The Fe-S cluster biosynthesis in Enterococcus faecium is essential for anaerobic growth and gastrointestinal colonization.

The facultative anaerobic Gram-positive bacterium Enterococcus faecium is a ubiquitous member of the human gut microbiota. However, it has gradually evolved into a pathogenic and multidrug resistant lineage that causes nosocomial infections. The establishment of high-level intestinal colonization by enterococci represents a critical step of infection. The majority of current research on Enterococcus has been conducted under aerobic conditions, while limited attention has been given to its physiological characteristics in anaerobic environments, which reflects its natural colonization niche in the gut. In this study, a high-density transposon mutant library containing 26,620 distinct insertion sites was constructed. Tn-seq analysis identified six genes that significantly contribute to growth under anaerobic conditions. Under anaerobic conditions, deletion of sufB (encoding Fe-S cluster assembly protein B) results in more extensive and significant impairments on carbohydrate metabolism compared to aerobic conditions. Consistently, the pathways involved in this utilization-restricted carbohydrates were mostly expressed at significantly lower levels in mutant compared to wild-type under anaerobic conditions. Moreover, deletion of sufB or pflA (encoding pyruvate formate lyase-activating protein A) led to failure of gastrointestinal colonization in mice. These findings contribute to our understanding of the mechanisms by which E. faecium maintains proliferation under anaerobic conditions and establishes colonization in the gut.

Serological Surveillance of the H1N1 and H3N2 Swine Influenza A Virus in Chinese Swine between 2016 and 2021.

Background: Swine influenza A virus (IAV-S) is a common cause of respiratory disease in pigs and poses a major public health threat. However, little attention and funding have been given to such studies. The aim of this study was to assess the prevalence of the Eurasian avian-like H1N1 (EA H1N1), 2009 pandemic H1N1 (pdm/09 H1N1), and H3N2 subtype antibodies in unvaccinated swine populations through serological investigations. Such data are helpful in understanding the prevalence of the IAV-S. Methods: A total of 40,343 serum samples from 17 regions in China were examined using hemagglutination inhibition (HI) tests against EA H1N1, pdm/09 H1N1, and H3N2 IAV-S from 2016 to 2021. The results were analyzed based on a reginal distribution, seasonal distribution, and in different breeding stages. Results: A total of 19,682 serum samples out of the 40,343 were positive for IAV-S (48.79%). The positivity rates to the EA H1N1 subtype, pdm/09 H1N1 subtype, and H3N2 subtype were 24.75% (9,986/40,343), 7.94% (3,205/40,343), and 0.06% (24/40,343), respectively. The occurrences of coinfections from two or more subtypes were also detected. In general, the positivity rates of serum samples were related to the regional distribution and feeding stages. Conclusions: The results of this study showed that the anti-EA H1N1 subtype and pdm/09 H1N1 subtype antibodies were readily detected in swine serum samples. The EA H1N1 subtype has become dominant in the pig population. The occurrences of coinfections from two or more subtypes afforded opportunities for their reassortment to produce new viruses. Our findings emphasized the need for continuous surveillance of influenza viruses.

Pathogenicity of novel reassortant Eurasian avian-like H1N1 influenza virus in pigs.

Reassortant Eurasian avian-like (EA) H1N1 virus, possessing 2009 pandemic (pdm/09) and triple-reassortant (TR)-derived internal genes, namely G4 genotype, has replaced the G1 genotype EA H1N1 virus (all the genes were of EA origin) and become predominant in swine populations in China. Understanding the pathogenicity of G4 viruses in pigs is of great importance for disease control. Here, we conducted comprehensive analyses of replication and pathogenicity of G4 and G1 EA H1N1 viruses in pigs. G4 virus exhibited enhanced replication, increased duration of virus shedding, and caused more severe respiratory lesions in pigs compared with G1 virus. G4 virus, with viral ribonucleoprotein (vRNP) complex genes of pdm/09 origin, exhibited higher levels of nuclear accumulation and higher polymerase activity, which is essential for improved replication of G4 virus. These findings indicate that G4 virus poses a great threat to both swine industry and public health, and control measures should be urgently implemented.

The role of 14-3-3 proteins in cell signalling pathways and virus infection.

14-3-3 proteins are highly conserved in species ranging from yeast to mammals and regulate numerous signalling pathways via direct interactions with proteins carrying phosphorylated 14-3-3-binding motifs. Recent studies have shown that 14-3-3 proteins can also play a role in viral infections. This review summarizes the biological functions of 14-3-3 proteins in protein trafficking, cell-cycle control, apoptosis, autophagy and other cell signal transduction pathways, as well as the associated mechanisms. Recent findings regarding the role of 14-3-3 proteins in viral infection and innate immunity are also reviewed.

Complex Internal Microstructure of Feather Follicles on Chicken Skin Promotes the Bacterial Cross-Contamination of Carcasses During the Slaughtering Process.

Chicken skin is considered the most susceptible to bacterial contamination during slaughter. It is rich in bushy feather follicles with complex internal structures that can absorb bacteria via cross-contamination during slaughter. Until now, the microstructural changes and local bacterial composition of feather follicles during slaughter have not been thoroughly investigated. This study used hematoxylin-eosin (HE) staining of the tissue paraffin section to investigate the structure of the feather follicles on chicken skin. In addition, the biopsy sampling method was employed for the high-throughput sequencing of 16S RNA genes to study the composition and source of bacterial contamination during slaughter. The results show that the feather follicles on chicken skin form a closed cavity structure during the slaughtering process. The volume of the irregular follicle cavity was about Ø: 200 µm × D: 1040 µm, which provides a place for the bacteria to absorb and resist the cleaning and disinfection during the slaughtering process. The composition of bacteria in the feather follicle was mainly Acinetobacter (37%), Psychrobacter (8%), Macrococcus (5%), and Comamonas (2%). The heat map obtained via the species abundance analysis of the feather follicle samples as well as the slaughter environment samples suggests that the gastrointestinal feces contaminated the feather follicles on the chicken skin mainly during the evisceration, defeathering, and chilling processes, and the last-stage chilling water also caused severe cross-contamination to the feather follicles during the chilling process.

The tail domain of PRRSV NSP2 plays a key role in aggrephagy by interacting with 14-3-3ε.

Porcine reproductive and respiratory syndrome (PRRS) caused by PRRS virus (PRRSV) is one of the most severe swine diseases that affects almost all swine-breeding countries. Nonstructural protein 2 (NSP2) is one of the most important viral proteins in the PRRSV life cycle. Our previous study showed that PRRSV NSP2 could induce the formation of aggresomes. In this study we explored the effects of aggresome formation on cells and found that NSP2 could induce autophagy, which depended on aggresome formation to activate aggrephagy. The transmembrane and tail domains of NSP2 contributed to aggrephagy and the cellular protein 14-3-3ε played an important role in NSP2-induced autophagy by binding the tail domain of NSP2. These findings provide information on the function of the C-terminal domain of NSP2, which will help uncover the function of NSP2 during PRRSV infection.

Porcine Reproductive and Respiratory Syndrome Virus Structural Protein GP3 Regulates Claudin 4 To Facilitate the Early Stages of Infection.

Claudins (CLDN) are a family of proteins that represent the most important components of tight junctions, where they establish the paracellular barrier that controls the flow of molecules in the intercellular space between epithelial cells. Several types of viruses make full use of CLDN to facilitate entry into cells. Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important pathogens in the swine industry. In this study, we found that CLDN4 functions as an anti-PRRSV factor by blocking its absorption during the early stages of infection. The small extracellular loop (ECL2) of CLDN4 restricted the viral particles outside cells by binding to GP3. A novel function of GP3-mediated regulation of CLDN4 transcription was suggested. CLDN4 can be decreased through downregulating the level of CLDN4 transcription by ubiquitinating the transcription factor, SP1. The mechanism by which highly pathogenic PRRSV infects the epithelium was proposed. Importantly, ECL2 was found to block PRRSV absorption and infection and neutralize the virus. A more in-depth understanding of PRRSV infection is described, and novel therapeutic antiviral strategies are discussed.IMPORTANCE In the present study, the role of CLDN4 in PRRSV infection was studied. The results showed that CLDN4 blocked absorption into cells and restricted extracellular viral particles via the interaction between the CLDN4 small extracellular loop, ECL2, and the viral surface protein GP3. GP3 was found to downregulate CLDN4 through ubiquitination of the transcription factor SP1 to facilitate viral entry. The mechanism by which highly pathogenic PRRSV infects the epithelium is suggested. A novel function of GP3 in regulating gene transcription was discovered. Moreover, ECL2 could block PRRSV absorption and infection, as well as neutralizing the virus in the supernatant, which may lead to the development of novel therapeutic antiviral strategies.

Methane Elimination Using Biofiltration Packed With Fly Ash Ceramsite as Support Material.

Methane is a greenhouse gas and significantly contributes to global warming. Methane biofiltration with immobilized methane-oxidizing bacteria (MOB) is an efficient and eco-friendly approach for methane elimination. To achieve high methane elimination capacity (EC), it is necessary to use an exceptional support material to immobilize MOB. The MOB consortium was inoculated in biofilters to continuusly eliminate 1% (v/v) of methane. Results showed that the immobilized MOB cells outperformed than the suspended MOB cells. The biofilter packed with fly ash ceramsite (FAC) held the highest average methane EC of 4.628 g h-1 m-3, which was 33.4% higher than that of the biofilter with the suspended MOB cells. The qPCR revealed that FAC surface presented the highest pmoA gene abundance, which inferred that FAC surface immobilized the most MOB biomass. The XPS and contact angle measurement indicated that the desirable surface elemental composition and stronger surface hydrophilicity of FAC might favor MOB immobilization and accordingly improve methane elimination.

Evolution and Pathogenicity of the H1 and H3 Subtypes of Swine Influenza Virus in Mice between 2016 and 2019 in China.

Pigs are considered a "mixing vessel" that can produce new influenza strains through genetic reassortments, which pose a threat to public health and cause economic losses worldwide. The timely surveillance of the epidemiology of the swine influenza virus is of importance for prophylactic action. In this study, 15 H1N1, one H1N2, and four H3N2 strains were isolated from a total of 4080 nasal swabs which were collected from 20 pig farms in three provinces in China between 2016 and 2019. All the isolates were clustered into four genotypes. A new genotype represented by the H1N2 strain was found, whose fragments came from the triple reassortant H1N2 lineage, classical swine influenza virus (cs-H1N1) lineage, and 2009 H1N1 pandemic virus lineage. A/Sw/HB/HG394/2018(H1N1), which was clustered into the cs-H1N1 lineage, showed a close relationship with the 1918 pandemic virus. Mutations determining the host range specificity were found in the hemagglutinin of all isolates, which indicated that all the isolates had the potential for interspecies transmission. To examine pathogenicity, eight isolates were inoculated into 6-week-old female BALB/c mice. The isolates replicated differently, producing different viral loadings in the mice; A/Swine/HB/HG394/2018(H1N1) replicated the most efficiently. This suggested that the cs-H1N1 reappeared, and more attention should be given to the new pandemic to pigs. These results indicated that new reassortments between the different strains occurred, which may increase potential risks to human health. Continuing surveillance is imperative to monitor swine influenza A virus evolution.

Improved nitrogen conservation capacity during composting of dairy manure amended with oil shale semi-coke as the porous bulking agent.

Oil shale semi-coke is the solid waste produced from the retorting process of oil shale, which may cause pollution to the environment without reasonable disposing. In this study, semi-coke was used as the bulking agent during composting to accelerate biodegradation of the organics as well as decrease the nitrogen loss. Results showed that the addition of semi-coke could accelerate biodegradation of the organics, with a raise in the organic matter loss from 44.99 % to 47.05 % compared with the control. Furthermore, the nitrogen loss significantly decreased from 40.00%-14.70 % in the treatment added with semi-coke due to less emission of NH3 and much more transformation of NH4+-N to NO3--N by nitrification, which could be explained by the increasing abundance of ammonia-oxidizing bacteria and archaea at the late composting stage and drastic shift of the microbial community like Chloroflexi, Firmicutes and Actinobacteria. After the composting cycle, the maturity of the produced compost was elevated greatly in the treatments amended with semi-coke. The result of PAHs detection suggested that there were low PAHs content in the raw oil shale semi-coke and they could be removed effectively to within the range for land application by composting especially when the surfactant was added.

Succession of the bacterial community and functional characteristics during continuous thermophilic composting of dairy manure amended with recycled ceramsite.

This study aimed to investigate variations of bacterial community and functional characteristics during the continuous thermophilic composting (CTC). Also their differences were discussed when amended with ceramsite and recycled ceramsite as the porous bulking agent. Results showed that the bacterial community shifted greatly and bacterial diversity increased as the CTC proceeded. Firmicutes and Chloroflexi was one of the major phyla at the active and late phase respectively. While Actinobacteria was the dominant phyla during the whole CTC. With the addition of ceramsite and recycled ceramsite, no significant difference was found of the overall bacterial variation trends. But the major phyla of Chloroflexi and Actinobacteria and major genes related to amino acid metabolism and carbohydrate metabolism increased significantly, especially when the recycled ceramsite was added. Redundancy analysis indicated that the succession of bacterial community was tightly related with the pH, water soluble organic carbon, NH4+-N, organic matter and germination index.

14-3-3ε acts as a proviral factor in highly pathogenic porcine reproductive and respiratory syndrome virus infection.

The highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) emerged in 2006 in China and caused great economic losses for the swine industry because of the lack of an effective vaccine. 14-3-3 proteins are generating significant interest as potential drug targets by allowing the targeting of specific pathways to elicit therapeutic effects in human diseases. In a previous study, 14-3-3s were identified to interact with non-structural protein 2 (NSP2) of PRRSV. In the present study, the specific subtype 14-3-3ε was confirmed to interact with NSP2 and play a role in the replication of the HP-PRRSV TA-12 strain. Knockdown of 14-3-3ε in Marc-145 cells and porcine alveolar macrophages (PAMs) caused a significant decrease in TA-12 replication, while stable overexpression of 14-3-3ε caused a significant increase in the replication of TA-12 and low pathogenic PRRSV (LP-PRRSV) CH-1R. The 14-3-3 inhibitor difopein also decreased TA-12 and CH-1R replication in Marc-145 cells and PAMs. These findings are consistent with 14-3-3ε acting as a proviral factor and suggest that 14-3-3ε siRNA and difopein are therapeutic candidates against PRRSV infection.

Sigma factors mediated signaling in Mycobacterium tuberculosis.

Activation of signaling cascades is critical for Mycobacterium tuberculosis (Mtb) to adapt the macrophage lifestyle. Parallel to several signal systems, sigma factor systems, especially the extra-cytoplasmic function sigma factors, are crucial for Mtb signaling. Most sigma factors lack a signal sensory domain and often are activated by various proteins that perceive the environmental cues and relay the signals through variegated post-translational modifications via the activity of antisigma factor, protein kinase and related transcriptional regulators. Antisigma factors are further controlled by multiple mechanisms. SigK senses the environmental redox state directly. Phosphorylation and lysine acetylation added another dimension to the regulatory hierarchy. This review will provide insights into Mtb pathogenesis, and lay the foundation for the discovery of novel approaches for therapeutic interventions.

A New Second Messenger: Bacterial c-di-AMP.

Nucleotide-based second messengers transduce signals originating from both outside and inside the cell to adaptive responses accordingly. c-di-AMP is a newly established second messenger employed by many organisms. We summarize recent advances in bacterial c-di-AMP-mediated signaling, especially the interaction between c-di-AMP signaling and the host.

Mycobacterium tuberculosis PPE family protein Rv1808 manipulates cytokines profile via co-activation of MAPK and NF-κB signaling pathways.

BACKGROUND/AIMS: Mycobacterium tuberculosis is an extremely successful intracellular pathogen armed with multiple tactics to subvert host immunity. PPE (Pro-Pro-Glu) family exclusively distributed in mycobacteria might be responsible for the virulence and pathogenicity of M.tuberculosis. The up-regulation of Rv1808 (PPE32) in many conditions prompted us to define its role in host innate immune response. METHODS: The Rv1808 encoding gene was expressed in nonpathogenic fast growing Mycobacterium smegmatis, mycobacteria- Escherichia coli shuttle plasmid pNITmyc served as control. RT-PCR and ELISA were used to detect the transcription and translation of host cytokines in culture supernatant from macrophage incubated with purified Rv1808 protein. Pharmacological inhibitors were applied to confirm the specificity of the effector interfering of host signaling. RESULTS: Recombinant Ms_Rv1808 survived better than Ms_pNITmyc within macrophage, accompanied by slightly higher host cell death. Rv1808 protein is associated with the cell wall and exposed on the cell surface. Physical binding of Rv1808 to TLR2 resulted in increase in the secretion of anti-inflammatory cytokine interleukin-10 (IL-10) and pro-inflammatory cytokines tumor necrosis factor (TNF-α) and interleukin-6 (IL-6) possibly via co-activation of NF-κB and MAPK (p38MAPK, JNK and ERK) signalling. CONCLUSION: Cell wall associated Rv1808 protein manipulated the host cytokines via MAPK and NF-κB signaling pathways.

Tuberculosis and sexual inequality: the role of sex hormones in immunity.

The role of sex hormones is profound and diverse. The gender and age differences in TB incidences suggest a role of hormones. These data, together with their relevance to the epidemiology of tuberculosis, are gathered and analyzed in this review. The underlying network of hormones functionalities in TB is also proposed.

Protein secondary structure prediction using NMR chemical shift data.

Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q(3) accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at http://monod.uwaterloo.ca/nmr/succes.

A novel algorithm for minimum recombinant haplotyping on pedigrees by zero recombinant block partition.

Haplotype inference based on pedigree data under the Mendelian law of inheritance and the minimum recombination principle is imperative for the construction of haplotype maps and the study of disease genes. But this problem has been proven to be NP-hard, exact algorithms previously known can't be applied to handle large-scale genotype datasets while heuristic algorithms can't gain high accuracy. This paper presents an algorithm named zero recombinant block algorithm (ZRBA) based on a new strategy using zero recombinant blocks (ZRB) as intermediate structure to reconstruct the haplotype configurations, theoretical analysis shows that this strategy can reduce the possible haplotype configurations exponentially, and following experiments demonstrate that our algorithm runs much faster than existing exact haplotyping algorithms with comparable accuracy.

MBA: a literature mining system for extracting biomedical abbreviations.

BACKGROUND: The exploding growth of the biomedical literature presents many challenges for biological researchers. One such challenge is from the use of a great deal of abbreviations. Extracting abbreviations and their definitions accurately is very helpful to biologists and also facilitates biomedical text analysis. Existing approaches fall into four broad categories: rule based, machine learning based, text alignment based and statistically based. State of the art methods either focus exclusively on acronym-type abbreviations, or could not recognize rare abbreviations. We propose a systematic method to extract abbreviations effectively. At first a scoring method is used to classify the abbreviations into acronym-type and non-acronym-type abbreviations, and then their corresponding definitions are identified by two different methods: text alignment algorithm for the former, statistical method for the latter. RESULTS: A literature mining system MBA was constructed to extract both acronym-type and non-acronym-type abbreviations. An abbreviation-tagged literature corpus, called Medstract gold standard corpus, was used to evaluate the system. MBA achieved a recall of 88% at the precision of 91% on the Medstract gold-standard EVALUATION Corpus. CONCLUSION: We present a new literature mining system MBA for extracting biomedical abbreviations. Our evaluation demonstrates that the MBA system performs better than the others. It can identify the definition of not only acronym-type abbreviations including a little irregular acronym-type abbreviations (e.g., ), but also non-acronym-type abbreviations (e.g., ).