The influence of topography on the biogeochemical cycle of mercury (Hg) has received relatively little attention. Here, we report the measurement of Hg species and their corresponding isotope composition in soil sampled along an elevational gradient transect on Mt. Leigong in subtropical southwestern China. The data are used to explain orography-related effects on the fate and behaviour of Hg species in montane environments. The total- and methyl-Hg concentrations in topsoil samples show a positive correlation with elevation. However, a negative elevation dependence was observed in the mass-dependent fractionation (MDF) and mass-independent fractionation (MIF) signatures of Hg isotopes. Both a MIF (Δ199Hg) binary mixing approach and the traditional inert element method indicate that the content of Hg derived from the atmosphere distinctly increases with altitude.
In addition to being an important mediator of migration and invasion of tumor cells, β3 integrin can also enhance TGF-β1 signaling. However, it is not known whether β3 might influence the induction of metastatic phenotype of tumor cells, especially non-metastatic tumor cells which express low level of β3. Here we report that H2O2 and HOCl, the reactive oxygen species produced by neutrophils, could cooperate with TGF-β1 to induce metastatic phenotype of non-metastatic hepatocellular carcinoma (HCC) cells. TGF-β1/H2O2/HOCl, but not TGF-β1 or H2O2/HOCl, induced β3 expression by triggering the enhanced activation of p38 MAPK. Intriguingly, β3 in turn promoted TGF-β1/H2O2/HOCl-mediated induction of metastatic phenotype of HCC cells by enhancing TGF-β1 signaling. β3 promoted TGF-β1/H2O2/HOCl-induced expression of itself via positive feed-back effect on p38 MAPK activation, and also promoted TGF-β1/H2O2/HOCl-induced expression of α3 and SNAI2 by enhancing the activation of ERK pathway, thus resulting in higher invasive capacity of HCC cells. By enhancing MAPK activation, β3 enabled TGF-β1 to augment the promoting effect of H2O2/HOCl on anoikis-resistance of HCC cells. TGF-β1/H2O2/HOCl-induced metastatic phenotype was sufficient for HCC cells to extravasate from circulation and form metastatic foci in an experimental metastasis model in nude mice. Inhibiting the function of β3 could suppress or abrogate the promoting effects of TGF-β1/H2O2/HOCl on invasive capacity, anoikis-resistance, and extravasation of HCC cells. These results suggest that β3 could function as a modulator to promote TGF-β1/H2O2/HOCl-mediated induction of metastatic phenotype of non-metastatic tumor cells, and that targeting β3 might be a potential approach in preventing the induction of metastatic phenotype of non-metastatic tumor cells.
Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as that from X-ray, NMR and cryo-EM, and theoretical/mathematical models, such as molecular dynamics, the Poisson-Boltzmann equation and the Nernst-Planck equation. In this work, we present a family of variational multiscale geometric models for macromolecular systems. Our models are able to combine multiresolution geometric modeling with multiscale electrostatic modeling in a unified variational framework. We discuss a suite of techniques for molecular surface generation, molecular surface meshing, molecular volumetric meshing, and the estimation of Hadwiger’s functionals. Emphasis is given to the multiresolution representations of biomolecules and the associated multiscale electrostatic analyses as well as multiresolution curvature characterizations. The resulting fine resolution representations of a biomolecular system enable the detailed analysis of solvent-solute interaction, and ion channel dynamics, while our coarse resolution representations highlight the compatibility of protein-ligand bindings and possibility of protein-protein interactions.
Variational multiscale modeling; Multiresolution surface; Energy functional; Meshing; Curvature; Electrostatics
Failing cardiomyocytes exhibit decreased efficiency of excitation-contraction (E-C) coupling. The down-regulation of junctophilin-2 (JP2), a protein anchoring the sarcoplasmic reticulum (SR) to T-tubules (TTs), has been identified as a major mechanism underlying the defective E-C coupling. However, the regulatory mechanism of JP2 remains unknown.
To determine whether microRNAs regulate JP2 expression.
Methods and Results
Bioinformatic analysis predicted two potential binding sites of miR-24 in the 3′-untranslated regions of JP2 mRNA. Luciferase assays confirmed that miR-24 suppressed JP2 expression by binding to either of these sites. In the aortic stenosis model, miR-24 was up-regulated in failing cardiomyocytes. Adenovirus-directed over-expression of miR-24 in cardiomyocytes decreased JP2 expression and reduced Ca2+ transient amplitude and E-C coupling gain.
MiR-24-mediated suppression of JP2 expression provides a novel molecular mechanism for E-C coupling regulation in heart cells, and suggests a new target against heart failure.
myocardial contractility; excitation-contraction coupling; heart failure; calcium signaling; heart failure
Non-human primates (NHP) represent an emerging animal model for the study of physical function, and provide opportunities for exploration of relationships of muscle biomolecular changes with age. One such primate model, the African green vervet monkey, has been used extensively in biomedical research but little is known regarding skeletal muscle composition, expression of myosin heavy chain (MHC) isoforms, and changes with age. In the present study we examined the effects of age on vastus lateralis (VL) muscle fiber-type composition, fiber cross-sectional area (CSA), and MHC isoforms expressed in 4 young and 4 older adult vervet monkeys. Proteomics analysis, using a human and nonhuman primate protein database, showed five MHC isoforms (I, IIA, IIX, IIB, and IIB′) expressed in female vervet VL muscle, which matched the human MHC isoforms. Fast type II fibers predominated and no pure type IIB or IIB′ containing fibers were detected. Hybrid fibers containing IIB/IIB′ MHC decreased in the old vervets. The CSA of both type I and type II fibers was significantly smaller in older vervet while type IIA fibers showed the most severity of atrophy. The decrease of fast MHC and atrophy of muscle fiber with aging recapitulate observations in human VL muscle. These findings, along with its homology of MHC between the vervet and human suggested that the vervet monkey may be a suitable preclinical model for understanding the cellular and molecular basis of sarcopenia and for developing new interventions to ameliorate the impact of disorders that affect skeletal muscle structure and function.
myosin heavy chain; aging; non-human primate; vervet
In the battle against malaria in China, the rate of elementary and high school students’ awareness on malaria knowledge is an important index for malaria elimination, but only rare data is available. This study aimed to investigate the level of malaria awareness in students at elementary and high schools in malaria endemic areas of China, and to provide the baseline information for the malaria elimination.
This cross-sectional survey was conducted in 20 different malaria-endemic provinces in the first year of China’s National Malaria Elimination Programme (NMEP). A structured questionnaire was administrated to students at elementary and high schools enrolled. A total of 44,519 questionnaires were effective while 1,220 were excluded because of incomplete survey responses.
More than 60% of students were aware of malaria, but only 9,013 of them answered correctly to all five questions, and there were still 1,862 students unaware of malaria. There were significant differences of the awareness of malaria among different age groups, between male and female, between two different education levels.
The study reveals that students at elementary and high school levels did not have adequate knowledge of malaria about biology, pathogenicity, transmitting vectors and preventive methods and so on at the beginning of NMEP in China. Further emphasis should be paid on health education campaigns in China to increase students’ public awareness of malaria about vector control, treatment, prevention.
Awareness; Malaria; Students; China
To identify treatable risk factors for aspiration in older adults—particularly those associated with sarcopenia – we examined tongue composition. We hypothesized that 1) isometric and swallowing posterior tongue strength would positively correlate with posterior tongue adiposity, and 2) healthy older adults who aspirate would have greater tongue adiposity than healthy older adults who did not aspirate.
Participants were 40 healthy adults, comprised of 20 aspirators (Mean age = 78 years) and 20 non-aspirators (Mean age = 81 years), as identified via flexible endoscopic evaluation of swallowing. Measures of maximal isometric posterior tongue strength and posterior swallowing tongue strength were acquired via tongue manometry. An index of posterior tongue adiposity was acquired via computed tomography for a 1 cm region of interest.
Posterior tongue adiposity was correlated with posterior tongue isometric (r = .32, p = 0.05) but not swallowing pressures (p > 0.05) as examined with separate partial correlation analyses. Tongue adiposity did not significantly differ as a function of age, gender, or aspiration status (p > 0.05).
Lower posterior isometric tongue strength was associated with greater posterior tongue adiposity. However, aspiration in healthy older adults was not affected by posterior tongue adiposity. This finding offers insight into the roles of tongue composition and strength in healthy older adults.
Tongue; Adiposity; Fat; Swallowing; Older Adults; Computed Tomography
To evaluate the association of coronary artery endothelial function and plasma levels of low density lipoprotein cholesterol (LDL-C) and high density lipoprotein cholesterol (HDL-C) in patients with Type 2 Diabetes Mellitus (DM).
We investigated 90 participants from our institution between October 2007 to March 2010: non-DM (n = 60) and DM (n = 30). As an indicator of coronary endothelial dysfunction, we used non-invasive Doppler echocardiography to quantify coronary flow velocity reserve (CFVR) in the distal part of the left descending artery after rest and after intravenous adenosine administration.
Plasma level of LDL-C was significantly higher in patients with DM than in non-DM (3.21 ± 0.64 vs. 2.86 ± 0.72 mmo/L, P < 0.05), but HDL-C level did not differ between the groups (1.01 ± 0.17 vs. 1.05 ± 0.19 mmo/L). Furthermore, the CFVR value was lower in DM patients than non-diabetics (2.45 ± 0.62 vs. 2.98 ± 0.68, P < 0.001). Plasma levels of LDL-C were negatively correlated with CFVR in all subjects (r = −0.35, P < 0.001; 95% confidence interval (CI): −0.52 – −0.15) and in the non-DM (r = −0.29, P < 0.05; 95% CI: −0.51– −0.05), with an even stronger negative correlation in the DM group (r = −0.42, P < 0.05; 95% CI: −0.68 – −0.06). Age (β = −0.019, s = 0.007, sβ = −0.435, 95% CI: −0.033 – −0.005, P = 0.008), LDL-C (β = −0.217, s = 0.105, sβ = −0.282, 95% CI: −0.428 – −0.005, P = 0.045) remained independently correlated with CFVR in the DM group. However, we found no correlation between HDL-C level and CFVR in any group.
Diabetes may contribute to coronary artery disease (CAD) by inducing dysfunction of the coronary artery endothelium. Increased LDL-C level may adversely impair coronary endothelial function in DM. HDL-C may lose its endothelial-protective effects, in part as a result of pathological conditions, especially under abnormal glucose metabolism.
Coronary flow velocity reserve; Low-density lipoprotein cholesterol; Endothelial function; Diabetes mellitus; High-density lipoprotein cholesterol
Laryngeal muscles are specialized for fine control of voice, speech and swallowing, and may differ from limb muscles in many aspects. Since muscles and their controlling motor neurons communicate via neuromuscular junctions (NMJ), we hypothesized that NMJs in laryngeal muscles have specialized characteristics different from limb muscles.
In vivo study.
Single muscle fibers from 12 Sprague-Dawley rats (6 male, 6 female) were used to analyze the postsynaptic side of NMJs from laryngeal thyroarytenoid (TA), cricothyroid (CT), posterior cricoarytenoid (PCA), limb soleus (SOL), and extensor digitorum longus (EDL) muscles. NMJs were labeled with rhodamine-conjugated-α-bungarotoxin. With confocal microscopy, we counted cluster fragments, and measured the NMJ area, both absolute and normalized (corrected by muscle fiber diameter) for at least 10 single fibers from each muscle of each animal. Differences between genders were also compared.
Cluster fragments of postsynaptic NMJs were more numerous in PCA and TA compared to CT, SOL and EDL muscles (P <.01) in both male and female rats. NMJ cluster fragments were more numerous in female than in male rats only in the TA muscle (P <.01). The absolute area covered by the NMJs showed SOL>EDL>PCA>CT>TA (P <.01), however, with normalization, the SOL=EDL=PCA>CT=TA.
Differences found in NMJ surface and organization between laryngeal and limb muscle fibers may relate to specialized laryngeal muscle functions. Differences in NMJs between male and female rats were found only in the TA muscle, suggesting an underlying mechanism for some gender-specific laryngeal disorders related to abnormal TA muscle activity.
Level of Evidence
Laryngeal muscle; neuromuscular junction; single fiber; cluster fragments; gender difference; rat
Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multi-protein complexes have emerged as a leading interest in structural biology. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics. This paper introduces a suite of computational tools for volumetric data processing, information extraction, surface mesh rendering, geometric measurement, and curvature estimation of biomolecular complexes. Particular emphasis is given to the modeling of cryo-electron microscopy data. Lagrangian-triangle meshes are employed for the surface presentation. On the basis of this representation, algorithms are developed for surface area and surface-enclosed volume calculation, and curvature estimation. Methods for volumetric meshing have also been presented. Because the technological development in computer science and mathematics has led to multiple choices at each stage of the geometric modeling, we discuss the rationales in the design and selection of various algorithms. Analytical models are designed to test the computational accuracy and convergence of proposed algorithms. Finally, we select a set of six cryo-electron microscopy data representing typical subcellular complexes to demonstrate the efficacy of the proposed algorithms in handling biomolecular surfaces and explore their capability of geometric characterization of binding targets. This paper offers a comprehensive protocol for the geometric modeling of subcellular structures, organelles, and multiprotein complexes.
macromolecules; geometric modeling; Laplace–Beltrami operator; high-order geometric PDEs; surface meshing; Gaussian curvature; mean curvature
This study examined the relations of school-age children’s depressive symptoms, frontal EEG asymmetry, and maternal history of childhood-onset depression (COD). Participants were 73 children, 43 of whom had mothers with COD. Children’s EEG was recorded at baseline and while watching happy and sad film clips. Depressive symptoms were measured using parent-report of Children’s Depression Inventory. The key findings are the interaction effects between baseline and film frontal EEG asymmetry on child depressive symptoms. Specifically, relative right frontal EEG asymmetry while watching happy or sad film clip was associated with elevated depressive symptoms for children who also exhibited right frontal EEG asymmetry at baseline. Results suggest that right frontal EEG asymmetry that is consistent across situations may be an marker of depression-prone children.
EEG symmetry; emotion; childhood depression; maternal depression
GH15 is a polyvalent phage that shows activity against a wide range of Staphylococcus aureus strains. In this work, the complete genome sequence of GH15 was determined. With a genome size of 139,806 bp (double-stranded DNA), GH15 is the largest staphylococcal phage sequenced to date. The complete genome encodes 214 open reading frames (ORFs) and 4 tRNAs. The closest relatives are the class III staphylococcal myobacteriophages, including K, A5W, ISP, Sb-1, and G1. Interestingly, although corresponding gene sequences demonstrate very high similarity, all the introns and inteins present in the phages listed above are absent in GH15. As such, GH15 can be considered phylogenetically unique among the staphylococcal myobacteriophages, indicating the diversity of this family.
The Mycobacterium tuberculosis H37Rv and BCG effects on the host cell transcriptional profile consider a main research point. In the present study the transcriptome profiling analysis of RAW264.7 either infected with Mycobacterium tuberculosis H37Rv or BCG have been reported using Solexa/Illumina digital gene expression (DGE).
The DGE analysis showed 1,917 different expressed genes between the BCG and H37Rv group. In addition, approximately 5% of the transcripts appeared to be predicted genes that have never been described before. KEGG Orthology (KO) annotations showed more than 71% of these transcripts are possibly involved in approximately 210 known metabolic or signaling pathways. The gene of the 28 pathways about pathogen recognition receptors and Mycobacterium tuberculosis interaction with macrophages were analyzed using the CLUSTER 3.0 available, the Tree View tool and Gene Orthology (GO). Some genes were randomly selected to confirm their altered expression levels by quantitative real-time PCR (qRT-PCR).
The present study used DGE from pathogen recognition receptors and Mycobacterium tuberculosis interaction with macrophages to understand the interplay between Mycobacterium tuberculosis and RAW264.7. Meanwhile find some important host protein which was affected by Mycobacterium tuberculosis to provide evidence for the further improvement of the present efficacy of existing Mycobacterium tuberculosis therapy and vaccine.
Little is known about the role of ODD dimensions on the temporal unfolding of CD and depression in girls between childhood and adolescence.
The year-to-year associations between CD and depressive symptomatology were examined using nine waves of annually collected data (ages 8 through 16 years) from 1215 participants of the Pittsburgh Girls Study. A series of autoregressive path models were tested that included ODD-Emotion Dysregulation (ODD-ED) and ODD-Defiance, as time varying covariates on CD predicting depression severity in the following year, and vice versa.
Conduct problems, depression, and ODD dimensions were relatively stable throughout childhood and adolescence, and a moderate degree of covariance was observed between these variables. Path analyses showed that CD often preceded depression across this developmental period, although the effect sizes were small. There was less consistent prediction from depression to CD. The overlap between ODD-ED and CD partially explained the prospective relations from CD to depression, whereas these paths were fully explained by the overlap between ODD-ED and depression. The overlap between ODD-Defiance and CD did not account for the prospective relations from CD to depression. In contrast, the overlap between ODD-Defiance and depression accounted for virtually all paths from CD to depression. Accounting for the overlap between ODD dimensions and both CD and depression eliminated all significant predictive paths.
Symptoms of CD tend to precede depression in girls during childhood and adolescence. However, covariance between depression and both ODD-ED and ODD-Defiance accounts for these prospective relations. ODD dimensions should be assessed when evaluating risk for comorbid depression in girls with conduct problems, and emotion dysregulation and defiance aspects of ODD should be identified as targets for treatment in order to prevent depression in the future.
Conduct Disorder; Depression; Oppositional Defiant Disorder; Comorbidity; Girls; Longitudinal
Bacteriophage could be an alternative to conventional antibiotic therapy against multidrug-resistant bacteria. However, the emergence of resistant variants after phage treatment limited its therapeutic application.
In this study, an approach, named “Step-by-Step” (SBS), has been established. This method takes advantage of the occurrence of phage-resistant bacteria variants and ensures that phages lytic for wild-type strain and its phage-resistant variants are selected. A phage cocktail lytic for Klebsiella pneumoniae was established by the SBS method. This phage cocktail consisted of three phages (GH-K1, GH-K2 and GH-K3) which have different but overlapping host strains. Several phage-resistant variants of Klebsiella pneumoniae were isolated after different phages treatments. The virulence of these variants was much weaker [minimal lethal doses (MLD)>1.3×109 cfu/mouse] than that of wild-type K7 countpart (MLD = 2.5×103 cfu/mouse). Compared with any single phage, the phage cocktail significantly reduced the mutation frequency of Klebsiella pneumoniae and effectively rescued Klebsiella pneumoniae bacteremia in a murine K7 strain challenge model. The minimal protective dose (MPD) of the phage cocktail which was sufficient to protect bacteremic mice from lethal K7 infection was only 3.0×104 pfu, significantly smaller (p<0.01) than that of single monophage. Moreover, a delayed administration of this phage cocktail was still effective in protection against K7 challenge.
Our data showed that the phage cocktail was more effective in reducing bacterial mutation frequency and in the rescue of murine bacteremia than monophage suggesting that phage cocktail established by SBS method has great therapeutic potential for multidrug-resistant bacteria infection.
The current study was performed to investigate mitochondrial protection and anti-aging activity of Astragalus polysaccharides (APS) and the potential underlying mechanism. Lipid peroxidation of liver and brain mitochondria was induced by Fe2+–Vit C in vitro. Thiobarbituric acid (TBA) colorimetry was used to measure the content of thiobarbituric acid reactive substances (TBARS). Mouse liver mitochondrial permeability transition (PT) was induced by calcium overload in vitro and spectrophotometry was used to measure it. The scavenging activities of APS on superoxide anion (O2•−) and hydroxyl radical (•OH), which were produced by reduced nicotinamide adenine dinucleotide (NADH)—N-Methylphenazonium methyl sulfate (PMS) and hydrogen peroxide (H2O2)–Fe2+ system respectively, were measured by 4-nitrobluetetrazolium chloride (NBT) reduction and Fenton reaction colorimetry respectively. The Na2S2O3 titration method was used to measure the scavenging activities of APS on H2O2. APS could inhibit TBARS production, protect mitochondria from PT, and scavenge O2•−, •OH and H2O2 significantly in a concentration-dependent manner respectively. The back of the neck of mice was injected subcutaneously with D-galactose to induce aging at a dose of 100 mg/kg/d for seven weeks. Moreover, the activities of catalase (CAT), surperoxide dismutase (SOD) and glutathione peroxidase (GPx) and anti-hydroxyl radical which were assayed by using commercial monitoring kits were increased significantly in vivo by APS. According to this research, APS protects mitochondria by scavenging reactive oxygen species (ROS), inhibiting mitochondrial PT and increasing the activities of antioxidases. Therefore, APS has the effect of promoting health.
Astragalus polysaccharides; mitochondria; anti-aging; antioxidant; reactive oxygen species; mitochondrial permeability transition
Somatosensory feedback from the larynx plays a critical role in regulation of normal upper airway functions, such as breathing, deglutition, and voice production, while altered laryngeal sensory feedback is known to elicit a variety of pathological reflex responses, including persistent coughing, dysphonia, and laryngospasm. Despite its clinical impact, the central mechanisms underlying the development of pathological laryngeal responses remain poorly understood. We examined the effects of persistent vocal fold (VF) inflammation and trauma, as frequent causes of long-lasting modulation of laryngeal sensory feedback, on brainstem immunoreactivity in the rat. Combined VF inflammation and trauma were induced by injection of lipopolysaccharide (LPS) solution and compared to VF trauma alone from injection of vehicle solution and to controls without any VF manipulations. Using a c-fos marker, we found significantly increased Fos-like immunoreactivity (FLI) in the bilateral intermediate/parvicellular reticular formation (IRF/PCRF) with a trend in the left solitary tract nucleus (NTS) only in animals with combined LPS-induced VF inflammation and trauma. Further, FLI in the right NTS was significantly correlated with the severity of LPS-induced VF changes. However, increased brainstem FLI response was not associated with FLI changes in the first-order neurons of the laryngeal afferents located in the nodose and jugular ganglia in either group. Our data indicate that complex VF alterations (i.e., inflammation/trauma vs. trauma alone) may cause prolonged excitability of the brainstem nuclei receiving a direct sensory input from the larynx, which, in turn, may lead to (mal)plastic changes within the laryngeal central sensory control.
larynx; inflammation; brainstem; immunoreactivity; rat
Transforming growth factor-β (TGF-β) signaling is critical for the differentiation of smooth muscle cells (SMCs) into quiescent cells expressing a full repertoire of contractile proteins. Heterozygous mutations in TGF-β receptor type II (TGFBR2) disrupt TGF-β signaling and lead to genetic conditions that predispose to thoracic aortic aneurysms and dissections (TAADs). The aim of this study is to determine the molecular mechanism by which TGFBR2 mutations cause TAADs.
Methods and results
Using aortic SMCs explanted from patients with TGFBR2 mutations, we show decreased expression of SMC contractile proteins compared with controls. Exposure to TGF-β1 fails to increase expression of contractile genes in mutant SMCs, whereas control cells further increase expression of these genes. Analysis of fixed and frozen aortas from patients with TGFBR2 mutations confirms decreased in vivo expression of contractile proteins relative to unaffected aortas. Fibroblasts explanted from patients with TGFBR2 mutations fail to transform into mature myofibroblasts with TGF-β1 stimulation as assessed by expression of contractile proteins.
These data support the conclusion that heterozygous TGFBR2 mutations lead to decreased expression of SMC contractile protein in both SMCs and myofibroblasts. The failure of TGFBR2-mutant SMCs to fully express SMC contractile proteins predicts defective contractile function in these cells and aligns with a hypothesis that defective SMC contractile function contributes to the pathogenesis of TAAD.
Thoracic aortic aneurysms and dissections; Smooth muscle cell differentiation; TGF-β; TGFBR2 mutations; Myofibroblast
To apply a diathesis × stress model to testing the association between peer victimization and depression in a sample of preadolescent girls.
DSM-IV symptoms of depression symptoms were measured at ages 9 and 11, assertiveness and peer victimization were assessed by youth report at age 9.
The interaction of low levels of assertiveness and high peer victimization at age 9 was predictive of depression symptoms at age 11, controlling for earlier depression symptoms.
The results extend the literature on peer relations and depression by identifying a group of girls who may be particularly vulnerable to the stress of negative peer interactions.
girls; depression; peer victimization; assertiveness
To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.
Models of developmental psychopathology emphasize both mediation and moderation processes among child and caregiving attributes; however, little research has examined both these processes simultaneously on the development of internalizing problems. This study tested a moderated mediation model that related early childhood shyness, emotion regulation and maternal negative control to school-age internalizing problems among 257 boys from low-income families. Shyness and maternal negative control was assessed at ages 1.5–2, emotion regulation was observed at age 3.5, and internalizing symptoms were assessed by mothers and teachers at age 6 or 7. Results indicated that 1) the active distraction regulation strategy mediated the relations between early shyness and maternal report of internalizing symptoms; 2) the passive/dependent regulation strategy mediated the relations between shyness and teacher report of internalizing symptoms; and 3) both mediation processes were moderated by maternal negative control. The results are discussed in relation to implications for early prevention and intervention.
Temperament; Emotion regulation; Internalizing symptoms; Parenting; Moderated mediation
Tight regulation of TGF-β superfamily signaling is important for normal cellular functions and tissue homeostasis. Since TGF-β superfamily signaling pathways are activated by a short phosphorylation cascade, from receptor phosphorylation to subsequent phosphorylation and activation of downstream signal transducer R-Smads, reversible phosphorylation serves as a critical step to assure the proper TGF-β signaling. This article will review the current progress on the understanding of dynamic phosphorylation in TGF-β signaling and the essential role of protein phosphatases in this process.
TGF-β signaling; Smads; phosphorylation; dephosphorylation; protein phosphatases
In eukaryotes, regulation of signaling mediators/effectors in the nucleus is one of the principal mechanisms that govern duration and strength of signaling. Smads are a family of structurally related intracellular proteins that serve as signaling effectors for TGF-β and TGF-β-related proteins. Accumulating evidence demonstrate that Smads possess intrinsic nucleocytoplasmic shuttling capacity, which enables them to transmit TGF-β signals from cell membrane to nucleus. We recently identified two important steps in the termination of nuclear Smad signaling. The first step is initiated by a serine/threonine phosphatase PPM1A that dephosphorylates Smad2/3 in the nucleus, thereby shutting down signaling capacity of phosphorylated Smad2/3. The second step involves nuclear export of dephosphorylated Smad2/3 with the aid of nuclear protein RanBP3 to terminate Smad signaling. This chapter introduces methods for examining nuclear export of Smad2/3 in TGF-β signaling.
Smad; PPM1A; RanBP3; nuclear phosphatase; nuclear export; signal transduction
We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor–binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor–binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.
Phage-coded lysin is an enzyme that destroys the cell walls of bacteria. Phage lysin could be an alternative to conventional antibiotic therapy against pathogens that are resistant to multiple antibiotics. In this study, a novel staphylococcal phage, GH15, was isolated, and the endogenous lytic enzyme (LysGH15) was expressed and purified. The lysin LysGH15 displayed a broad lytic spectrum; in vitro treatment killed a number of Staphylococcus aureus strains rapidly and completely, including methicillin-resistant S. aureus (MRSA). In animal experiments, a single intraperitoneal injection of LysGH15 (50 μg) administered 1 h after MRSA injections at double the minimum lethal dose was sufficient to protect mice (P < 0.01). Bacteremia in unprotected mice reached colony counts of about 107 CFU/ml within 3.5 h after challenge, whereas the mean colony count in lysin-protected mice was less than 104 CFU/ml (and ultimately became undetectable). These results indicate that LysGH15 can kill S. aureus in vitro and can protect mice efficiently from bacteremia in vivo. The phage lysin LysGH15 might be an alternative treatment strategy for infections caused by MRSA.