Bacterial community drives soil organic carbon transformation in vanadium titanium magnetite tailings through remediation using Pongamia pinnata.

With continuous mine exploitation, regional ecosystems have been damaged, resulting in a decline in the carbon sink capacity of mining areas. There is a global shortage of effective soil ecological restoration techniques for mining areas, especially for vanadium (V) and titanium (Ti) magnetite tailings, and the impact of phytoremediation techniques on the soil carbon cycle remains unclear. Therefore, this study aimed to explore the effects of long-term Pongamia pinnata remediation on soil organic carbon transformation of V-Ti magnetite tailing to reveal the bacterial community driving mechanism. In this study, it was found that four soil active organic carbon components (ROC, POC, DOC, and MBC) and three carbon transformation related enzymes (S-CL, S-SC, and S-PPO) in vanadium titanium magnetite tailings significantly (P < 0.05) increased with P. pinnata remediation. The abundance of carbon transformation functional genes such as carbon degradation, carbon fixation, and methane oxidation were also significantly (P < 0.05) enriched. The network nodes, links, and modularity of the microbial community, carbon components, and carbon transformation genes were enhanced, indicating stronger connections among the soil microbes, carbon components, and carbon transformation functional genes. Structural equation model (SEM) analysis revealed that the bacterial communities indirectly affected the soil organic carbon fraction and enzyme activity to regulate the soil total organic carbon after P. pinnata remediation. The soil active organic carbon fraction and free light fraction carbon also directly regulated the soil carbon and nitrogen ratio by directly affecting the soil total organic carbon content. These results provide a theoretical reference for the use of phytoremediation to drive soil carbon transformation for carbon sequestration enhancement through the remediation of degraded ecosystems in mining areas.

Genome-wide identification of resistance genes and response mechanism analysis of key gene knockout strain to catechol in Saccharomyces cerevisiae.

Engineering Saccharomyces cerevisiae for biodegradation and transformation of industrial toxic substances such as catechol (CA) has received widespread attention, but the low tolerance of S. cerevisiae to CA has limited its development. The exploration and modification of genes or pathways related to CA tolerance in S. cerevisiae is an effective way to further improve the utilization efficiency of CA. This study identified 36 genes associated with CA tolerance in S. cerevisiae through genome-wide identification and bioinformatics analysis and the ERG6 knockout strain (ERG6Δ) is the most sensitive to CA. Based on the omics analysis of ERG6Δ under CA stress, it was found that ERG6 knockout affects pathways such as intrinsic component of membrane and pentose phosphate pathway. In addition, the study revealed that 29 genes related to the cell wall-membrane system were up-regulated by more than twice, NADPH and NADP+ were increased by 2.48 and 4.41 times respectively, and spermidine and spermine were increased by 2.85 and 2.14 times, respectively, in ERG6Δ. Overall, the response of cell wall-membrane system, the accumulation of spermidine and NADPH, as well as the increased levels of metabolites in pentose phosphate pathway are important findings in improving the CA resistance. This study provides a theoretical basis for improving the tolerance of strains to CA and reducing the damage caused by CA to the ecological environment and human health.

Diversity and composition of microbial communities in Jinsha earthen site under different degree of deterioration.

Earthen sites are the important cultural heritage that carriers of human civilization and contains abundant history information. Microorganisms are one of important factors causing the deterioration of cultural heritage. However, little attention has been paid to the role of biological factors on the deterioration of earthen sites at present. In this study, microbial communities of Jinsha earthen site soils with different deterioration types and degrees as well as related to environmental factors were analyzed. The results showed that the concentrations of Mg2+ and SO42- were higher in the severe deterioration degree soils than in the minor deterioration degree soils. The Chao1 richness and Shannon diversity indices of bacteria in different type deterioration were higher in the summer than in the winter; the Chao1 and Shannon indices of fungi were lower in the summer. The differences in bacterial and fungal communities were associated with differences in Na+, K+, Mg2+ and Ca2+ contents. Based on both the relative abundances in amplicon sequencing and isolated strains, the bacterial phyla Actinobacteria, Firmicutes and Proteobacteria, and the Ascomycota genera Aspergillus, Cladosporium and Penicillium were common in all soils. The OTUs enriched in the severe deterioration degree soils were mostly assigned to Actinobacteria and Proteobacteria, whereas the Firmicutes OTUs differentially abundant in the severe deterioration degree were all depleted. All bacterial isolates produced alkali, implying that the deterioration on Jinsha earthen site may be accelerated through alkali production. The fungal isolates included both alkali and acid producing strains. The fungi with strong ability to produce acid were mainly from the severe deterioration degree samples and were likely to contribute to the deterioration. Taken together, the interaction between soil microbial communities and environment may affect the soil deterioration, accelerate the deterioration process and threaten the long-term preservation of Jinsha earthen site.

Insights into antibiotic and heavy metal resistance interactions in Escherichia coli isolated from livestock manure and fertilized soil.

Heavy metal and antibiotic-resistant bacteria from livestock feces are ecological and public health problems. However, the distribution and relationships of antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs), and virulence factors (VFs) and their transmission mechanisms remain unclear. Therefore, we investigated the resistance of Escherichia coli, the prevalence of its ARGs, HMRGs, and VFs, and their transmission mechanisms in livestock fresh feces (FF), composted feces (CF), and fertilized soil (FS). In total, 99.54% (n = 221) and 91.44% (n = 203) of E. coli were resistant to at least one antibiotic and one heavy metal, respectively. Additionally, 72.52% (n = 161) were multi-drug resistant (MDR), of which Cu-resistant E. coli accounted for 72.67% (117/161). More than 99.34% (88/89) of E. coli carried multidrug ARGs, VFs, and the Cu resistance genes cueO and cusABCRFS. The Cu resistance genes cueO and cusABCRFS were mainly located on chromosomes, and cueO and cusF were positively associated with HMRGs, ARGs, and VFs. The Cu resistance genes pcoABCDRS were located on the plasmid pLKYL-P02 flanked by ARGs in PF18C from FF group and on chromosomes flanked by HMRGs in SAXZ1-1 from FS group. These results improved our understanding of bacterial multidrug and heavy metal resistance in the environment.

Genome-wide identification of resistance genes and cellular analysis of key gene knockout strain under 5-hydroxymethylfurfural stress in Saccharomyces cerevisiae.

In bioethanol production, the main by-product, 5-hydroxymethylfurfural (HMF), significantly hinders microbial fermentation. Therefore, it is crucial to explore genes related to HMF tolerance in Saccharomyces cerevisiae for enhancing the tolerance of ethanol fermentation strains. A comprehensive analysis was conducted using genome-wide deletion library scanning and SGAtools, resulting in the identification of 294 genes associated with HMF tolerance in S. cerevisiae. Further KEGG and GO enrichment analysis revealed the involvement of genes OCA1 and SIW14 in the protein phosphorylation pathway, underscoring their role in HMF tolerance. Spot test validation and subcellular structure observation demonstrated that, following a 3-h treatment with 60 mM HMF, the SIW14 gene knockout strain exhibited a 12.68% increase in cells with abnormal endoplasmic reticulum (ER) and a 22.41% increase in the accumulation of reactive oxygen species compared to the BY4741 strain. These findings indicate that the SIW14 gene contributes to the protection of the ER structure within the cell and facilitates the clearance of reactive oxygen species, thereby confirming its significance as a key gene for HMF tolerance in S. cerevisiae.

Phenotypic and comparative transcriptomics analysis of RDS1 overexpression reveal tolerance of Saccharomyces cerevisiae to furfural.

The yeast Saccharomyces cerevisiae able to tolerate lignocellulose-derived inhibitors like furfural. Yeast strain performance tolerance has been measured by the length of the lag phase for cell growth in response to the furfural inhibitor challenge. The aims of this work were to obtain RDS1 yeast tolerant strain against furfural through overexpression using a method of in vivo homologous recombination. Here, we report that the overexpressing RDS1 recovered more rapidly and displayed a lag phase at about 12 h than its parental strain. Overexpressing RDS1 strain encodes a novel aldehyde reductase with catalytic function for reduction of furfural with NAD(P)H as the co-factor. It displayed the highest specific activity (24.8 U/mg) for furfural reduction using NADH as a cofactor. Fluorescence microscopy revealed improved accumulation of reactive oxygen species resistance to the damaging effects of inhibitor in contrast to the parental. Comparative transcriptomics revealed key genes potentially associated with stress responses to the furfural inhibitor, including specific and multiple functions involving defensive reduction-oxidation reaction process and cell wall response. A significant change in expression level of log2 (fold change >1) was displayed for RDS1 gene in the recombinant strain, which demonstrated that the introduction of RDS1 overexpression promoted the expression level. Such signature expressions differentiated tolerance phenotypes of RDS1 from the innate stress response of its parental strain. Overexpression of the RDS1 gene involving diversified functional categories is accountable for stress tolerance in yeast S. cerevisiae to survive and adapt the furfural during the lag phase.

Study on diversity, nitrogen-fixing capacity, and heavy metal tolerance of culturable Pongamia pinnata rhizobia in the vanadium-titanium magnetite tailings.

Introduction: The diversity, nitrogen-fixing capacity and heavy metal tolerance of culturable rhizobia in symbiotic relationship with Pongamia pinnata surviving in vanadium (V) - titanium (Ti) magnetite (VTM) tailings is still unknown, and the rhizobia isolates from the extreme barren VTM tailings contaminated with a variety of metals would provide available rhizobia resources for bioremediation. Methods: P. pinnata plants were cultivated in pots containing the VTM tailings until root nodules formed, and then culturable rhizobia were isolated from root nodules. The diversity, nitrogen-fixing capacity and heavy metal tolerance of rhizobia were performed. Results: Among 57 rhizobia isolated from these nodules, only twenty strains showed different levels of tolerance to copper (Cu), nickel (Ni), manganese (Mn) and zinc (Zn), especially strains PP1 and PP76 showing high tolerance against these four heavy metals. Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi. Some rhizobia isolates showed a high nitrogen-fixing capacity and promoted P. pinnata growth by increasing nitrogen content by 10%-145% in aboveground plant part and 13%-79% in the root. R. pachyrhizi PP1 showed the strongest capacity of nitrogen fixation, plant growth promotion and resistance to heavy metals, which provided effective rhizobia strains for bioremediation of VTM tailings or other contaminated soils. This study demonstrated that there are at least three genera of culturable rhizobia in symbiosis with P. pinnata in VTM tailings. Discussion: Abundant culturable rhizobia with the capacity of nitrogen fixation, plant growth promotion and resistance to heavy metals survived in VTM tailings, indicating more valuable functional microbes could be isolated from extreme soil environments such as VTM tailings.

Discovery of new strains for furfural degradation using adaptive laboratory evolution in Saccharomyces cerevisiae.

In industrial production, the excessive discharge of furfural can pose harm to soil microorganisms, aquatic animals and plants, as well as humans. Therefore, it is crucial to develop efficient and cost-effective methods for degrading furfural in the environment. Currently, the use of Saccharomyces cerevisiae for furfural degradation in water has shown effectiveness, but there is a need to explore improved efficiency and tolerance in S. cerevisiae for this purpose. In this study, we isolated and evolved highly efficient furfural degradation strains, namely YBA_08 and F60C. These strains exhibited remarkable capabilities, degrading 59% and 99% furfural in the YPD medium after 72 h of incubation, significantly higher than the 31% achieved by the model strain S288C. Through analysis of the efficient degradation mechanism in the evolutionary strain F60C, we discovered a 326% increase in the total amount of NADH and NADPH. This increase likely promotes faster furfural degradation through intracellular aldehyde reductases. Moreover, the decrease in NADPH content led to a 406% increase in glutathione content at the background level, which protects cells from damage caused by reactive oxygen species. Mutations and differential expression related to cell cycle and cell wall synthesis were observed, enabling cell survival in the presence of furfural and facilitating rapid furfural degradation and growth recovery. Based on these findings, it is speculated that strains YBA_08 and F60C have the potential to contribute to furfural degradation in water and the production of furfuryl alcohol, ethanol, and FDCA in biorefinery processes.

Contribution of YPRO15C Overexpression to the Resistance of Saccharomyces cerevisiae BY4742 Strain to Furfural Inhibitor.

Lignocellulosic biomass is still considered a feasible source of bioethanol production. Saccharomyces cerevisiae can adapt to detoxify lignocellulose-derived inhibitors, including furfural. Tolerance of strain performance has been measured by the extent of the lag phase for cell proliferation following the furfural inhibitor challenge. The purpose of this work was to obtain a tolerant yeast strain against furfural through overexpression of YPR015C using the in vivo homologous recombination method. The physiological observation of the overexpressing yeast strain showed that it was more resistant to furfural than its parental strain. Fluorescence microscopy revealed improved enzyme reductase activity and accumulation of oxygen reactive species due to the harmful effects of furfural inhibitor in contrast to its parental strain. Comparative transcriptomic analysis revealed 79 genes potentially involved in amino acid biosynthesis, oxidative stress, cell wall response, heat shock protein, and mitochondrial-associated protein for the YPR015C overexpressing strain associated with stress responses to furfural at the late stage of lag phase growth. Both up- and down-regulated genes involved in diversified functional categories were accountable for tolerance in yeast to survive and adapt to the furfural stress in a time course study during the lag phase growth. This study enlarges our perceptions comprehensively about the physiological and molecular mechanisms implicated in the YPR015C overexpressing strain's tolerance under furfural stress. Construction illustration of the recombinant plasmid. a) pUG6-TEF1p-YPR015C, b) integration diagram of the recombinant plasmid pUG6-TEF1p-YPR into the chromosomal DNA of Saccharomyces cerevisiae.

Transcriptomic profiling revealed important roles of amino acid metabolism in fruiting body formation at different ripening times in Hypsizygus marmoreus.

Introduction: Hypsizygus marmoreus is an industrial mushroom that is widely cultivated in East Asia. Its long postripening stage before fruiting severely limits its industrialized production. Methods: Five different mycelial ripening times (30, 50, 70, 90, and 100 d) were chosen and primordia (30P, 50P, 70P, 90P, and 110P) were collected for comparative transcriptomic analyses. The corresponding substrates (30F, 50F, 70F, 90F, and 110F) were used for nutrient content and enzyme activity determination. Results: In pairwise comparisons between 110P and other primordia, a total of 1,194, 977, 773, and 697 differentially expressed genes (DEGs) were identified in 30P_110P, 50P_110P, 70P_110P, and 90P_110P, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes Genomes (KEGG) functional enrichment analyses revealed that the DEGs were mainly associated with amino acid metabolism, and lipid and carbohydrate metabolism pathways. Tyrosine, tryptophan, phenylalanine and histidine metabolism were enriched in all groups. Among the main carbon nutrients, the contents of cellulose and hemicellulose were high, and the lignin content decreased with the extension of the ripening time. Laccase had the highest activity, and acid protease activity decreased with the extension of the ripening time. Discussion: The highly enrichment for amino acid metabolic pathways in primordia reveals that these pathways are essential for fruiting body formation in H. marmoreus, and these results will provide a basis for the optimization of its cultivation.

Chelativorans petroleitrophicus sp. nov., a paraffin oil-degrading bacterium isolated from a mixture of oil-based drill cuttings and paddy soil.

We isolated a paraffin oil-degrading bacterial strain from a mixture of oil-based drill cutting and paddy soil, and characterized the strain using a polyphasic approach. The Gram-positive, aerobic, rod-shaped and non-spore-forming strain (SCAU 2101T) grew optimally at 50 °C, pH 7.0 and 0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that the strain represented a distinct clade in the genus Chelativorans, neighbouring Chelativorans intermedius LMG 28482T (97.1 %). The genome size and DNA G+C content of the strain were 3 969 430 bp and 63.1 mol%, respectively. Whole genome based phylogenomic analyses showed that the average nucleotide identity and digital DNA-DNA hybridization values between strain SCAU 2101T and C. intermedius LMG 28482T were 77.5 and 21.2 %, respectively. The major respiratory quinone was Q-10. The dominant fatty acids were C19 : 0 cyclo ω8c (50.6 %), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 22.5 %) and C18 : 0 (13.8 %). The polar lipids of the strain included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. Based on the results, strain SCAU 2101T was considered to represent a novel species in the genus Chelativorans, for which the name Chelativorans petroleitrophicus sp. nov. is proposed. The type strain is SCAU 2101T (= CCTCC AB 2021125T=KCTC 92067T).

MyoG-enhanced circGPD2 regulates chicken skeletal muscle development by targeting miR-203a.

Circular RNAs (circRNAs) are a subclass of RNA macromolecules that are reported to be involved in the regulation of skeletal muscle development. However, the functions and regulatory mechanisms of circRNAs in chicken myogenesis are still largely unclear. Here, we identified a novel circRNA, circGPD2, an RNA macromolecule with a calculated molecular weight of 215 kDa. We discovered that circGPD2 is a muscle-specific circRNA and is strongly expressed in the breast muscle of broilers by utilizing the comparison model of layers and broilers. Functional analysis revealed circGPD2 has a positive role in the proliferation and differentiation of myoblasts, and circGPD2 performs function through the release of the inhibition effect of miR-203a on c-JUN and MEF2C. Besides, the myogenic regulatory factor MyoG enhanced the expression of circGPD2 by targeting the E-box element on the GPD2 promoter. Importantly, lentivirus-mediated circGPD2 knockdown resulted in the breast muscle mass loss of the chicks. Overall, we revealed the crucial role of circGPD2 in chicken myogenesis in vitro and in vivo, and analyzed the upstream and downstream regulation mechanisms of circGPD2. Our study provides an attractive target for molecular marker-assisted breeding to improve the meat yield in the chicken meat industry.

Enhanced Effects of Iron on Mycelial Growth, Metabolism and In Vitro Antioxidant Activity of Polysaccharides from Lentinula edodes.

The polysaccharides found in Lentinula edodes have a variety of medicinal properties, such as anti-tumor and anti-viral effects, but their content in L. edodes sporophores is very low. In this study, Fe2+ was added to the liquid fermentation medium of L. edodes to analyze its effects on mycelial growth, polysaccharide and enzyme production, gene expression, and the activities of enzymes involved in polysaccharide biosynthesis, and in vitro antioxidation of polysaccharides. The results showed that when 200 mg/L of Fe2+ was added, with 7 days of shaking at 150 rpm and 3 days of static culture, the biomass reached its highest value (0.28 mg/50 mL) 50 days after the addition of Fe2+. Besides, Fe2+ addition also enhanced intracellular polysaccharide (IPS) and exopolysaccharide (EPS) productions, the levels of which were 2.98- and 1.79-fold higher than the control. The activities of the enzymes involved in polysaccharides biosynthesis, including phosphoglucomutase (PGM), phosphoglucose isomerase (PGI), and UDPG-pyrophosphorylase (UGP) were also increased under Fe2+ addition. Maximum PGI activity reached 1525.20 U/mg 30 days after Fe2+ addition, whereas PGM and UGP activities reached 3607.05 U/mg and 3823.27 U/mg 60 days after Fe2+ addition, respectively. The Pearson correlation coefficient showed a strong correlation (p < 0.01) between IPS production and PGM and UGP activities. The corresponding coding genes of the three enzymes were also upregulated. When evaluating the in vitro antioxidant activities of polysaccharides, EPS from all Fe2+-treated cultures exhibited significantly better capacity (p < 0.05) for scavenging -OH radicals. The results of the two-way ANOVA indicated that the abilities of polysaccharides to scavenge O2− radicals were significantly (p < 0.01) affected by Fe2+ concentration and incubation time. These results indicated that the addition of iron provided a good way to achieve desirable biomass, polysaccharide production, and the in vitro antioxidation of polysaccharides from L. edodes.

Gga-miR-146b-3p promotes apoptosis and attenuate autophagy by targeting AKT1 in chicken granulosa cells.

The normal development of follicles determines the reproductive performance of females. Granulosa cells (GC) play crucial roles in follicular maturation. Numerous studies have shown that miRNAs are involved in the regulation of GC. According to our previous sequencing data, gga-miR-146b-3p was differentially expressed in normal and atretic chicken follicles. In this study, we verified that gga-miR-146b-3p attenuated proliferation and autophagy but promoted apoptosis in chicken GC. Threonine kinase1 (AKT1), a key member of the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway, was predicted to be a target gene of gga-miR-146b-3p via bioinformatic analysis. Dual-luciferase reporter gene assays were used to determine target relationships. Moreover, knockout of AKT1 decelerated proliferation and autophagy while accelerating the apoptosis of GC. However, overexpression of AKT1 reversed these results. In summary, our results demonstrated that gga-miR-146b-3p repressed the proliferation and autophagy of chicken GC while up-regulating apoptosis by targeting AKT1 through the PI3K/AKT signaling pathway. These findings may provide great insights for further exploration of the molecular regulation of gga-miR-146b-3p and AKT1 on the functions of GC during folliculogenesis.

Role of rhizobia in promoting non-enzymatic antioxidants to mitigate nitrogen-deficiency and nickel stresses in Pongamia pinnata.

The contribution of rhizobia in the mitigation of non-enzymatic antioxidants against nitrogen deficiency and heavy metal toxicity for legume plant is not clear. Therefore, it is hypothesized that the inoculation of rhizobia could mitigate nitrogen deficiency and nickel (Ni) stresses in P. pinnata tissues by enhancing the formation of certain non-enzymatic antioxidants. The effect of symbiotic nitrogen-fixing rhizobia on the mitigation of nitrogen-deficiency and Ni stresses in P. pinnata was evaluated by inoculating two different rhizobia, i.e., Rhizobium pisi PZHK2 and Ochrobacterium pseudogrignonense PZHK4, around the rhizosphere of P. pinnata grown in soil containing 40 mg kg-1 Ni2+ and without nitrogen addition. The inoculation with both rhizobial strains promoted the growth of P. pinnata under nickel stress or nitrogen-deficiency condition, increased nitrogen content in all plant tissues and nickel content in shoots and leaves, but reduced nickel accumulation in roots. The four non-enzymatic antioxidants including glutathione (GSH), proanthocyanidin (OPC), ascorbic acid (ASA) and flavonoids (FLA) distributed in roots, shoots and leaves were followed in descending order: GSH > OPC > ASA > FLA. The four non-enzymatic antioxidants showed different levels of change under the nitrogen-deficiency and nickel stresses and in the non-stress control. The inoculation of PZHK2 and PZHK4 significantly (p < 0.05) increased the four non-enzymatic antioxidants in P. pinnata tissues, especially in roots. Some non-enzymatic antioxidants showed correlations with nickel or nitrogen in P. pinnata tissues, and the four non-enzymatic antioxidants also had correlations among each other. Therefore, this research revealed an excellent role of rhizobia in promoting non-enzymatic antioxidants to mitigate nitrogen-deficiency or nickel stress for P. pinnata.

Bio-Matrix Pot Addition Enhanced the Vegetation Process of Iron Tailings by Pennisetum giganteum.

The barrenness of large mine tailing sand reservoirs increases the risks for landslides and erosion that may be accompanied with transfer of contaminants into the surrounding environment. The tailing sand is poor in nutrients, which effectively complicates the vegetation process. We investigated direct planting of Pennisetum giganteum into tailing sand using two pit planting methods: the plants were transplanted either directly into pits filled with soil or into soil-filled bio-matrix pots made of organic material. After growing P. giganteum in iron tailing sand for 360 days, the dry weight of the plants grown in the bio-matrix pot (T2) was approximately twofold higher than that of the plants grown in soil placed directly into the sand (T1). At 360 days, the organic matter (OM) content in the soil below the pit was the lowest in the not-planted treatment (T0) and the highest in T2, the available N (AN) contents were higher in T1 and T2 than in T0, and the available P and K contents were the highest in T2. At 360 days, the Shannon diversity of the soil microbial communities was higher in T1 and T2 than in T0, and the community compositions were clearly separated from each other. The profiles of predicted C cycle catabolism functions and N fixation-related functions in T1 and T2 at 360 days were different from those in the other communities. The results showed that P. giganteum grew well in the iron tailing sand, especially in the bio-matrix pot treatment, and the increased nutrient contents and changes in microbial communities indicated that using the bio-matrix pot in planting had potential to improve the vegetation process in iron tailing sands effectively.

miRNA sequencing analysis of healthy and atretic follicles of chickens revealed that miR-30a-5p inhibits granulosa cell death via targeting Beclin1.

BACKGROUND: The egg production performance of chickens is affected by many factors, including genetics, nutrition and environmental conditions. These factors all play a role in egg production by affecting the development of follicles. MicroRNAs (miRNAs) are important non-coding RNAs that regulate biological processes by targeting genes or other non-coding RNAs after transcription. In the animal reproduction process, miRNA is known to affect the development and atresia of follicles by regulating apoptosis and autophagy of granulosa cells (GCs). RESULTS: In this study, we identified potential miRNAs in the atretic follicles of broody chickens and unatretic follicles of healthy chickens. We identified gga-miR-30a-5p in 50 differentially expressed miRNAs and found that gga-miR-30a-5p played a regulatory role in the development of chicken follicles. The function of miR-30a-5p was explored through the transfection test of miR-30a-5p inhibitor and miR-30a-5p mimics. In the study, we used qPCR, western blot and flow cytometry to detect granulosa cell apoptosis, autophagy and steroid hormone synthesis. Confocal microscopy and transmission electron microscopy are used for the observation of autophagolysosomes. The levels of estradiol (E2), progesterone (P4), malondialdehyde (MDA) and superoxide dismutase (SOD) were detected by ELISA. The results showed that miR-30a-5p showed a negative effect on autophagy and apoptosis of granulosa cells, and also contributed in steroid hormones and reactive oxygen species (ROS) production. In addition, the results obtained from the biosynthesis and dual luciferase experiments showed that Beclin1 was the target gene of miR-30a-5p. The rescue experiment conducted further confirmed that Beclin1 belongs to the miR-30a-5p regulatory pathway. CONCLUSIONS: In summary, after deep miRNA sequencing on healthy and atretic follicles, the results indicated that miR-30a-5p inhibits granulosa cell death by inhibiting Beclin1.

Prevalence of antibiotic resistance pattern in shigella isolates procured from pediatric patients at Faisalabad - Pakistan.

Shigella infection (shigellosis) is an intestinal disease caused by a shigella isolates belongs to a family Enterobacteriacea. Watery diarrhea, abdominal pain and tenesmus are the prominent symptoms of shigella infection. The present study was designed to determine period prevalence and antimicrobial susceptibility of Shigella species recovered from stool specimens obtained from diarrheal paediatric patients under 5 years of age. This cross-sectional study was carried out for a period of six months (Jan to June, 2016). All Shigella isolates were identified based on colony morphology, microscopic characteristics, and biochemical characteristics. After applying Kirby Baur disc diffusion method only 22 (18.96%) stool specimens were found positive for Shigella isolates among the 116 stool specimens. The isolates were also found susceptible to Levofloxacin (72.72%), Azithromycin (59.09%), and Cefotaxime (40.90%). However, the said isolates were resistant to Lincomycin (100%) and Penicillin-G (100%), followed by Amoxicillin (95.45%) and Oxacillin (95.45%). The chi-square test was used to check the close association among antimicrobial agents used and as highly significant (p-value < 2.2e-16). Based on antimicrobial susceptibility findings, Levofloxacin, Azithromycin and Cefotoxime were found effective for the control of shigellosis.

Cultivating Lentinula edodes on Substrate Containing Composted Sawdust Affects the Expression of Carbohydrate and Aromatic Amino Acid Metabolism-Related Genes.

In mushroom cultivation, composting the substrate can make the nutrients more easily absorbed by hyphae due to the degradation of lignin, cellulose, and other organic matter. However, the effects of cultivating Lentinula edodes on composted substrate and the related molecular mechanisms have not been studied systemically. We applied transcriptomics, qRT-PCR, and proteomics to study L. edodes cultivated on substrates with fresh (CK) and composted (ND) sawdust, focusing on the brown film formation stage. The time of brown film formation was shorter and the mycelium growth rate and crude polysaccharide content of the brown film were higher in ND than in CK. The faster growth rate in ND may have been due to the higher nitrogen content in ND than in CK. Among the 9,455 genes annotated using transcriptomics, 96 were upregulated and 139 downregulated in ND compared with CK. Among the 2,509 proteins identified using proteomics sequencing, 74 were upregulated and 113 downregulated. In the KEGG pathway analyses, both differentially expressed genes and proteins were detected in cyanoamino acid metabolism, inositol phosphate metabolism, pentose and glucuronate interconversions, phosphatidylinositol signaling system, RNA polymerase, starch and sucrose metabolism, and tyrosine metabolism pathways. A large number of differentially expressed genes (DEGs) related to aromatic amino acid metabolic and biosynthetic process were upregulated in ND. Most of the DEGs annotated to carbohydrate active enzymes were downregulated in L. edodes growing on composted sawdust containing substrate, possibly due to the lower hemicellulose and cellulose contents in the composted sawdust. The results suggested that using composted substrate may decrease the cultivation time and improve the quality of L. edodes and revealed the underlying molecular mechanisms. IMPORTANCE Composted substrates are not commonly used in the cultivation of Lentinula edodes, thus the effects of cultivating L. edodes on composted substrate and the related molecular mechanisms have not been studied systemically. We studied L. edodes cultivated on substrates with fresh (CK) and composted (ND) sawdust, focusing on the brown film formation stage, and determined the composting related differences in the substrate and in the growth and gene expression of L. edodes. Cultivation on composted substrate was beneficial and showed potential for decreasing the cultivation time and improving the quality of L. edodes. Analyzing the expression levels of genes and proteins in brown film revealed gene and metabolism pathway level changes that accompanied the cultivation on composted substrate.

Changes in the taxonomic and functional structures of microbial communities during vegetable waste mixed silage fermentation.

Silage fermentation, a sustainable method of using vegetable waste resources, is a complex process driven by a variety of microorganisms. We used lettuce waste as the main raw material for silage, analyzed changes in the physicochemical characteristics and bacterial community composition of silage over a 60-day fermentation period, identified differentially abundant taxa, predicted the functional profiles of bacterial communities, and determined the associated effects on the quality of silage. The largest changes occurred during the early stages of silage fermentation. Changes in the physicochemical characteristics included a decrease in pH and an increase in the ammonia nitrogen to total nitrogen ratio and lactic acid content. The number of lactic acid bacteria (LAB) increased, while molds, yeasts, and aerobic bacteria decreased. The bacterial communities and their predicted functions on day 0 were different from those on day 7 to day 60. The relative abundances of phylum Firmicutes and genus Lactobacillus increased. Nitrite and nitrate ammonification were more prevalent after day 0. The differences in the predicted functions were associated with differences in pH and amino acid, protein, carbohydrate, NH3-N, ether extract, and crude ash contents.