CBEA: Competitive balances for taxonomic enrichment analysis

Research in human-associated microbiomes often involves the analysis of taxonomic count tables generated via high-throughput sequencing. It is difficult to apply statistical tools as the data is high-dimensional, sparse, and compositional. An approachable way to alleviate high-dimensionality and sparsity is to aggregate variables into pre-defined sets. Set-based analysis is ubiquitous in the genomics literature and has demonstrable impact on improving interpretability and power of downstream analysis. Unfortunately, there is a lack of sophisticated set-based analysis methods specific to microbiome taxonomic data, where current practice often employs abundance summation as a technique for aggregation. This approach prevents comparison across sets of different sizes, does not preserve inter-sample distances, and amplifies protocol bias. Here, we attempt to fill this gap with a new single-sample taxon enrichment method that uses a novel log-ratio formulation based on the competitive null hypothesis commonly used in the enrichment analysis literature. Our approach, titled competitive balances for taxonomic enrichment analysis (CBEA), generates sample-specific enrichment scores as the scaled log-ratio of the subcomposition defined by taxa within a set and the subcomposition defined by its complement. We provide sample-level significance testing by estimating an empirical null distribution of our test statistic with valid p-values. Herein, we demonstrate, using both real data applications and simulations, that CBEA controls for type I error, even under high sparsity and high inter-taxa correlation scenarios. Additionally, CBEA provides informative scores that can be inputs to downstream analyses such as prediction tasks.     

AvrRps4 effector family processing and recognition in lettuce

During pathogenesis, effector proteins are secreted from the pathogen to the host plant to provide virulence activity for invasion of the host. However, once the host plant recognizes one of the delivered effectors, effector‐triggered immunity activates a robust immune and hypersensitive response (HR). In planta, the effector AvrRps4 is processed into the N‐terminus (AvrRps4^N) and the C‐terminus (AvrRps4^C). AvrRps4^C is sufficient to trigger HR in turnip and activate AtRRS1/AtRPS4‐mediated immunity in Arabidopsis; on the other hand, AvrRps4^N induces HR in lettuce. Furthermore, AvrRps4^N‐mediated HR requires a conserved arginine at position 112 (R112), which is also important for full‐length AvrRps4 (AvrRps4^F) processing. Here, we show that effector processing and effector recognition in lettuce are uncoupled for the AvrRps4 family. In addition, we compared effector recognition by lettuce of AvrRps4 and its homologues, HopK1 and XopO. Interestingly, unlike for AvrRps4 and HopK1, mutation of the conserved R111 in XopO by itself was insufficient to abolish recognition. The combination of amino acid substitutions arginine 111 to leucine with glutamate 114 to lysine abolished the XopO‐mediated HR, suggesting that AvrRps4 family members have distinct structural requirements for perception by lettuce. Together, our results provide an insight into the processing and recognition of AvrRps4 and its homologues.     

MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments

Hi-C is a genome-wide chromosome conformation capture technology that detects interactions between pairs of genomic regions and exploits higher order chromatin structures. Conceptually Hi-C data counts interaction frequencies between every position in the genome and every other position. Biologically functional interactions are expected to occur more frequently than transient background and artefactual interactions. To identify biologically relevant interactions, several background models that take biases such as distance, GC content and mappability into account have been proposed. Here we introduce MaxHiC, a background correction tool that deals with these complex biases and robustly identifies statistically significant interactions in both Hi-C and capture Hi-C experiments. MaxHiC uses a negative binomial distribution model and a maximum likelihood technique to correct biases in both Hi-C and capture Hi-C libraries. We systematically benchmark MaxHiC against major Hi-C background correction tools including Hi-C significant interaction callers (SIC) and Hi-C loop callers using published Hi-C, capture Hi-C, and Micro-C datasets. Our results demonstrate that 1) Interacting regions identified by MaxHiC have significantly greater levels of overlap with known regulatory features (e.g. active chromatin histone marks, CTCF binding sites, DNase sensitivity) and also disease-associated genome-wide association SNPs than those identified by currently existing models, 2) the pairs of interacting regions are more likely to be linked by eQTL pairs and 3) more likely to link known regulatory features including known functional enhancer-promoter pairs validated by CRISPRi than any of the existing methods. We also demonstrate that interactions between different genomic region types have distinct distance distributions only revealed by MaxHiC. MaxHiC is publicly available as a python package for the analysis of Hi-C, capture Hi-C and Micro-C data.     

Inhibitory role of TRIP-Br1 oncoprotein in anticancer drug-mediated programmed cell death via mitophagy activation

Chemotherapy has been widely used as a clinical treatment for cancer over the years. However, its effectiveness is limited because of resistance of cancer cells to programmed cell death (PCD) after treatment with anticancer drugs. To elucidate the resistance mechanism, we initially focused on cancer cell-specific mitophagy, an autophagic degradation of damaged mitochondria. This is because mitophagy has been reported to provide cancer cells with high resistance to anticancer drugs. Our data showed that TRIP-Br1 oncoprotein level was greatly increased in the mitochondria of breast cancer cells after treatment with various anticancer drugs including staurosporine (STS), the main focus of this study. STS treatment increased cellular ROS generation in cancer cells, which triggered mitochondrial translocation of TRIP-Br1 from the cytosol via dephosphorylation of TRIP-Br1 by protein phosphatase 2A (PP2A). Up-regulated mitochondrial TRIP-Br1 suppressed cellular ROS levels. In addition, TRIP-Br1 rapidly removed STS-mediated damaged mitochondria by activating mitophagy. It eventually suppressed STS-mediated PCD via degradation of VDACI, TOMM20, and TIMM23 mitochondrial membrane proteins. TRIP-Br1 enhanced mitophagy by increasing expression levels of two crucial lysosomal proteases, cathepsins B and D. In conclusion, TRIP-Br1 can suppress the sensitivity of breast cancer cells to anticancer drugs by activating autophagy/mitophagy, eventually promoting cancer cell survival.     

Development of a Peristaltic Micropump for Bio-Medical Applications Based on Mini LIPCA

This paper presents the design, fabrication, and experimental characterization of a peristaltic micropump. The micropump is composed of two layers fabricated from Polydimethylsiloxane （PDMS） material. The first layer has a rectangular channel and two valve seals. Three rectangular mini lightweight piezo-composite actuators are integrated in the second layer, and used as actuation parts. Two layers are bonded, and covered by two Polymethyl Methacrylate （PMMA） plates, which help increase the stiffness of the micropump. A maximum flow rate of 900μL.min 1 and a maximum backpressure of 1.8 kPa are recorded when water is used as pump liquid. We measured the power consumption of the micropump. The micropump is found to be a promising candidate for bio-medical application due to its bio-compatibility, portability, bidirectionality, and simple effective design.     

mTORC1-independent translation control in mammalian cells by methionine adenosyltransferase 2A and S-adenosylmethionine

Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine (SAM). As the sole methyl-donor for methylation of DNA, RNA, and proteins, SAM levels affect gene expression by changing methylation patterns. Expression of MAT2A, the catalytic subunit of isozyme MAT2, is positively correlated with proliferation of cancer cells; however, how MAT2A promotes cell proliferation is largely unknown. Given that the protein synthesis is induced in proliferating cells and that RNA and protein components of translation machinery are methylated, we tested here whether MAT2 and SAM are coupled with protein synthesis. By measuring ongoing protein translation via puromycin labeling, we revealed that MAT2A depletion or chemical inhibition reduced protein synthesis in HeLa and Hepa1 cells. Furthermore, overexpression of MAT2A enhanced protein synthesis, indicating that SAM is limiting under normal culture conditions. In addition, MAT2 inhibition did not accompany reduction in mechanistic target of rapamycin complex 1 activity but nevertheless reduced polysome formation. Polysome-bound RNA sequencing revealed that MAT2 inhibition decreased translation efficiency of some fraction of mRNAs. MAT2A was also found to interact with the proteins involved in rRNA processing and ribosome biogenesis; depletion or inhibition of MAT2 reduced 18S rRNA processing. Finally, quantitative mass spectrometry revealed that some translation factors were dynamically methylated in response to the activity of MAT2A. These observations suggest that cells possess an mTOR-independent regulatory mechanism that tunes translation in response to the levels of SAM. Such a system may acclimate cells for survival when SAM synthesis is reduced, whereas it may support proliferation when SAM is sufficient.     

The beta chorionic gonadotropin-beta luteinizing gene cluster maps to human chromosome 19

Summary We used a cloned human cDNA probe homologous to the placenta chorionic gonadotropin subunit (CGB) and to the pituitary luteinizing hormone subunit (LHB) and Southern blotting techniques to analyse DNA from a series of rodent x human somatic cell hybrids for the presence of specific gonadotropin subunit related sequences. Our results provide evidence for the assignment and linkage of the eight genes (or pseudogenes) coding for the subunit of these glycoprotein hormones to chromosome 19. Moreover, we observed a strict concordance between the permissivity of mouse x man hybrid cells to enteroviruses (which is linked to the presence of specific cell receptors encoded by human chromosome 19) and the presence of CGB and LHB related sequences, thus confirming the localization of the structural genes for the subunits on chromosome 19.This work was supported in part by INSERM grants CRL 81 1041 and by MRC grant MT 4860     

越南铁线莲属一新种

本文描述的产于越南的毛茛科Ranunculaceae铁线莲属Clematis一新种C. hagiangensis N. T. Do是欧亚大陆第一个具单性花的种, 在花构造方面与单性铁线莲组单性铁线莲亚组sect. Aspidanthera Spach subsect. Dioicae (Prantl) W. T. Wang的种类近缘, 但叶均为单叶, 萼片呈卵形或宽卵形而不同。在单性铁线莲亚组的种, 叶通常为复叶, 只在C. dimorphophylla W. T. Wang和C. variifolia W. T. Wang同时为单叶和复叶, 此外萼片呈长圆形、倒披针形或狭卵形。     

河静黑叶猴果实性食物组成、选择及其对种子的扩散作用

喀斯特森林的生态环境较其他类型的森林更为脆弱.由于抗干扰和恢复能力低,喀斯特森林中种子扩散对维持植物种群的续存与更新具极其重要的作用.叶猴以叶为主要食物,果实是仅列其后的第二大食物资源.对分布于喀斯特生境的叶猴来说,它们对果实的取食具有潜在的种子传播作用.基于此,于2009年7月-2010年12月,在越南广平的风芽-格邦国家自然公园,通过实地跟踪观察结合粪便收集调查了河静黑叶猴(Trachypithecus francoisi hatinhensis)对果实的选择及其对种子的潜在扩散作用.河静黑叶猴全年共采食果实类食物38科131种,取食的果实种类和取食高峰持续期均高于其他地区黑叶猴对果实的取食.这得益于当地原始雨林中丰富的果实食物资源.河静黑叶猴对果实种类没有明显的选择偏好(-0.3＜S112种果实＜0.3),果实资源的可获得性亦不影响其对果实的取食频次(r=-0.13,P=0.15＞0.05),在雨季的果实食物种类和取食强度上均高于旱季(z=-2.903,P=0.02＜0.05).在果实性状的选择上,河静黑叶猴对处理难度较小的浆果和核果(两种类型的果实共106种,占80.9％)有明显的选择偏好,更多地选择黄色(46种)、红色(29种)和绿色(14种)(三种颜色的果实占果实种类的68.7％),重量多为5 g以上较大的果实(共104种,占果实种类的79.4％),更多地选择果实内仅有1-2颗种子的果实.河静黑叶猴多吞食直径小于3 cm的种子,在猴群的粪便中发现了85种果实的种子,尤以肉质的浆果和核果最多,如垂叶榕(Ficus benjamina)、柿叶青梅(Vatica diospyroides)、构树(Broussonetia papyrifera)等.最远传播距离可达397 m.对其他的果实,则以吐出或丢弃的方式短距离传播,多集中在6-20 m范围.河静黑叶猴是一些果实较大或果皮较硬的植物重要的潜在扩散媒介,因为此类种子不能依靠鸟类吞食传播,如水浦桃(Syzygium jambos)、红毛丹(Nephelium lappaceum)和木奶果(Baccaurea ramiflora)等.河静黑叶猴一年中在雨季的夏秋两季(8-12月)对果实的取食强度达到高峰,这期间每月在猴群粪便中发现的种子数量均超过1000.结果反映出河静黑叶猴对喀斯特森林中的果实植物种子有潜在的传播作用.