Repression of Germline RNAi Pathways in Somatic Cells by Retinoblastoma Pathway Chromatin Complexes

The retinoblastoma (Rb) tumor suppressor acts with a number of chromatin cofactors in a wide range of species to suppress cell proliferation. The Caenorhabditis elegans retinoblastoma gene and many of these cofactors, called synMuv B genes, were identified in genetic screens for cell lineage defects caused by growth factor misexpression. Mutations in many synMuv B genes, including lin-35/Rb, also cause somatic misexpression of the germline RNA processing P granules and enhanced RNAi. We show here that multiple small RNA components, including a set of germline-specific Argonaute genes, are misexpressed in the soma of many synMuv B mutant animals, revealing one node for enhanced RNAi. Distinct classes of synMuv B mutants differ in the subcellular architecture of their misexpressed P granules, their profile of misexpressed small RNA and P granule genes, as well as their enhancement of RNAi and the related silencing of transgenes. These differences define three classes of synMuv B genes, representing three chromatin complexes: a LIN-35/Rb-containing DRM core complex, a SUMO-recruited Mec complex, and a synMuv B heterochromatin complex, suggesting that intersecting chromatin pathways regulate the repression of small RNA and P granule genes in the soma and the potency of RNAi. Consistent with this, the DRM complex and the synMuv B heterochromatin complex were genetically additive and displayed distinct antagonistic interactions with the MES-4 histone methyltransferase and the MRG-1 chromodomain protein, two germline chromatin regulators required for the synMuv phenotype and the somatic misexpression of P granule components. Thus intersecting synMuv B chromatin pathways conspire with synMuv B suppressor chromatin factors to regulate the expression of small RNA pathway genes, which enables heightened RNAi response. Regulation of small RNA pathway genes by human retinoblastoma may also underlie its role as a tumor suppressor gene

A Linear Approximate Algorithm for Earth Mover's Distance with Thresholded Ground Distance

Effective and efficient image comparison plays a vital role in content-based image retrieval (CBIR). The earth mover’s distance (EMD) is an enticing measure for image comparison, offering intuitive geometric interpretation and modelling the human perceptions of similarity. Unfortunately, computing EMD, using the simplex method, has cubic complexity. FastEMD, based on min-cost flow, reduces the complexity to (O(N2log⁡N)). Although both methods can obtain the optimal result, the high complexity prevents the application of EMD on large-scale image datasets. Thresholding the ground distance can make EMD faster and more robust, since it can decrease the impact of noise and reduce the range of transportation. In this paper, we present a new image distance metric, EMD+, which applies a threshold to the ground distance. To compute EMD+, the FastEMD approach can be employed. We also propose a novel linear approximation algorithm. Our algorithm achieves ON complexity with the benefit of qualified bins. Experimental results show that (1) our method is 2 to 3 orders of magnitude faster than EMD (computed by FastEMD) and 2 orders of magnitude faster than FastEMD and (2) the precision of our approximation algorithm is no less than the precision of FastEMD

The ATP-Dependent Protease ClpP Inhibits Biofilm Formation by Regulating Agr and Cell Wall Hydrolase Sle1 in Staphylococcus aureus

Biofilm causes hospital-associated infections on indwelling medical devices. In Staphylococcus aureus, Biofilm formation is controlled by intricately coordinated network of regulating systems, of which the ATP-dependent protease ClpP shows an inhibitory effect. Here, we demonstrate that the inhibitory effect of ClpP on biofilm formation is through Agr and the cell wall hydrolase Sle1. Biofilm formed by clpP mutant consists of proteins and extracellular DNA (eDNA). The increase of the protein was, at least in part, due to the reduced protease activity of the mutant, which was caused by the decreased activity of agr. On the other hand, the increase of eDNA was due to increased cell lysis caused by the higher level of Sle1. Indeed, as compared with wild type, the clpP mutant excreted an increased level of eDNA, and showed higher sensitivity to Triton-induced autolysis. The deletion of sle1 in the clpP mutant decreased the biofilm formation, the level of eDNA, and the Triton-induced autolysis to wild-type levels. Despite the increased biofilm formation capability, however, the clpP mutant showed significantly reduced virulence in a murine model of subcutaneous foreign body infection, indicating that the increased biofilm formation capability cannot compensate for the intrinsic functions of ClpP during infection

Genetic Heterogeneity of Oesophageal Cancer in High-Incidence Areas of Southern and Northern China

BACKGROUND AND OBJECTIVE: Oesophageal cancer is one of the most common and deadliest cancers worldwide. Our previous population-based study reported a high prevalence of oesophageal cancer in Chaoshan, Guangdong Province, China. Ancestors of the Chaoshan population migrated from the Taihang Mountain region of north-central China, which is another high-incidence area for oesophageal cancer. The purpose of the present study was to obtain evidence of inherited susceptibility to oesophageal cancer in the Chaoshan population, with reference to the Taihang Mountain population, with the eventual goal of molecular identification of the disease genes. METHODS: We conducted familial correlation, commingling, and complex segregation analyses of 224 families from the Chaoshan population and 403 families from the Taihang population using the FPMM program of S.A.G.E. version 5.3.0. A second analysis focused on specific families having large numbers of affected individuals or early onset of the disease. RESULTS: For the general population, moderate sib-sib correlation was noticed for esophageal cancer. Additionally, brother-brother correlation was even higher. Commingling analyses indicated that a three-component distribution model best accounts for the variation in age of onset of oesophageal cancer, and that a multifactorial model provides the best fit to the general population data. An autosomal dominant mode and a dominant or recessive major gene with polygenic inheritance were found to be the best models of inherited susceptibility to oesophageal cancer in some large families. CONCLUSIONS: The current results provide evidence for inherited susceptibility to oesophageal cancer in certain high-risk groups in China, and support efforts to identify the susceptibility genes

Progress and challenges in maternal health in western China:a Countdown to 2015 national case study

Background China is one of the few Countdown countries to have achieved Millennium Development Goal 5 (75% reduction in maternal mortality ratio between 1990 and 2015). We aimed to examine the health systems and contextual factors that might have contributed to the substantial decline in maternal mortality between 1997 and 2014. We chose to focus on western China because poverty, ethnic diversity, and geographical access represent particular challenges to ensuring universal access to maternal care in the region. Methods In this systematic assessment, we used data from national census reports, National Statistical Yearbooks, the National Maternal and Child Health Routine Reporting System, the China National Health Accounts report, and National Health Statistical Yearbooks to describe changes in policies, health financing, health workforce, health infrastructure, coverage of maternal care, and maternal mortality by region between 1997 and 2014. We used a multivariate linear regression model to examine which contextual and health systems factors contributed to the regional variation in maternal mortality ratio in the same period. Using data from a cross-sectional survey in 2011, we also examined equity in access to maternity care in 42 poor counties in western China. Findings Maternal mortality declined by 8·9% per year between 1997 and 2014 (geometric mean ratio for each year 0·91, 95% CI 0·91–0·92). After adjusting for GDP per capita, length of highways, female illiteracy, the number of licensed doctors per 1000 population, and the proportion of ethnic minorities, the maternal mortality ratio was 118% higher in the western region (2·18, 1·44–3·28) and 41% higher in the central region (1·41, 0·99–2·01) than in the eastern region. In the rural western region, the proportion of births in health facilities rose from 41·9% in 1997 to 98·4% in 2014. Underpinning such progress was the Government’s strong commitment to long-term strategies to ensure access to delivery care in health facilities—eg, professionalisation of maternity care in large hospitals, effective referral systems for women medically or socially at high risk, and financial subsidies for antenatal and delivery care. However, in the poor western counties, substantial disparity by education level of the mother existed in access to health facility births (44% of illiterate women vs 100% of those with college or higher education), antenatal care (17% vs 69%) had at least four visits), and caesarean section (8% vs 44%). Interpretation Despite remarkable progress in maternal survival in China, substantial disparities remain, especially for the poor, less educated, and ethnic minority groups in remote areas in western China. Whether China’s highly medicalised model of maternity care will be an answer for these populations is uncertain. A strategy modelled after China’s immunisation programme, whereby care is provided close to the women’s homes, might need to be explored, with township hospitals taking a more prominent role

The Cassiopeia Filament: A Blown Spur of the Local Arm

We present wide-field and high-sensitivity CO(1-0) molecular line observations toward the Cassiopeia region, using the 13.7m millimeter telescope of the Purple Mountain Observatory (PMO). The CO observations reveal a large-scale highly filamentary molecular cloud within the Galactic region of 132\fdg0\,$\geq$\,$l$\,$\geq$\,122\fdg0 and -1\fdg0\,$\leq$\,$b$\,$\leq$\,3\fdg0 and the velocity range from approximately +1 to +4 km/s. The measured length of the large-scale filament, referred to as the Cassiopeia Filament, is about 390 pc. The observed properties of the Cassiopeia Filament, such as length, column density, and velocity gradient, are consistent with those synthetic large-scale filaments in the inter-arm regions. Based on its observed properties and location on the Galactic plane, we suggest that the Cassiopeia Filament is a spur of the Local arm, which is formed due to the galactic shear. The western end of the Cassiopeia Filament shows a giant arc-like molecular gas shell, which is extending in the velocity range from roughly -1 to +7 km/s. Finger-like structures, with systematic velocity gradients, are detected in the shell. The CO kinematics suggest that the large shell is expanding at a velocity of ~6.5 km/s. Both the shell and finger-like structures outline a giant bubble with a radius of ~16 pc, which is likely produced by stellar wind from the progenitor star of a supernova remnant. The observed spectral linewidths suggest that the whole Cassiopeia Filament was quiescent initially until its west part was blown by stellar wind and became supersonically turbulent.Comment: 46 pages, 19 figures, to be published by the A

Golgi-associated LC3 lipidation requires V-ATPase in noncanonical autophagy

Autophagy is an evolutionarily conserved catabolic process by which cells degrade intracellular proteins and organelles in the lysosomes. Canonical autophagy requires all autophagy proteins (ATGs), whereas noncanonical autophagy is activated by diverse agents in which some of the essential autophagy proteins are dispensable. How noncanonical autophagy is induced and/or inhibited is still largely unclear. In this study, we demonstrated that AMDE-1, a recently identified chemical that can induce canonical autophagy, was able to elicit noncanonical autophagy that is independent of the ULK1 (unc-51-like kinase 1) complex and the Beclin1 complex. AMDE-1-induced noncanonical autophagy could be specifically suppressed by various V-ATPase (vacuolar-type H(+)-ATPase) inhibitors, but not by disturbance of the lysosome function or the intracellular ion redistribution. Similar findings were applicable to a diverse group of stimuli that can induce noncanonical autophagy in a FIP200-independent manner. AMDE-1-induced LC3 lipidation was colocalized with the Golgi complex, and was inhibited by the disturbance of Golgi complex. The integrity of the Golgi complex was also required for multiple other agents to stimulate noncanonical LC3 lipidation. These results suggest that the Golgi complex may serve as a membrane platform for noncanonical autophagy where V-ATPase is a key player. V-ATPase inhibitors could be useful tools for studying noncanonical autophagy

Evaluation of 17 microsatellite markers for parentage testing and individual identification of domestic yak (Bos grunniens)

Background Yak (Bos grunniens) is the most important domestic animal for people living at high altitudes. Yak ordinarily feed by grazing, and this behavior impacts the accuracy of the pedigree record because it is difficult to control mating in grazing yak. This study aimed to evaluate the pedigree system and individual identification in polled yak. Methods A total of 71 microsatellite loci were selected from the literature, mostly from the studies on cattle. A total of 35 microsatellite loci generated excellent PCR results and were evaluated for the parentage testing and individual identification of 236 unrelated polled yaks. A total of 17 of these 35 microsatellite loci had polymorphic information content (PIC) values greater than 0.5, and these loci were in Hardy–Weinberg equilibrium without linkage disequilibrium. Results Using multiplex PCR, capillary electrophoresis, and genotyping, very high exclusion probabilities were obtained for the combined core set of 17 loci. The exclusion probability (PE) for one candidate parent when the genotype of the other parent is not known was 0.99718116. PE for one candidate parent when the genotype of the other parent is known was 0.99997381. PE for a known candidate parent pair was 0.99999998. The combined PEI (PE for identity of two unrelated individuals) and PESI (PE for identity of two siblings) were >0.99999999 and 0.99999899, respectively. These findings indicated that the combination of 17 microsatellite markers could be useful for efficient and reliable parentage testing and individual identification in polled yak. Discussion Many microsatellite loci have been investigated for cattle paternity testing. Nevertheless, these loci cannot be directly applied to yak identification because the two bovid species have different genomic sequences and organization. A total of 17 loci were selected from 71 microsatellite loci based on efficient amplification, unambiguous genotyping, and high PIC values for polled yaks, and were suitable for parentage analysis in polled yak populations

Microbiome and Metabolomics Reveal the Effects of Different Feeding Systems on the Growth and Ruminal Development of Yaks

The change in the feeding system can greatly improve the growth performance of the yak (Bos grunniens), an important livestock species in the plateau region. Here, we comprehensively compared the effects of different feeding systems on the growth performance and ruminal development of yaks, and investigated the effects of ruminal microorganisms and metabolites using the 16S rRNA gene sequencing and liquid chromatograph–mass spectrometer (LC-MS) technologies. We found that compared to traditional grazing feeding, house feeding significantly improved the growth performance (such as average daily gain and net meat weight) and rumen development of the yaks. At the genus level, the abundance of Rikenellaceae RC9 Gut group, Christensenellaceae R-7 group, Lachnospiraceae NK3A20 group, Ruminococcaceae UCG-014, and Prevotellaceae UCG-003 showed significant differences and was closely related to rumen development in the two distinct feeding systems. Also, metabolomics revealed that the change in the feeding system significantly affected the concentration and metabolic pathways of the related rumen metabolites. The metabolites with significant differences were significantly enriched in purine metabolism (xanthine, adenine, inosine, etc.), tyrosine metabolism (L-tyrosine, dopaquinone, etc.), phenylalanine metabolism (dihydro-3-caumaric acid, hippuric acid, etc.), and cAMP signaling pathway [acetylcholine, (-)-epinephrine, etc.]. This study scientifically support the house fattening feeding system for yaks. Also, our results provide new insights into the composition and function of microbial communities that promote ruminal development and in general growth of the yaks