Green synthesis of NiO NPs for metagenome-derived laccase stabilization: Detoxifying pollutants and wastes

Laccases play a crucial role in neutralizing environmental pollutants, including antibiotics and phenolic compounds, by converting them into less harmful substances via a unique oxidation process. This study introduces an environmentally sustainable remediation technique, utilizing NiO nanoparticles (NPs) synthesized through green chemistry to immobilize a metagenome-derived laccase, PersiLac1, enhancing its application in pollutant detoxification. Salvadora persica leaf extract was used for the synthesis of NiO nanoparticles, utilizing its phytochemical constituents as reducing and capping agents, followed by characterization through different analyses. Characterization of NiO nanoparticles revealed distinctive FTIR absorption peaks indicating the nanoparticulate structure, while FESEM showed structured NiO with robust interconnections and dimensionality of about 50nm, confirmed by EDX analysis to have a consistent distribution of Ni and O. The immobilized PersiLac1 demonstrated enhanced thermal stability, with 85.55 % activity at 80 °C and reduced enzyme leaching, retaining 67.93 % activity across 15 biocatalytic cycles. It efficiently reduced rice straw (RS) phenol by 67.97 % within 210 min and degraded 70-78 % of tetracycline (TC) across a wide pH range (4.0-8.0), showing superior performance over the free enzyme. Immobilized laccase achieved up to 71 % TC removal at 40-80 °C, significantly outperforming the free enzyme. Notably, 54 % efficiency was achieved at 500 mg/L TC by immobilized laccase at 120 min. This research showed the potential of green-synthesized NiO nanoparticles to effectively immobilize laccase, presenting an eco-friendly approach to purify pollutants such as phenols and antibiotics. The durability and reusability of the immobilized enzyme, coupled with its ability to reduce pollutants, indicates a viable method for cleaning the environment. Nonetheless, the production costs and scalability of NiO nanoparticles for widespread industrial applications pose significant challenges. Future studies should focus on implementation at an industrial level and examine a wider range of pollutants to fully leverage the environmental clean-up capabilities of this innovative technology.

Orally Administered Lactobacillus rhamnosus CY12 Alleviates DSS-Induced Colitis in Mice by Restoring the Intestinal Barrier and Inhibiting the TLR4-MyD88-NF-κB Pathway via Intestinal Microbiota Modulation

Oral ingestion of probiotics is a promising approach to relieving inflammatory disease through regulating the gut microbiota. A newly discovered strain, Lactobacillus rhamnosus CY12 (LCY12), obtained from cattle-yak milk, displayed numerous probiotic properties. These included enhanced viability in low pH and bile environments, adhesion capabilities, and potent antimicrobial effects. The research aimed to explore the beneficial impacts of the novel LCY12 strain on colitis in mice induced by dextran sulfate sodium (DSS) and to elucidate the underlying molecular mechanisms. The results of the study showed that administration of LCY12 effectively helped to reduce the negative effects of DSS-induced body weight loss, disease activity index score, colon length shortening, loss of goblet cells, and overall histopathological scores in the intestines. Simultaneously, LCY12 administration significantly alleviated intestinal inflammation and safeguarded intestinal barrier integrity by enhancing IL-10 levels, while dampening IL-6, IL-1β, and TNF-α production. Additionally, LCY12 boosted the presence of tight junction proteins. Furthermore, LCY12 hindered the TLR4/MyD88/NF-κB signaling pathway by downregulating TLR4 and MyD88 expression, inactivating phosphorylated IκBα, and preventing translocation of NF-κB p65 from the cytoplasm to the nucleus. The LCY12 also increased specific intestinal microbial communities and short-chain fatty acid (SCFA) production. Altogether, LCY12 oral administration alleviated colitis induced with DSS in mice by improving intestinal barrier function and regulating inflammatory cytokines, SCFA production, and intestinal microbiota.

Unveiling the population genetic structure of Iranian horses breeds by whole-genome resequencing analysis

Preserving genetic diversity is pivotal for enhancing genetic improvement and facilitating adaptive responses to selection. This study focuses on identifying key genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs), while exploring the genomic evolutionary connectedness among seven Iranian horses representing five indigenous breeds: Caspian, Turkemen, DareShuri, Kurdish, and Asil. Using whole-genome resequencing, we generated 2.7 Gb of sequence data, with raw reads ranging from 1.2 Gb for Caspian horses to 0.38 Gb for Turkoman horses. Post-filtering, approximately 1.9 Gb of reads remained, with ~ 1.5 Gb successfully mapped to the horse reference genome (EquCab3.0), achieving mapping rates between 76.4% (Caspian) and 98.35% (Turkoman). We identified 2,909,816 SNPs in Caspian horses, constituting around 0.1% of the genome. Notably, 71% of these SNPs were situated in intergenic regions, while 8.5 and 6.8% were located upstream and downstream, respectively. A comparative analysis of SNPs between Iranian and non-Iranian horse breeds showed that Caspian horses had the lowest number of shared SNPs with Turkoman horses. Instead, they showed a closer genetic relationship with DareShuri, Quarter, Arabian, Standardbred, and Asil breeds. Hierarchical clustering highlighted Caspian horses as a distinct cluster, underscoring their distinctive genomic signature. Caspian horses exhibit a unique genetic profile marked by an enrichment of private mutations in neurological genes, influencing sensory perception and awareness. This distinct genetic makeup shapes mating preferences and signifies a separate evolutionary trajectory. Additionally, significant non-synonymous single nucleotide polymorphisms (nsSNPs) in reproductive genes offer intervention opportunities for managing Caspian horses. These findings reveal the population genetic structure of Iranian horse breeds, contributing to the advancement of knowledge in areas such as conservation, performance traits, climate adaptation, reproduction, and resistance to diseases in equine science.

Precision enzyme discovery through targeted mining of metagenomic data

Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.

Proteomics provides insights into the theranostic potential of extracellular vesicles

Extracellular vesicles (EVs) encompass a diverse range of membranous structures derived from cells, including exosomes and microvesicles. These vesicles are present in biological fluids and play vital roles in various physiological and pathological processes. They facilitate intercellular communication by enabling the exchange of proteins, lipids, and genetic material between cells. Understanding the cellular processes that govern EV biology is essential for unraveling their physiological and pathological functions and their potential clinical applications. Despite significant advancements in EV research in recent years, there is still much to learn about these vesicles. The advent of improved mass spectrometry (MS)-based techniques has allowed for a deeper characterization of EV protein composition, providing valuable insights into their roles in different physiological and pathological conditions. In this chapter, we provide an overview of proteomics studies conducted to identify the protein contents of EVs, which contribute to their therapeutic and pathological features. We also provided evidence on the potential of EV proteome contents as biomarkers for early disease diagnosis, progression, and treatment response, as well as factors that influence their composition. Additionally, we discuss the available databases containing information on EV proteome contents, and finally, we highlight the need for further research to pave the way toward their utilization in clinical settings.

Forage lignocellulose is an important factor in driving the seasonal dynamics of rumen anaerobic fungi in grazing yak and cattle

Anaerobic fungi (AF) inhabit the gastrointestinal tract of ruminants and play an important role in the degradation of fiber feed. However, limited knowledge is available on seasonal dynamics and inter-species differences in rumen AF community in yak and cattle under natural grazing systems. Using the random forests model, the null model, and structural equation model, we investigated the seasonal dynamics and key driving factors of fiber-associated rumen AF in grazing yak and cattle throughout the year on the Qinghai-Tibet Plateau (QTP). We found that the richness and diversity of rumen AF of grazing yak and cattle in cold season were significantly higher than those in warm season (P < 0.05). We identified 12 rumen AF genera, among which , Cyllamyces, and Orpinomyces were predominant in the rumen of both grazing yak and cattle. LEfSe and random forest analysis showed that Feramyces, Tahromyces, and Buwchfawromyces were important seasonal indicator of rumen AF in grazing yak (P < 0.05), and Caecomyces, Cyllamyces, and Piromyces in grazing cattle (P < 0.05). Null model analysis revealed that the dynamic changes of rumen AF community structure were mainly affected by deterministic factors. Notably, mantel test and structural equation model revealed that forage physical-chemical properties, including dry matter (DM), neutral detergent fiber (NDF), and hemicellulose contents (HC) were the key factors driving the seasonal variations of the rumen AF community (P < 0.05). The results revealed that forage lignocellulose was probably an important factor affecting the seasonal dynamics and inter-species differences of the rumen AF community under natural grazing conditions. IMPORTANCE The seasonal dynamics of rumen anaerobic fungi in nature grazing yak and cattle were determined during cold and warm seasons based on pasture nutritional quality and environmental data sets. The main driving factors of anaerobic fungi in yak and cattle rumen were explored by combining random forest and structural equation models. In addition, the dynamic differences in the composition of the anaerobic fungi community in the yak and cattle in different seasons were characterized. It was found that some rumen anaerobic fungi have contributed to high fiber degradation rate in yak. These novel findings improve our understanding of the association of environmental and dietary seasonal variations with anaerobic fungal community, facilitating yak adaptation to high altitude.

Heritability and recursive influence of host genetics on the rumen microbiota drive body weight variance in male Hu sheep lambs

BACKGROUND

Heritable rumen microbiota is an important modulator of ruminant growth performance. However, no information exists to date on host genetics-rumen microbiota interactions and their association with phenotype in sheep. To solve this, we curated and analyzed whole-genome resequencing genotypes, 16S rumen-microbiota data, and longitudinal body weight (BW) phenotypes from 1150 sheep.

RESULTS

A variance component model indicated significant heritability of rumen microbial community diversity. Genome-wide association studies (GWAS) using microbial features as traits identified 411 loci-taxon significant associations (P < 10-8). We found a heritability of 39% for 180-day-old BW, while also the rumen microbiota likely played a significant role, explaining that 20% of the phenotypic variation. Microbiota-wide association studies (MWAS) and GWAS identified four marker genera (Bonferroni corrected P < 0.05) and five novel genetic variants (P < 10-8) that were significantly associated with BW. Integrative analysis identified the mediating role of marker genera in genotype influencing phenotype and unravelled that the same genetic markers have direct and indirect effects on sheep weight.

CONCLUSIONS

This study reveals a reciprocal interplay among host genetic variations, the rumen microbiota and the body weight traits of sheep. The information obtained provide insights into the diverse microbiota characteristics of rumen and may help in designing precision microbiota management strategies for controlling and manipulating sheep rumen microbiota to increase productivity. Video Abstract.

Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses

Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available. Firmicutes use free enzymes and cellulosomes to degrade the polysaccharides. Fibrobacters either aggregate lignocellulose-degrading enzymes on their cell surface or release them into the extracellular medium in membrane vesicles, a mechanism that has proven extremely effective in the breakdown of recalcitrant cellulose. Based on current metagenomic analyses, rumen Bacteroidetes and Firmicutes are categorized as generalist microbes that can degrade a wide range of polysaccharides, while other members adapted toward specific polysaccharides. Particularly, there is ample evidence that Verrucomicrobia and Spirochaetes have evolved enzyme systems for the breakdown of complex polysaccharides such as xyloglucans, peptidoglycans, and pectin. It is concluded that diversity in degradation mechanisms is required to ensure that every component in feeds is efficiently degraded, which is key to harvesting maximum energy by host animals.

Comparative metabolomics of root-tips reveals distinct metabolic pathways conferring drought tolerance in contrasting genotypes of rice

Background

The mechanisms underlying rice root responses to drought during the early developmental stages are yet unknown.

Results

This study aimed to determine metabolic differences in IR64, a shallow-rooting, drought-susceptible genotype, and Azucena, a drought-tolerant and deep-rooting genotype under drought stress. The morphological evaluation revealed that Azucena might evade water stress by increasing the lateral root system growth, the root surface area, and length to access water. At the same time, IR64 may rely mainly on cell wall thickening to tolerate stress. Furthermore, significant differences were observed in 49 metabolites in IR64 and 80 metabolites in Azucena, for which most metabolites were implicated in secondary metabolism, amino acid metabolism, nucleotide acid metabolism and sugar and sugar alcohol metabolism. Among these metabolites, a significant positive correlation was found between allantoin, galactaric acid, gluconic acid, glucose, and drought tolerance. These metabolites may serve as markers of drought tolerance in genotype screening programs. Based on corresponding biological pathways analysis of the differentially abundant metabolites (DAMs), biosynthesis of alkaloid-derivatives of the shikimate pathway, fatty acid biosynthesis, purine metabolism, TCA cycle and amino acid biosynthesis were the most statistically enriched biological pathway in Azucena in drought response. However, in IR64, the differentially abundant metabolites of starch and sucrose metabolism were the most statistically enriched biological pathways.

Conclusion

Metabolic marker candidates for drought tolerance were identified in both genotypes. Thus, these markers that were experimentally determined in distinct metabolic pathways can be used for the development or selection of drought-tolerant rice genotypes.

Efficiency of an alkaline, thermostable, detergent compatible, and organic solvent tolerant lipase with hydrolytic potential in biotreatment of wastewater

Discharging the tannery wastewater into the environment is a serious challenge worldwide due to the release of severe recalcitrant pollutants such as oil compounds and organic materials. The biological treatment through enzymatic hydrolysis is a cheap and eco-friendly method for eliminating fatty substances from wastewater. In this context, lipases can be utilized for bio-treatment of wastewater in multifaceted industrial applications. To overcome the limitations in removing pollutants in the effluent, we aimed to identify a novel robust stable lipase (PersiLipase1) from metagenomic data of tannery wastewater for effective bio-degradation of the oily wastewater pollution. The lipase displayed remarkable thermostability and maintained over 81 % of its activity at 60 °C.After prolonged incubation for 35 days at 60°C, the PersiLipase1 still maintained 53.9 % of its activity. The enzyme also retained over 67 % of its activity in a wide range of pH (4.0 to 9.0). In addition, PersiLipase1 demonstrated considerable tolerance toward metal ions and organic solvents (e.g., retaining >70% activity after the addition of 100 mM of chemicals). Hydrolysis of olive oil and sheep fat by this enzyme showed 100 % efficiency. Furthermore, the PersiLipase1 proved to be efficient for biotreatment of oil and grease from tannery wastewater with the hydrolysis efficiency of 90.76 % ± 0.88. These results demonstrated that the metagenome-derived PersiLipase1 from tannery wastewater has a promising potential for the biodegradation and management of oily wastewater pollution.

Extracellular Vesicles as reconfigurable therapeutics for eye diseases: Promises and hurdles

A large number of people worldwide suffer from visual impairment. However, most available therapies rely on impeding the development of a particular eye disorder. Therefore, there is an increasing demand for effective alternative treatments, specifically regenerative therapies. Extracellular vesicles, including exosomes, ectosomes, or microvesicles, are released by cells and play a potential role in regeneration. Following an introduction to EV biogenesis and isolation methods, this integrative review provides an overview of our current knowledge about EVs as a communication paradigm in the eye. Then, we focused on the therapeutic applications of EVs derived from conditioned medium, biological fluid, or tissue and highlighted some recent developments in strategies to boost the innate therapeutic potential of EVs by loading various kinds of drugs or being engineered at the level of producing cells or EVs. Challenges faced in the development of safe and effective translation of EV-based therapy into clinical settings for eye diseases are also discussed to pave the road toward reaching feasible regenerative therapies required for eye-related complications.

Efficient bioconversion of lignocellulosic waste by a novel computationally screened hyperthermostable enzyme from a specialized microbiota

A large amount of lignocellulosic waste is generated every day in the world, and their accumulation in the agroecosystems, integration in soil compositions, or incineration for energy production has severe environmental pollution effects. Using enzymes as biocatalysts for the biodegradation of lignocellulosic materials, especially in harsh processing conditions, is a practical step towards green energy and environmental biosafety. Hence, the current study focuses on enzyme computationally screened from camel rumen metagenomics data as specialized microbiota that have the capacity to degrade lignocellulosic-rich and recalcitrant materials. The novel hyperthermostable xylanase named PersiXyn10 with the performance at extreme conditions was proper activity within a broad temperature (30-100 ℃) and pH range (4.0-11.0) but showed the maximum xylanolytic activity in severe alkaline and temperature conditions, pH 8.0 and temperature 90 ℃. Also, the enzyme had highly resistant to metals, surfactants, and organic solvents in optimal conditions. The introduced xylanase had unique properties in terms of thermal stability by maintaining over 82% of its activity after 15 days of incubation at 90 ℃. Considering the crucial role of hyperthermostable xylanases in the paper industry, the PersiXyn10 was subjected to biodegradation of paper pulp. The proper performance of hyperthermostable PersiXyn10 on the paper pulp was confirmed by structural analysis (SEM and FTIR) and produced 31.64 g/L of reducing sugar after 144 h hydrolysis. These results proved the applicability of the hyperthermostable xylanase in biobleaching and saccharification of lignocellulosic biomass for declining the environmental hazards.

Enhancing the ethanol production by exploiting a novel metagenomic-derived bifunctional xylanase/β-glucosidase enzyme with improved β-glucosidase activity by a nanocellulose carrier

Some enzymes can catalyze more than one chemical conversion for which they are physiologically specialized. This secondary function, which is called underground, promiscuous, metabolism, or cross activity, is recognized as a valuable feature and has received much attention for developing new catalytic functions in industrial applications. In this study, a novel bifunctional xylanase/β-glucosidase metagenomic-derived enzyme, PersiBGLXyn1, with underground β-glucosidase activity was mined by in-silico screening. Then, the corresponding gene was cloned, expressed and purified. The PersiBGLXyn1 improved the degradation efficiency of organic solvent pretreated coffee residue waste (CRW), and subsequently the production of bioethanol during a separate enzymatic hydrolysis and fermentation (SHF) process. After characterization, the enzyme was immobilized on a nanocellulose (NC) carrier generated from sugar beet pulp (SBP), which remarkably improved the underground activity of the enzyme up to four-fold at 80°C and up to two-fold at pH 4.0 compared to the free one. The immobilized PersiBGLXyn1 demonstrated 12 to 13-fold rise in half-life at 70 and 80°C for its underground activity. The amount of reducing sugar produced from enzymatic saccharification of the CRW was also enhanced from 12.97 g/l to 19.69 g/l by immobilization of the enzyme. Bioethanol production was 29.31 g/l for free enzyme after 72 h fermentation, while the immobilized PersiBGLXyn1 showed 51.47 g/l production titre. Overall, this study presented a cost-effective in-silico metagenomic approach to identify novel bifunctional xylanase/β-glucosidase enzyme with underground β-glucosidase activity. It also demonstrated the improved efficacy of the underground activities of the bifunctional enzyme as a promising alternative for fermentable sugars production and subsequent value-added products.

Proteomic analysis of the meristematic root zone in contrasting genotypes reveals new insights in drought tolerance in rice

Drought is responsible for major losses in rice production. Root tips contain meristematic and elongation zones that play major roles in determination of root traits and adaptive strategies to drought. In this study we analysed two contrasting genotypes of rice: IR64, a lowland, drought-susceptible, and shallow-rooting genotype; and Azucena, an upland, drought-tolerant, and deep-rooting genotype. Samples were collected of root tips of plants grown under control and water deficit stress conditions. Quantitative proteomics analysis resulted in the identification of 7294 proteins from the root tips of IR64 and 6307 proteins from Azucena. Data are available via ProteomeXchange with identifier PXD033343. Using a Partial Least Square Discriminant Analysis on 4170 differentially abundant proteins, 1138 statistically significant proteins across genotypes and conditions were detected. Twenty two enriched biological processes showing contrasting patterns between two genotypes in response to stress were detected through gene ontology enrichment analysis. This included identification of novel proteins involved in root elongation with specific expression patterns in Azucena, including four Expansins and seven Class III Peroxidases. We also detected an antioxidant network and a metallo-sulfur cluster assembly machinery in Azucena, with roles in reactive oxygen species and iron homeostasis, and positive effects on root cell cycle, growth and elongation.

Age-dependent changes of hindgut microbiota succession and metabolic function of Mongolian cattle in the semi-arid rangelands

Dietary changes have significant effects on gut microbiota and host health. Weaning is an important stage of dietary change in ruminants. The gastrointestinal tract (GIT) microbiota of calf in the early life undergo some changes, and the plasticity of the calf is beneficial to cope with these changes and challenges. However, the complex development of hindgut microorganisms in post-weaning ruminants is not fully understood. In this study, we used 16S rRNA sequencing and untargeted metabolomic analysis to determine the cecal and colonic bacterial community and associated metabolome of Mongolian cattle at age of the 5th (at weaning), 18th, and 36th months. Moreover, the maturation patterns of the hindgut bacterial community and the dynamic changes of metabolites were also explored. Sequencing results showed that Firmicutes and Bacteroidetes were the dominant phyla in the cecum and colon. The linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed bacterial features that were stage-specific in the cecum and colon. The relative abundance of Ruminococcaceae, a microbial family related to fiber degradation, gradually increased with age in the cecum, while the relative abundance of Bacteroides and Alistipes, which are related to immunity, gradually increased in the colon. The differential metabolites in the cecum and colon were mainly enriched in steroid hormone biosynthesis, primary bile acid biosynthesis, and arachidonic acid metabolism between different ages of Mongolian cattle after weaning. Consequently, this dual omics analysis provided important information on the changes in microbial and metabolite interactions in Mongolian cattle after weaning. The microorganisms and metabolites in the cecum and colon further enhanced the abiotic stress resistance of Mongolian cattle to the harsh environment. The information obtained in this study is of great significance for future strategies of cecum and colon microbiota regulation of post-weaning Mongolian cattle in the harsh Mongolian Plateau ecosystem.

DELAY OF GERMINATION 1 (DOG1) regulates dormancy in dimorphic seeds of Xanthium strumarium

Seed dormancy ensures plant survival but many mechanisms remain unclear. A high-throughput RNA-seq analysis investigated the mechanisms involved in the establishment of dormancy in dimorphic seeds of Xanthium strumarium (L.) developing in one single burr. Results showed that DOG1 , the main dormancy gene in Arabidopsis thaliana L., was over-represented in the dormant seed leading to the formation of two seeds with different cell wall properties. Less expression of DME /EMB1649 , UBP26 , EMF2, MOM, SNL2, and AGO4 in the non-dormant seed was observed, which function in the chromatin remodelling of dormancy-associated genes through DNA methylation. However, higher levels of ATXR7 /SDG25, ELF6 , and JMJ16/PKDM7D in the non-dormant seed that act at the level of histone demethylation and activate germination were found. Dramatically lower expression in the splicing factors SUA, PWI , and FY in non-dormant seed may indicate that variation in RNA splicing for ABA sensitivity and transcriptional elongation control of DOG1 is of importance for inducing seed dormancy. Seed size and germination may be influenced by respiratory factors, and alterations in ABA content and auxin distribution and responses. TOR (a serine/threonine-protein kinase) is likely at the centre of a regulatory hub controlling seed metabolism, maturation, and germination. Over-representation of the respiration-associated genes (ACO3 , PEPC3 , and D2HGDH ) was detected in non-dormant seed, suggesting differential energy supplies in the two seeds. Degradation of ABA biosynthesis and/or proper auxin signalling in the large seed may control germinability, and suppression of endoreduplication in the small seed may be a mechanism for cell differentiation and cell size determination.

Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates

Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.

Maternal Fecal Microbes Contribute to Shaping the Early Life Assembly of the Intestinal Microbiota of Co-inhabiting Yak and Cattle Calves

The Qinghai-Tibetan Plateau offers one of the most extreme environments for yaks (Bos grunniens). Although the genetic adaptability of yak and rumen metagenomes is increasingly understood, the relative contribution of host genetics and maternal symbiotic microbes throughout early intestinal microbial successions in yaks remains elusive. In this study, we assessed the intestinal microbiota succession of co-inhabiting yak and cattle (Bos taurus) calves at different weeks after birth as well as the modes of transmission of maternal symbiotic microbes (i.e., rumen fluid, feces, oral cavity, and breast skin) to their calves’ intestinal microbiota colonization. We found that the fecal microbiota of yak and cattle calves after birth was dominated by members of the families Ruminococcaceae, Bacteroidaceae, and Lachnospiraceae. The Source Tracker model revealed that maternal fecal microbes played an important role (the average contribution was about 80%) in the intestinal microbial colonization of yak and cattle calves at different weeks after birth. Unlike cattle calves, there was no significant difference in the fecal microbiota composition of yak calves between 5 and 9 weeks after birth (Wilcoxon test, P &gt; 0.05), indicating that yak may adapt to its natural extreme environment to stabilize its intestinal microbiota composition. Additionally, our results also find that the intestinal microbial composition of yak and cattle calves, with age, gradually tend to become similar, and the differences between species gradually decrease. The findings of this study are vital for developing strategies to manipulate the intestinal microbiota in grazing yaks and cattle for better growth and performance on the Qinghai-Tibetan Plateau.

Y Chromosome Genes May Play Roles in the Development of Neural Rosettes from Human Embryonic Stem Cells

BACKGROUND

The human Y chromosome harbors genes that are mainly involved in the growth, development, sexual dimorphism, and spermatogenesis process. Despite many studies, the function of the male-specific region of the Y chromosome (MSY) awaits further clarification, and a cell-based approach can help in this regard.

RESULTS

In this study, we have developed four stable transgenic male embryonic stem cell (ESCs) lines that can overexpress male-specific genes HSFY1, RBMY1A1, RPS4Y1, and SRY. As a proof of principle, we differentiated one of these cell lines (RPS4Y1 over-expressing ESCs) to the neural stem cell (rosette structure) and characterized them based on the expression level of lineage markers. RPS4Y1 expression in the Doxycycline-treated group was significantly higher than control groups at transcript and protein levels. Furthermore, we found Doxycycline-treated group had a higher differentiation efficiency than the untreated control groups.

CONCLUSIONS

Our results suggest that the RPS4Y1 gene may play a critical role in neurogenesis. Also, the generated transgenic ESC lines can be widely employed in basic and preclinical studies, such as sexual dimorphism of neural and cardiac functions, the development of cancerous and non-cancerous disease models, and drug screening.

Comparison of Dynamics of Udder Skin Microbiota From Grazing Yak and Cattle During the Perinatal Period on the Qinghai–Tibetan Plateau

The perinatal period has an important impact on the health of ruminants, and the imbalance of udder skin microbiota might be an important inducement of bovine mastitis. However, it is not clear how the perinatal period affects the microbial structure and stability of the udder skin of yak and cattle. Here, we used 16S rRNA gene high-throughput sequencing to analyze the udder skin microbiota of yak and cattle during the perinatal period. We found that the diversity and richness of microbiota of bovine udder skin during 1–2 weeks postpartum were significantly lower than those in the 1–2 weeks prenatal and 1-month postpartum period (Wilcoxon, p < 0.05). Besides, we found sharing of 2,533 OTUs in the udder skin microbiota of yak and cattle during the perinatal period, among which the core microbiota at the genera level was mainly composed of Staphylococcus, Moraxella, and Acinetobacter. However, the genus Acinetobacter was significantly abundant in the udder skin of cattle during 1–2 weeks postpartum. The NMDS and LEfSe results showed that the perinatal period had more effects on the composition and stability of microbial community in the udder skin of cattle compared to yak, particularly during 1–2 weeks postpartum. In addition, the average content of total whey proteins and immunoglobulin G of whey protein were significantly higher in the yak colostrum when compared to those found in the cattle (p < 0.05). In conclusion, the structure of udder skin microbiota of yak during the perinatal period is more stable than that of cattle in the same habitat, and 1–2 weeks postpartum may be a potential window period to prevent cattle mastitis.

Impact of environmental variables on yield related traits and bioactive compounds of the Persian fenugreek (Trigonella foenum-graecum L.) populations

Trigonella foenum-graecum is widely distributed worldwide and grown under a wide range of climatic conditions. The current research was conducted to study the effects of the environmental variables on yield related traits and metabolite contents of 50 different Persian fenugreeks at various geographical locations. Accordingly, multivariate statistical techniques including canonical correspondence analysis (CCA), hierarchical clustering on principal components, and partial least squares regression (PLSR) were applied to determine important proxy variables and establish a relevant model to predict bioactive compounds in fenugreeks. The interrelation of clustered groups emphasized the importance of functional groups of bioactive compounds and several yield related traits. The CCA indicated that two climatic variables of temperature and solar irradiation contributed prominently to 4-hydroxyisoleucine accumulation. The predicted model based on PLSR revealed climatic variables such as temperature, solar, and rain. The precursor of isoleucine was the predictive power for 4-hydroxyisoleucine accumulation while seed weight predicted trigonelline content. The current study's findings may provide helpful information for the breeding strategies of this multipurpose crop.

Simultaneous hydrolysis of various protein-rich industrial wastes by a naturally evolved protease from tannery wastewater microbiota

Elimination of protein-rich waste materials is one of the vital environmental protection requirements. Using of non-naturally occurring chemicals for their remediation properties can potentially induce new pollutants. Therefore, enzymes encoded in the genomes of microorganisms evolved in the same environment can be considered suitable alternatives to chemicals. Identification of efficient proteases that can hydrolyze recalcitrant, protein-rich wastes produced by various industrial processes has been widely welcomed as an eco-friendly waste management strategy. In this direction, we attempted to screen a thermo-halo-alkali-stable metagenome-derived protease (PersiProtease1) from tannery wastewater. The PersiProtease1 exhibited high pH stability over a wide range and at 1 h in pH 11.0 maintained 87.59% activity. The enzyme possessed high thermal stability while retaining 76.64% activity after 1 h at 90 °C. Moreover, 65.34% of the initial activity of the enzyme remained in the presence of 6 M NaCl, showing tolerance against high salinity. The presence of various metal ions, inhibitors, and organic solvents did not remarkably inhibit the activity of the discovered protease. The PersiProtease1 was extracted from the tannery wastewater microbiota and efficiently applied for biodegradation of real sample tannery wastewater protein, chicken feathers, whey protein, dehairing sheepskins, and waste X-ray films. PersiProtease1 proved its enormous potential in simultaneous biodegradation of solid and liquid protein-rich industrial wastes based on the results.

Highly efficient removal of dyes from wastewater using nanocellulose from quinoa husk as a carrier for immobilization of laccase

In this study, the synthesis of nanocellulose (NC) from an agro-waste of quinoa husks (QS) was reported for the first time. The NC nano-carrier was utilized for immobilization of a model laccase enzyme (PersiLac1) providing an innovative, green, and practical nano-biocatalyst for efficient removal of two different model dyes (malachite green (MG) and congo red (CR)) from water. This nano-biocatalyst developed a synergistic adsorption-degradation approach leading the dye molecules easily gathered near the nano-carrier by adsorption and then degraded effectively by the enzyme. Upon enzyme immobilization, the dye removals (%) were remarkably improved for both 150 mg/L of dyes (from 54% and 12%, for MG and CR, respectively, in case of the pristine NCs, to 98% and 60% for the immobilized enzyme). The immobilized PersiLac1 could decolorize the concentrated dye solutions and showed superior reusability (up to 83% dye removal after 18th runs for MG) and remarkable performance from complex real textile effluents.

Changes in root microbiome during wheat evolution

Background

Although coevolutionary signatures of host-microbe interactions are considered to engineer the healthy microbiome of humans, little is known about the changes in root-microbiome during plant evolution. To understand how the composition of the wheat and its ancestral species microbiome have changed over the evolutionary processes, we performed a 16S rRNA metagenomic analysis on rhizobacterial communities associated with a phylogenetic framework of four Triticum species T. urartu, T. turgidum, T. durum, and T. aestivum along with their ancestral species Aegilops speltoides, and Ae. tauschii during vegetative and reproductive stages.

Results

In this study, we illustrated that the genome contents of wild species Aegilops speltoides and Ae. tauschii can be significant factors determining the composition of root-associated bacterial communities in domesticated bread wheat. Although it was found that domestication and modern breeding practices might have had a significant impact on microbiome-plant interactions especially at the reproductive stage, we observed an extensive and selective control by wheat genotypes on associated rhizobacterial communities at the same time. Our data also showed a strong genotypic variation within species of T. aestivum and Ae. tauschii, suggesting potential breeding targets for plants surveyed.

Conclusions

This study performed with different genotypes of Triticum and Aegilops species is the first study showing that the genome contents of Ae. speltoides and Ae. tauschii along with domestication-related changes can be significant factors determining the composition of root-associated bacterial communities in bread wheat. It is also indirect evidence that shows a very extensive range of host traits and genes are probably involved in host-microbe interactions. Therefore, understanding the wheat root-associated microbiome needs to take into consideration of its polygenetic mosaic nature.

Genome-Wide Expression Analysis of Root Tips in Contrasting Rice Genotypes Revealed Novel Candidate Genes for Water Stress Adaptation

Root system architecture (RSA) is an important agronomic trait with vital roles in plant productivity under water stress conditions. A deep and branched root system may help plants to avoid water stress by enabling them to acquire more water and nutrient resources. Nevertheless, our knowledge of the genetics and molecular control mechanisms of RSA is still relatively limited. In this study, we analyzed the transcriptome response of root tips to water stress in two well-known genotypes of rice: IR64, a high-yielding lowland genotype, which represents a drought-susceptible and shallow-rooting genotype; and Azucena, a traditional, upland, drought-tolerant and deep-rooting genotype. We collected samples from three zones (Z) of root tip: two consecutive 5 mm sections (Z1 and Z2) and the following next 10 mm section (Z3), which mainly includes meristematic and maturation regions. Our results showed that Z1 of Azucena was enriched for genes involved in cell cycle and division and root growth and development whereas in IR64 root, responses to oxidative stress were strongly enriched. While the expansion of the lateral root system was used as a strategy by both genotypes when facing water shortage, it was more pronounced in Azucena. Our results also suggested that by enhancing meristematic cell wall thickening for insulation purposes as a means of confronting stress, the sensitive IR64 genotype may have reduced its capacity for root elongation to extract water from deeper layers of the soil. Furthermore, several members of gene families such as NAC, AP2/ERF, AUX/IAA, EXPANSIN, WRKY, and MYB emerged as main players in RSA and drought adaptation. We also found that HSP and HSF gene families participated in oxidative stress inhibition in IR64 root tip. Meta-quantitative trait loci (QTL) analysis revealed that 288 differentially expressed genes were colocalized with RSA QTLs previously reported under drought and normal conditions. This finding warrants further research into their possible roles in drought adaptation. Overall, our analyses presented several major molecular differences between Azucena and IR64, which may partly explain their differential root growth responses to water stress. It appears that Azucena avoided water stress through enhancing growth and root exploration to access water, whereas IR64 might mainly rely on cell insulation to maintain water and antioxidant system to withstand stress. We identified a large number of novel RSA and drought associated candidate genes, which should encourage further exploration of their potential to enhance drought adaptation in rice.

Efficient saccharification of ionic liquid-pretreated rice straw in a one-pot system using novel metagenomics derived cellulases

Ionic liquids (ILs)-resistant cellulase enzymes can facilitate the saccharification of IL- pretreated biomass in a one-pot wash-free method. Using a bioinformatics approach, two cellulases, Persicel7 and Persicel8, with convincing evidence for ionic liquid tolerance were identified. Subsequently, these enzymes were heterologously expressed and biochemically characterized. Persicel7 and Persicel8 exhibited endo-β-1, 4-glucanase activity and were resistant to inhibitors and several organic solvents. Their activity in 10% (v/v) 1-ethyl-3-methylimidazolium chloride and 1-butyl-3-methylimidazolium chloride were 130% higher compared with IL-free control. The half-life of cellulases was improved up to 11-fold when incubated with 20% (v/v) solution of ion liquids. In addition, a one-pot IL-pretreatment and enzymatic saccharification of rice straw enhanced the saccharification rate by 33% compared to the untreated reaction. The Persicel7 and Persicel8 unique properties make them attractive candidates for industrial applications, particularly hydrolyzing ion liquid activated biomass in a one-pot system.

Transcriptomic and Metabolomic Analyses Reveal Inhibition of Hepatic Adipogenesis and Fat Catabolism in Yak for Adaptation to Forage Shortage During Cold Season

Animals have adapted behavioral and physiological strategies to conserve energy during periods of adverse conditions. Hepatic glucose is one such adaptation used by grazing animals. While large vertebrates have been shown to have feed utilization and deposition of nutrients—fluctuations in metabolic rate—little is known about the regulating mechanism that controls hepatic metabolism in yaks under grazing conditions in the cold season. Hence, the objective of this research was to integrate transcriptomic and metabolomic data to better understand how the hepatic responds to chronic nutrient stress. Our analyses indicated that the blood parameters related to energy metabolism (glucose, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, lipoprotein lipase, insulin, and insulin-like growth factor 1) were significantly (p &lt; 0.05) lower in the cold season. The RNA-Seq results showed that malnutrition inhibited lipid synthesis (particularly fatty acid, cholesterol, and steroid synthesis), fatty acid oxidation, and lipid catabolism and promoted gluconeogenesis by inhibiting the peroxisome proliferator-activated receptor (PPAR) and PI3K-Akt signaling pathways. For metabolite profiles, 359 metabolites were significantly altered in two groups. Interestingly, the cold season group remarkably decreased glutathione and phosphatidylcholine (18:2 (2E, 4E)/0:0). Moreover, integrative analysis of the transcriptome and metabolome demonstrated that glycolysis or gluconeogenesis, PPAR signaling pathway, fatty acid biosynthesis, steroid biosynthesis, and glutathione metabolism play an important role in the potential relationship between differential expression genes and metabolites. The reduced lipid synthesis, fatty acid oxidation, and fat catabolism facilitated gluconeogenesis by inhibiting the PPAR and PI3K-Akt signaling pathways to maintain the energy homeostasis of the whole body in the yak, thereby coping with the shortage of forages and adapting to the extreme environment of the Qinghai-Tibetan Plateau (QTP).

Y chromosome is moving out of sex determination shadow

Although sex hormones play a key role in sex differences in susceptibility, severity, outcomes, and response to therapy of different diseases, sex chromosomes are also increasingly recognized as an important factor. Studies demonstrated that the Y chromosome is not a ‘genetic wasteland’ and can be a useful genetic marker for interpreting various male-specific physiological and pathophysiological characteristics. Y chromosome harbors male‑specific genes, which either solely or in cooperation with their X-counterpart, and independent or in conjunction with sex hormones have a considerable impact on basic physiology and disease mechanisms in most or all tissues development. Furthermore, loss of Y chromosome and/or aberrant expression of Y chromosome genes cause sex differences in disease mechanisms. With the launch of the human proteome project (HPP), the association of Y chromosome proteins with pathological conditions has been increasingly explored. In this review, the involvement of Y chromosome genes in male-specific diseases such as prostate cancer and the cases that are more prevalent in men, such as cardiovascular disease, neurological disease, and cancers, has been highlighted. Understanding the molecular mechanisms underlying Y chromosome-related diseases can have a significant impact on the prevention, diagnosis, and treatment of diseases.

Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach

Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA-related MQTLs were detected and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance-associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA), and lignification (e.g. C4H, PAL, PRX and CAD). The genes located within both the SNP peak positions and the QTL-overview peaks for RSA are suggested as novel candidate genes for further functional analysis. The promising candidate genes and MQTLs can be used as basis for genetic engineering and MQTL-assisted breeding of root phenotypes to improve yield potential, stability and performance in a water-stressed environment.

The novel homologue of the human α-glucosidase inhibited by the non-germinated and germinated quinoa protein hydrolysates after in vitro gastrointestinal digestion

Quinoa (Chenopodium quinoa Willd) is a potential source of protein with ideal amino acid profiles which its bioactive compounds can be improved during germination and gastrointestinal digestion. The present investigation studies the impact of germination for 24 hr and simulated gastrointestinal digestion on α-glucosidase inhibitory activity of the quinoa protein and bioactive peptides against the novel homologue of human α-glucosidase, PersiAlpha-GL1. The sprouted quinoa after gastroduodenal digestion was the most effective α-glucosidase inhibitor showing 81.10% α-glucosidase inhibition at concentration 4 mg/ml with the half inhibition rate (IC₅₀ ) of 0.07 mg/ml. Based on the kinetic analysis, both the germinated and non-germinated samples before and after digestion were competitive-type inhibitors of α-glucosidase. Results of this study showed the improved α-glucosidase inhibitory activity of the quinoa bioactive peptides after germination and gastrointestinal digestion and highlighted the potential of metagenome-derived PersiAlpha-GL1 as a novel homologue of the human α-glucosidase for developing the future anti-diabetic drugs. PRACTICAL APPLICATIONS: This study aimed to evaluate the effect of germination and gastrointestinal digestion of the quinoa protein and bioactive peptides on α-glucosidase inhibitory activity against the novel PersiAlpha-GL1. Metagenomic data were used to identify the novel α-glucosidase structurally and functionally homologue of human intestinal. The results showed the highest inhibition on PersiAlpha-GL1 by a germinated quinoa after gastroduodenal digestion and confirmed the potential of PersiAlpha-GL1 to enhance the effectiveness of the anti-diabetic drugs for industrial application.

Application of free and immobilized novel bifunctional biocatalyst in biotransformation of recalcitrant lignocellulosic biomass

Herein, an innovative, green, and practical biocatalyst was developed using conjugation of a novel bifunctional mannanase/xylanase biocatalyst (PersiManXyn1) to the modified cellulose nanocrystals (CNCs). Firstly, PersiManXyn1 was multi-stage in-silico screened from rumen macrobiota, and then cloned, expressed, and purified. Next, CNCs were synthesized from sugar beet pulp using enzymatic and acid hydrolysis processes, and then Fe₃O₄ NPs were anchored on their surface to produce magnetic CNCs (MCNCs). This hybrid was modified by dopamine providing DA/MCNCs nano-carrier. The bifunctional PersiManXyn1 demonstrated the superior hydrolysis activity on corn cob compared with the monofunctional xylanase enzyme (PersiXyn2). Moreover, the immobilization of PersiManXyn1 on the nano-carrier resulted in an improvement of the thermal stability, kinetic parameters (K_cat), and storage stability of the enzyme. Incorporation of the Fe₃O₄ NPs on the CNCs made magnetic nano-carrier with high magnetization value (25.8 emu/g) which exhibited rapid response toward the external magnetic fields. Hence, the immobilized biocatalyst could be easily separated from the products by a magnet, and reused up to 8 cycles with maintaining more than 50% of its original activity. The immobilized PersiManXyn1 generated 22.2%, 38.7%, and 35.1% more reducing sugars after 168 h hydrolysis of the sugar beet pulp, coffee waste, and rice straw, respectively, compared to the free enzyme. Based on the results, immobilization of the bifunctional PersiManXyn1 exhibited the superb performance of the enzyme to improve the conversion of the lignocellulosic wastes into high value products and develop the cost-competition biomass operations.

Proteomics study reveals the molecular mechanisms underlying cryotolerance induced by mild sublethal stress in human sperm

The preconditioning of human sperm with sublethal nitrosative stress before cryopreservation can potentially improve the thawed sperm quality. However, the underlying mechanisms behind this protective strategy are not entirely understood. We compared the cryosurvival of human sperm exposed to 0.01 μM nitric oxide (NO) throughout the cryopreservation and used multiplexed quantitative proteomics approach to identify changes in the proteome profile of preconditioned sperm cells. Semen samples were obtained from 30 normospermia donors and then each sample was divided into three equal parts: fresh (F), frozen-control (C), and frozen exposed to nitric oxide (NO). The sperm undergoing mild sublethal stress showed higher values for motility and viability compared to the frozen control sperm. Moreover, out of 2912 identified proteins, 248 proteins were detected as differentially abundant proteins (DAPs) between cryopreserved groups and fresh group (F) (p < 0.05). Gene ontology (GO) analysis of differentially abundant proteins indicated that the abundance of proteins associated with glycolysis, gluconeogenesis, and fertilization processes was reduced while oxidative phosphorylation pathway was increased in abundance in cryopreserved sperm compared to the fresh sperm. Moreover, redox protein such as thioredoxin 17 was increased in abundance in the NO group compared to the control freezing group. Therefore, the pre-conditioning of sperm prior to cryopreservation may play an important role in maintaining the redox balance in mitochondria of sperm after freezing. Overall, our results indicate that arylsulfatase A (ARSA), serine protease 37 (PRSS37), and sperm surface protein (SP17) may potentially serve as protein biomarkers associated with screening the fertilization potential of the thawed sperm.

Zeolite-based nanocomposite as a smart pH-sensitive nanovehicle for release of xylanase as poultry feed supplement

Xylanase improves poultry nutrition by degrading xylan in the cell walls of feed grains and release the entrapped nutrients. However, the application of xylanase as a feed supplement is restricted to its low stability in the environment and gastrointestinal (GI) tract of poultry. To overcome these obstacles, Zeozyme NPs as a smart pH-responsive nanosystem was designed based on xylanase immobilization on zeolitic nanoporous as the major cornerstone that was modified with L-lysine. The immobilized xylanase was followed by encapsulating with a cross-linked CMC-based polymer. Zeozyme NPs was structurally characterized using TEM, SEM, AFM, DLS, TGA and nitrogen adsorption/desorption isotherms at liquid nitrogen temperature. The stability of Zeozyme NPs was evaluated at different temperatures, pH, and in the presence of proteases. Additionally, the release pattern of xylanase was investigated at a digestion model mimicking the GI tract. Xylanase was released selectively at the duodenum and ileum (pH 6-7.1) and remarkably preserved at pH ≤ 6 including proventriculus, gizzard, and crop (pH 1.6-5). The results confirmed that the zeolite equipped with the CMC matrix could enhance the xylanase thermal and pH stability and preserve its activity in the presence of proteases. Moreover, Zeozyme NPs exhibited a smart pH-dependent release of xylanase in an in vitro simulated GI tract.

Efficient removal of various textile dyes from wastewater by novel thermo-halotolerant laccase

A novel thermostable/halotolerant metagenome-derived laccase (PersiLac2) from tannery wastewater was purified to remove textile dyes in this study. The enzyme was highly active over a wide temperature and pH range and maintained 73.35% of its initial activity after 30 days, at 50 °C. The effect of various metal and organic-solvent tolerance on PersiLac2 showed, retaining greater than 53% activity at 800 mM of metal ions, 52.12% activity at 6 M NaCl, and greater than 44.09% activity at 20% organic solvents. PersiLac2 manifested effective removal of eight different textile dyes from azo, anthraquinone, and triphenylmethane families. It decolorized 500 mg/L of Alizarin yellow, Carmine, Congo red and Bromothymol blue with 99.74-55.85% efficiency after 15 min, at 50 °C, without mediator. This enzyme could practically remove dyes from a real textile effluent and it displayed significant detoxification in rice seed germination tests. In conclusion, PersiLac2 could be useful in future for decolorization/detoxification of wastewater.

Highly Efficient Computationally Derived Novel Metagenome α-Amylase With Robust Stability Under Extreme Denaturing Conditions

α-Amylases are among the very critical enzymes used for different industrial purposes. Most α-amylases cannot accomplish the requirement of industrial conditions and easily lose their activity in harsh environments. In this study, a novel α-amylase named PersiAmy1 has been identified through the multistage in silico screening pipeline from the rumen metagenomic data. The long-term storage of PersiAmy1 in low and high temperatures demonstrated 82.13 and 71.01% activities after 36 days of incubation at 4 and 50°C, respectively. The stable α-amylase retained 61.09% of its activity after 180 min of incubation at 90°C and was highly stable in a broad pH range, showing 60.48 and 86.05% activities at pH 4.0 and pH 9.0 after 180 min of incubation, respectively. Also, the enzyme could resist the high-salinity condition and demonstrated 88.81% activity in the presence of 5 M NaCl. PersiAmy1 showed more than 74% activity in the presence of various metal ions. The addition of the detergents, surfactants, and organic solvents did not affect the α-amylase activity considerably. Substrate spectrum analysis showed that PersiAmy1 could act on a wide array of substrates. PersiAmy1 showed high stability in inhibitors and superb activity in downstream conditions, thus useful in detergent and baking industries. Investigating the applicability in detergent formulation, PersiAmy1 showed more than 69% activity after incubation with commercial detergents at different temperatures (30–50°C) and retained more than 56% activity after incubation with commercial detergents for 3 h at 10°C. Furthermore, the results of the wash performance analysis exhibited a good stain removal at 10°C. The power of PersiAmy1 in the bread industry revealed soft, chewable crumbs with improved volume and porosity compared with control. This study highlights the intense power of robust novel PersiAmy1 as a functional bio-additive in many industrial applications.

Inner retinal injury in experimental glaucoma is prevented upon AAV mediated Shp2 silencing in a caveolin dependent manner

SH2 domain containing tyrosine phosphatase 2 (Shp2; PTPN11) regulates several intracellular pathways downstream of multiple growth factor receptors. Our studies implicate that Shp2 interacts with Caveolin-1 (Cav-1) protein in retinal ganglion cells (RGCs) and negatively regulates BDNF/TrkB signaling. This study aimed to investigate the mechanisms underlying the protective effects of shp2 silencing in the RGCs in glaucomatous conditions.

Methods: Shp2 was silenced in the Cav-1 deficient mice and the age matched wildtype littermates using adeno-associated viral (AAV) constructs. Shp2 expression modulation was performed in an acute and a chronic mouse model of experimental glaucoma. AAV2 expressing Shp2 eGFP-shRNA under a strong synthetic CAG promoter was administered intravitreally in the animals' eyes. The contralateral eye received AAV-eGFP-scramble-shRNA as control. Animals with Shp2 downregulation were subjected to either microbead injections or acute ocular hypertension experimental paradigm. Changes in inner retinal function were evaluated by measuring positive scotopic threshold response (pSTR) while structural and biochemical alterations were evaluated through H&E staining, western blotting and immunohistochemical analysis of the retinal tissues.

Results: A greater loss of pSTR amplitudes was observed in the WT mice compared to Cav-1^-/- retinas in both the models. Silencing of Shp2 phosphatase imparted protection against inner retinal function loss in chronic glaucoma model in WT mice. The functional rescue also translated to structural preservation of ganglion cell layer in the chronic glaucoma condition in WT mice which was not evident in Cav-1^-/- mice retinas.

Conclusions: This study indicates that protective effects of Shp2 ablation under chronic experimental glaucoma conditions are dependent on Cav-1 in the retina, suggesting in vivo interactions between the two proteins.

Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen

Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated cattle. Our metagenome sequencing provided novel genomic insights into functional potential of 523 uncultured bacteria and 15 mostly uncultured archaea in the rumen. The assembled genomes belonged mainly to Bacteroidota, Firmicutes, Verrucomicrobiota, and Fibrobacterota and were enriched for genes related to the degradation of lignocellulosic polymers and the fermentation of degraded products into short chain volatile fatty acids. We also found a shift from copiotrophic to oligotrophic taxa during the course of rumen fermentation, potentially important for the digestion of recalcitrant lignocellulosic substrates in the physiochemically complex and varying environment of the rumen. Differential colonization of forages (the incubated lignocellulosic materials) by rumen microbiota suggests that taxonomic and metabolic diversification is an evolutionary adaptation to diverse lignocellulosic substrates constituting a major component of the cattle's diet. Our data also provide novel insights into the key role of unique microbial diversity and associated gene functions in the degradation of recalcitrant lignocellulosic materials in the rumen.

Bi-functionalized aminoguanidine-PEGylated periodic mesoporous organosilica nanoparticles: a promising nanocarrier for delivery of Cas9-sgRNA ribonucleoproteine

BACKGROUND

There is a great interest in the efficient intracellular delivery of Cas9-sgRNA ribonucleoprotein complex (RNP) and its possible applications for in vivo CRISPR-based gene editing. In this study, a nanoporous mediated gene-editing approach has been successfully performed using a bi-functionalized aminoguanidine-PEGylated periodic mesoporous organosilica (PMO) nanoparticles (RNP@AGu@PEG1500-PMO) as a potent and biocompatible nanocarrier for RNP delivery.

RESULTS

The bi-functionalized MSN-based nanomaterials have been fully characterized using electron microscopy (TEM and SEM), nitrogen adsorption measurements, thermogravimetric analysis (TGA), X-ray powder diffraction (XRD), Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR), and dynamic light scattering (DLS). The results confirm that AGu@PEG1500-PMO can be applied for gene-editing with an efficiency of about 40% as measured by GFP gene knockdown of HT1080-GFP cells with no notable change in the morphology of the cells.

CONCLUSIONS

Due to the high stability and biocompatibility, simple synthesis, and cost-effectiveness, the developed bi-functionalized PMO-based nano-network introduces a tailored nanocarrier that has remarkable potential as a promising trajectory for biomedical and RNP delivery applications.

Mouse model of Alzheimer's disease demonstrates differential effects of early disease pathology on various brain regions

Different parts of the brain are affected distinctively in various stages of the Alzheimer's disease (AD) pathogenesis. Identifying the biochemical changes in specific brain regions is key to comprehend the neuropathological mechanisms in early pre-symptomatic phases of AD. Quantitative proteomics profiling of four distinct areas of the brain of young APP/PS1 mouse model of AD was performed followed by biochemical pathway enrichment analysis. Findings revealed fundamental compositional and functional shifts even in the early stages of the disease. This novel study highlights unique proteome and biochemical pathway alterations in specific regions of the brain that underlie the early stages of AD pathology and will provide a framework for future longitudinal studies. The proteomics data were deposited into the ProteomeXchange Consortium via PRIDE with the identifier PXD019192.

The Contribution of Y Chromosome Genes to Spontaneous Differentiation of Human Embryonic Stem Cells into Embryoid Bodies In Vitro

Objective

Sexual dimorphism in mammals can be described as subsequent transcriptional differences from their distinct sex chromosome complements. Following X inactivation in females, the Y chromosome is the major genetic difference between sexes. In this study, we used a male embryonic stem cell line (Royan H6) to identify the potential role of the male-specific region of the Y chromosome (MSY) during spontaneous differentiation into embryoid bodies (EBs) as a model of early embryonic development.

Materials and Methods

In this experimental study, RH6 cells were cultured on inactivated feeder layers and Matrigel. In a dynamic suspension system, aggregates were generated in the same size and were spontaneously differentiated into EBs. During differentiation, expression patterns of specific markers for three germ layers were compared with MSY genes.

Results

Spontaneous differentiation was determined by downregulation of pluripotent markers and upregulation of fourteen differentiation markers. Upregulation of the ectoderm markers was observed on days 4 and 16, whereas mesoderm markers were upregulated on the 8th day and endodermic markers on days 12-16. Mesoderm markers correlated with 8 MSY genes namely DDX3Y, RPS4Y1, KDM5D, TBL1Y, BCORP1, PRY, DAZ, and AMELY, which were classified as a mesoderm cluster. Endoderm markers were co-expressed with 7 MSY genes, i.e. ZFY, TSPY, PRORY, VCY, EIF1AY, USP9Y, and RPKY, which were grouped as an endoderm cluster. Finally, the ectoderm markers correlated with TXLNGY, NLGN4Y, PCDH11Y, TMSB4Y, UTY, RBMY1, and HSFY genes of the MSY, which were categorized as an ectoderm cluster. In contrast, 2 MSY genes, SRY and TGIF2LY, were more highly expressed in RH6 cells compared to EBs.

Conclusion

We found a significant correlation between spontaneous differentiation and upregulation of specific MSY genes. The expression alterations of MSY genes implied the potential responsibility of their gene co-expression clusters for EB differentiation. We suggest that these genes may play important roles in early embryonic development.

In-silico discovery of bifunctional enzymes with enhanced lignocellulose hydrolysis from microbiota big data

Due to the importance of using lignocellulosic biomass, it is always important to find an effective novel enzyme or enzyme cocktail or fusion enzymes. Identification of bifunctional enzymes through a metagenomic approach is an efficient method for converting agricultural residues and a beneficial way to reduce the cost of enzyme cocktail and fusion enzyme production. In this study, a novel stable bifunctional cellulase/xylanase, PersiCelXyn1 was identified from the rumen microbiota by the multi-stage in-silico screening pipeline and computationally assisted methodology. The enzyme exhibited the optimal activity at pH 5 and 50°C. Analyzing the enzyme activity at extreme temperature, pH, long-term storage, and presence of inhibitors and metal ions, confirmed the stability of the bifunctional enzyme under harsh conditions. Hydrolysis of the rice straw by PersiCelXyn1 showed its capability to degrade both cellulose and hemicellulose polymers. Also, the enzyme improved the degradation of various biomass substrates after 168 h of hydrolysis. Our results demonstrated the power of the multi-stage in-silico screening to identify bifunctional enzymes from metagenomic big data for effective bioconversion of lignocellulosic biomass.

Diversity of microbes colonizing forages of varying lignocellulose properties in the sheep rumen

Background

The rumen microbiota contributes strongly to the degradation of ingested plant materials. There is limited knowledge about the diversity of taxa involved in the breakdown of lignocellulosic biomasses with varying chemical compositions in the rumen.

Method

We aimed to assess how and to what extent the physicochemical properties of forages influence the colonization and digestion by rumen microbiota. This was achieved by placing nylon bags filled with candidate materials in the rumen of fistulated sheep for a period of up to 96 h, followed by measuring forage's chemical characteristics and community structure of biofilm-embedded microbiota.

Results

Rumen degradation for all forages appeared to have occurred mainly during the first 24 h of their incubation, which significantly slowed down after 48 h of rumen incubation, depending on their chemical properties. Random Forest analysis predicted the predominant role of Treponema and Butyrivibrio in shaping microbial diversity attached to the forages during the course of rumen incubation. Exploring community structure and composition of fiber-attached microbiota revealed significant differential colonization rates of forages depending on their contents for NDF and cellulose. The correlation analysis highlighted the significant contribution of Lachnospiraceae and Veillonellaceae to fiber degradation in the sheep rumen.

Conclusion

Our findings suggested that forage cellulose components are critical in shaping the pattern of microbial colonization and thus their final digestibility in the rumen.

Application of the immobilized enzyme on magnetic graphene oxide nano-carrier as a versatile bi-functional tool for efficient removal of dye from water

Herein, we report bi-functional applications of a novel immobilized enzyme on the modified magnetic graphene oxide (GO) for effective removal of dyes from water. The amine functionalized GO nano-carrier was covalently attached to a model enzyme (PersiManXyn1). The enzyme assays showed that the specific activities of the free and immobilized enzyme were 856.05 and 1141.1 µmolmin^-1mg^-1, respectively. While the free enzyme showed only 5% of its maximum activity, the immobilized PersiManXyn1 preserved more than 35% of its activity, at 90 °C. After four weeks storage, the free enzyme has been deactivated, but the immobilized enzyme retained 54% of its initial activity. The immobilized PersiManXyn1 was proficiently applied for dye removal from water using two strategies. While only pristine nano-carrier and free enzyme showed no considerable catalytic ability, the immobilized PersiManXyn1 could catalytically reduce the concentrated dye solutions within 150 s with superior reusability (94% dye removal after 15^th cycle). Proficient treatment of a real textile effluent by the immobilized PersiManXyn1 approved its practical applications in the water remediation.

Immobilization of enzyme cocktails on dopamine functionalized magnetic cellulose nanocrystals to enhance sugar bioconversion: A biomass reusing loop

A combined enzymatic treatment/acid hydrolysis technique was utilized to synthesize cellulose nanocrystals (CNCs) from sugar beet pulp. CNCs were functionalized with magnetite nanoparticles and dopamine making a versatile nano-carrier (DA/Fe₃O₄NPs@CNCs) for covalent enzyme immobilization. Oxygene/amine functionalities, high magnetization value, and specific surface area of DA/Fe₃O₄NPs@CNCs made it a reusable and green candidate for conjugation to hydrolytic enzyme cocktails (three cellulases, two hemicellulases, and their combinations) to prepare an innovative and practical nano-biocatalyst for biomass conversion. The conjugated enzymes showed an enhanced optimum temperature (∼ 10 °C), improved thermal stability, and shifted optimum pH toward alkaline pHs. Covalent attachment could successfully suppress the enzyme leaching and provide easy recovery/reuse of the nano-biocatalyst up to 10 cycles, with > 50% of initial activity. Application of the nano-biocatalyst in hydrolysis of rice straw and sugar beet pulp showed an increase (20-76%) in the yield of fermentable sugars compared to the free enzyme cocktails.