/or its treatment.


Genetic variants rs1994016 and rs3825807 in ADAMTS7 affect its mRNA expression in atherosclerotic occlusive peripheral arterial disease

Abstract: AIM Peripheral artery disease (PAD) is a vascular disease affecting peripheral circulation.

Abstract: Recently, genome-wide association studies revealed a relationship between single nucleotide polymorphisms (SNPs) in ADAMTS7 (a disintegrin and metalloprotease with thrombospondin motif 7) and atherosclerosis.

Abstract: In this study, we aimed to determine ADAMTS7 expression in peripheral blood mononuclear cells (PBMCs) and the frequency of ADAMTS7 rs1994016 and rs3825807 polymorphisms in a sample of Turkish patients with PAD, and to evaluate the association of matrix metalloproteinase (MMP) levels with PAD development.

Abstract: METHODS In this case-control study, ADAMTS7mRNA and protein expression was determined using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and western blot, respectively, and rs1994016 and rs3825807 variants in ADAMTS7 were determined by real-time PCR in 115 PAD patients and 116 healthy controls.

Abstract: Plasma levels of nine MMPs were determined using a multiplex immunoassay system.

Abstract: RESULTS ADAMTS7mRNA levels were significantly higher in PAD patients than in controls (t=-2.75, P=.007).

Abstract: There was no significant difference in the frequencies of rs1994016 and rs3825807 between PAD patients and controls (P>.05).

Abstract: In PAD patients, ADAMTS7mRNA levels were significantly increased for the CC genotype of rs1994016 (t=-2.31, P=.026) and TT genotype of rs3825807 (t=-2.23, P=.032).

Abstract: Furthermore, plasma levels of MMP-1, MMP-3, MMP-7, MMP-10, MMP-12, and MMP-13 were significantly higher in PAD patients than in controls (P<.05).

Abstract: CONCLUSION This is the first report of the relationship between PAD and ADAMTS7 expression and the effects of the rs1994016 and rs3825807 variants on PAD development.

Abstract: ADAMTS7 may be associated with PAD development.


Distinct Parietal and Temporal Pathways to the Homologues of Broca's Area in the Monkey

Abstract: The homologues of the two distinct architectonic areas 44 and 45 that constitute the anterior language zone (Broca's region) in the human ventrolateral frontal lobe were recently established in the macaque monkey.

Abstract: Although we know that the inferior parietal lobule and the lateral temporal cortical region project to the ventrolateral frontal cortex, we do not know which of the several cortical areas found in those regions project to the homologues of Broca's region in the macaque monkey and by means of which white matter pathways.

Abstract: We have used the autoradiographic method, which permits the establishment of the cortical area from which axons originate (i.e., the site of injection), the precise course of the axons in the white matter, and their termination within particular cortical areas, to examine the parietal and temporal connections to area 44 and the two subdivisions of area 45 (i.e., areas 45A and 45B).

Abstract: The results demonstrated a ventral temporo-frontal stream of fibers that originate from various auditory, multisensory, and visual association cortical areas in the intermediate superolateral temporal region.

Abstract: These axons course via the extreme capsule and target most strongly area 45 with a more modest termination in area 44.

Abstract: By contrast, a dorsal stream of axons that originate from various cortical areas in the inferior parietal lobule and the adjacent caudal superior temporal sulcus was found to target both areas 44 and 45.

Abstract: These axons course in the superior longitudinal fasciculus, with some axons originating from the ventral inferior parietal lobule and the adjacent superior temporal sulcus arching and forming a simple arcuate fasciculus.

Abstract: The cortex of the most rostral part of the inferior parietal lobule is preferentially linked with the ventral premotor cortex (ventral area 6) that controls the orofacial musculature.

Abstract: The cortex of the intermediate part of the inferior parietal lobule is linked with both areas 44 and 45.

Abstract: These findings demonstrate the posterior parietal and temporal connections of the ventrolateral frontal areas, which, in the left hemisphere of the human brain, were adapted for various aspects of language production.

Abstract: These precursor circuits that are found in the nonlinguistic, nonhuman, primate brain also exist in the human brain.

Abstract: The possible reasons why these areas were adapted for language use in the human brain are discussed.

Abstract: The results throw new light on the prelinguistic precursor circuitry of Broca's region and help understand functional interactions between Broca's ventrolateral frontal region and posterior parietal and temporal association areas.


MIRA-seq for DNA methylation analysis of CpG islands

Abstract: AIM To develop a reliable method for whole genome analysis of DNA methylation.

Abstract: MATERIALS & METHODS Genome-scale analysis of DNA methylation includes affinity-based approaches such as enrichment using methyl-CpG-binding proteins.

Abstract: One of these methods, the methylated-CpG island recovery assay (MIRA), is based on the high affinity of the MBD2b-MBD3L1 complex for CpG-methylated DNA.

Abstract: Here we provide a detailed description of MIRA and combine it with next generation sequencing platforms (MIRA-seq).

Abstract: RESULTS We assessed the performance of MIRA-seq and compared the data with whole genome bisulfite sequencing.

Abstract: CONCLUSION MIRA-seq is a reliable, genome-scale DNA methylation analysis platform for scoring DNA methylation differences at CpG-rich genomic regions.

Abstract: The method is not limited by primer or probe design and is cost effective.


How many images are in an auditory scene?

Abstract: If an auditory scene consists of many spatially separated sound sources, how many sound sources can be processed by the auditory system?

Abstract: Experiment I determined how many speech sources could be localized simultaneously on the azimuth plane.

Abstract: Different words were played from multiple loudspeakers, and listeners reported the total number of sound sources and their individual locations.

Abstract: In experiment II the accuracy of localizing one speech source in a mixture of multiple speech sources was determined.

Abstract: An extra sound source was added to an existing set of sound sources, and the task was to localize that extra source.

Abstract: In experiment III the setup and task were the same as in experiment I, except that the sounds were tones.

Abstract: The results showed that the maximum number of sound sources that listeners could perceive was limited to approximately four spatially separated speech signals and three for tonal signals.

Abstract: The localization errors increased along with the increase of total number of sound sources.

Abstract: When four or more speech sources already existed, the accuracy in localizing an additional source was near chance.


Mobilization of intracellular copper stores by the ctr2 vacuolar copper transporter.

Abstract: Copper plays an essential role in processes including signaling to the transcription and protein trafficking machinery, oxidative phosphorylation, iron mobilization, neuropeptide maturation, and normal development.

Abstract: Whereas much is known about intracellular mobilization of ions such as calcium, little information is available on how eukaryotic cells mobilize intracellular copper stores.

Abstract: We describe a mechanism by which the Saccharomyces cerevisiae Ctr2 protein provides bioavailable copper via mobilization of intracellular copper stores.

Abstract: Whereas Ctr2 exhibits structural similarity to the Ctr1 plasma membrane copper importer, microscopic and biochemical fractionation studies localize Ctr2 to the vacuole membrane.

Abstract: We demonstrate that Ctr2 mobilizes vacuolar copper stores in a manner dependent on amino acid residues conserved between the Ctr1 and Ctr2 copper transport family and that ctr2 Delta mutants hyper-accumulate vacuolar copper.

Abstract: Furthermore, a Ctr2 mutant that is mislocalized to the plasma membrane stimulates extracellular copper uptake, supporting a direct role for Ctr2 in copper transport across membranes.

Abstract: These studies identify a novel mechanism for copper mobilization and suggest that organisms cope with copper deprivation via the use of intracellular vesicular stores.


Peroxisomes Are Signaling Platforms for Antiviral Innate Immunity

Abstract: Peroxisomes have long been established to play a central role in regulating various metabolic activities in mammalian cells.

Abstract: These organelles act in concert with mitochondria to control the metabolism of lipids and reactive oxygen species.

Abstract: However, while mitochondria have emerged as an important site of antiviral signal transduction, a role for peroxisomes in immune defense is unknown.

Abstract: Here, we report that the RIG-I-like receptor (RLR) adaptor protein MAVS is located on peroxisomes and mitochondria.

Abstract: We find that peroxisomal and mitochondrial MAVS act sequentially to create an antiviral cellular state.

Abstract: Upon viral infection, peroxisomal MAVS induces the rapid interferon-independent expression of defense factors that provide short-term protection, whereas mitochondrial MAVS activates an interferon-dependent signaling pathway with delayed kinetics, which amplifies and stabilizes the antiviral response.

Abstract: The interferon regulatory factor IRF1 plays a crucial role in regulating MAVS-dependent signaling from peroxisomes.

Abstract: These results establish that peroxisomes are an important site of antiviral signal transduction.


Two-sided confidence intervals for the single proportion: comparison of seven methods. Stat. Med

Abstract: Simple interval estimate methods for proportions exhibit poor coverage and can produce evidently inappropriate intervals.

Abstract: Criteria appropriate to the evaluation of various proposed methods include: closeness of the achieved coverage probability to its nominal value; whether intervals are located too close to or too distant from the middle of the scale; expected interval width; avoidance of aberrations such as limits outside [0,1] or zero width intervals; and ease of use, whether by tables, software or formulae.

Abstract: Seven methods for the single proportion are evaluated on 96,000 parameter space points.

Abstract: Intervals based on tail areas and the simpler score methods are recommended for use.

Abstract: In each case, methods are available that aim to align either the minimum or the mean coverage with the nominal 1 -alpha.


Nuclear accumulation of HDAC4 in ATM deficiency promotes neurodegeneration in ataxia-telangiectasia

Abstract: Ataxia telangiectasia is a neurodegenerative disease caused by mutation of the Atm gene.

Abstract: Here we report that ataxia telangiectasia mutated (ATM) deficiency causes nuclear accumulation of histone deacetylase 4 (HDAC4) in neurons and promotes neurodegeneration.

Abstract: Nuclear HDAC4 binds to chromatin, as well as to myocyte enhancer factor 2A (MEF2A) and cAMP-responsive element binding protein (CREB), leading to histone deacetylation and altered neuronal gene expression.

Abstract: Blocking either HDAC4 activity or its nuclear accumulation blunts these neurodegenerative changes and rescues several behavioral abnormalities of ATM-deficient mice.

Abstract: Full rescue of the neurodegeneration, however, also requires the presence of HDAC4 in the cytoplasm, suggesting that the ataxia telangiectasia phenotype results both from a loss of cytoplasmic HDAC4 as well as its nuclear accumulation.

Abstract: To remain cytoplasmic, HDAC4 must be phosphorylated.

Abstract: The activity of the HDAC4 phosphatase, protein phosphatase 2A (PP2A), is downregulated by ATM-mediated phosphorylation.

Abstract: In ATM deficiency, enhanced PP2A activity leads to HDAC4 dephosphorylation and the nuclear accumulation of HDAC4.

Abstract: Our results define a crucial role of the cellular localization of HDAC4 in the events leading to ataxia telangiectasia neurodegeneration.


Regulation and function of the E-cadherin/catenin complex in cells of the monocyte-macrophage lineage and DCs.

Abstract: E-cadherin is best characterized as adherens junction protein, which through homotypic interactions contributes to the maintenance of the epithelial barrier function.

Abstract: In epithelial cells, the cytoplasmic tail of E-cadherin forms a dynamic complex with catenins and regulates several intracellular signal transduction pathways, including Wnt/β-catenin, PI3K/Akt, Rho GTPase, and NF-κB signaling.

Abstract: Recent progress uncovered a novel and critical role for this adhesion molecule in mononuclear phagocyte functions.

Abstract: E-cadherin regulates the maturation and migration of Langerhans cells, and its ligation prevents the induction of a tolerogenic state in bone marrow-derived dendritic cells (DCs).

Abstract: In this respect, the functionality of β-catenin could be instrumental in determining the balance between immunogenicity and tolerogenicity of DCs in vitro and in vivo.

Abstract: Fusion of alternatively activated macrophages and osteoclasts is also E-cadherin-dependent.

Abstract: In addition, the E-cadherin ligands CD103 and KLRG1 are expressed on DC-, T-, and NK-cell subsets and contribute to their interaction with E-cadherin-expressing DCs and macrophages.

Abstract: Here we discuss the regulation, function, and implications of E-cadherin expression in these central orchestrators of the immune system.


Polymorphism and ligand dependent changes in human glucagon-like peptide-1 receptor (GLP-1R) function: allosteric rescue of loss of function mutation.

Abstract: The glucagon-like peptide-1 receptor (GLP-1R) is a key physiological regulator of insulin secretion and a major therapeutic target for the treatment of type II diabetes.

Abstract: However, regulation of GLP-1R function is complex with multiple endogenous peptides that interact with the receptor, including full-length (1-37) and truncated (7-37) forms of GLP-1 that can exist in an amidated form (GLP-1(1-36)NH₂ and GLP-1(7-36)NH₂) and the related peptide oxyntomodulin.

Abstract: In addition, the GLP-1R possesses exogenous agonists, including exendin-4, and the allosteric modulator, compound 2 (6,7-dichloro-2-methylsulfonyl-3-tert-butylaminoquinoxaline).

Abstract: The complexity of this ligand-receptor system is further increased by the presence of several single nucleotide polymorphisms (SNPs) that are distributed across the receptor.

Abstract: We have investigated 10 GLP-1R SNPs, which were characterized in three physiologically relevant signaling pathways (cAMP accumulation, extracellular signal-regulated kinase 1/2 phosphorylation, and intracellular Ca²⁺ mobilization); ligand binding and cell surface receptor expression were also determined.

Abstract: We demonstrate both ligand- and pathway-specific effects for multiple SNPs, with the most dramatic effect observed for the Met¹⁴⁹ receptor variant.

Abstract: At the Met¹⁴⁹ variant, there was selective loss of peptide-induced responses across all pathways examined, but preservation of response to the small molecule compound 2.

Abstract: In contrast, at the Cys³³³ variant, peptide responses were preserved but there was attenuated response to compound 2.

Abstract: Strikingly, the loss of peptide function at the Met¹⁴⁹ receptor variant could be allosterically rescued by compound 2, providing proof-of-principle evidence that allosteric drugs could be used to treat patients with this loss of function variant.


Neuronal circuitry mechanism regulating adult quiescent neural stem cell fate decision

Abstract: Adult neurogenesis arises from neural stem cells within specialized niches.

Abstract: Neuronal activity and experience, presumably acting on this local niche, regulate multiple stages of adult neurogenesis, from neural progenitor proliferation to new neuron maturation, synaptic integration and survival.

Abstract: It is unknown whether local neuronal circuitry has a direct impact on adult neural stem cells.

Abstract: Here we show that, in the adult mouse hippocampus, nestin-expressing radial glia-like quiescent neural stem cells (RGLs) respond tonically to the neurotransmitter γ-aminobutyric acid (GABA) by means of γ2-subunit-containing GABAA receptors.

Abstract: Clonal analysis of individual RGLs revealed a rapid exit from quiescence and enhanced symmetrical self-renewal after conditional deletion of γ2.

Abstract: RGLs are in close proximity to terminals expressing 67-kDa glutamic acid decarboxylase (GAD67) of parvalbumin-expressing (PV+) interneurons and respond tonically to GABA released from these neurons.

Abstract: Functionally, optogenetic control of the activity of dentate PV+ interneurons, but not that of somatostatin-expressing or vasoactive intestinal polypeptide (VIP)-expressing interneurons, can dictate the RGL choice between quiescence and activation.

Abstract: Furthermore, PV+ interneuron activation restores RGL quiescence after social isolation, an experience that induces RGL activation and symmetrical division.

Abstract: Our study identifies a niche cell–signal–receptor trio and a local circuitry mechanism that control the activation and self-renewal mode of quiescent adult neural stem cells in response to neuronal activity and experience.


Global vitamin D levels in relation to age, gender, skin pigmentation and latitude: an ecologic meta-regression analysis

Abstract: We performed a meta-analysis of cross-sectional studies on serum 25(OH)D status globally.

Abstract: Serum 25(OH)D levels on average were 54 nmol/l, were higher in women than men, and higher in Caucasians than in non-Caucasians.

Abstract: There was no trend in serum 25(OH)D level with latitude.

Abstract: Vitamin D deficiency was widespread.

Abstract: We studied vitamin D status (expressed as serum 25-hydroxy-vitamin D [25(OH)D]) in native subjects worldwide.

Abstract: Meta-analysis and meta-regression of studies reporting on 25(OH)D in healthy subjects retrieved from Pubmed, Embase and Web of Science using the terms “serum”, “25-hydroxy-vitamin D”, “cholecalciferol”, and “human”.

Abstract: A total of 394 studies were included.

Abstract: The mean 25(OH)D level was 54 nmol/l (95% CI: 52–57 nmol/l).

Abstract: Women had borderline significantly higher 25(OH)D levels than men, and Caucasians had higher levels than non-Caucasians.

Abstract: 25(OH)D levels were higher in subjects aged >15 years than in younger subjects.

Abstract: Unadjusted there was no significant decrease in 25(OH)D with latitude (slope of curve −0.03 ± 0.12 nmol/l per degree latitude north or south of equator, p = 0.8).

Abstract: There was a significant decline with latitude for Caucasians (−0.69 ± 0.30 nmol/l per degree, p = 0.02), but not for non-Caucasians (0.03 ± 0.39 nmol/l per degree, p = 0.14).

Abstract: After adjustment for age, gender, and ethnicity, no overall correlation was present between 25(OH)D and latitude (−0.29 ± 0.24 nmol/l per degree, p = 0.23).

Abstract: There was no overall influence of latitude on 25(OH)D. However, in separate analyses 25(OH)D decreased with latitude in Caucasians but not in non-Caucasians.

Abstract: A widespread global vitamin D insufficiency was present compared with proposed threshold levels.


Identification and characterization of a novel monocyte/macrophage differentiation-dependent gene that is responsive to lipopolysaccharide, ceramide, and lysophosphatidylcholine.

Abstract: A novel differentiation-dependent cDNA (DIF-2) has been isolated from human mononuclear phagocytes by differential display.

Abstract: The full-length cDNA was cloned and sequenced.

Abstract: DIF-2 consists of 156 amino acids and has a predicted isoelectric point of 8.84.

Abstract: The mRNA is expressed in freshly isolated monocytes and is downregulated significantly when monocytes are subjected to differentiation.

Abstract: A similar differentiation-dependent downregulation is observed in normal hepatocytes compared to undifferentiated HepG2 cells.

Abstract: The mRNA expression in monocytes is sensitive to lipopolysaccharide and ceramide which both strongly increase DIF-2 transcription, while lysophosphatidylcholine results in a weaker upregulation of DIF-2 expression.

Abstract: A DIF-2 homologous gene has been previously isolated from mouse fibroblasts and was shown to be a serum growth factor-inducible immediate early gene.

Abstract: Our results indicate that DIF-2 represents a gene which is regulated in differentiation processes and strongly responsive to lipopolysaccharide, ceramide and lysophosphatidylcholine.


A Novel 3-Hydroxysteroid Dehydrogenase That Regulates Reproductive Development and Longevity

Abstract: Endogenous small molecule metabolites that regulate animal longevity are emerging as a novel means to influence health and life span.

Abstract: In C. elegans, bile acid-like steroids called the dafachronic acids (DAs) regulate developmental timing and longevity through the conserved nuclear hormone receptor DAF-12, a homolog of mammalian sterol-regulated receptors LXR and FXR.

Abstract: Using metabolic genetics, mass spectrometry, and biochemical approaches, we identify new activities in DA biosynthesis and characterize an evolutionarily conserved short chain dehydrogenase, DHS-16, as a novel 3-hydroxysteroid dehydrogenase.

Abstract: Through regulation of DA production, DHS-16 controls DAF-12 activity governing longevity in response to signals from the gonad.

Abstract: Our elucidation of C. elegans bile acid biosynthetic pathways reveals the possibility of novel ligands as well as striking biochemical conservation to other animals, which could illuminate new targets for manipulating longevity in metazoans.


An Argonaute transports siRNAs from the cytoplasm to the nucleus.

Abstract: Ribonucleoprotein complexes consisting of Argonaute-like proteins and small regulatory RNAs function in a wide range of biological processes.

Abstract: Many of these small regulatory RNAs are predicted to act, at least in part, within the nucleus.

Abstract: We conducted a genetic screen to identify factors essential for RNA interference (RNAi) in nuclei of Caenorhabditis elegans and identified the Argonaute protein NRDE-3.

Abstract: In the absence of small interfering RNAs (siRNAs), NRDE-3 resides in the cytoplasm.

Abstract: NRDE-3 binds siRNAs generated by RNA-dependent RNA polymerases acting on messenger RNA templates in the cytoplasm and redistributes to the nucleus.

Abstract: Nuclear redistribution of NRDE-3 requires a functional nuclear localization signal, is required for nuclear RNAi, and results in NRDE-3 association with nuclear-localized nascent transcripts.

Abstract: Thus, specific Argonaute proteins can transport specific classes of small regulatory RNAs to distinct cellular compartments to regulate gene expression.