The role of NF-kappaB-inducing kinase (NIK) in cytokine signaling remains controversial. To identify the physiologic functions NIK, we disrupted NIK locus by gene targeting. Although NIK-/- mice displayed abnormalities both lymphoid tissue development and antibody responses, cells manifested normal NF-kappaB DNA binding activity when treated with a variety cytokines, including tumor necrosis factor (TNF), interleukin-1 (IL-1), lymphotoxin-beta (LTbeta). However, was selectively required for...

Shewanella oneidensis is a highly motile organism by virtue of polar flagellum. Unlike most flagellated bacteria, it contains only one major chromosome segment encoding the components flagellum with exception motor proteins. In this region, three genes encode flagellinsaccording to original genome annotation. However, we find that flaA and flaB functional filament subunits. Although these two genesare under control different promoters, they are actively transcribed subsequently translated,...

Shewanella are renowned for their ability to utilize a wide range of electron acceptors (EA) respiration, which has been partially accredited the presence large number c-type cytochromes. To investigate involvement cytochrome proteins in aerobic and anaerobic respiration oneidensis Mr -1, 36 in-frame deletion mutants, among possible 41 predicted, genes were obtained. The potential each individual reduction variety EAs was assessed individually as well competition experiments. While results...

Abstract Background Members of the Erysipelotrichaceae family have a high abundance in intestinal tract mammals, and been reported to be associated with host metabolic disorders inflammatory diseases. In our previous study, we found that strains cecum was concentration N-acetylgalactosamine (GalNAc). However, only few members isolated cultured, their main characteristics, genomic information functional capacity carbohydrate metabolism remain unknown. Results this tested 10 different kinds...

We have often observed unexpected state transitions of complex systems. are thus interested in how to steer a system from an desired state. Here we introduce the concept transittability networks and derive new sufficient necessary condition for which can be efficiently verified. define steering kernel as minimal set nodes control signals must directly applied transition between two specific states network propose graph-theoretic algorithm identify states. our 27 real networks, finding that...

Astragalus membranaceus var. mongholicus (AMM), a member of the Leguminosae, is one most important medicinal plants worldwide. The dried roots AMM have wide range pharmacological effects and are traditional Chinese medicine. Here, we report first chromosome-level reference genome AMM, comprising nine pseudochromosomes with total size 1.47 Gb 27 868 protein-encoding genes. Comparative genomic analysis reveals that has not experienced an independent whole-genome duplication (WGD) event after...

A joint maintenance decision-making framework is proposed to optimise the long-term plan and lower cost for offshore wind farms. The historical speed data are screened by using method of k-means clustering, Markov chains established in different seasons. On this basis, approach chain Monte Carlo applied simulate distribution repair vessel's waiting time maintenance, where impact on availability considered. Moreover, components turbines divided into four states according their effective ages,...

Abstract Background Although solid surface-associated biofilm development of S. oneidensis has been extensively studied in recent years, pellicles formed at the air-liquid interface are largely overlooked. The goal this work was to understand basic requirements and mechanism pellicle formation . Results We demonstrated that can be completed when oxygen certain cations were present. Ca(II), Mn(II), Cu(II), Zn(II) essential for process evidenced by fully rescuing from EDTA treatment while Mg...

Biomolecules do not perform their functions alone, but interactively with one another to form so called biomolecular networks. It is well known that a complex disease stems from the malfunctions of corresponding Therefore, important tasks identify drug targets In this study, target identification formulated as problem finding steering nodes in networks while concept network output controllability applied identification. By applying control signals these nodes, are expected be transited state...

We report a previously undescribed mechanism for the rugose morphotype in Shewanella oneidensis, research model investigating redox transformations of environmental contaminants. Bacteria may form smooth or colonies on agar plates. In general, conversion from to colony is attributed increased production exopolysaccharide (EPS). this work, we discovered that aflagellate S. oneidensis mutants grew into colonies, whereas those with nonfunctional flagellar filaments remained smooth. EPS was not...

Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of library a key step NGS. Therefore, various construction methods have been explored. However, are still limited by some shortcomings. This study developed new NGS method, Single strand Adaptor Library Preparation (SALP), using novel single adaptor (SSA). SSA double-stranded oligonucleotide with 3′ overhang 3 random nucleotides, which can be efficiently ligated end DNA T4 ligase....

Studying the controllability of biomolecular networks can result in profound knowledge about molecular biological systems. However, there is no comprehensive and easy-to-use platform for analyzing although various algorithms complex network have been proposed recently. In this application note, we develop CytoCtrlAnalyser which a Cytoscape app to provide networks. Nine integrated CytoCtrlAnalyser. With topologies customized control settings imported into CytoCtrlAnalyser, users identify...

The metabolism of gut microbiota produces bioactive metabolites that modulate host physiology and promote self-growth. Erysipelotrichaceae is one the most common anaerobic microorganism families in gut, which has been discovered to play a vital role metabolic disorders inflammatory diseases. Our previous study found N-acetylgalactosamine (GalNAc) caecal content pigs significantly affected abundance strains. However, it remains unknown how GalNAc feeding vitro culture affects expression...

Recently we have identified a novel protein NIP45 (nuclear factor of activated T cells [NFAT]-interacting protein) which substantially augments interleukin (IL)-4 gene transcription. The provision together with NFAT and the helper cell type 2 (Th2)-specific transcription c-Maf to normally refractory IL-4 production, such as B or Th1 clones, results in substantial secretion levels that approximate those produced by primary Th2 cells. In studies designed further our understanding activity,...

Many systems of interests in practices can be represented as complex networks. For biological systems, biomolecules do not perform their functions alone but interact with each other to form so-called biomolecular A system is said controllable if it steered from any initial state final finite time. The network controllability has become essential study the dynamics networks and understand importance individual nodes Some interesting phenomena have been discovered terms structural Most current...

Escherichia coli sequence type 167 (ST167) is an international multiresistant high-risk clone associated with New Delhi metallo-beta-lactamase (NDM) carbapenemase. Here, we report the whole genome of ST167 clinical isolate (EC16), obtained from a patient abdominal infection in China, coharbouring blaNDM-5, blaCTX-M-55, fosA3, aac(3)-IV, and qnrS1 genes. E. strain EC16 was subjected to antimicrobial susceptibility testing by broth microdilution method. Whole-genome sequencing performed using...

Maternal gut microbiota is an important regulator for the metabolism and immunity of fetus during pregnancy. Recent studies have indicated that maternal intestinal closely linked to development infant health. Some bacterial metabolites are considered be directly involved in immunoregulation However, detailed mechanisms largely unknown. In this study, we exploited potential correlation between pregnant sows occurrence stillborn piglets by combining 16S rRNA gene metagenomic sequencing data,...

Complex networks are ubiquitous in nature. In biological systems, biomolecules interact with each other to form so-called biomolecular networks, which determine the cellular behaviors of living organisms. Controlling by regulating certain network is one most concerned problems systems biology. Recently, connections between and structural control theory have been explored, uncovering some interesting phenomena. Some researchers paid attentions controllability notion minimum steering sets...

Cell free DNA (cfDNA) in human plasma carries abundant information, which has therefore been the key sample for noninvasive prenatal testing (NIPT) and liquid biopsy. Especially by using rapidly developed next-generation sequencing (NGS) techniques, genetic epigenetic information embedded cfDNA effectively extensively decoded. In this process, a step is to construct NGS library. Due its high degradation, single strand-based method was reported be more qualified library of cfDNA. order...

Abstract Background As the characteristic functional component in ginger, gingerols possess several health-promoting properties. Long non-coding RNAs (lncRNAs) act as crucial regulators of diverse biological processes. However, lncRNAs ginger are not yet identified so far, and their potential roles gingerol biosynthesis still unknown. In this study, metabolomic transcriptomic analyses were performed three main cultivars (leshanhuangjiang, tonglingbaijiang, yujiang 1 hao) China to understand...