Biology subjects

Lin, W.

Publications and source records attributed to Lin, W..

At least 163 records · Page 9Linked to original sources

bioRxiv2019

Physiological and genomic analysis of Candidatus Nitrosocosmicus agrestis, an ammonia tolerant ammonia-oxidizing archaeon from vegetable soil

The presences of ammonia tolerant ammonia-oxidizing archaea (AOA) in environments are always underestimated and their adaption to complex habitats has also rarely been reported. Here we present the physiological and genomic characteristics of an ammonia tolerant soil AOA strain Candidatus Nitrosocosmicus agrestis. This strain was able to form aggregates and adhere on the surface of hydrophobic matrix. Ammonia-oxidizing activities were still observed at 200 mM NH4+ (> 1500 M of free ammonia) and 50 mM NO2-. Urea could be used as sole energy source but exogenous organics had no significant effect on the ammonia oxidation. Besides the genes involving in ammonia oxidation, carbon fixation and urea hydrolysis, the genome also encodes a full set of genes (GTs, GHs, CEs, MOP, LPSE, etc) that responsible for polysaccharide metabolism and secretion, suggesting the potential production of extracellular polymeric substances (EPS). Moreover, a pathway connecting urea cycle, polyamines synthesis and excretion was identified in the genome, which indicates the NH4+ in cytoplasm could potentially be converted into polyamines and excreted out of cell, and then contributes to the high ammonia tolerance. Genes encoding the cytoplasmic carbonic anhydrase and putative polyamine exporter are unique in Ca. Nitrosocosmicus agrestis or the genus Ca. Nitrosocosmicus, suggesting the prevalence of ammonia tolerance in this clade. The proposed mechanism of ammonia tolerance via polyamines synthesis and export was verified by using transcriptional gene regulation and polyamines determination. IMPORTANCEAOA are ubiquitous in different environments and play a major role in nitrification. Though AOA have higher affinities for ammonia, their maximum specific cell activity and ammonia tolerance are usually much lower than AOB, resulting in low contribution to the global ammonia oxidation and N2O production. However, in some agricultural soils, the AOA activity would not be suppressed by the fertilization with high concentration of ammonium nitrogen, suggesting the presence of some ammonia tolerant species. This study provides some physiological and genomic characteristics for an ammonia tolerant soil AOA strain Ca. Nitrosocosmicus agrestis and proposes some mechanisms of this AOA adapting to a variety of environments and tolerating to high ammonia. Ammonia tolerance of AOA was always underestimated in many previous studies, physiological and genomic analyses of this AOA clade are benefit to uncover the role of AOA playing in global environmental patterns.

microbiology↗

bioRxiv2019

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription

All organisms--bacteria, archaea, and eukaryotes--have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription-initiation-factor structural module pre-organizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription-initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate, and define details of, stepwise, RNA-extension-driven displacement of the "{sigma} finger" of the bacterial transcription initiation factor {sigma}. The structures reveal that--for both the primary {sigma} factor and extracytoplasmic (ECF) {sigma} factors, and for both 5-triphosphate RNA and 5-hydroxy RNA--the "{sigma} finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5-end, upon extension of nascent RNA from [~]5 nt to [~]10 nt. SIGNIFICANCE STATEMENTThe "{sigma} finger" of the bacterial initiation factor {sigma} binds within the RNA polymerase active-center cleft and blocks the path of nascent RNA. It has been hypothesized that the {sigma} finger must be displaced during initial transcription. By determining crystal structures defining successive steps in initial transcription, we demonstrate that the {sigma} finger is displaced in stepwise fashion, driven by collision with the RNA 5-end, as nascent RNA is extended from [~]5 nt to [~]10 nt during initial transcription, and we show that this is true for both the primary {sigma} factor and alternate {sigma} factors. Stepwise displacement of the {sigma} finger can be conceptualized as stepwise compression of a "protein spring" that stores energy for subsequent breakage of protein-DNA and protein-protein interactions in promoter escape.

biochemistry↗

bioRxiv2019

Development of Dynamic Functional Architecture during Early Infancy

Understanding the moment-to-moment dynamics of functional connectivity (FC) in the human brain during early development is crucial for uncovering neuro-mechanisms of the emerging complex cognitive functions and behaviors. Instead of calculating FC in a static perspective, we leveraged a longitudinal resting-state functional magnetic resonances imaging dataset from fifty-one typically developing infants and, for the first time, thoroughly investigated how the temporal variability of the FC architecture develops at the global (entire brain), meso- (functional system) and local (brain region) levels in the first two years of age. Our results revealed that, in such a pivotal stage, 1) the whole-brain FC dynamics is linearly increased; 2) the high-order functional systems display increased FC dynamics for both within- and between-network connections, while the primary systems show the opposite trajectories; 3) many frontal regions have increasing FC dynamics despite large heterogeneity in developmental trajectories and velocities. All these findings indicate that the brain is gradually reconfigured towards a more flexible, dynamic, and adaptive system with globally increasing but locally heterogeneous trajectories in the first two postnatal years, explaining why infants have emerging and rapidly developing high-order cognitive functions and complex behaviors.

neuroscience↗

bioRxiv2019

Auxin-induced nanoclustering of membrane signaling complexes underlies cell polarity establishment in Arabidopsis

Cell polarity is fundamental to the development of both eukaryotic and prokaryotic organisms, yet the mechanism of its establishment remains poorly understood. Here we show that signal-activated nanoclustering of membrane proteins and a cytoskeleton-based feedback loop provide an important mechanism for the establishment of cell polarity. The phytohormone auxin promoted sterol-dependent nanoclustering of cell surface transmembrane receptor-like kinase 1 (TMK1) to initiate cell polarity during the morphogenesis of Arabidopsis puzzle piece-shaped leaf pavement cells (PC). Auxin-triggered nanoclustering of TMK1 stabilized flotillin-associated ordered nanodomains, which were essential for auxin-mediated formation of ROP6 GTPase nanoclusters that act downstream TMK1 to promote cortical microtubule ordering. Mathematical modeling further demonstrated the essential role of this auxin-mediated stabilization of TMK1 and ROP6 nanoclusters, and predicted the additional requirement of ROP6-dependent cortical microtubules for further stabilization of TMK1-sterol nanodomains and the polarization of PC. This prediction was experimentally validated by genetic and biochemical data. Our studies reveal a new paradigm for polarity establishment: A diffusive signal triggers cell polarization by activating cell surface receptor-mediated lateral segregation of signaling components and a cytoskeleton-mediated positive feedback loop of nanodomain stabilization.\n\nHighlightsO_LISterols are required for cell polarity in Arabidopsis leaf epidermal cells\nC_LIO_LIAuxin promotes lipid ordering and polar distribution of ordered lipid nanodomains at the plasma membrane (PM)\nC_LIO_LIAuxin stabilizes sterol-dependent nanoclustering of transmembrane kinase (TMK1), a PM auxin signal transducer\nC_LIO_LIAuxin-induced TMK1 nanoclustering is required but insufficient for cell polarization\nC_LIO_LIMicrotubule-based feedback stabilization of the auxin-induced TMK1 nanodomains can generate cell polarity\nC_LI

cell biology↗

bioRxiv2019

Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled genomes

Metagenomic studies have claimed the existence of novel lineages with unprecedented properties never before observed in prokaryotes. Such lineages include Asgard archaea1-3, which are purported to represent archaea with eukaryotic cell complexity, and the Candidate Phyla Radiation (CPR), a novel domain level taxon erected solely on the basis of metagenomic data4. However, it has escaped the attention of most biologists that these metagenomic sequences are not assembled into genomes by sequence overlap, as for cultured archaea and bacteria. Instead, short contigs are sorted into computer files by a process called binning in which they receive taxonomic assignment on the basis of sequence properties like GC content, dinucleotide frequencies, and stoichiometric co-occurrence across samples. Consequently, they are not genome sequences as we know them, reflecting the gene content of real organisms. Rather they are metagenome assembled genomes (MAGs). Debates that Asgard data are contaminated with individual eukaryotic sequences5-7 are overshadowed by the more pressing issue that no evidence exists to indicate that any sequences in binned Asgard MAGs actually stem from the same chromosome, as opposed to simply stemming from the same environment. Here we show that Asgard and CPR MAGs fail spectacularly to meet the most basic phylogenetic criterion8 fulfilled by genome sequences of all cultured prokaryotes investigated to date: the ribosomal proteins of Asgard and CPR MAGs do not share common evolutionary histories. Their phylogenetic behavior is anomalous to a degree never observed with genomes of real organisms. CPR and Asgard MAGs are binning artefacts, assembled from environments where up to 90% of the DNA is from dead cells9-12. Asgard and CPR MAGs are unnatural constructs, genome-like patchworks of genes that have been stitched together into computer files by binning.

evolutionary biology↗

bioRxiv2019

A mutation in Hnrnph1 that decreases methamphetamine-induced reinforcement, reward, and dopamine release and increases synaptosomal hnRNP H and mitochondrial proteins

Individual variation in the addiction liability of amphetamines has a heritable genetic component. We previously identified Hnrnph1 (heterogeneous nuclear ribonucleoprotein H1) as a quantitative trait gene underlying decreased methamphetamine-induced locomotor activity in mice. Here, mice (both male and female) with a heterozygous mutation in the first coding exon of Hnrnph1 (H1+/-) showed reduced methamphetamine reinforcement and intake and dose-dependent changes in methamphetamine reward as measured via conditioned place preference. Furthermore, H1+/- mice showed a robust decrease in methamphetamine-induced dopamine release in the nucleus accumbens with no change in baseline extracellular dopamine, striatal whole tissue dopamine, dopamine transporter protein, or dopamine uptake. Immunohistochemical and immunoblot staining of midbrain dopaminergic neurons and their forebrain projections for tyrosine hydroxylase did not reveal any major changes in staining intensity, cell number, or in the number of forebrain puncta. Surprisingly, there was a two-fold increase in hnRNP H protein in the striatal synaptosome of H1+/- mice with no change in whole tissue levels. To gain insight into the molecular mechanisms linking increased synaptic hnRNP H with decreased methamphetamine-induced dopamine release and behaviors, synaptosomal proteomic analysis identified an increased baseline abundance of several mitochondrial complex I and V proteins that rapidly decreased at 30 min post-methamphetamine administration in H1+/- mice. In contrast, the much lower level of basal synaptosomal mitochondrial proteins in wild-type mice showed a rapid increase in response to methamphetamine. We conclude that H1+/- decreases methamphetamine-induced dopamine release, reward, and reinforcement and induces dynamic changes in basal and methamphetamine-induced synaptic mitochondrial function.\n\nSIGNIFICANCE STATEMENTMethamphetamine dependence is a significant public health concern with no FDA-approved treatment. We discovered a role for the RNA binding protein hnRNP H in methamphetamine reward and reinforcement. Hnrnph1 mutation also blunted methamphetamine-induced dopamine release in the nucleus accumbens - a key neurochemical event contributing to methamphetamine addiction liability. Finally, Hnrnph1 mutants showed a marked increase in basal level of synaptosomal hnRNP H and mitochondrial proteins that decreased in response to methamphetamine whereas wild-type mice showed a methamphetamine-induced increase in synaptosomal mitochondrial proteins. Thus, we identified a potential role for hnRNP H in basal and dynamic mitochondrial function that informs methamphetamine-induced cellular adaptations associated with reduced addiction liability.

neuroscience↗

bioRxiv2019

CASLFA: CRISPR/Cas9-mediated lateral flow nucleic acid assay

The lateral flow assay is one of the oldest and most convenient analytical techniques for analyzing the immune response, but its applicability to precise genetic analyses is limited by the tedious and inefficient hybridization steps. Here, we have introduced a new version of the lateral flow assay, termed Cas9-mediated lateral flow nucleic acids assay (CASLFA), to address such issues. In this study, CASLFA is utilized to identify Listeria monocytogenes, genetically modified organisms (GMOs), and African swine fever virus (ASFV) at a sensitivity of hundreds of copies of genome samples with high specificity within 1 h. CASLFA satisfies some of the characteristics of a next-generation molecular diagnostics tool due to its rapidity and accuracy, allowing for point-of-care use without the need for technical expertise and complex ancillary equipment. This method has great potential for analyzing genes in resource-poor or nonlaboratory environments.

bioengineering↗

bioRxiv2019

First report of Telenomus remus parasitizing Spodoptera frugiperda and its natural parasitism in South China

The fall armyworm, Spodoptera frugiperda, is a lepidopteran pest that feeds on many economically important cereal crops such as corn, rice, sorghum, and sugarcane. Native to the Americas, it has become a serious invasive pest in Africa and Asia. Recently, this pest was found invaded China and has spread exceptionally fast across the country. As S. frugiperda will most likely become a major pest in China, Integrated Pest Management strategies, including biological control methods, should be developed to win the battle against it. Here, we report the detection of Telenomus remus parasitizing S. frugiperda eggs in cornfields in South China based on morphological and molecular evidence. Our preliminary surveys indicated that the natural parasitism rates of T. remus on S. frugiperda could reach 30% and 50% for egg masses and per egg mass, respectively. Further application of T. remus against S. frugiperda in biological control programs are discussed.

zoology↗

bioRxiv2019

MicroRNA-378 suppressed osteogenesis of mesenchymal stem cells and impaired bone formation via inactivating Wnt/β-catenin signaling

MicroRNAs (miRNAs) have been reported to serve as silencers to repress gene expression at post-transcriptional level. Multiple miRNAs have been demonstrated to play important roles in osteogenesis. MiR-378, a conserved miRNA, was reported to mediate bone metabolism and influence bone development, but the detailed function and underlying mechanism remain obscure. In this study, the miR-378 transgenic (TG) mouse was developed to study the role of miR-378 in osteogenic differentiation as well as bone formation. The abnormal bone tissues and impaired bone quality were displayed in the miR-378 TG mice, and a delayed healing effect was observed during bone fracture of the miR-378 TG mice. The osteogenic differentiation of MSCs derived from this TG mouse was also inhibited. We also found that miR-378 mimics suppressed while anti-miR-378 promoted osteogenesis of human MSCs. Two Wnt family members Wnt6 and Wnt10a were identified as bona fide targets of miR-378, and their expression were decreased by this miRNA, which eventually induced the inactivation of Wnt/{beta}-catenin signaling. Finally, the sh-miR-378 modified MSCs were locally injected into the fracture sites in an established mouse fracture model. The results indicated that miR-378 inhibitor therapy could promote bone formation and stimulate healing process in vivo. In conclude, miR-378 suppressed osteogenesis and bone formation via inactivating Wnt/{beta}-catenin signaling, suggesting miR-378 may be a potential therapeutic target for bone diseases.

cell biology↗

bioRxiv2019

Characteristics and Evolutionary analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from streamlined plasmids to chromids

Aerobic anoxygenic photoheterotrophic bacteria (AAPB) represent intermediates in the evolution from photoautotrophic to heterotrophic metabolisms. Substantial evidence indicates that highly conserved photosynthetic gene clusters (PGCs) of AAPB can be transferred between species, genera, and even phyla. Furthermore, analysis of recently discovered PGCs carried by extrachromosomal replicons (exPGCs) suggests that extrachromosomal replicons (ECRs) play an important role in the transfer of PGCs. In the present study, thirteen Roseobacter clade genomes from seven genera that harbored exPGCs were used to analyze characteristics and evolution of PGCs. The identification of plasmid-like and chromid-like ECRs from PGC-containing ECRs revealed two different functions: the spread of PGCs among strains and the maintenance of PGCs within genomes. Phylogenetic analyses indicated two independent origins of exPGCs, corresponding to PufC-containing and PufX-containing photosynthetic reaction complexes. Furthermore, the two different types of complexes were observed within different strains of the same Tateyamaria and Jannaschia genera. The two different complexes were also differentially carried by chromosomes and ECRs in the strains, respectively, which provided clear evidence for ECR-mediated PGC transfer. Multiple recombination events of exPGCs were also observed, wherein the majority of exPGCs were inserted by replication modules at the same genomic positions. However, the exPGCs of the Jannaschia strains comprised superoperons without evidence of insertion, and therefore likely represent an initial evolutionary stage where the PGC was translocated from chromosomes to ECRs without further combinations. Lastly, a scenario of PGC gain and loss is proposed that specifically focuses on ECR-mediated exPGC transfer to explain the evolution and patchy distribution of AAPB within the Roseobacter clade.\n\nImportanceThe evolution of photosynthesis was a significant event during the diversification of biological life. Aerobic anoxygenic heterotrophic bacteria (AAPB) share physiological characteristics with both photoautotrophs and heterotrophs and are therefore suggested to be evolutionary intermediates between the two lifestyles. Here, characterization and evolutionary analyses were conducted for thirteen bacterial strains that contained photosynthetic gene clusters (PGCs) carried by extrachromosomal replicons (ECRs) to shed light on the evolution of photosynthesis in bacteria. Specifically, these analyses improved the \"Think Pink\" scenario of PGC transfer that is mediated by ECRs in Roseobacter clade strains. This study advances our understanding of the importance of ECRs in the transfer of PGCs within marine photoheterotrophic bacteria.

genomics↗

bioRxiv2019

Whole-genome sequencing of 128 camels across Asia provides insights into origin and migration of domestic Bactrian camels

The domestic Bactrian camels were treated as the principal means of locomotion between the eastern and western cultures in history. To address the question of their origin, we performed whole-genome sequencing of 128 camels across Asia, including representative populations of domestic Bactrian camels from the Mongolian Plateau to the Caspian Sea, as well as the extant wild Bactrian camels and dromedaries. The domestic and wild Bactrian camels showed remarkable genetic divergence since they were split from dromedaries, confirming they were separated species. The wild Bactrian camels made also little contribution to the ancestry of domestic ones. Among the domestic Bactrian camels, those from Iran exhibited the largest genetic distance from others, and were the first population to separate in the phylogeny. Although evident admixture was observed between domestic Bactrian camels and dromedaries living around the Caspian Sea, the large genetic distance and basal position of Iranian Bactrian camels could not be explained by introgression alone. Taken together, our study favored the Iranian origin of domestic Bactrian camels, which were then immigrated eastward to Mongolia where the native wild Bactrian camels inhabited. This study illustrated the complex genomic landscape of migration underlying domestication in Bactrian camels.

genomics↗

bioRxiv2019

Universal and naked-eye gene detection platform based on CRISPR/Cas12a/13a system

Colorimetric gene detection based on gold nanoparticles (AuNPs) is an attractive detection format due to its simplicity. Here, we report a new design for a colorimetric gene-sensing platform based on the CRISPR/Cas system that has improved specificity, sensitivity, and universality. CRISPR/Cas12a and CRISPR/Cas13a have two distinct catalytic activities and are used for specific target gene recognition. Programmable recognition of DNA by Cas12a/crRNA and RNA by Cas13a/crRNA with a complementary sequence activates the nonspecific trans-ssDNA or -RNA cleavage, respectively, thus degrading the ssDNA or RNA linkers which are designed as a hybridization template for the AuNP-DNA probe pair. Target-induced trans -ssDNA or RNA cleavage leads to a distance-dependent color change for the AuNP-DNA probe pair. In this platform, naked eye detection of transgenic rice, African swine fever virus (ASFV), and a miRNA can be completed within 1 hour. Our colorimetric gene-sensing method shows superior characteristics, such as probe universality, isothermal reaction conditions, on-site detection capability, and sensitivity that is comparable to that of the fluorescent detection; thus, this method represents a robust next generation gene detection platform.

bioengineering↗

bioRxiv2018

Hypoxic Training Increases the Concentration of Serum Irisin and Reduces Weight in Diet-induced Obese Rats

Irisin promotes browning of white fat, improves energy metabolism, and-weight loss. In this study, we investigated the effects of different oxygen concentrations during hypoxic training on the serum irisin and the PGC-1(peroxisome proliferator-activated receptor gamma coactivator 1-alpha)-FNDC5(fibronectin type III domain containing 5)-UCPl(uncoupling protein 1) signaling pathway in the skeletal muscle of obese rats. Male Sprague-Dawley Obese rats (n=80) were randomly divided into 8 groups as follows: the control group (group A, n=10); the endurance exercise group (AE group, n=10), which involved animal treadmill training at slope 0{degrees}, 20 m/min, 40 min/d, and 5 d/w; the 16.3% hypoxia exposure group (group B, n=10), 13.3% hypoxia exposure group (group C, n=10), and 11.3% hypoxia exposure group (group D, n=10), which were exposed to a low oxygen environment with oxygen concentrations of 16.3%, 13.3%, and 11.3%, respectively, for 12 h/d; and the 16.3% hypoxic training group (BE group, n=10), 13.3% hypoxic training group (CE group, n=10), and 11.3% hypoxic training group (DE group, n=10) with animal treadmill training during hypoxia exposure. After 8 weeks, the serum irisin concentrations in the AE, BE, CE, and DE groups were significantly higher than that in the A group (p<0.05). Hypoxia exposure and hypoxic training at the three different concentrations significantly increased PGC-1 and FNDC5 gene expression in the skeletal muscle. The PGC-1 and FNDC5 protein contents were significantly higher in the skeletal muscle of the obese rats in the C, AE, and DE groups than those in group A (p<0.05). UCP1 protein expression was significantly higher in groups C, CE, D, and DE than in group A (p<0.05). To conclude, training at oxygen concentrations of 13.3% and 11.3% significantly increased the serum irisin level, and 11.3% hypoxic training enhanced the effects of the PGC-l-Irisin-UCP1 signaling pathway in skeletal muscle.

biochemistry↗

bioRxiv2018

HiAlc Klebsiella pneumonia, one of potential chief culprits of non-alcoholic fatty liver disease: through generation of endogenous ethanol

Non-alcoholic fatty liver disease (NAFLD), a prelude of cirrhosis and hepatocellular carcinoma, is the most common chronic liver disease worldwide. NAFLD has been considerated to be associated with the composition of gut microbiota. However, causal relationship between change of gut microbiome and NAFLD remains unclear. Here we show that Klebsiella pneumoniae was significantly associated with NAFLD through inducing generation of endogenous ethanol. A strain of high alcohol-producing Klebsiella pneumoniae (HiAlc Kpn) was initially isolated from fecal samples of patient with non-alcoholic steatohepatitis (NASH) accompanied with auto-brewery syndrome (ABS). Gavage of HiAlc Kpn was capable of inducing murine model of fatty liver disease (FLD) in which had typical pathological changes of hepatic steatosis and similar liver gene expression profiles to those of alcohol intake in mice. Data derived from germ-free mice by gnotobiotic gavage further demonstrated that the HiAlc Kpn is the major cause of the changes in FLD mice. Furthermore, using proteomic and metabolitic analysis, we found that HiAlc Kpn induced generation of endogenous alcohol through the 2,3-butanediol fermentation pathway. More interestingly, the blood alcohol concentration was elevated in FLD mice induced by HiAlc Kpn after glucose intake. Clinical analysis showed that HiAlc Kpn were observed in up to 60% of patients with NAFLD. Our results suggested that HiAlc Kpn make important contribution to NAFLD, possibly through generation of the endogenous alcohol. Thus, targeting these bacteria might provide a novel therapeutic for clinical treatment of NAFLD.\n\nIn BriefFatty liver disease induced by high alcohol-producing Klebsiella pneumoniae\n\nCompeting Financial Interest StatementThe authors declare no conflicts of interest.

microbiology↗

bioRxiv2018

SuperCT: A supervised-learning-framework to enhance the characterization of single-cell transcriptomic profiles

Characterization of individual cell types is fundamental to the study of multicellular samples such as tumor tissues. Single-cell RNAseq techniques, which allow high-throughput expression profiling of individual cells, have significantly advanced our ability of this task. Currently, most of the scRNA-seq data analyses are commenced with unsupervised clustering of cells followed by visualization of clusters in a low-dimensional space. Clusters are often assigned to different cell types based on canonical markers. However, the efficiency of characterizing the known cell types in this way is low and limited by the investigator[s] knowledge. In this study, we present a technical framework of training the expandable supervised-classifier in order to reveal the single-cell identities based on their RNA expression profiles. Using multiple scRNA-seq datasets we demonstrate the superior accuracy, robustness, compatibility and expandability of this new solution compared to the traditional methods. We use two examples of model upgrade to demonstrate how the projected evolution of the cell-type classifier is realized.

bioinformatics↗

bioRxiv2018

Structural basis of ECF-sigma-factor-dependent transcription initiation.

Extracytoplasmic (ECF) {sigma} factors, the largest class of alternative {sigma} factors, are related to primary {sigma} factors, but have simpler structures, comprising only two of the six conserved functional modules present in primary {sigma} factors: region 2 ({sigma}R2) and region 4 ({sigma}R4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF {sigma} factor {sigma}L, and promoter DNA. The structures show that {sigma}R2 and {sigma}R4 of the ECF {sigma} factor occupy the same sites on RNAP as in primary {sigma} factors, show that the connector between {sigma}R2 and {sigma}R4 of the ECF {sigma} factor--although unrelated in sequence--follows the same path through RNAP as in primary {sigma} factors, and show that the ECF {sigma} factor uses the same strategy to bind and unwind promoter DNA as primary {sigma} factors. The results define protein-protein and protein-DNA interactions involved in ECF-{sigma}-factor-dependent transcription initiation.

molecular biology↗

bioRxiv2018

Low nutrient levels reduce the fitness cost of MexCD-OprJ efflux pump overexpression in ciprofloxacin-resistant Pseudomonas aeruginosa

The long-term persistence of antibiotic resistance in the environment is a public health concern. Expression of an efflux pump, an important mechanism of resistance to antibiotics, is usually associated with a fitness cost in bacteria. In this study, we aimed to determine why antibiotic resistance conferred by overexpression of an efflux pump persists in environments such as drinking and source water in which antibiotic selective pressure may be very low or even absent. Competition experiments between wild-type Pseudomonas aeruginosa and ciprofloxacin-resistant mutants revealed that the fitness cost of ciprofloxacin resistance (strains cip_1, cip_2, and cip_3) significantly decreased (P < 0.05) under low-nutrient (0.5 mg/l total organic carbon (TOC)) relative to high-nutrient (500 mg/l TOC) conditions. Mechanisms underlying this fitness cost were analyzed. MexD gene expression in resistant bacteria (cip_3 strain) was significantly lower (P < 0.05) in low-nutrient conditions, with 10 mg/l TOC (8.01 {+/-} 0.82-fold), than in high-nutrient conditions, with 500 mg/l TOC (48.89 {+/-} 4.16-fold). Moreover, rpoS gene expression in resistant bacteria (1.36 {+/-} 0.13-fold) was significantly lower (P < 0.05) than that in the wild-type strain (2.78 {+/-} 0.29-fold) under low-nutrient conditions (10 mg/l TOC), suggesting a growth advantage. Furthermore, the difference in metabolic activity between the two competing strains was significantly smaller (P < 0.05) in low-nutrient conditions (5 and 0.5 mg/l TOC). These results suggest that nutrient levels are a key factor in determining the persistence and spread of antibiotic resistance conferred by efflux pumps in the natural environment with trace amounts or no antibiotics.\n\nImportanceThe widespread of antibiotic resistance has led to an increasing concern about the environmental and public health risks. Mechanisms associated with antibiotic resistance including efflux pumps often increase bacterial fitness cost. Our study showed that the fitness cost of ciprofloxacin resistance conferred by overexpression of MexCD-OprJ efflux pump significantly decreased under low-nutrient relative to high-nutrient conditions. The significance of our research is to reveal that nutrient levels are key factor in determining the persistence of antibiotic resistance conferred by efflux pumps under conditions with trace amounts or no antibiotics, which can be mediated by some mechanisms including MexD gene expression, SOURs differences, and rpoS gene regulation.

microbiology↗

bioRxiv2018

Velocity and Diameter Measurements of Penetrating Arteries by Model Based Analysis of Complex Difference Images in Phase Contrast MRI

Pathological changes of penetrating arteries (PAs) within deep white matter (WM) may be an important contributing factor of cerebral small vessel disease (SVD). Quantitative characterization of the PAs is important for further illuminating their roles in SVD but remains challenging due to their sub-voxel sizes. We propose a quantitative MRI approach for measuring the diameters and flow velocities of PAs based on model based analysis of complex difference images in phase contrast MRI. The complex difference image of each PA is fitted by a model image calculated by taking into account the partial volume effect and signal enhancement due to in flow effects to obtain velocity [Formula], diameter (D), and volume flow rate (VFR) of the PAs. Simulation, phantom, and in vivo studies were carried out to evaluate the accuracy and measurement errors of the proposed method. Our results suggest that PAs with velocities [≥] 0.8 cm/s can be accurately measured with [Formula], D, and VFR errors of 0.28 cm/s, 20 m, and 0.024 mm3/s, respectively, although the mean lumen area occupies only 18% of the acquired pixel area. The PAs have a [Formula] distribution peak at ~1.2 cm/s and diameters distribution mostly in the range of 88 - 200 m Quantitative measurements of PAs with the MBAC method may serve as an invaluable tool for illuminating the role of PAs in the aetiopathogenesis of cerebral SVD.

biophysics↗