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• Whole genomes between hyper-aerotolerant (HAT) C. coli and oxygen-sensitive (OS) C. coli strains from swine were compared. • Expressions of genes involved in oxidative stress and iron transport/uptake between HAT C. coli and OS C. coli were compared. • No genetic differences according to aerotolerance levels of C. coli at genomic structure were identified. • Higher expression of oxidative stress-related genes under aerobic stress may be responsible for the emergence of HAT C. coli. Although Campylobacter , an obligate microaerophilic foodborne pathogen, is susceptible to oxygen, aerotolerant/hyper-aerotolerant (HAT) Campylobacter can survive under aerobic conditions. Here, we aimed to reveal what affects the enhanced aerotolerance in HAT Campylobacter coli at genome and gene expression levels. We compared the whole genomes between HAT and oxygen-sensitive (OS) C. coli isolates from swine and analyzed the relative expressions of oxidative stress-related (sodB , ahpC , katA , and trxB) and iron transport/uptake-related (cfbpA , ceuE , feuB , and feoB) genes. The comparative genomics showed no relation between the clustering of the strains and aerotolerance levels. The reactive oxygen species-related factors involved in respiration, stress response, and iron acquisition/uptake were similar among the strains, regardless of their aerotolerance levels. However, the expressions of the oxidative stress-related genes under aerobic conditions compared to that of microaerobic conditions increased in the HAT strains, while decreased in the OS strains. Our findings suggest that what influences differences in aerotolerance between HAT and OS C. coli may be due to the differential expressions of oxidative stress-related genes despite the similarities in genomic structure. This study provides insights into the genetic basis of aerotolerance in C. coli. Therefore, it could assist in managing HAT C. coli that has the potential to be easily transmitted to humans through the food chain. [ABSTRACT FROM AUTHOR]

Hickory ( Carya cathayensis ) is a critical tree species of the genus Carya from the Juglandaceae family that contains nutrient-rich nuts. Due to large-scale soil degradation, the pests and diseases of hickory are becoming more and more serious. Thaumatin-like proteins (TLPs) are vital proteins involved in the complex defense process of plant pathogens. In this study, 40 CcTLP genes were identified genome-widely and phylogenetically grouped into three subfamilies. The sequence of CcTLPs had a conservative pattern, such as eight stable disulfide bonds, REDDD, and G-X-[GF]-X-C-X-T-[GA]-D-C-X(1,2)-G-X-(2,3)-C structure. In total, 57 cis -elements related to stress-responsive, light-responsive, phytohormone-responsive, and plant-responsive were discovered. Under salicylate (SA), methyl jasmonate (MeJA), and ethephon (ETH) treatments, the expressions of CcTLP28, CcTLP29, CcTLP30, CcTLP31, CcTLP32, CcTLP33, CcTLP37, CcTLP38 , and CcTLP39 had different patterns. This is an indication that most of the TLP genes were upregulated by SA and downregulated by MeJA. Notably, seven TLP genes were significantly upregulated under the Botryosphaeria dothidea inoculation, especially CcTLP31 , with an over 20-fold change. Nine genes were shown by subcellular localization analysis to be located at the plasma membrane and cytoplasm. The knowledge of the disease-resistant function of the CcTLP family in hickory is promoted by these results. A foundation reference for the molecular breeding of this plant in the future is provided by our findings., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Li, Xu, Wang, Guo, Gu, Lyu, Huang, Lin, Huang, Xu and Li.)

High-throughput technologies produce gene expression time-series data that need fast and specialized algorithms to be processed. While current methods already deal with different aspects, such as the non-stationarity of the process and the temporal correlation, they often fail to take into account the pairing among replicates. We propose PairGP, a non-stationary Gaussian process method to compare gene expression time-series across several conditions that can account for paired longitudinal study designs and can identify groups of conditions that have different gene expression dynamics. We demonstrate the method on both simulated data and previously unpublished RNA sequencing (RNA-seq) time-series with five conditions. The results show the advantage of modeling the pairing effect to better identify groups of conditions with different dynamics. The pairing effect model displays good capabilities of selecting the most probable grouping of conditions even in the presence of a high number of conditions. The developed method is of general application and can be applied to any gene expression time series dataset. The model can identify common replicate effects among the samples coming from the same biological replicates and model those as separate components. Learning the pairing effect as a separate component, not only allows us to exclude it from the model to get better estimates of the condition effects, but also to improve the precision of the model selection process. The pairing effect that was accounted before as noise, is now identified as a separate component, resulting in more accurate and explanatory models of the data., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

This study evaluates the effects of longan seed powder (LS) on the growth performance, immunological response, and immune-antioxidant related gene expression of Nile tilapia (Oreochromis niloticus). Three hundred fish (13.82 ± 0.06 g) were divided into five experiments and fed 5 diets, including the basal diet (control without LS) and basal diet containing 10 (LS10), 20 (LS20), 40 (LS40), and 80 (LS80) g kg -1 LS for eight weeks. A completely randomized design (CRD) with three replications was utilised. The growth performance and immune response were measured at weeks 4 and 8 post feeding, while the gene expressions were determined at the end of the feeding trial. The results revealed that administration of LS could significantly (P < 0.05) improve specific growth rate (SGR), weight gain (WG), and feed conversion ratio (FCR) in Nile tilapia as compared to the control group. However, no significant differences (P > 0.05) were observed in survival rates among treatments. LS-supplemented diets showed enhanced serum peroxidase activity (SPA), serum lysozyme activity (SLA), skin mucus lysozyme activity (MLA), and skin mucus peroxidase activity (MPA) at weeks 4 and 8 post-feeding, with the highest values observed in the LS20 diet (P < 0.05). Additionally, LS-supplemented diets significantly up-regulated (P < 0.05) immune and antioxidant related gene expressions (IL1, IL8, LBP, GSTa, GPX, and GSR) in the liver and intestine, with highest values observed in the LS20 treatment. The present results confirmed the beneficial effects of LS as a functional feed additive and immunostimulant for Nile Tilapia culture in a biofloc system., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

• 45 CsGRX genes were identified in cucumber genome. • CC-type GRX genes were differential expression under abiotic stresses. • CsGRX6, CsGRX8 , and CsGRX14 are localized to the nucleus. • Overexpression of CsGRX4 increased sensitivity to salt stress. Glutaredoxins (GRX s) are key regulators in the cellular redox state and play pivotal roles in both plant development and responses to stress stimuli. Here, we found 45 GRX gene members in cucumber, 16 of which were classified as CC-type. These CC-type GRX s were shown to be highly conserved among cucumber, Arabidopsis thaliana , and rice, according to our bioinformatic analyzes results. Cucumber CC-type GRX (CsGRX) genes showed varying expression levels in different plant organs and in response to different abiotic stresses. CsGRX1, CsGRX5, CsGRX9, CsGRX13 , and CsGRX16 expression was induced from 3 to 6 h by salicylic acid (SA) treatments, whereas CsGRX1, CsGRX3, CsGRX8, CsGRX13, CsGRX14 , and CsGRX17 expression was induced from 3 to 12 h with methyl jasmonate (MeJA) treatments. Moreover, CsGRX11 expression was strongly induced from 0 to 24 h by MeJA treatment, whereas CsGRX3 and CsGRX11 expression was strongly induced at the early stages of 42 °C treatments and at the later stages of the methyl viologen treatments. CsGRX4, CsGRX6, CsGRX7, CsGRX13 and CsGRX11 expression was induced by PEG and NaCl treatments. These results indicated the versatile roles of GRX genes in response to stress stimuli. The subcellular localization results for three CsGRX –green fluorescent protein (GFP) fusion proteins indicated that some orthologs were localized to the nucleus. CsGRX4 that responded to salt stress were heterologously expressed in Arabidopsis , and its transgenic lines demonstrated salt sensitivity, showing lower seed germination rate and shorter root length than their wild type counterparts under salt stress. Our results provide a foundation for future studies on GRX genes in cucumber. [ABSTRACT FROM AUTHOR]

Bacterial LPS is a heat-stable endotoxin and wall components of gram negative bacteria, which can exhibit a toxicological effect on physiology and biochemical activities of fish. In this study, we investigated the effect of LPS exposure on cell viability, oxidative stress, caspase activity and immune-related gene expressions in cultured fin cell lines of red crucian carp, white crucian carp and their hybrid offspring. LPS stimulation could reduce fish cell viability, whereas gene expression levels and promoter activities in inflammatory signals increased dramatically. Moreover, enhanced levels of intracellular oxidative stress and decreased levels of mitochondrial membrane potential (MMP) were observed in LPS-induced fish cells. N-Acetyl-L-cysteine (NAC) could alleviate LPS-stimulated reactive oxygen species (ROS) generation and caspase-3 activity in fish cells. These results suggested that ROS-mediated cytotoxic stress was involved in LPS-induced inflammation and mitochondrial damage in cultured fish cells. [Display omitted] • LPS exposure could increase inflammatory signals in three lines of fish fibroblast cells. • LPS treatment could cause oxidative stress and lead to mitochondrial damage. • NAC could alleviate ROS generation and caspase-3 activity in LPS-stimulated fish cells. [ABSTRACT FROM AUTHOR]

Acetyl-CoA carboxylase is the rate-limiting enzyme in the biogenesis of long chain fatty acids. There is a single copy of the gene for acetyl-CoA carboxylase per haploid chromosome set. The gene contains two promoters whose primary transcripts are differentially spliced resulting in multiple forms of acetyl-CoA carboxylase mRNA. These mRNA species are different in the 5′-untranslated region, but contain the same coding region. Generation of different forms of the mRNA is tissue specific and controlled by physiological conditions. Two promoters contain an extensive array of cis-elements that perceive changes in the cellular environment signalling repression and induction of long chain fatty acid synthesis. The ability of the gene to respond to various lipogenic signals and the presence of the same coding sequence in all acetyl-CoA carboxylase mRNA species suggest that the biosynthesis of fatty acids required for multiple functions in the cells is primarily regulated at the gene level. [ABSTRACT FROM AUTHOR]

Chemosensory proteins (CSPs) are important for insect chemoreception, which bind, solubilize and transport hydrophobic chemical molecules from external environment to dendrite membrane of chemosensory neurons. Moreover, CSPs are also involved in non-sensory physiological activities. The peach fruit borers Carposina sasakii Matsumura (Lepidoptera: Carposinidae) seriously damage fruit trees and their chemoreception mainly occurs in the adult stage. We identified 10 putative CSPs (Csas CSP1 ~ Csas CSP10) from head transcriptomes of C. sasakii adult males and females, all of which are classic CSPs that have 4 conserved cysteines with a spacing pattern C 1 –X 6 –C 2 –X 17 – 18 –C 3 –X 2 –C 4. Their phylogenetic characteristics were also described. An analysis using fluorescence quantitative PCR showed Csas CSP2 has the highest level of expression in the heads, so it is more likely to be involved in C. sasakii chemoreception than the other C. sasakii CSPs. Csas CSP1, Csas CSP3, Csas CSP4, Csas CSP6, Csas CSP7 and Csas CSP8 are expressed dominantly in the wings; Csas CSP5 and Csas CSP10 have the highest expression level in the thoraxes; Csas CSP9 is dominantly and equally expressed in the thoraxes and abdomens. This study contributes to understanding physiological functions of C. sasakii CSPs and chemosensory mechanism at C. sasakii molecular level. Relative expressions of putative C. sasakii CSPs (Csas CSP1 ~ Csas CSP10) in C. sasakii heads, wings, thoraxes and abdomens. Gene expressions in different tissues are normalized, relative to that in heads. Data are displayed as the mean of three replicates with standard deviation (the bar). Significant differences in the relative expressions between different tissues are indicated by different letters at the bars (P < 0.05; LSD test). [Display omitted] • 10 putative chemosensory proteins are identified from Carposina sasakii. • Phylogenetic characteristics of these chemosensory proteins are shown. • Tissue- and sex-specific expressions of these chemosensory proteins were studied. [ABSTRACT FROM AUTHOR]

Todays, with the industrialization of human societies, pollution of aquatic ecosystems with plastics derivatives are a serious concern, affecting the life of their organisms. The present study was conducted to investigate the size effects of micro-plastic, polystyrene on some physiological lesions of the goldfish, Carassius auratus. Fish were exposed to two sizes (0.25 and 8 μm) polystyrene at different environmentally relevant concentrations. The exposure trial was done in two steps. First, fish exposed to a stable concentration of 300 mg/L polystyrene for 168 h. Gill, intestine, and liver tissues were sampled every 24 h to investigate the accumulation of polystyrene. Then, fish were exposed in three replicates to 0 (control), 0.05, 0.5, and 5 mg/L polystyrene in two sizes of 0.25 and 8 μm for 28 days. After the exposure period, gill, liver, and intestine tissues were sampled for histological study, also, serum samples were collected for biochemical assays. Fluorescent microscope observations confirmed the accumulation of polystyrene in tissue samples with time. In addition, histological lesions were found in the liver, intestine, and gill of the exposed fish. The severity of lesions showed a size and dose-dependent pattern. Polystyrene induced the antioxidant system of exposed fish through elevating the levels of SOD and CAT activity and significant difference in expression of antioxidant related genes (CAT, SOD and HSP70). In conclusion, the results of the present study confirmed the toxic effects of microplastic, polystyrene on goldfish. [Display omitted] • The severity of lesions showed a size and dose dependent pattern. • Size effects of 0.25 µm MPs was sever than 8 µm. • SOD, CAT and antioxidant genes were the most relevant biomarkers of MPs. • MPs affect many physiological indices of goldfish as an aquatics model. [ABSTRACT FROM AUTHOR]

Simple Summary: Supplementation of agriculture by-product as functional feed additives in combination with biofloc technology (a sustainable and environmentally friendly technology) has recently gained much attention in aquaculture. In the present study, sugarcane bagasse powder can possibly be applied as a feed additive to improve growth performance, immune response, and immune and antioxidant-related gene expression. We investigated, herein, the effects of dietary inclusion of sugarcane bagasse powder (SB) on Nile tilapia development, mucosal and serum immunities, and relative immune and antioxidant genes. Fish (15.12 ± 0.04 g) were provided a basal diet (SB0) or basal diet incorporated with SB at 10 (SB10), 20 (SB20), 40 (SB40), or 80 (SB80) g kg−1 for 8 weeks. Our results demonstrated that the dietary incorporation of sugarcane bagasse powder (SB) at 20 and 40 g kg−1 significantly ameliorated FW, WG, and SGR as opposed to fish fed basal, SB10, and SB80 diets. However, no significant changes in FCR and survivability were observed between the SB supplemented diets and the control (basal diet). The mucosal immunity exhibited significantly higher SMLA and SMPA activities (p < 0.005) in fish treated with SB diets after eight weeks. The highest SMLA and SMPA levels were recorded in fish fed SB80 followed by SB20, SB40, and SB10, respectively. For serum immunity, fish fed SB incorporated diets significantly ameliorated SL and RB levels (p < 0.05) compared with the control. However, SP was not affected by the inclusion of SB in any diet throughout the experiment. The expression of IL1, IL8, LBP, GSTa, GPX, and GSR genes in the fish liver was significantly increased in fish fed the SB20 and SB10 diets relative to the basal diet fed fish (p < 0.05); whereas only the IL8, LBP, and GPX genes in the intestines were substantially augmented via the SB20 and SB80 diets (p < 0.05). IL1 and GSR were not influenced by the SB incorporated diets (p > 0.05). In summary, sugarcane bagasse powder (SB) may be applied as a feed additive to improve growth performance, immune response, and immune and antioxidant-related gene expression in Nile tilapia. [ABSTRACT FROM AUTHOR]

The potential protective role of priming wheat seeds with maize green extract (MGE) against the stress effects of drought was studied. Pretreatment using MGE, MGE enriched with polyamines (MGEPA), and drought treatments (irrigation deficit of 30% (severe drought) or 60% (moderate drought) versus 90% relative water content of soil as a control) were applied in a factorial completely randomized design. Under moderate drought, pretreatment with MGEPA outperformed MGE and control, while severely stressed plants died even with pretreatments. Both extracts enhanced normal plant growth and yield and mitigated the deleterious effect of moderately stressed plants. Application of both extracts markedly increased photosynthetic efficiency, membrane stability, relative water content, and accumulation of antioxidants, osmoprotectants, trans- and cis-zeatin, polyamines, and their gene expressions, while levels of superoxide (O2•−) and hydrogen peroxide (H2O2), lipid peroxidation, and electrolyte leakage were decreased. Enzymatic antioxidants and glyoxalase system activities were improved in moderately stressed plants and were further improved with pretreatment with both extracts, thus protecting plants from oxidative damage by up-regulation of the ascorbate–glutathione cycle. Glycine betaine, soluble sugars, and proline levels were greatly increased in pretreated plants, thus maintaining membrane stability and photosynthetic efficiency. The interaction between drought and pretreatment using MGEPA was significant in growing wheat plants in dry environments with 60% relative water content of soil. [ABSTRACT FROM AUTHOR]

Remedies toward sustainable aquaculture rely upon research that unveils the molecular mechanisms behind host immunity and their interactions with pathogens. Antiviral defense is a major innate immune response in fish. The antiviral protein GCHV-induced gene-2 (Gig2), a member of the interferon-stimulated gene (ISG), was identified and characterized from rockfish (Sebastes schlegelii). Gig2 exists in two isoforms, namely, SsGig2-I1 and SsGig2-I2, in rockfish with lengths of 163 and 223 bp, respectively. Bioinformatic analysis indicated the availability of poly (ADP-ribose) polymerase domain in both proteins, and 51.3% identity and 71.3% similarity between both isoforms were observed. The basal expression pattern revealed the highest tissue-specific expression in rockfish gills for both isoforms. The immune challenge experiment disclosed a distinctive and strong expression of each transcript in the presence of poly I:C. Both isoforms are localized in the endoplasmic reticulum. Interferon (IFN) pathway gene analysis revealed no significant upregulation of IFN related genes. Viral hemorrhagic septicemia virus (VHSV) gene expression analysis revealed strong downregulation of viral transcripts after 48 h of infection in the presence of Gig2 isoforms. Collectively, these results indicate the protective role of Gig2 in rockfish against VHSV infection and help broaden our understanding of the innate immunity of fish., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

• UV-C + MAP exhibited synergistic effects in retaining physiological quality. • UV-C + MAP reduced total microbial growth. • UV-C + MAP retarded lignin synthesis by suppressing related enzyme activities. • UV-C + MAP inhibited gene expressions of phenolic metabolism-related enzymes. The present study investigated influences of ultraviolet light C (UV-C; 2 kJ m−2) irradiation and high-oxygen modified atmosphere packaging (MAP; 80 % O 2 , 10 % CO 2 and 10 % N 2) on physiological quality, microbial growth and lignification metabolism of fresh-cut carrots. After 15-d cold storage, comparing with either treatment alone, the combination of UV-C irradiation and high-oxygen MAP (abbr. UV-C + MAP) more obviously inhibited firmness, weight loss, ascorbic acid, total carotenoid and γ-aminobutyric acid declines, reduced respiration and ethylene production rates as well as delayed bacterial growth. UV-C + MAP more strongly restrained whiteness index, total phenolic, lignin and malondialdehyde increases. Furthermore, UV-C + MAP treatment more efficiently retarded lignin synthesis by suppressing phenolic metabolism-related enzyme (phenylalanine ammonialyase, PAL; polyphenoloxidase, PPO; peroxidase, POD) activities and their gene (DcPAL ; DcPPO ; DcPOD) expressions. Above results indicated that UV-C + MAP exhibited synergistic effects in retaining physiological quality, delayed senescence process, reducing microbial growth, alleviating lignification degree, and lessened surface whitening. Therefore, UV-C + MAP could maintain overall quality and extend shelf-life during storage of fresh-cut carrots. [ABSTRACT FROM AUTHOR]

Simple Summary: Crossbreeding using exotic breeds is usually employed to improve the growth characteristics of indigenous chickens. This mating not only provides growth but adversely affects excess fat deposition as well. This deposition was regulated by a complicated cellular mechanism including peroxisome proliferator-activated receptors (PPARs) function. Thus, we hypothesized that native chickens breed percentage might be related to PPARs gene expression. This study aimed to study the role of PPARs on fat deposition in chickens which was the different native genetic background. Our results indicated that increasing commercial breed percentage in the chicken leads to increased fat deposition via the increasing of PPARG gene expression. Therefore, the PPARG gene notable as a major gene of cellular fat deposition and might be applied in further study. This study aimed to study the role of PPARs on fat deposition in native crossbred chicken. We studied the growth, abdominal, subcutaneous, and intramuscular fat, and mRNA expression of PPARA and PPARG in adipose and muscle tissues of four chicken breeds (CH breed (100% Thai native chicken), KM1 (50% CH background), KM2 (25% CH background), and broiler (BR)). The result shows that the BR chickens had higher abdominal fat than other breeds (p < 0.05) and the KM2 had an abdominal fat percentage higher than KM1 and CH respectively (p < 0.05). The intramuscular fat of BR was greater than KM1 and CH (p < 0.05). In adipose tissue, PPARA expression was different among the chicken breeds. However, there were breed differences in PPARG expression. Study of abdominal fat PPARG expression showed the BR breed, KM1, and KM2 breed significantly greater (p < 0.05) than CH. In 8 to 12 weeks of age, the PPARG expression of the CH breed is less than (p < 0.05) KM2. Crossbreeding improved the growth of the Thai native breed, there was also a corresponding increase in carcass fatness. However, there appears to be a relationship between PPARG expression and fat deposition traits. therefore, PPARG activity hypothesized to plays a key role in lipid accumulation by up-regulation. [ABSTRACT FROM AUTHOR]

The effects of added probiotics on growth performance, blood chemical, and hematological responses; as well as immune-related gene expression in Nile tilapia (Oreochromis niloticus) under transportation stress were evaluated. Fish were treated over a period of 120 days in three groups: T 1 , the control group (no probiotic), T 2 , 5.6 × 108 cfu g−1 of Saccharomyces cerevisiae , and T 3 , 1 × 106 cfu g−1 of Bacillus spp. The fish were then exposed to the transportation stress experiment for four hours (h). The resulted revealed that there were no significant differences in survival rate during and after transportation in all treatments. However, the survival rate of the control group significant decreased (p <.05) after 24 h post transportation stress, and significantly higher rate of cortisol, glucose, aspartate aminotransferase (AST), and alanine aminotransferase (ALT) were observed in the T 1 group, compared to the T 2 and T 3 groups. However, significantly lower malondialdehyde (MDA) was found in T 3 compared to those of T 1 and T 2 after 24 to 72 h post-transportation. The expression of heat shock proteins (Hsp 70) and tumor necrosis factor-alpha (TNF- α) levels in the control group were significantly higher (p <.05) than those of T 2 and T 3 groups, especially at 0 h post-transportation stress. No significant differences in lysozyme activity and hematological profiles were detected between the control (T 1) and probiotic groups (T 2 and T 3). In conclusion, Nile tilapia reared for 120 days in aqueous probiotic showed significantly improved health tolerance under transportation stress. • Significant lower blood chemical was observed in probiotics treated fish. • Significant lower levels of Hsp70 and TNF- α were observed in probiotics treated fish compared to the control. • No significant differences in survival rates were during or after transportation. [ABSTRACT FROM AUTHOR]

• LAS deteriorated the pollutants removal efficiency in SBRs. • LAS disrupted the sludge structure and reduced the biomass in SBRs. • The microbial community was altered with the reduction of functional bacterial. • The metabolic activity was decreased, i.e. ATP and expression of functional genes. Linear alkylbenzene sulfonates (LAS) are widely detected in wastewater, and pose potential risks to environment. The influences of LAS on the typical pollutants removal in sequencing batch reactors (SBRs) were evaluated. The results indicated that the removal efficiency of COD, NH 4 + and PO 4 3− was respectively reduced by 10.5–27.5%, 5.4–7.3% and11.6–28.9% with the exposure of 10–50 mg/L LAS. Mechanisms investigation found that LAS disrupted the sludge structure and reduced the biomass in reactors due to the saponification effects. Also, the presence of LAS altered the microbial community of activated sludge, and reduced the abundances of functional bacterial responsible for pollutants removal (i.e.Candidatus Accumulibacter , Nitrospira , Denitratisoma and etc.). Moreover, the LAS exhibited negative impacts on the microbial activity with increased LDH release but decreased ATP concentration. The genes expressions for microbial metabolism (i.e. carbohydrate metabolisms, energy metabolism) and typical pollutants removal (i.e. electron transport, phosphonate transport) were all downregulated in LAS-exposed SBRs. [ABSTRACT FROM AUTHOR]

Myocardial infarction (MI) eventually exacerbates inflammatory response due to the release of inflammatory and pro-inflammatory factors. The aim of this study is to explore the protective efficacy of piperine supplementation against the inflammatory response in isoproterenol (ISO)-induced MI. Masson Trichome staining was executed to determine myocardial tissue architecture. Immunohistochemistry was performed for IL-6, TNF-α. RT-PCR studies were performed to ascertain the gene expression of IL-6, TNF-α, iNOS, eNOS, MMP-2, MMP-9, and collagen-III. Western blotting was performed to determine expression of HIF-1α, VEGF, Nrf-2, NF-ƙB, Cox-2, p-38, phospho-p38, ERK-1/2, phospho-ERK-1/2, and collagen-I. HIF-1α, VEGF, and iNOS expression were significantly upregulated with concomitant decline in eNOS expression in the heart myocardial tissue of rats received ISO alone whereas piperine pretreatment prevented these changes in ISO administered rats. Current results revealed ROS-mediated activation of MAPKs, namely, p-p38, p-ERK1/2 in the heart tissue of ISO administered group. Piperine pretreatment significantly prevented these changes in ISO treated group. NF-κB is involved in the modulation of gene expressions responsible for tissue repair. ISO-induced NF-κB-p65 expression was significantly reduced in the group pretreated with piperine and mitigated extent of myocardial inflammation. A significant increase in cardiac fibrosis upon ISO treatment was reported due to the increased hydroxyproline content, MMP-2 & 9 and upregulation of collagen-I protein compared to control group. All these cardiac hypertrophy markers were decreased in ' piperine pretreated ISO administered group ' compared to group received ISO injection. Current findings concluded that piperine as a nutritional intervention could prevent inflammation of myocardium in ISO-induced MI. Image 1 [ABSTRACT FROM AUTHOR]

Native to China, spine grapes (Vitis davidii Foex) are an important wild grape species. Here, the quality characteristics of one white and three red spine grape clones were evaluated via targeted metabolomic and transcription level analysis. Xiangzhenzhu (XZZ) had the highest soluble sugar and organic acid content. Malvidin-3-acetyl-glucoside and cyanidin-3-glucoside were the characteristic anthocyanins in spine grapes, and significant differences in anthocyanin composition between different clones were detected. Anthocyanins were not detected in Baiyu (BY) grapes. The transcript levels of VdGST, VdF3′H, VdOMT, VdLDOX, and VdUFGT were significantly related to the anthocyanin biosynthesis and proportions. A total of 27 kinds of glycosidically bound volatiles (including alcohols, monoterpenes, esters, aldehydes, ketones, and phenolic acid) were identified in spine grapes, with Gaoshan #4 (G4) and BY grapes having the highest concentrations. The VdGT expression levels were closely related to glycosidically bound volatile concentrations. These results increase our understanding of the quality of wild spine grapes and further promote the development and use of wild grape resources. [ABSTRACT FROM AUTHOR]

Today, data mining and gene expressions are at the forefront of modern data analysis. Here we introduce a novel probability distribution that is applicable in these fields. This paper develops the proposed spherical-Dirichlet distribution designed to fit vectors located at the positive orthant of the hypersphere, as it is often the case for data in these fields, avoiding unnecessary probability mass. Basic properties of the proposed distribution, including normalizing constants and moments are developed. Relationships with other distributions are also explored. Estimators based on classical inferential statistics, such as method of moments and maximum likelihood estimators are obtained. Two applications are developed: the first one uses simulated data, and the second uses a real text mining example. Both examples are fitted using the proposed spherical-Dirichlet distribution and their results are discussed. [ABSTRACT FROM AUTHOR]

The Superposing Significant Interaction Rules (SSIR) method is a combinatorial procedure that deals with symbolic descriptors of samples. It is able to rank the series of samples when those items are classified into two classes. The method selects preferential descriptors and, with them, generates rules that make up the rank by means of a simple voting procedure. Here, two application examples are provided. In both cases, binary or multilevel strings encoding gene expressions are considered as descriptors. It is shown how the SSIR procedure is useful for ranking the series of patient transcription data to diagnose two types of cancer (leukemia and prostate cancer) obtaining Area Under Receiver Operating Characteristic (AU-ROC) values of 0.95 (leukemia prediction) and 0.80–0.90 (prostate). The preferential selected descriptors here are specific gene expressions, and this is potentially useful to point to possible key genes. [ABSTRACT FROM AUTHOR]

The continuous and rapid emergence of new viral strains calls for a better understanding of the fundamental changes occurring within the host cell upon viral infection. In this study, we analyzed RNA-seq transcriptome data from Calu-3 human lung epithelial cells infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compared to five other viruses namely, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East Respiratory Syndrome (SARS-MERS), influenzavirus A (FLUA), influenzavirus B (FLUB), and rhinovirus (RHINO) compared to mock-infected cells and characterized their coding and noncoding RNA transcriptional portraits. The induction of interferon, inflammatory, and immune response was a hallmark of SARS-CoV-2 infection. Comprehensive bioinformatics revealed the activation of immune response and defense response to the virus as a common feature of viral infection. Interestingly however, the degree of functional categories and signaling pathways activation varied among different viruses. Ingenuity pathways analysis highlighted altered conical and casual pathways related to TNF, IL1A, and TLR7, which are seen more predominantly during SARS-CoV-2 infection. Nonetheless, the activation of chemotaxis and lipid synthesis was prominent in SARS-CoV-2-infected cells. Despite the commonality among all viruses, our data revealed the hyperactivation of chemotaxis and immune cell trafficking as well as the enhanced fatty acid synthesis as plausible mechanisms that could explain the inflammatory cytokine storms associated with severe cases of COVID-19 and the rapid spread of the virus, respectively. [ABSTRACT FROM AUTHOR]

The global spread of COVID-19, caused by pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for an imminent response from medical research communities to better understand this rapidly spreading infection. Employing multiple bioinformatics and computational pipelines on transcriptome data from primary normal human bronchial epithelial cells (NHBE) during SARS-CoV-2 infection revealed activation of several mechanistic networks, including those involved in immunoglobulin G (IgG) and interferon lambda (IFNL) in host cells. Induction of acute inflammatory response and activation of tumor necrosis factor (TNF) was prominent in SARS-CoV-2 infected NHBE cells. Additionally, disease and functional analysis employing ingenuity pathway analysis (IPA) revealed activation of functional categories related to cell death, while those associated with viral infection and replication were suppressed. Several interferon (IFN) responsive gene targets (IRF9, IFIT1, IFIT2, IFIT3, IFITM1, MX1, OAS2, OAS3, IFI44 and IFI44L) were highly upregulated in SARS-CoV-2 infected NBHE cell, implying activation of antiviral IFN innate response. Gene ontology and functional annotation of differently expressed genes in patient lung tissues with COVID-19 revealed activation of antiviral response as the hallmark. Mechanistic network analysis in IPA identified 14 common activated, and 9 common suppressed networks in patient tissue, as well as in the NHBE cell model, suggesting a plausible role for these upstream regulator networks in the pathogenesis of COVID-19. Our data revealed expression of several viral proteins in vitro and in patient-derived tissue, while several host-derived long noncoding RNAs (lncRNAs) were identified. Our data highlights activation of IFN response as the main hallmark associated with SARS-CoV-2 infection in vitro and in human, and identified several differentially expressed lncRNAs during the course of infection, which could serve as disease biomarkers, while their precise role in the host response to SARS-CoV-2 remains to be investigated. [ABSTRACT FROM AUTHOR]

The modified Cholesky decomposition (MCD) is a powerful tool for estimating a covariance matrix. The regularization can be conveniently imposed on the linear regressions to encourage the sparsity in the estimated covariance matrix to accommodate the high-dimensional data. In this paper, we propose a Cholesky-based sparse ensemble estimate for covariance matrix by averaging a set of Cholesky factor estimates obtained from multiple variable orderings used in the MCD. The sparse estimation is enabled by encouraging the sparsity in the Cholesky factor. The theoretical consistent property is established under some regular conditions. The merits of the proposed method are illustrated through simulation and a maize genes data set.

Endometriosis is a common, benign, and hormone-dependent gynaecological disorder that displays altered immunoinflammatory profiles. Myeloid-derived suppressor cells (MDSCs) suppressed immunosurveillance in endometriosis in human and mouse model. Receptor tyrosine kinase inhibitor Sunitinib can induce MDSC apoptosis and suppress the progression of cancer. However, the effects of Sunitinib on MDSCs in endometriosis and the underlying mechanism are not clear. In this study, we employed an animal study of the endometriosis model in mice for treatment of Sunitinib. After syngeneic endometrium transplantation and treatment, endometriotic lesion volume, weight, and histology were compared. Peritoneal fluid, peripheral blood, and bone marrow MDSC subsets and their molecular signaling were monitored by flow cytometry. Peritoneal cytokines were assayed by ELISA. The gene expression profiles of isolated CD11b+Ly6G+Ly6C lo cells were studied by RNA sequencing. We found that Sunitinib significantly decreased the endometriotic lesion size and weight after 1 and 3 weeks, and decreased p-STAT3 activation in MDSCs after 1 week of treatment. In the first week, Sunitinib specifically increased the G-MDSC population in peritoneal fluid but the isolated CD11b+Ly6G+Ly6C lo MDSCs after Sunitinib treatment were presented as mature polynuclear MDSCs, while the control group had immature mononuclear MDSCs. Importantly, we found Sunitinib differentially suppressed gene expressions of immunosuppressive function and differentiation in peritoneal G-MDSCs. Apelin signaling pathway associated genes and inflammation related genes were upregulated, and amino acid metabolism regulator genes were downregulated in bone marrow G-MDSCs. For endometriotic lesions, the PPARG gene governing glucose metabolism and fatty acid storage, which is important for the development of endometriosis was upregulated. In conclusion, Sunitinib inhibited endometriotic lesions, by promoting peritoneal fluid MDSCs maturation and inhibiting the immunosuppressive function. These findings suggest that Sunitinib changed the immune microenvironment and inhibited the development of endometriosis, which has potential therapeutic effects as novel immunotherapy to promote MDSCs maturation, differentiation, and metabolism for the treatment of endometriosis., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 He, Hung, Liang, Zhang, Gao, Chu, Zhang, Xu, Chung and Wang.)

Background: The diamondback moth (Plutella xylostella) is one of the most destructive lepidopteran pests on cruciferous vegetables. However, resistance has emerged to current chemical and biological insecticides used for P. xylostella control, indicating the necessity of screening new targets on P. xylostella, and finding new insecticides against P. xylostella. In particular, octopamine receptors are representative G protein-coupled receptors found only in invertebrates and are potential targets for identifying novel insecticides., Results: A β-adrenergic-like octopamine receptor gene (PxOA2B1) was cloned, and its pharmacological characteristics in P. xylostella were studied. The results demonstrated that octopamine could activate the PxOA2B1 receptor, with a half-maximal effective concentration (EC 50 ) of 49.5 nm. Amitraz, an insecticide and acaricide, and its metabolite (N-2,4-dimethylphenyl-N'-methylformamidine; DPMF) were also found to act as PxOAB1R agonists. We synthesized phenyl imidazolidin-2-one derivatives 3a-h using DPMF as the lead compound, and compounds 3a-h showed similar antagonist activities as phentolamine, mianserin and chlorpromazine. In particular, 3d, with an EC 50 of 25.2 nm, showed very similar antagonist activity to mianserin., Conclusion: This research found that PxOAB1R might be a potential target for P. xylostella control. Phenyl imidazolidin-2-ones could be novel potential antagonists targeted at octopamine receptors and would be useful tools for the design and development of novel insecticides. © 2021 Society of Chemical Industry., (© 2021 Society of Chemical Industry.)

Objective: Alpha and beta-adrenoceptors (ADR-α1, 2, and β2) play a regulatory role in the folliculogenesis and steroidogenesis in the ovarian follicles. This study aimed to measure these adrenoceptors mRNA and its protein levels in cumulus cells (CCs) culture of poor ovarian reserve (POR) and polycystic ovarian syndrome (PCOS) infertile women (IVF candidate) and the effect of clonidine treatment at CCs culture., Methods: This case/control study was conducted in 2017 includes a control (donation oocytes) and two studies (PCO and POR) groups. The ovulation induction drugs were prescribed in all groups. After the oocyte puncture, the follicular fluid was collected and CCs were isolated were cultured. RNA was extracted and cDNA was synthesized and designed the primer for the ADR-α1, 2 and ADR-β2 gene expression. The protein levels were investigated by Western Blot., Results: The results showed a high level of three adrenergic expressions in PCO women compared to the control group ( p -value <.001), which can be reduced by clonidine. POR group showed a significant decrease in the gene expression of ADR-α1 ( p -value = .004) and ADR-α2 ( p -value = .003) compared to the control group and clonidine treatment had no effect., Conclusion: The significant increase of three adrenoceptors gene expression and protein levels in CCs culture indicate to the hyperactivity of the ovarian sympathetic nervous system at the receptor levels in women with PCOS, and clonidine confirmed it by reducing this expression. In POR women, the reduction of ADR-α1, 2 expressions maybe lead to the aging process in the ovary.

In the study of gene expression data, network analysis has played a uniquely important role. To accommodate the high dimensionality and low sample size and generate interpretable results, regularized estimation is usually conducted in the construction of gene expression Gaussian Graphical Models (GGM). Here we use GeO-GGM to represent gene-expression-only GGM. Gene expressions are regulated by regulators. gene-expression-regulator GGMs (GeR-GGMs), which accommodate gene expressions as well as their regulators, have been constructed accordingly. In practical data analysis, with a "lack of information" caused by the large number of model parameters, limited sample size, and weak signals, the construction of both GeO-GGMs and GeR-GGMs is often unsatisfactory. In this article, we recognize that with the regulation between gene expressions and regulators, the sparsity structures of a GeO-GGM and its GeR-GGM counterpart can satisfy a hierarchy. Accordingly, we propose a joint estimation which reinforces the hierarchical structure and use the construction of a GeO-GGM to assist that of its GeR-GGM counterpart and vice versa. Consistency properties are rigorously established, and an effective computational algorithm is developed. In simulation, the assisted construction outperforms the separation construction of GeO-GGM and GeR-GGM. Two The Cancer Genome Atlas data sets are analyzed, leading to findings different from the direct competitors., (© 2021 Wiley Periodicals LLC.)