Identification of the three subtypes and the prognostic characteristics of stomach adenocarcinoma: analysis of the hypoxia-related long non-coding RNAs

Functional & Integrative Genomics - Stomach adenocarcinoma (STAD) is one of the most commonly diagnosed cancers. This study analyzed the subtypes and characteristics of STAD subtypes by...     

Mechanical analysis of deep tissue injury during sitting in patients with spinal cord injury via parametric finite element model

Biomechanics and Modeling in Mechanobiology - Spinal cord injury patients are prone to develop deep tissue injury because of long-term mechanical load. However, there is a lack of statistical...     

高寒草甸植物物种丧失对草原毛虫的影响

植物多样性是调控食物网结构和生态系统功能最重要的生物因素, 植物多样性丧失深刻影响食草动物, 但由于小型食草动物种群数量波动明显、统计随机性较大等困难, 我们对植物多样性丧失如何影响小型食草动物依然知之甚少。基于在青藏高原高寒草甸设置的长期植物物种剔除试验, 本研究于2016-2020年7-8月连续调查了植物物种剔除各处理中草原毛虫(Gynaephora alpherakiif)的数量, 分析了植物物种及功能群丧失对草原毛虫的影响。结果表明, 虽然时空差异及统计随机性是影响草原毛虫数量变化的主要因素, 但植物物种剔除介导的群落差异对草原毛虫数量的影响依然显著: (1)在各观测时段, 优势种线叶嵩草(Kobresia capillifolia)的丧失导致群落中草原毛虫数量显著减少; 禾草类物种丧失也会减少草原毛虫数量, 但其影响仅在8月显著; (2)杂类草物种丧失通过增加群落中禾草物种多度, 可增加草原毛虫数量; 豆科物种丧失使莎草增多, 也会增加草原毛虫数量; (3)各植物功能群部分物种剔除并未显著影响草原毛虫数量。本研究证实了高寒草甸中草原毛虫数量会因优势植物嵩草和禾草的多度减少或禾草物种丧失而显著减少, 但群落总生物量、个体数和物种丰富度、豆科多度以及各功能群植物同比减少, 都对草原毛虫数量没有明显影响。这些结果说明在随机作用主导下, 植物群落中的特定功能群相对多度(而非物种多样性)变化深刻影响草原毛虫适合度, 进而影响生态系功能及服务; 未来生物多样性研究及草地虫害生物防控中应更多考虑统计随机性及植物功能多样性对小型食草动物的影响。     

2021年膜翅目新增分类单元

本文对2021年发表的膜翅目昆虫新分类单元进行了梳理和总结。结合数据库检索, 基于标本记录, 全球膜翅目学者于2021年发表该目新分类单元的期刊论文355篇, 新增分类单元条目共1,152条, 隶属于21总科66科416属, 包括5新科4新亚科83新属3新亚属1,054新种和3新亚种。现生类群相关期刊论文309篇, 新增分类单元条目980条, 隶属于18总科52科332属, 包括2新科26新属3新亚属946新种和3新亚种。绝灭类群相关期刊论文46篇, 新增分类单元条目172条, 隶属于14总科27科86属, 包括3新科4新亚科57新属和108新种。2021年中国膜翅目新增分类单元的相关期刊论文83篇, 新增分类单元条目235条, 隶属于17总科34科91属, 包括3新属(绝灭类群1新属)和232新种(绝灭类群2新种); 现生类群中新增的2属分别记录自台湾和浙江, 新种数量排前五位的省级行政单位有云南(54个)、浙江(42个)、福建(18个)、西藏(18个)和新疆(16个)。在全球现生、绝灭和中国现生膜翅目总科新物种数量的对比中, 姬蜂总科新种数量最多, 分别约占全球现生、绝灭和中国现生膜翅目新种总数的32.5% (307个/946个)、19.4% (21个/108个)和37.0% (85个/230个)。有关现生膜翅目新种发表情况, 在洲级地理单元中, 亚洲发表新种数量最多, 约占56.9% (538个); 在洲级地理亚单元中, 东亚发表新种数量最多, 约占28.6% (271个); 在国家和地区行政单元中, 中国发表新种数量最多, 约占24.3% (230个)。在76种期刊的355篇论文中, 有348篇英文论文、4篇中文论文和3篇法语论文。这些结果表明, 中国膜翅目分类在全球膜翅目分类中发挥着十分重要的作用。     

MicroRNA-638 inhibits human airway smooth muscle cell proliferation and migration through targeting cyclin D1 and NOR1

Abnormal airway smooth muscle cell (ASMC) proliferation and migration contribute significantly to increased ASM mass associated with asthma. MicroRNA (miR)-638 is a primate-specific miRNA that plays important roles in development, DNA damage repair, hematopoiesis, and tumorigenesis. Although it is highly expressed in ASMCs, its function in ASM remodeling remains unknown. In the current study, we found that in response to various mitogenic stimuli, including platelet-derived growth factor-two B chains (PDGF-BB), transforming growth factor β1, and fetal bovine serum, the expression of miR-638, as determined by quantitative real-time polymerase chain reaction (qRT-PCR), was significantly downregulated in the proliferative human ASMCs. Both gain- and loss-of-function studies were performed to study the role of miR-638 in ASMC proliferation and migration. We found that adenovirus-mediated miR-638 overexpression markedly inhibits ASMC proliferation and migration, while ablation of miR-638 by anti-miR-638 markedly increases cell proliferation and migration, as determined by WST-8 proliferation and scratch wound assays. Dual-luciferase reporter assay, qRT-PCR, and immunoblot analysis were used to investigate the effects of miR-638 on the expression of the downstream target genes in ASMCs. Our results demonstrated that miR-638 overexpression significantly reduced the expression of downstream target cyclin D1 and NOR1, both of which have been shown to be essential for cell proliferation and migration. Together, our study provides the first in vitro evidence highlighting the antiproliferative and antimigratory roles of miR-638 in human ASMC remodeling and suggests that targeted overexpression of miR-638 in ASMCs may provide a novel therapeutic strategy for preventing ASM hyperplasia associated with asthma.     

Brain-derived neurotrophic factor: A steroidogenic regulator of Leydig cells

The brain-derived neurotrophic factor (BDNF) was first recognized for its roles in the peripheral and central nervous systems, and its complex functions on mammalian organs have been extended constantly. However, to date, little is known about its effects on the male reproductive system, including the steroidogenesis of mammals. The purpose of this study was to elucidate the effects of BDNF on testosterone generation of Leydig cells and the underlying mechanisms. We found that BDNF-induced proliferation of TM3 Leydig cells via upregulation of proliferating cell nuclear antigen ( Pcna) and promoted testosterone generation as a result of upregulation of steroidogenic acute regulatory protein ( Star), 3b-hydroxysteroid dehydrogenase ( Hsd3b1), and cytochrome P450 side-chain cleavage enzyme ( Cyp11a1) both in primary Leydig cells and TM3 Leydig cells, which were all attenuated in Bdnf knockdown TM3 Leydig cells. Furthermore, the possible mechanism of testosterone synthesis was explored in TM3 Leydig cells. The results showed that BDNF enhanced extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) phosphorylation, and the effect was disrupted by Bdnf deletion. Moreover, PD98059, a potent selective inhibitor of ERK1/2 activation, compromised BDNF-induced testosterone generation and upregulation of Star, Hsd3b1, and Cyp11a1. The Bdnf knockdown assay, on the other hand, indicated the autocrine effect of BDNF on steroidogenesis in TM3 Leydig cells. On the basis of these results, we concluded that BDNF, acting as an autocrine factor, induced testosterone generation as a result of the upregulation of Star, Hsd3b1, and Cyp11a1 via stimulation of the ERK1/2 pathway.     

Prediction analysis for microbiome sequencing data

One goal of human microbiome studies is to relate host traits with human microbiome compositions. The analysis of microbial community sequencing data presents great statistical challenges, especially when the samples have different library sizes and the data are overdispersed with many zeros. To address these challenges, we introduce a new statistical framework, called predictive analysis in metagenomics via inverse regression (PAMIR), to analyze microbiome sequencing data. Within this framework, an inverse regression model is developed for overdispersed microbiota counts given the trait, and then a prediction rule is constructed by taking advantage of the dimension‐reduction structure in the model. An efficient Monte Carlo expectation‐maximization algorithm is proposed for maximum likelihood estimation. The method is further generalized to accommodate other types of covariates. We demonstrate the advantages of PAMIR through simulations and two real data examples.     

Construction of a sensitive pyrogen-testing cell model by site-specific knock-in of multiple genes

A pyrogen test is crucial for evaluating the safety of drugs and medical equipment, especially those involved in injections. As existing pyrogen tests, including the rabbit pyrogen test, the limulus amoebocyte lysate (LAL) test and the monocyte activation test have limitations, development of new models for pyrogen testing is necessary. Here we develop a sensitive cell model for pyrogen test based on the lipopolysaccharides (LPS) signal pathway. TLR4, MD2, and CD14 play key roles in the LPS-mediated pyrogen reaction. We established a new TLR4/MD2/CD14-specific overexpressing knock-in cell model using the CRISPR/CAS9 technology and homologous recombination to detect LPS. Stimulation of our TLR4/CD14/MD2 knock-in cell line model with LPS leads to the release of the cytokines IL-6 and TNF-alpha, with a detection limit of 0.005 EU/ml, which is greatly lower than the lower limit of 0.015 EU/ml detected by the Tachypleus amebocyte lysate (TAL) assay.     

Quantitative phosphoproteomic analyses provide evidence for extensive phosphorylation of regulatory proteins in the rhizobia–legume symbiosis

Plant Molecular Biology - PsLecRLK overexpression in rice provides tolerance against salinity stress and cause upregulation of SOS1 pathway genes, which are responsible for extrusion of excess Na+...