ARIP: A Tool for Precise Interatomic Contact Area and Volume Calculation in Proteins.

The interplay patterns of amino acid residues are pivotal in determining the tertiary structure and flexibility of proteins, which in turn are intricately linked to their functionality and interactions with other molecules. Here, we introduce ARIP, a novel tool designed to identify contact residues within proteins. ARIP employs a modified version of the dr_sasa algorithm and an atomic overlap weighted algorithm to directly calculate the contact area and volume between atoms based on their van der Waals radius. It also allows for the selection of solvent radii, recognizing that not every atom in proteins can interact with water molecules. The solvent parameters were derived from the analysis of approximately 5000 protein and nucleic acid structures with water molecules determined using X-ray crystallography. One advantage of the modified algorithm is its capability to analyze multiple models within a single PDB file, making it suitable for molecular dynamic capture. The contact volume is symmetrically distributed between the interacting atoms, providing more informative results than contact area for the analysis of intra- and intermolecular interactions and the development of scoring functions. Furthermore, ARIP has been applied to four distinct cases: capturing key residue-residue contacts in NMR structures of P4HB, protein-drug binding of CYP17A1, protein-DNA binding of SPI1, and molecular dynamic simulations of BRD4.

vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data.

Virus-encoded small RNAs (vsRNA) have been reported to play an important role in viral infection. Unfortunately, there is still a lack of an effective method for vsRNA identification. Herein, we presented vsRNAfinder, a de novo method for identifying high-confidence vsRNAs from small RNA-Seq (sRNA-Seq) data based on peak calling and Poisson distribution and is publicly available at https://github.com/ZenaCai/vsRNAfinder. vsRNAfinder outperformed two widely used methods namely miRDeep2 and ShortStack in identifying viral miRNAs with a significantly improved sensitivity. It can also be used to identify sRNAs in animals and plants with similar performance to miRDeep2 and ShortStack. vsRNAfinder would greatly facilitate effective identification of vsRNAs from sRNA-Seq data.

Colicins of Escherichia coli Lead to Resistance against the Diarrhea-Causing Pathogen Enterotoxigenic E. coli in Pigs.

Gut microbes can affect host adaptation to various environment conditions. Escherichia coli is a common gut species, including pathogenic strains and nonpathogenic strains. This study was conducted to investigate the effects of different E. coli strains in the gut on the health of pigs. In this study, the complete genomes of two E. coli strains isolated from pigs were sequenced. The whole genomes of Y18J and the enterotoxigenic E. coli strain W25K were compared to determine their roles in pig adaptation to disease. Y18J was isolated from feces of healthy piglets and showed strong antimicrobial activity against W25K in vitro. Gene knockout experiments and complementation analysis followed by modeling the microbe-microbe interactions demonstrated that the antagonistic mechanism of Y18J against W25K relied on the bacteriocins colicin B and colicin M. Compared to W25K, Y18J is devoid of exotoxin-coding genes and has more secondary-metabolite-biosynthetic gene clusters. W25K carries more genes involved in genome replication, in accordance with a shorter cell cycle observed during a growth experiment. The analysis of gut metagenomes in different pig breeds showed that colicins B and M were enriched in Laiwu pigs, a Chinese local breed, but were scarce in boars and Duroc pigs. IMPORTANCE This study revealed the heterogeneity of E. coli strains from pigs, including two strains studied by both in silico and wet experiments in detail and 14 strains studied by bioinformatics analysis. E. coli Y18J may improve the adaptability of pigs toward disease resistance through the production of colicins B and M. Our findings could shed light on the pathogenic and harmless roles of E. coli in modern animal husbandry, leading to a better understanding of intestinal-microbe-pathogen interactions in the course of evolution.

Transcriptomic landscape of sodium butyrate-induced growth inhibition of human colorectal cancer organoids.

Butyrate, a short-chain fatty acid, is predominantly produced by the decomposition of dietary fiber in the colon. Recent studies have shown that sodium butyrate (NaB) can inhibit cell proliferation and stimulate cell apoptosis in colorectal cancer (CRC) cells. However, the molecular mechanism behind NaB is still elusive. In this study, we aimed to explore the deeper mechanism of NaB in CRC by establishing a novel model - organoid. Organoids were generated from healthy and cancerous sites of CRC patients. RNA-seq experiments were undertaken using RNA isolated from the CRC organoids treated with NaB. Gene ontology analyses suggested that cell adhesion, cell-cell signaling, and extracellular matrix (ECM) organization were significantly enriched, with the manifested ECM related to the cell morphology variation in NaB-induced CRC organoids. The KEGG pathway and PPI analysis mainly focused on ECM-receptor interactions, as well as the PI3K-Akt signaling pathway. Interestingly, further analysis suggested that the upregulation of the expression of ITGB7 and ITGA2B was significantly associated with death by NaB-induced CRC organoids. In addition, NaB might further induce cell cycle arrest via the PI3K-Akt pathway, and thus cause cell death. Cumulatively, these results provide evidence that the ECM-integrin/PI3K axis may mediate phenotypic changes in the NaB-treated CRC organoid, which provides a broader perspective of the treatment and prognosis monitoring of CRC.

Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets.

BACKGROUND: In modern animal husbandry, breeders pay increasing attention to improving sow nutrition during pregnancy and lactation to favor the health of neonates. Sow milk is a main food source for piglets during their first three weeks of life, which is not only a rich repository of essential nutrients and a broad range of bioactive compounds, but also an indispensable source of commensal bacteria. Maternal milk microorganisms are important sources of commensal bacteria for the neonatal gut. Bacteria from maternal milk may confer a health benefit on the host. METHODS: Sow milk bacteria were isolated using culturomics followed by identification using 16S rRNA gene sequencing. To screen isolates for potential probiotic activity, the functional evaluation was conducted to assess their antagonistic activity against pathogens in vitro and evaluate their resistance against oxidative stress in damaged Drosophila induced by paraquat. In a piglet feeding trial, a total of 54 newborn suckling piglets were chosen from nine sows and randomly assigned to three treatments with different concentrations of a candidate strain. Multiple approaches were carried out to verify its antioxidant function including western blotting, enzyme activity analysis, metabolomics and 16S rRNA gene amplicon sequencing. RESULTS: The 1240 isolates were screened out from the sow milk microbiota and grouped into 271 bacterial taxa based on a nonredundant set of 16S rRNA gene sequencing. Among 80 Pediococcus isolates, a new Pediococcus pentosaceus strain (SMM914) showed the best performance in inhibition ability against swine pathogens and in a Drosophila model challenged by paraquat. Pretreatment of piglets with SMM914 induced the Nrf2-Keap1 antioxidant signaling pathway and greatly affected the pathways of amino acid metabolism and lipid metabolism in plasma. In the colon, the relative abundance of Lactobacillus was significantly increased in the high dose SMM914 group compared with the control group. CONCLUSION: P. pentosaceus SMM914 is a promising probiotic conferring antioxidant capacity by activating the Nrf2-Keap1 antioxidant signaling pathway in piglets. Our study provided useful resources for better understanding the relationships between the maternal microbiota and offspring. Video Abstract.

An Anti-Cancer Peptide LVTX-8 Inhibits the Proliferation and Migration of Lung Tumor Cells by Regulating Causal Genes' Expression in p53-Related Pathways.

Spider venom has been found to show its anticancer activity in a variety of human malignancies, including lung cancer. In this study, we investigated the anti-cancer peptide toxin LVTX-8, with linear amphipathic alpha-helical conformation, designed and synthesized from the cDNA library of spider Lycosa vittata. Multiple cellular methods, such as CCK-8 assay, flow cytometry, colony formation assay, Transwell invasion and migration assay, were performed to detect peptide-induced cell growth inhibition and anti-metastasis in lung cancer cells. Our results demonstrated that LVTX-8 displayed strong cytotoxicity and anti-metastasis towards lung cancer in vitro. Furthermore, LVTX-8 could suppress the growth and metastasis of lung cancer cells (A549 and H460) in nude mouse models. Transcriptomics, integrated with multiple bioinformatics analysis, suggested that the molecular basis of the LVTX-8-mediated inhibition of cancer cell growth and metastasis manifested in two aspects: Firstly, it could restrain the activity of cancer cell division and migration through the functional pathways, including "p53 hypoxia pathway" and "integrin signaling". Secondly, it could regulate the expression level of apoptotic-related proteins, which may account for programmed apoptosis of cancer cells. Taken together, as an anticancer peptide with high efficiency and acceptable specificity, LVTX-8 may become a potential precursor of a therapeutic agent for lung cancer in the future.

Homologous recombination shapes the genetic diversity of African swine fever viruses.

The African swine fever virus (ASFV) has severely influenced the swine industry of the world. Currently, there is no effective vaccine or drugs against the ASFV. How to effectively control the virus is challenging. In this study, we have analyzed all the publicly available ASFV genomes and demonstrated that there was a large genetic diversity of ASFV genomes. Interestingly, the genetic diversity was mainly caused by extensive genomic insertions and/or deletions (indels) instead of the point mutations. Further analyses showed that the indels may be attributed much to the homologous recombination, as supported by significant associations between the occurrence of extensive recombination events and the indels in the ASFV genomes. Besides, the homologous recombination also led to changes of gene content of ASFVs. Finally, repeated elements of dozens of nucleotides in length were observed to widely distribute and cluster in the adjacent positions of ASFV genomes, which may facilitate the occurrence of homologous recombination. This work highlighted the importance of homologous recombination in shaping the genetic diversity of the ASFVs, and could help understand the evolution of the virus.

Rapid identification of human-infecting viruses.

Viruses have caused much mortality and morbidity to humans and pose a serious threat to global public health. The virome with the potential of human infection is still far from complete. Novel viruses have been discovered at an unprecedented pace as the rapid development of viral metagenomics. However, there is still a lack of methodology for rapidly identifying novel viruses with the potential of human infection. This study built several machine learning models to discriminate human-infecting viruses from other viruses based on the frequency of k-mers in the viral genomic sequences. The k-nearest neighbor (KNN) model can predict the human-infecting viruses with an accuracy of over 90%. The performance of this KNN model built on the short contigs (≥1 kb) is comparable to those built on the viral genomes. We used a reported human blood virome to further validate this KNN model with an accuracy of over 80% based on very short raw reads (150 bp). Our work demonstrates a conceptual and generic protocol for the discovery of novel human-infecting viruses in viral metagenomics studies.

RAEdb: a database of enhancers identified by high-throughput reporter assays.

High-throughput reporter assays have been recently developed to directly and quantitatively assess enhancer activity for thousands of regulatory elements. However, there is still no database to collect these enhancers. We developed RAEdb, the first database to collect enhancers identified by high-throughput reporter assays. RAEdb includes 538 320 enhancers derived from eight studies, most of which were from six human cell lines. An activity score was assigned to each enhancer based on reporter assays. Based on these enhancers, 7658 epromoters (promoters with enhancer activity) were identified and stored in the database. RAEdb provides two ways of searches: the first is to search studies by species and cell line; the other is to search enhancers or epromoters by position, activity score, sequence and gene. RAEdb also provides a genome browser to query, visualize and compare enhancers. All data in RAEdb is freely available for download.

FOXA1 defines cancer cell specificity.

A transcription factor functions differentially and/or identically in multiple cell types. However, the mechanism for cell-specific regulation of a transcription factor remains to be elucidated. We address how a single transcription factor, forkhead box protein A1 (FOXA1), forms cell-specific genomic signatures and differentially regulates gene expression in four human cancer cell lines (HepG2, LNCaP, MCF7, and T47D). FOXA1 is a pioneer transcription factor in organogenesis and cancer progression. Genomewide mapping of FOXA1 by chromatin immunoprecipitation sequencing annotates that target genes associated with FOXA1 binding are mostly common to these cancer cells. However, most of the functional FOXA1 target genes are specific to each cancer cell type. Further investigations using CRISPR-Cas9 genome editing technology indicate that cell-specific FOXA1 regulation is attributable to unique FOXA1 binding, genetic variations, and/or potential epigenetic regulation. Thus, FOXA1 controls the specificity of cancer cell types. We raise a "flower-blooming" hypothesis for cell-specific transcriptional regulation based on these observations.

Effect of Huanshuai Recipe Oral Liquid ([characters: see text]) on renal dysfunction progression in patients with atherosclerotic renal artery stenosis.

OBJECTIVE: To investigate the effect of Huanshuai Recipe Oral Liquid ([characters: see text], HSR) on retarding the progression of renal dysfunction in patients with atherosclerotic renal artery stenosis (ARAS). METHODS: A total of 52 ARAS patients with the Chinese medicine (CM) syndrome of qi deficiency and blood stasis, phlegm and dampness retention were recruited and randomly assigned into the treatment group (36 cases) and the control group (16 cases). Both groups received a basic treatment (high-quality low-protein diet, blood pressure control, lipid-lowering, correcting the acidosis, etc.). In addition, the treatment group received 20 mL HSR and the control group received placebo, 3 times a day for 6 months. Renal function (serum creatinine, blood urea nitrogen and uric acid) and blood lipids (cholesterol, triglycerides and low density lipoprotein) were examined monthly. The estimated glomerular filtration rate (eGFR) and CM syndrome score were compared between groups. RESULTS: After treatment, compared with the control group, the serum creatinine level, uric acid level and CM syndrome score of the treatment group were significantly decreased (P<0.05 or P<0.01), and the eGFR in the treatment group were significantly increased (P<0.05). CONCLUSION: HSR can effectively improve the renal function and clinical symptoms of ARAS patients.

CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana.

BACKGROUND: The cytochrome P450 (CYP) superfamily enables terrestrial plants to adapt to harsh environments. CYPs are key enzymes involved in a wide range of metabolic pathways. It is particularly useful to be able to analyse the three-dimensional (3D) structure when investigating the interactions between CYPs and their substrates. However, only two plant CYP structures have been resolved. In addition, no currently available databases contain structural information on plant CYPs and ligands. Fortunately, the 3D structure of CYPs is highly conserved and this has made it possible to obtain structural information from template-based modelling (TBM). DESCRIPTION: The CYP Structure Interface (CYPSI) is a platform for CYP studies. CYPSI integrated the 3D structures for 266 A. thaliana CYPs predicted by three TBM methods: BMCD, which we developed specifically for CYP TBM; and two well-known web-servers, MUSTER and I-TASSER. After careful template selection and optimization, the models built by BMCD were accurate enough for practical application, which we demonstrated using a docking example aimed at searching for the CYPs responsible for ABA 8'-hydroxylation. CYPSI also provides extensive resources for A. thaliana CYP structure and function studies, including 400 PDB entries for solved CYPs, 48 metabolic pathways associated with A. thaliana CYPs, 232 reported CYP ligands and 18 A. thaliana CYPs docked with ligands (61 complexes in total). In addition, CYPSI also includes the ability to search for similar sequences and chemicals. CONCLUSIONS: CYPSI provides comprehensive structure and function information for A. thaliana CYPs, which should facilitate investigations into the interactions between CYPs and their substrates. CYPSI has a user-friendly interface, which is available at http://bioinfo.cau.edu.cn/CYPSI.

Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization.

BACKGROUND: Work on protein structure prediction is very useful in biological research. To evaluate their accuracy, experimental protein structures or their derived data are used as the 'gold standard'. However, as proteins are dynamic molecular machines with structural flexibility such a standard may be unreliable. RESULTS: To investigate the influence of the structure flexibility, we analysed 3,652 protein structures of 137 unique sequences from 24 protein families. The results showed that (1) the three-dimensional (3D) protein structures were not rigid: the root-mean-square deviation (RMSD) of the backbone Cα of structures with identical sequences was relatively large, with the average of the maximum RMSD from each of the 137 sequences being 1.06 Å; (2) the derived data of the 3D structure was not constant, e.g. the highest ratio of the secondary structure wobble site was 60.69%, with the sequence alignments from structural comparisons of two proteins in the same family sometimes being completely different. CONCLUSION: Proteins may have several stable conformations and the data derived from resolved structures as a 'gold standard' should be optimized before being utilized as criteria to evaluate the prediction methods, e.g. sequence alignment from structural comparison. Helix/ß-sheet transition exists in normal free proteins. The coil ratio of the 3D structure could affect its resolution as determined by X-ray crystallography.

Study on the relationship between blood stasis syndrome and clinical pathology in 227 patients with primary glomerular disease.

OBJECTIVE: To investigate the relationship between the severity of Chinese medicine (CM) blood stasis syndrome (BSS) with clinical features and renal lesion indexes of the primary glomerular disease. METHODS: An epidemiological survey was conducted to collect the data of 227 patients diagnosed as chronic primary glomerular diseases, and their severity of BSS were scored three days before renal biopsies were performed. The following clinical indexes were analyzed: age, course of glomerular diseases, 24-h urine protein ration (Upro), hypertension and blood pressure (BP) progress, serum creatinine levels (Scr), estimation of glomerular filtration rate based on the predigesting equation of MDRD (eGFR), blood urea nitrogen (BUN), uric acid (UA), triglyceride (TG), cholesterol (CHO), haematoglobin (HGB), albumin (ALB), and the correlation among renal pathological types, pathology lesion indexes, and BSS scores. RESULTS: (1) Among the 227 patients, 207 (91.19%) were diagnosed as BSS, in which 95 cases were considered as moderate and the rest 112 cases as severe. (2) There was a negative correlation between age, gender, grades of the hypertension, and the BSS score. Multiple stepwise regression analysis showed that Upro, CHO, TG, and eGFR were positively related to the BSS score (P<0.05). (3) The BSS score has a positive correlation with indexes of chronic renal pathology, especially the tubular atrophy and interstitial fibrosis. The severity of proliferation and glomerular sclerosis was accompanied with higher BSS scores with a significant difference (P<0.05). CONCLUSIONS: BSS is one of the most common CM syndromes among patients with the primary glomerular diseases; the BSS score has a positive correlation with Upro, CHO, TG, eGFR, as well as the index of chronic renal pathology. Based on these observations, the BSS may be used as an indicator of the development of renal diseases. Being positively diagnosed as BSS could indicate the beginning of the chronic phase of the primary glomerular diseases.

Synthesis and discovery of autophagy inducers for A549 and H460 lung cancer cells, novel 1-(2'-hydroxy-3'-aroxypropyl)-3-aryl-1H-pyrazole-5-carbohydrazide derivatives.

A series of novel 1-(2'-hydroxy-3'-aroxypropyl)-3-aryl-1H-pyrazole-5-carbohydrazide derivatives were synthesized, and the effects of the compounds on A549 cell growth were investigated. The results showed that all of the 1-(2'-hydroxy-3'-aroxypropyl)-3-aryl-1H-pyrazole-5-carbohydrazide derivatives 2 could inhibit the growth of A549 cells in dosage- and time-dependent manners. Typically, compound 2a and 2d induced A549 cells to autophagy but did not cause apoptosis and necrosis in the cells, and 2d had the most autophagy inducing effect in H460 cells. More importantly, 2a and 2d did not inhibit the growth of HUVEC cells.