Biology subjects

Ren, H.

Publications and source records attributed to Ren, H..

122 records · Page 7Linked to original sources

bioRxiv2019

Age-dependent sexual dimorphism in the adult human gut microbiota

A decade of studies has established the importance of the gut microbiome in human health. In spite of sex differences in the physiology, lifespan, and prevalence of many age-associated diseases, sex and age disparities in the gut microbiota have been little studied. Here we show age-related sex differences in the adult gut microbial composition and functionality in two community-based cohorts from Northern China and the Netherlands. Consistently, women harbour a more diverse and stable microbial community across broad age ranges, whereas men exhibit a more variable gut microbiota strongly correlated with age. Reflecting the sex-biased age-gut microbiota interaction patterns, sex differences observed in younger adults are considerably reduced in the elderly population. Our findings highlight the age- and sex-biased differences in the adult gut microbiota across two ethnic population and emphasize the need for considering age and sex in studies of the human gut microbiota.

genomics↗

bioRxiv2019

Dynamic chromosome rearrangements of the white-spotted bamboo shark shed light on cartilaginous fish diversification mechanisms

Cartilaginous fishes have a very high phenotypical diversity, a phenomenon for which the mechanisms have been largely unexplored. Here, we report the genome of the white-spotted bamboo shark as the first chromosome-level genome assembly of cartilaginous fish. Using this genome, we illustrated a dynamic chromosome rearrangement process in the bamboo shark, which resulted in the formation of 13 chromosomes, all of which were sparsely distributed with conserved genes and fast-evolving. We found the fast-evolving chromosomes to be enriched in immune-related genes with two chromosomes harboring the major genes for developing the single-chain antibody. We also found chromosome rearrangements to have resulted in the loss of two genes (p2rx3 and p2rx5) which we also showed were involved in cartilage development using a CRISPR/Cas9 approach in zebrafish. Our study highlighted the significance of chromosome rearrangements in the phenotypical evolution of cartilaginous fishes, providing clues to inform further studies on mechanisms for fish diversification.

genomics↗

bioRxiv2019

Conservation of structure, function and inhibitor binding in UNC-51-like kinase 1 and 2 (ULK1/2)

Autophagy is essential for cellular homeostasis and when deregulated this survival mechanism has been associated with disease development. Inhibition of autophagy initiation by inhibiting the kinase ULK1 has been proposed as a potential cancer therapy. While inhibitors and crystal structures of ULK1 have been reported, little is known about the other closely related kinase ULK2. Here we present the crystal structure of ULK2 in complex with ATP competitive inhibitors. Surprisingly, the ULK2 structure revealed a dimeric assembly reminiscent of dimeric arrangements of auto-activating kinases suggesting a role for this association in ULK activation. Screening of a kinase focused library of pre-clinical and clinical compounds revealed several potent ULK1/2 inhibitors and good correlation of inhibitor binding behavior with both ULK kinases. Aurora A was identified as a major off-target of currently used ULK1 inhibitors. Autophagic flux assays demonstrated that this off-target activity by strongly inducing autophagy in different cellular systems conferred an additional layer of complexity in the interpretation of cellular data. The data presented here provides structural models and chemical starting points for the development of ULK1/2 dual inhibitors with improved selectivity for future exploitation of autophagy inhibition.

biochemistry↗

bioRxiv2019

Different subtypes of influenza A viruses target different human proteins and pathways leading to different pathogenic phenotypes

Different subtypes of Influenza A viruses cause different pathogenic phenotypes after infecting human bodies. Direct binary interactions between viral proteins and human proteins provide an important background for influenza viruses to cause complex pathologies of hosts. Here, we demonstrated the different impacts on the TNF--induced NF-{kappa}B activation of H1N1 and H5N1 virus proteins. By further examining the virus-host protein-protein interactions (PPI), we found that the same segment protein of the H1N1 and H5N1 viruses target on different host proteins. We then performed a yeast two-hybrid analysis of a highly pathogenic avian H5N1 influenza virus and human proteins. Influenza-host protein-protein interaction networks of three strains of influenza A viruses (including two other reported influenza-host PPI networks) were systematically compared and mapped on the network level and the pathway level. The results show subtype-specific characters of the influenza-host protein interactome, which may response for the specific pathogenic mechanisms of different subtypes of influenza viruses. ImportanceInfluenza A virus (IAV) can cause contagious respiratory illness, namely influenza (flu). The symptoms of infections from different subtypes of IAVs vary from mild to severe illness. The mechanism of these different pathogenic phenotypes remains poorly understood. Our results show that the same NA and NP segments from H1N1 and H5N1 virus cause different impacts on the TNF--induced NF-{kappa}B pathway. Furthermore, we generated a yeast two-hybrid protein-protein interaction (PPI) network between H5N1 and human proteins. By systematically comparing the influenza-host PPI networks of three strains of IAVs, we show that different subtypes of IAVs target different human proteins and pathways, which may have led to different pathogenic phenotypes.

microbiology↗

bioRxiv2019

Nonobese subjects of Bacteroides and Prevotella enterotypes responded differentially to calorie restriction intervention

Calorie restriction (CR), which has the potential effect to weight loss and blood amino acids, has been demonstrated to associate with gut microbiota in human, especially in obese individuals. However, studies for simultaneously evaluating enterotype-dependent impacts of CR on the gut microbiota and blood amino acids in nonobese individuals are still limited.\n\nHere, 41 nonobese individuals received a 3-week CR diet with approximately 50% fewer calories than normal diet. We measured their BMI and blood amino acid concentration, along with the gut microbiota before and after the intervention. In this trial, 28 Enterotype Bacteroides (ETB) subjects and 13 Enterotype Prevotella (ETP) subjects were identified before the intervention. Short-term CR dietary intervention decreased the body mass index (BMI) in most subjects but varied in subjects with different enterotypes. ETP subjects exhibited significantly higher BMI loss ratio than the ETB subjects. CR additionally induced substantial enterotype-independent changes in blood amino acids, but only minor changes in gut microbial composition.\n\nWe further built a prediction model based on baseline relative abundances of 7 gut microbial species showing high performance in predicting CR-associated BMI loss ratio. Among them, the relative abundance of ETB-enriched Clostridium bolteae and C. ramosum were negatively correlated with BMI loss ratio while the relative abundance of Dorea longicatena which was slightly enriched in ETP subjects, was positively correlated with BMI loss ratio.\n\nTogether, our work points out that the individual variation of BMI loss after CR could be partially correlated with different microbial composition and highlights the potential application for microbiome stratification in personalized nutrition intervention.

microbiology↗

bioRxiv2018

Novel 3,6-Dihydroxypicolinic Acid Decarboxylase Mediated Picolinic Acid Catabolism in Alcaligenes faecalis JQ135

Alcaligenesfaecalis strain JQ135 utilizes picolinic acid (PA) as sole carbon and nitrogen source for growth. In this study, we screened a 6-hydroxypicolinic acid (6HPA) degradation-deficient mutant through random transposon mutagenesis. The mutant hydroxylated 6HPA into an intermediate, identified as 3,6-dihydroxypicolinic acid (3,6DHPA) with no further degradation. A novel decarboxylase PicC was identified that was found to be responsible for the decarboxylation of 3,6DHPA to 2.5-dihydroxypyridine. Although, PicC belonged to amidohydrolase_2 family, it shows low similarity (<45%) when compared to other reported amidohydrolase_2 family decarboxylases. Moreover, PicC was found to form a monophyletic group in the phylogenetic tree constructed using PicC and related proteins. Further, the genetic deletion and complementation results demonstrated that picC was essential for PA degradation. The PicC was Zn2+-dependent non-oxidative decarboxylase that can specifically catalyze the irreversible decarboxylation of 3,6DHPA to 2.5-dihydroxypyridine. The Km and kcat towards 3,6DHPA were observed to be 13.44 M and 4.77 s-1, respectively. Site-directed mutagenesis showed that His163 and His216 were essential for PicC activity.\n\nImportancePicolinic acid is a natural toxic pyridine derived from L-tryptophan metabolism and some aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize picolinic acid for their growth, and thus, a microbial degradation pathway of picolinic acid has been proposed. Picolinic acid is converted into 6-hydroxypicolinic acid, 3,6-dihydroxypicolinic acid, and 2,5-dihydroxypyridine in turn. However, there was no physiological and genetic validation for this pathway. This study demonstrated that 3,6DHPA was an intermediate in PA catabolism process and further identified and characterized a novel amidohydrolase_2 family decarboxylase PicC. It was also shown that PicC could catalyze the decarboxylation process of 3,6-dihydroxypicolinic acid into 2,5-dihydroxypyridine. This study provides a basis for understanding PA degradation pathway and the underlying molecular mechanism.

microbiology↗

bioRxiv2018

Genome-wide identification and expression analysis of the FAR gene family in hexaploid wheat (Triticum aestivum L.)

Fatty acyl-CoA reductase (FAR) is involved in the biosynthesis of primary alcohols, which are waxy constituents that play an important role in plant stress. Previous studies have shown that primary alcohol is the most important component in the wheat seeding stage and accounts for more than 80% of the total composition. To date, eight FAR genes have been identified in wheat, but there has not been a systematic analysis. In this study, a comprehensive overview of the TaFAR gene family was performed, including analyses of the phylogenetic relationship, the multiple sequence alignment, the conserved motif distribution and the expression pattern. The result showed that a total of 41 wheat FAR genes were identified and designated TaFAR1-A-TaFAR22-D; all FAR genes were divided into six classes according to their phylogenetic relationship, and most of the FAR genes might be related to wheat cuticular wax synthesis. The analysis of the promoter binding site showed that TaFAR genes could be regulated by the MYB transcription factor and could be used as target genes for hormone regulation under adverse conditions, especially during a drought. This study provides a basis for further analyses of the TaFAR gene function and of upstream regulatory genes.

plant biology↗

bioRxiv2018

3’ Branch Ligation: A Novel Method to Ligate Non-Complementary DNA to Recessed or Internal 3’OH Ends in DNA or RNA

Nucleic acid ligases are crucial enzymes that repair breaks in DNA or RNA during synthesis, repair and recombination. Various molecular tools have been developed using the diverse activities of DNA/RNA ligases. Herein, we demonstrate a non-conventional ability of T4 DNA ligase to join 5 phosphorylated blunt-end double-stranded DNA to DNA breaks at 3 recessive ends, gaps, or nicks to form a 3 branch structure. Therefore, this base pairing-independent ligation is termed 3 branch ligation (3BL). In an extensive study of optimal ligation conditions, similar to blunt-end ligation, the presence of 10% PEG-8000 in the ligation buffer significantly increased ligation efficiency. A low level of nucleotide preference was observed at the junction sites using different synthetic DNAs. Furthermore, we discovered that T4 DNA ligase efficiently ligated DNA to the 3 recessed end of RNA, not to that of DNA, in a DNA/RNA hybrid, whereas RNA ligases are less efficient in this reaction. These novel properties of T4 DNA ligase can be utilized as a broad molecular technique in many important applications. We performed a proof-of-concept study of a new directional tagmentation protocol for next generation sequencing (NGS) library construction that eliminates inverted adapters and allows sample barcode insertion adjacent to genomic DNA. 3BL after single transposon tagmentation can theoretically achieve 100% usable template, and our empirical data demonstrate that the new approach produced higher yield compared with traditional double transposon or Y transposon tagmentation. We further explore the potential use of 3BL for preparing targeted RNA NGS libraries with mitigated structure-based bias and adapter dimer problems.

molecular biology↗

bioRxiv2018

Local Polyploidy Phenomenon in Escherichia coli and its significance in genetic engineering

Classic Helmstetter & Cooper model asserted that the multifork phenomenon in the process of replication. However, the impacts of the multifork on the evolution and genetic engineering are still vague. Here, we employed CRISPR/Cas9 technology to knock-out eighteen Escherichia coli chromosomal fragments (over 50 kb) that represent all areas of the chromosome. We demonstrated that a single cell could have wild-type, color-reporter, and antibiotic-resistant genes simultaneously in the same locus of the different branches of the duplication forks after multiple rounds of deletions and replacements. This phenomenon that a single cell had different genotypes in its local polyploid chromosomes, which was similar to eukaryotic heterozygote, was named as local polyploidy. Under a defined selective pressure condition, offspring cells containing at least a copy of conditionally beneficial mutation could be enriched, and other alleles could be kept silently and peacefully in the duplication fork(s) of the same cell. The significance of this phenomenon in the genetic engineering was discussed.

microbiology↗

bioRxiv2018

The thermodynamic landscape of carbon redox biochemistry

Redox biochemistry plays a key role in the transduction of chemical energy in living systems. However, the compounds observed in metabolic redox reactions are a minuscule fraction of chemical space. It is not clear whether compounds that ended up being selected as metabolites display specific properties that distinguish them from non-biological compounds. Here we introduce a systematic approach for comparing the chemical space of all possible redox states of linear-chain carbon molecules to the corresponding metabolites that appear in biology. Using cheminformatics and quantum chemistry, we analyze the physicochemical and thermodynamic properties of the biological and non-biological compounds. We find that, among all compounds, aldose sugars have the highest possible number of redox connections to other molecules. Metabolites are enriched in carboxylic acid functional groups and depleted of carbonyls, and have higher solubility than non-biological compounds. Upon constructing the energy landscape for the full chemical space as a function of pH and electron donor potential, we find that over a large range of conditions metabolites tend to have lower Gibbs energies than non-biological molecules. Finally, we generate Pourbaix phase diagrams that serve as a thermodynamic atlas to indicate which compounds are local and global energy minima in redox chemical space across a set of pH values and electron donor potentials. Our work yields insight into the physicochemical principles governing redox metabolism, and suggests that thermodynamic stability in aqueous environments may have played an important role in early metabolic processes.

systems biology↗

bioRxiv2018

A mixed quantum chemistry/machine learning approach for the fast and accurate prediction of biochemical redox potentials and its large-scale application to 315,000 redox reactions

A quantitative understanding of the thermodynamics of biochemical reactions is essential for accurately modeling metabolism. The group contribution method (GCM) is one of the most widely used approaches to estimating standard Gibbs energies and redox potentials of reactions for which no experimental measurements exist. Previous work has shown that quantum chemical predictions of biochemical thermodynamics are a promising approach to overcome the limitations of GCM. However, the quantum chemistry approach is significantly more expensive. Here we use a combination of quantum chemistry and machine learning to obtain a fast and accurate method for predicting the thermodynamics of biochemical redox reactions. We focus on predicting the redox potentials of carbonyl functional group reductions to alcohols and amines, two of the most ubiquitous carbon redox transformations in biology. Our method relies on semi-empirical quantum chemistry calculations calibrated with Gaussian Process (GP) regression against available experimental data. Our approach results in higher predictive power than the GCM at a low computational cost. We design and implement a network expansion algorithm that iteratively reduces and oxidizes a set of natural seed metabolites, and demonstrate the high-throughput applicability of our method by predicting the standard potentials of more than 315,000 redox reactions involving approximately 70,000 compounds. Additionally, we developed a novel fingerprint-based framework for detecting molecular environment motifs that are enriched or depleted across different regions of the redox potential landscape. We provide open access to all source code and data generated.

biophysics↗

bioRxiv2018

Quantum chemistry reveals the thermodynamic principles of redoxbiochemistry

Thermodynamics dictates the structure and function of metabolism. Redox reactions drive cellular energy and material flow. Hence, accurately quantifying the thermodynamics of redox reactions should reveal key design principles that shape cellular metabolism. However, only a limited number of redox potentials have been measured experimentally, and mostly with inconsistent, poorly-reported experimental setups. Here, we develop a quantum chemistry approach for the calculation of redox potentials of biochemical reactions. We demonstrate that our method predicts experimentally measured potentials with unparalleled accuracy. We calculate the reduction potentials of all redox pairs that can be generated from biochemically relevant compounds and highlight fundamental thermodynamic trends that define cellular redox biochemistry. We further use the calculated potentials to address the question of why NAD/NADP are used as the primary cellular electron carriers, demonstrating how their physiological redox range specifically fits the reactions of central metabolism and minimizes the concentration of reactive carbonyls. The use of quantum chemistry tools, as demonstrated in this study, can revolutionize our understanding of key biochemical phenomena by enabling fast and accurate calculation of large datasets of thermodynamic values.

biochemistry↗

bioRxiv2017

Acute and chronic toxicity assessment of benzylpenicillin G residue in cooked meat

The current level of penicillin use and its persisting residues in livestock is potentially concerning; the toxicity of penicillin residues in heat-treated animal food products (HAFP) is yet to be elucidated. In this study, the acute and chronic toxicity of benzylpenicillin G (BPG) residues in HAFP was investigated in a mouse model. The calculated LD50 of BPG heated to cooking temperature (BPHCT) was 933.04 mg kg-1 [b.w.] intraperitoneally corresponding to 3.75 times lower than its prototype. Mice fed on the experimental diet containing heat-treated beef with high BPG levels for 6 months displayed a reduction in body weight and altered serum values indicating for liver and renal function. Further, the organ ratios of intestinal and spleen were increased. Histopathological changes were observed in the liver, lung and parenchyma testis tissue. BPHCT residue induced sperm aberration and micronucleated polychromatic erythrocytes formation. Present results indicate that prolonged exposure of BPHCT at higher levels of residue might have an impact on public health. Importantly the toxic concentrations of BPHCT are relatively high compared with levels that would result from the degradation of antibiotic residues in meat from animals that have received a therapeutic dose of BPG.

pharmacology and toxicology↗

bioRxiv2017

Collaborations between CpG sites in DNA methylation

DNA methylation patterns have profound impacts on genome stability, gene expression, and development. The molecular base of DNA methylation patterns has long been focused at single CpG sites level. Here, we construct a kinetic model of DNA methylation with collaborations between CpG sites, from which a correlation function was established based on experimental data. The function consists of three parts that suggest three possible sources of the correlation: movement of enzymes along DNA, collaboration between DNA methylation and nucleosome modification, and global enzyme concentrations within a cell. Moreover, the collaboration strength between DNA methylation and nucleosome modification is universal for mouse early embryo cells. The obtained correlation function provide insightful understanding for the mechanisms of inheritance of DNA methylation patterns.

genetics↗