Organic acids and 2,4-Di-tert-butylphenol: major compounds of Weissella confusa WM36 cell-free supernatant against growth, survival and virulence of Salmonella Typhi
Background Salmonella Typhi (S. Typhi), the causative agent of typhoid fever, causes serious systemic disease in humans. Antibiotic treatment is required for the S. Typhi infection, while the inappropriate use of antibiotics causes increased drug-resistant S. Typhi. Hence, alternative therapies through non-antibiotic approaches are urgently needed. The use of beneficial lactic acid bacterium and/or its metabolites to control typhoid fever represent a promising approach, as it may exert protective actions through various mechanisms. Method In this study, the cell-free culture supernatant (CFCS) of Weissella confusa WM36 was evaluated via the antibacterial activity, and its metabolites were identified. In addition, the effects of CFCS on Salmonella virulence behaviors were also investigated. Result Based on strong inhibition the growth of S. Typhi DMST 22842, organic acids (lactic acid and acetic acid) and 2,4-Di-tert-butylphenol (2,4 DTBP), were the main antibacterial metabolites presented in CFCS of strain WM36. Minimum inhibitory concentration (MIC) at 40% WM36–CFCS dramatically reduced the S. Typhi population to more than 99.99% at 4 h and completely inhibited biofilm formation, while sub-MIC at 20% (v/v) and MIC could reduce 100% of motility. Additionally, sub-MIC at only 10% (v/v) WM36–CFCS did down-regulate the expression of virulence genes which are responsible for the type-III secretion system, effector proteins, and quorum sensing system in this pathogen. Conclusion W. confusa WM36 and its metabolites are shown to be a promising candidates, and an effective approach against typhoid Salmonella burden.
Pelyuntha et al. (2020) Organic acids and 2,4-Di-tert-butylphenol: major compounds of Weissella confusa WM36 cell-free supernatant against growth, survival and virulence of Salmonella Typhi. PeerJ 8:e8410 https://doi.org/10.7717/peerj.8410
Ecology of an ocelot population at the northern edge of the species’ distribution in northern Sonora, Mexico
We used data from eight years of camera trapping at Rancho El Aribabi, a cattle ranch and conservation property in northern Sonora, Mexico, to examine the ecology of the northern-most known breeding population of ocelots (Leopardus pardalis). Ocelots were found mostly in two discrete and disjunct areas: a riverine riparian canyon at just less than 1,000 masl elevation and along arroyos in an oak-mesquite savanna in the Sierra Azul at 1,266–1,406 masl. An ocelot was also detected at a site between those two areas, in an area of a Sonoran desertscrub-foothills thornscrub ecotone at 1,300 masl. At least 18 ocelots, both males and females, were detected during the 2007–2011 and 2014–2018 sampling periods. A female with a kitten was documented in 2011. No individual ocelots were photographed in both areas, which are separated by a minimum of 11.29 km, and no individuals were photographed in both time periods. In a binary logistic regression, key environmental variables predicting ocelot presence were, in order of importance, distance to a paved road, distance to human habitation, proximity to water, and an anthropogenic influences index that was dominated by cattle. Another analysis corroborated the finding regarding ocelot presence and cattle. Contrary to previous studies, ocelot presence was not tied to vegetation cover close to the ground. We present information about the types of habitats and sites ocelots used, short-term movements, daily and seasonal activity patterns, and behavior, including occurrence of different individuals at or near the same site over short periods of time. We discuss ocelot home range, density, and movements, but small sample sizes and study design problems limit the value of estimates derived from our work. Rancho El Aribabi is a private, conservation ranch for which the owners have made voluntary conservation commitments that provide habitat and protection for ocelots and other animals and plants. This northern-most known breeding population is a likely source of ocelots that are periodically detected in southeastern Arizona. Our results should help facilitate conservation of the ocelot in other semi-arid areas of northwestern Mexico and adjacent USA.
Rorabaugh et al. (2020) Ecology of an ocelot population at the northern edge of the species’ distribution in northern Sonora, Mexico. PeerJ 8:e8414 https://doi.org/10.7717/peerj.8414
Integrated bioinformatics analysis of potential pathway biomarkers using abnormal proteins in clubfoot
Background As one of the most common major congenital distal skeletal abnormalities, congenital talipes equinovarus (clubfoot) affects approximately one in one thousandth newborns. Although several etiologies of clubfoot have been proposed and several genes have been identified as susceptible genes, previous studies did not further explore signaling pathways and potential upstream and downstream regulatory networks. Therefore, the aim of the present investigation is to explore abnormal pathways and their interactions in clubfoot using integrated bioinformatics analyses. Methods KEGG, gene ontology (GO), Reactome (REAC), WikiPathways (WP) or human phenotype ontology (HP) enrichment analysis were performed using WebGestalt, g:Profiler and NetworkAnalyst. Results A large number of signaling pathways were enriched e.g. signal transduction, disease, metabolism, gene expression (transcription), immune system, developmental biology, cell cycle, and ECM. Protein-protein interactions (PPIs) and gene regulatory networks (GRNs) analysis results indicated that extensive and complex interactions occur in these proteins, enrichment pathways, and TF-miRNA coregulatory networks. Transcription factors such as SOX9, CTNNB1, GLI3, FHL2, TGFBI and HOXD13, regulated these candidate proteins. Conclusion The results of the present study supported previously proposed hypotheses, such as ECM, genetic, muscle, neurological, skeletal, and vascular abnormalities. More importantly, the enrichment results also indicated cellular or immune responses to external stimuli, and abnormal molecular transport or metabolism may be new potential etiological mechanisms of clubfoot.
Cai et al. (2020) Integrated bioinformatics analysis of potential pathway biomarkers using abnormal proteins in clubfoot. PeerJ 8:e8422 https://doi.org/10.7717/peerj.8422
Comparative analysis of cutaneous bacterial communities of farmed Rana dybowskii after gentamycin bath
Introduction Pathogenic bacteria limit the success of Rana dybowskii breeding. Gentamicin is used to treat R. dybowskii disease. To understand the effects of gentamicin on the composition and structure of the cutaneous bacterial community of R. dybowskii, three groups (control, gentamicin and recovery) were established in this study. Materials & Methods The V3–V4 hypervariable region of the 16S rRNA gene was analyzed in samples by high-throughput sequencing. Alpha diversity and beta diversity were evaluated to compare the cutaneous bacterial community diversity. Results A total of 1,159,668 valid sequences and 3,132 operational taxonomic units (OTUs) were obtained from these three experimental groups. The number of OTUs obtained in the control group, gentamicin group and recovery group were 2,194, 2,288, and 2,047, respectively, and the number of shared OTUs was 1,313. The alpha diversity of the cutaneous bacterial community was not significantly affected by gentamicin, while beta diversity was significantly affected. Discussion & Conclusions The effect of a gentamicin bath on relative species abundance was greater than the effect on the species composition. The changes in Proteobacteria, Acinetobacter, and Chryseobacterium were significant, and reductions were observed after the recovery period. Six potentially pathogenic genera were detected, including Aeromonas, Citrobacter, Chryseobacterium, Pseudomonas, Staphylococcus, and Streptococcus. Among them, Aeromonas and Chryseobacterium were significantly inhibited by the gentamicin bath. The results of this study provide a theoretical basis for the application of gentamicin in R. dybowskii breeding.
Bie et al. (2020) Comparative analysis of cutaneous bacterial communities of farmed Rana dybowskii after gentamycin bath. PeerJ 8:e8430 https://doi.org/10.7717/peerj.8430
Gini coefficients for measuring the distribution of sexually transmitted infections among individuals with different levels of sexual activity
Objectives Gini coefficients have been used to describe the distribution of Chlamydia trachomatis (CT) infections among individuals with different levels of sexual activity. The objectives of this study were to investigate Gini coefficients for different sexually transmitted infections (STIs), and to determine how STI control interventions might affect the Gini coefficient over time. Methods We used population-based data for sexually experienced women from two British National Surveys of Sexual Attitudes and Lifestyles (Natsal-2: 1999–2001; Natsal-3: 2010–2012) to calculate Gini coefficients for CT, Mycoplasma genitalium (MG), and human papillomavirus (HPV) types 6, 11, 16 and 18. We applied bootstrap methods to assess uncertainty and to compare Gini coefficients for different STIs. We then used a mathematical model of STI transmission to study how control interventions affect Gini coefficients. Results Gini coefficients for CT and MG were 0.33 (95% CI [0.18–0.49]) and 0.16 (95% CI [0.02–0.36]), respectively. The relatively small coefficient for MG suggests a longer infectious duration compared with CT. The coefficients for HPV types 6, 11, 16 and 18 ranged from 0.15 to 0.38. During the decade between Natsal-2 and Natsal-3, the Gini coefficient for CT did not change. The transmission model shows that higher STI treatment rates are expected to reduce prevalence and increase the Gini coefficient of STIs. In contrast, increased condom use reduces STI prevalence but does not affect the Gini coefficient. Conclusions Gini coefficients for STIs can help us to understand the distribution of STIs in the population, according to level of sexual activity, and could be used to inform STI prevention and treatment strategies.
Gsteiger et al. (2020) Gini coefficients for measuring the distribution of sexually transmitted infections among individuals with different levels of sexual activity. PeerJ 8:e8434 https://doi.org/10.7717/peerj.8434
Comparative analysis of the demographic parameters of seven spotted ladybird beetle (Coleoptera: Coccinellidae) reared on various host aphid species
Background The demographic parameters of the predacious seven spotted ladybird beetle Coccinella septempunctata Linnaeus (Coleoptera: Coccinellidae) reared on the following four host aphid species were compared: Rhopalosiphum padi Linnaeus (Hemiptera: Aphididae), Rhopalosiphum maidis Fitch (Hemiptera: Aphididae), Sitobion avenae Fabricius (Hemiptera: Aphididae), and Schizaphis graminum Rondani (Hemiptera: Aphididae). Methods The developmental period, fecundity, adult preoviposition period, total preoviposition period and population parameters were evaluated based on the two-sex age-stage life table. The duration of the developmental stages and the population parameters were calculated with the TWOSEX-MSChart program, whereas population size was projected based on the two-sex age-stage life table data with the TIMING-MSChart program. Results The intrinsic rate of increase (r) was the highest in the R. padi predators (0.1946 per day), followed by the S. graminum (0.1435 per day), S. avenae (0.1400 per day), and R. maidis (0.1180 per day) predators. The differences in the net reproductive rate (R0) and the finite rate of increase (λ) when C. septempunctata was reared on the four aphid species were consistent with the r values. This trend was reversed for the mean generation time (T), which ranged from 29.02 days for the lady beetles reared on R. padi to 39.75 days for the lady beetles reared on R. maidis. Interestingly, R. padi was the most suitable host, while the congeneric R. maidis was the least suitable. The results of this study may be useful for future investigations regarding the ecological effects of predatory species and the mass-production of C. septempunctata in the laboratory for an augmentative release of an aphid predator.
Farooq et al. (2020) Comparative analysis of the demographic parameters of seven spotted ladybird beetle (Coleoptera: Coccinellidae) reared on various host aphid species. PeerJ 8:e8313 https://doi.org/10.7717/peerj.8313
Evolution of sexual size dimorphism in the wing musculature of Drosophila
Male courtship songs in Drosophila are exceedingly diverse across species. While much of this variation is understood to have evolved from changes in the central nervous system, evolutionary transitions in the wing muscles that control the song may have also contributed to song diversity. Here, focusing on a group of four wing muscles that are known to influence courtship song in Drosophila melanogaster, we investigate the evolutionary history of wing muscle anatomy of males and females from 19 Drosophila species. We find that three of the wing muscles have evolved sexual dimorphisms in size multiple independent times, whereas one has remained monomorphic in the phylogeny. These data suggest that evolutionary changes in wing muscle anatomy may have contributed to species variation in sexually dimorphic wing-based behaviors, such as courtship song. Moreover, wing muscles appear to differ in their propensity to evolve size dimorphisms, which may reflect variation in the functional constraints acting upon different wing muscles.
Tracy et al. (2020) Evolution of sexual size dimorphism in the wing musculature of Drosophila. PeerJ 8:e8360 https://doi.org/10.7717/peerj.8360
Identification of key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis
Background Osteoarthritis (OA) is the most common chronic degenerative joint disease and is mainly characterized by cartilage degeneration, subcartilage bone hyperplasia, osteophyte formation and joint space stenosis. Recent studies showed that synovitis might also be an important pathological change of OA. However, the molecular mechanisms of synovitis in OA are still not well understood. Objective This study was designed to identify key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis. Materials and Methods The gene expression profiles of GSE12021, GSE55235 and GSE55457 were downloaded from the GEO database. The differentially expressed genes (DEGs) were identified by the LIMMA package in Bioconductor, and functional enrichment analyses were performed. A protein-protein interaction network (PPI) was constructed, and module analysis was performed using STRING and Cytoscape. The CIBERSORT algorithm was used to analyze the immune infiltration of synovial tissue between OA and normal controls. Results A total of 106 differentially expressed genes, including 68 downregulated genes and 38 upregulated genes, were detected. The PPI network was assessed, and the most significant module containing 14 hub genes was identified. Gene Ontology analysis revealed that the hub genes were significantly enriched in immune cell chemotaxis and cytokine activity. KEGG pathway analysis showed that the hub genes were significantly enriched in the rheumatoid arthritis signaling pathway, IL-17 signaling pathway and cytokine-cytokine receptor interaction signaling pathway. The immune infiltration profiles varied significantly between osteoarthritis and normal controls. Compared with normal tissue, OA synovial tissue contained a higher proportion of memory B cells, naive CD4+ T cells, regulatory T cells, resting dendritic cells and resting mast cells, while naive CD4+ T cells, activated NK cells, activated mast cells and eosinophils contributed to a relatively lower portion (P > 0.05). Finally, the expression levels of 11 hub genes were confirmed by RT-PCR. Conclusion The hub genes and the difference in immune infiltration in synovial tissue between osteoarthritis and normal controls might provide new insight for understanding OA development.
Cai et al. (2020) Identification of key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis. PeerJ 8:e8390 https://doi.org/10.7717/peerj.8390
Isolation, sequencing, and expression analysis of 30 AP2/ERF transcription factors in apple
Background AP2/ERF transcription factors are involved in the regulation of plant growth, development, and stress responses. Our research objective was to characterize novel apple (Malus × domestica Borkh.) genes encoding AP2/ERF transcription factors involved in regulation of plant growth, development, and stress response. The transcriptional level of apple AP2/ERF genes in different tissues and under various biotic and abiotic stress was determined to provide valuable insights into the function of AP2/ERF transcription factors in apple. Methods Thirty full-length cDNA sequences of apple AP2/ERF genes were isolated from ‘Zihong Fuji’ apple (Malus × domestica cv. Zihong Fuji) via homologous comparison and RT-PCR confirmation, and the obtained cDNA sequences and the deduced amino acid sequences were analyzed with bioinformatics methods. Expression levels of apple AP2/ERF genes were detected in 16 different tissues using a known array. Expression patterns of apple AP2/ERF genes were detected in response to Alternaria alternata apple pathotype (AAAP) infection using RNA-seq with existing data, and the expression of apple AP2/ERF genes was analyzed under NaCl and mannitol treatments using qRT-PCR. Results The sequencing results produced 30 cDNAs (designated as MdERF3-8, MdERF11, MdERF16-19, MdERF22-28, MdERF31-35, MdERF39, MdAP2D60, MdAP2D62-65, and MdRAV2). Phylogenetic analysis revealed that MdERF11/16, MdERF33/35, MdERF34/39, and MdERF18/23 belonged to groups A-2, A-4, A-5, and A-6 of the DREB subfamily, respectively; MdERF31, MdERF19, MdERF4/25/28/32, MdERF24, MdERF5/6/27, and MdERF3/7/8/17/22/26 belonged to groups B-1, B-2, B-3, B-4, B-5, and B-6 of the ERF subfamily, respectively; MdAP2D60 and MdAP2D62/63/64/65 belonged to the AP2 subfamily; and MdRAV2 belonged to the RAV subfamily. Array results indicated that 30 apple AP2/ERF genes were expressed in all examined tissues to different degrees. RNA-seq results using previously reported data showed that many members of the apple ERF and DREB subfamilies were induced by Alternaria alternate apple pathotype (AAAP) infection. Under salt treatment, many members in the apple ERF and DREB subfamilies were transcriptionally up or down-regulated. Under mannitol treatment, many members of the apple ERF, DREB, and AP2 subfamilies were induced at the transcriptional level. Taken together, the results indicated that the cloned apple AP2/ERF genes were expressed in all examined tissues. These genes were up-regulated or down-regulated in response to AAAP infection and to salt or mannitol treatment, which suggested they may be involved in regulating growth, development, and stress response in apple.
Li et al. (2020) Isolation, sequencing, and expression analysis of 30 AP2/ERF transcription factors in apple. PeerJ 8:e8391 https://doi.org/10.7717/peerj.8391
Autophagy-related genes prognosis signature as potential predictive markers for immunotherapy in hepatocellular carcinoma
Autophagy-related genes (ATGs) depress tumorigenesis. However, in tumor tissue, it promotes tumor progression. Here, we demonstrated that 63 ATGs were differentially expressed in normal tissues and tumor tissues of hepatocellular carcinoma (HCC), and seven prognostic-related genes were chosen to establish prognostic risk signatures. It is not just an independent prognostic factor for HCC, but also closely related to the degree of malignancy of HCC. Further, the hallmarks of PI3K–AKT–mTOR signaling was significantly enriched in the high-risk group. Moreover, AKT–pS473 and mTOR–pS2448 expression was down-regulated and correlated with patient prognosis in high-risk group. Finally, we demonstrate that the prognosis signature of ATGs is closely related to immune cell infiltration and PD-L1 expression. In conclusion, ATGs are a crucial factor in the malignant progression of HCC and will be a new prognostic marker for diagnosis and treatment. ATGs prognostic signatures are potentially useful for predicting PD-L1 therapeutic effects.
Mao et al. (2020) Autophagy-related genes prognosis signature as potential predictive markers for immunotherapy in hepatocellular carcinoma. PeerJ 8:e8383 https://doi.org/10.7717/peerj.8383