Current Research in Biotechnology最新文献

Lignocellulose, the Earth’s most abundant biopolymer, is degraded by wood-decaying fungi, specifically white rot fungi (WRF) and brown rot fungi (BRF), which use different strategies. This study examines the expression profiles of the AA9 and CDH enzymes of three WRF species (Heterobasidion annosum, Phanerochaete chrysosporium, and Pleurotus ostreatus) and two BRF species (Fomitopsis pinicola and Rhodonia placenta) from the Agaricomycetes class, grown on poplar wood or glucose as the sole carbon source. Mycelia were collected between days 10 and 12, revealing distinct lignocellulose degradation strategies between WRF and BRF, evidenced by the upregulation of AA9 LPMO (lytic polysaccharide monooxygenases) and AA3_1 (Cellobiose Dehydrogenase) genes, with the co-occurrence of both types of transcripts at the time of mycelial collection. The genome analysis showed variability in the number of AA9LPMO genes between WRF and BRF, which were differentially regulated depending on the carbon source. WRF exhibited a significant upregulation of AA9 LPMO genes,. In Phanerochaete chrysosporium, only one AA9LPMO gene was homologous to Pleurotus ostreatus, which had the highest number of AA9LPMO genes among the WRF studied. Some AA9 LPMO genes in Pleurotus ostreatus were associated to transposable elements (TEs, mainly footprints of LTRs) and grouped in clustered. LTRs were found either in the flanking or within the gene coding regions with no effect on gene transcription. In silico analysis of the AA9LPMO proteins in WRF uncovered distinct features at their C-terminal ends. Most of them lacked an appended module, but those with a CBM1 were highly induced in poplar wood media. The proportion of AA9 proteins with a CBM1 module was similar in Phanerochaete chrysosporium and Heterobasidion irregulare, but lower in Pleurotus ostreatus, which contained more AA9LPMO genes overall. In Pleurotus ostreatus, AA9LPMO proteins were grouped into three clades based on their C oxidizing type, with each clade containing proteins with specific features. The abundance (redundancy) of AA9LPMO genes in WRF especially associated to footprints LTRs in Pleurotus ostreatus suggests these genes may have other roles beyond lignocellulose degradation.

Plastic waste has become a significant global ecological concern due to its substantial harmful impacts. They are eventually colonized and transformed by diverse microbial communities known as the ‘‘plastisphere”. Only a limited group of microbes have been identified so far due to the prevalence of non-culturable strains that inhabit polymer substrates. We investigated the community diversity and predictive functionality of the plastisphere microbiota using a high-throughput next-generation sequencing (NGS) approach to unveil their plastic degrading potential. Samples were collected from four different plastic-enriched disposal sites adjacent to Kolkata, West Bengal, India, followed by processing, gDNA extraction, library preparation, and sequencing. The most prevalent phyla were Proteobacteria, followed by Bacteroidetes, Actinobacteria, Cyanobacteria, Firmicutes, and Verrucomicrobia. The functional profiling revealed that genes associated with metabolism, cellular processes, and signalling were most prevalent, followed by poorly characterized information storage and processing. In this study, we predicted the existence of a beneficial microbiome associated with bioremediation and plastic degradation, which suggests the potential utilization of plastics as primary carbon sources. Our findings also highlighted the existence of promising microbial enzymes associated with the biodegradation of several plastic substrates.

Furthermore, our research unveiled the enriched distribution of beneficial microbiome in the studied metagenome, which offers a diverse prospect. This investigation establishes a connection between the structure of microbial communities and diverse genes actively engaged in the biodegradation of plastic waste within plastic disposal sites. These beneficial degraders can be investigated further for broad-spectrum applications in plastic bioremediation. Subsequent explorations of their plastic degrading enzymes will provide profound contributions to plastic pollution mitigation.

To delineate the response mechanism of Nile tilapia (Oreochromis niloticus) to the riverine pollution of river Ganga, a comparative transcriptomic analysis was performed utilizing fresh liver through RNA-Seq technology. A total of 51.39 million and 32.8 million reads were obtained after excluding low quality sequences from non-polluted (Barrackpore) and polluted (Kanpur) sites of Nile tilapia. About 81.4 % and 95.3% reads were perfectly mapped with the reference sequence of O. niloticus. Transcriptional analysis generated 363 differential expressed genes (DEGs) including 131 up-regulated and 232 down-regulated genes. Gene Ontology (GO) enrichment analysis revealed that significant DEGs were associated with ribosome biogenesis, alpha-amino acid metabolic process, translational initiation etc. as biological process (BP); unfolded protein binding, vitamin binding, carboxylic acid binding and etc. as molecular function (MF); ribosome, and ribosomal subunit as cellular component (CC). The KEGG analysis indicated that these DEGs were highly involved in ribosome, Lysine degradation and RNA transport pathways. Additionally, ten hub genes participated in Translation, Ribonucleoprotein complex biogenesis as BP, Ribosome, Eukaryotic translation initiation factor 3 complex as CC and Structural constituent of ribosome, RNA binding as MF were affected in riverine pollution. Overall, this transcriptome investigation provided an extensive overview of pollution triggered transcriptional mechanisms in Tilapia liver and would be highly significant for further exploration of the molecular processes in response to pollution.

Citrus viral infections pose a substantial threat to the global citrus industry, resulting in multitudinous economic losses annually. Timely and precise identification of citrus viruses offers a promising avenue for proactive insights preemptively before the instigation of extensive infections. The present study was devised to expedite the prompt identification of the presence of Citrus tristeza virus (CTV) within Nepalese citrus species utilizing a Double Antibody Sandwich-Enzyme-Linked Immunosorbent Assay (DAS-ELISA), followed by its validation using reverse transcription PCR (RT-PCR). Samplings extracted from plants harvested from 74 out of the 77 administrative districts within Nepal provide substantial evidence of extensive propagation of viral contagion among citrus cultivars across 64 districts (86.48%) of the nation. A comprehensive analysis of the samples obtained from diverse geographical localities revealed that 36 districts (48.64%) exhibit mild infestation, while 9 districts (12.16%) evince moderate infestation. Moreover, samples harvested from 19 districts (25.67%) were highly infected; intriguingly, specimens from 10 districts (13.51%) manifest an absence of viral intrusion. The results have been validated with RT-PCR assay. Given the profound significance of citrus as a pivotal repository of vitamin C and its essential role in conferring advantageous health attributes to humankind, alongside its substantial contribution to the economic paradigm, a meticulous examination is imperative to safeguard these plants against an array of viral infections. Collectively, the DAS-ELISA methodology along with RT-PCR approaches constitutes an exquisitely sensitive and meticulously specific modality, poised to accelerate the expeditious detection of citrus-associated viruses within burgeoning economies like Nepal. This advancement supports timely and precise detection and diagnosis of agriculturally virulent conditions, thereby forestalling the eruption of viral epidemics and concomitantly curbing their financial repercussions.

This study was performed to optimize synbiotic formulations with Ligilactobacillus salivarius BF17 for augmenting gut health in Murrah buffalo calves. Prebiotic utilization, acidification profiles, prebiotic indices (PIs) and prebiotic activity scores (PAS) were performed to screen various prebiotics. The findings revealed significant differences (P < 0.05) in prebiotic utilization by probiotic bacteria. The fructooligosaccharides (FOS) and inulin performed better in terms of acidification and growth than did mannan-oligosaccharides (MOS), corn dextrin (CD) and wheat dextrin (WD). Furthermore, PI and PAS were highest for inulin. Hence, inulin was selected for the synbiotic formulation. Twenty-three neonatal Murrah buffalo calves (90 days experimental period) were randomly divided into four dietary groups; control (CON): basal diet alone; prebiotic (PRE): basal diet with chicory root powder (natural source of inulin, @ 8 g/d • calf); probiotic (PRO): basal diet with milk fermented with Lg. salivarius BF17 @10⁸ colony forming units (CFU)/g/d • calf and synbiotic (SYN): basal diet with both prebiotic and probiotic. The final BW (kg) of the buffalo calves was higher (P<0.05) in the SYN group (74.93 ± 0.56), followed by PRE (71.26 ± 0.97), and PRO (72.25 ± 0.53) groups compared to control (68.04 ± 0.77). Feed conversion efficiency was significantly (P<0.05) increased in all the supplemented groups (0.423 ± 0.008 in PRE; 0.428 ± 0.007 in PRO and 0.438 ± 0.010 in SYN) compared to CON (0.396 ± 0.003). Structural growth measurements also revealed a significant increase (P < 0.05) among the calves in the supplemented groups compared to control group. Nevertheless, in the SYN and PRO groups, there was a simultaneous increase (P < 0.05) in Lactobacillus and Bifidobacterium populations, coupled with a decrease in the coliform population. The average faecal score was decreased (P < 0.05) in all the treatment groups (1.72 ± 0.22 in PRE; 1.71 ± 0.20 in PRO and 1.62 ± 0.21 in SYN) as compared to CON group (1.97 ± 0.25). Compared with those in the control group, the fecal biomarkers in all supplemented groups were favorable. Overall, inulin was more effective in optimized synbiotic formulation with Lg. salivarius BF17. Moreover, supplementation with prebiotic, probiotic, and synbiotic improved growth and gut health in Murrah buffalo calves, with the SYN group yielding superior effects.

Microalgae synthesize valuable compounds like pigments, proteins, lipids and carbohydrates under stress conditions, which make them an interesting feedstock for different industries. The effect of GABA (Gamma-aminobutyric acid) supplementation under salinity stress conditions was investigated on growth, biomass, pigments, lipid and protein content of Pseudochlorella pringsheimii. Between the varying treatments, 5 g/L NaCl combined with 2.5 mM GABA was observed as the best concentration for stimulating the production of bioactive compounds in microalga P. pringsheimii. The results revealed a significant increase in biomass content by 93.24 %, compared with the control. Moreover, a significant increase was also observed in the production of chlorophyll (chl) a, chlorophyll (chl) b, total carotenoids (car), protein and lipid content by 112.15 %, 84 %, 29.94 %, 23.08 % and 35.63 %, respectively. However, as compared to control and salinity stress alone, the total carbohydrate content was sharply declined by 52.30 % and 101.79 % in GABA supplemented groups. In addition, the presence of fatty acids and different biomolecules were also confirmed by GC–MS and FTIR analysis. The existence of different essential and non-essential amino acids in substantial amounts was validated by UHPLC analysis. Collectively, the present work contributes to a novel strategy for boosting the coproduction of biomass, lipids, proteins and pigments in P. pringsheimii under unfavorable conditions.

This study aims to assess the immune status of septic acute lung injury (ALI) at various stages and to investigate whether probiotics can mitigate ALI in septic rats. Rats were randomly assigned to sham, caecal ligation and puncture (CLP), and probiotic treatment after CLP (CLP+PT) group. Intestinal contents, bronchoalveolar lavage fluid (BALF), and lung tissue were collected from rats at 6, 24 and 48 h after CLP. Results showed that Th17 level at 24 h in BALF is significantly higher than that at 6 and 48 h. The Treg level increased after CLP and reached its highest point at 48 h. Pathological damage in the alveolar interstitium intensified over time. At 24 h, Th17 percentage of BALF significantly increased in the CLP group while it significantly decreased in the CLP+PT group, and the Treg percentage of BALF at 48 h showed the same alteration trend. Alveolar interstitial pathological damage in the CLP+PT group was reduced at all time points compared to the CLP group. The abundance of Firmicutes was higher and Bacteroidetes lower in the sepsis group compared to the sham group. However, the abundance of these bacteria was similar between the probiotic and pseudo-probiotic groups. Actinomycetes levels differed significantly among the three groups, with the probiotic group exhibiting significantly higher levels. Bifidobacteria levels were significantly higher in the probiotic group compared to the sepsis group. Phenotype prediction indicated a higher proportion of biofilm formation in the probiotic group compared to the sepsis group. In conclusions, significant alterations in Th17 and Treg levels in BALF of septic rats suggest a shift in the distribution of important T lymphocytes in the lungs during sepsis. Probiotics modulated the gut microbiota of septic rats, downregulated the highest value of Th17 and Treg percentage in BAFL, resulting in mitigated lung injury in rats.

Applying (hyper)accumulators to remediate Cd-contaminated agricultural soils is vital to safeguard food safety and human health. Tagetes patula L. (Marigold) − an omnipresent hyperaccumulator − has been extensively explored with artificially Cd-contaminated soils. Little is known about its feasibility and potential for remediating naturally Cd-contaminated soils and field applications. In this study, the Cd remediation potential of Marigold was assessed with greenhouse and field studies, with the control groups of Solanum nigrum L. (Black nightshade), Amaranthus Hypochondriacus L. (Amaranth) and Pennisetum purpureum K. Schumach. × P. thyphoideum Rich. (King grass). The results of greenhouse experiment showed that Marigold obtained the highest shoot Cd (4.69 mg·kg⁻¹), Cd uptake amount (93.47 μg·pot⁻¹), translocation factor (TF, 2.80) and bioconcentration factor (BCF, 2.67) while remediating naturally Cd-contaminated soils. Moreover, the field study validated its superior phytoremediation potential of Cd – Marigold achieved 150.80 g·ha⁻¹ while treating a Cd-contaminated farmland (1.72 mg·kg⁻¹). Further, the meta-analysis corroborated Marigold’s strength over other control plants in remediating Cd-contaminated soils, holding the mean effect size of BCF and TF of 1.54 and 0.61, respectively. Taken together, Marigold is promising for the remediation of Cd-contaminated fields. Knowledge gleaned from this study provides an effective approach for the practical phytoremediation of Cd-contaminated soils.

Nanotechnology offers promising solutions for climate-resilient agriculture, countering challenges like stagnant yields, emerging pests, and environmental stresses posed by changing global climates. Nanoparticles (NPs) possess unique properties and biological interactions. Metal-based NPs have been tailored for functions like antimicrobial activity, insecticidal properties, and weed inhibition and hold promise for combating biotic stresses and offer the potential for plant pest control, disease detection and management, stress resilience, weed control, and enhancing biomass and crop yield. Metallic NPs repel pests, exhibit larvicidal and ovicidal properties, combat plant pathogens, deliver agrochemicals precisely, and prevent weed growth, eventually boosting agricultural productivity. Numerous NP-based metal and metal oxide nanoproducts, including nanocarriers for nanofertilizers and nanopesticides, nanobiosensors for early pathogen detection, and nanoclays for weed control have flooded the market. Though, mechanistic details of NPs action in mitigating biotic stresses are poorly accounted for, metallic NPs combat pathogens by incurring DNA damage and generating reactive oxygen species (ROS). They fortify plant defense by activation of regulatory factors, induction of antioxidant systems, activation of stress-related genes, and modulation of the metabolic pathways to enhance plant growth. Nevertheless, nanotechnology in agriculture is in its infancy yet, necessitating further research to comprehend its merits and demerits. The potential toxicological effects of NPs underscore the importance of optimizing their dosage to maximize benefits while minimizing negative impacts. Further, redressal of regulatory and safety concerns associated with NPs application in agriculture is essential to ensure their safe and sustainable usage. Clear universal guidelines and standardized testing protocols need to be mandated to uphold their global implementation to transform agriculture.

In recent years, small peptide and non-peptide AVPI-/Smac-mimetics have been developed as IAP antagonists and are in clinical trials to overcome resistance to apoptosis in various cancer types. In this study, we present molecular modeling studies and in vitro biological evaluation of a set of AVPI-mimetics, including parent AVPI, tetrapeptide AVPI-mimetics and AVPI-conjugates.

Combined molecular modeling studies and HYDE analyses provided valuable information regarding the protein–ligand interactions within the binding site of cIAP1-BIR3 and XIAP-BIR3 domains, showing that the binding part of both domains (cIAP1- and XIAP-BIR3) are formed from 22 amino acid residues, and their active part of 11 AAs. Moreover, 5 amino acids are defined common for both targets, namely Lys299, Gly306, Leu307, Trp310, and Trp323. Based on the observed docking models, six amino acid residues for cIAP1-BIR3 and five amino acids for XIAP-BIR3 are recognized actively involved in the formation of H-bonds with the respective ligand. The amino acid sequence 308 (Arg308 in cIAP1-BIR3, Thr308 in XIAP-BIR3), simultaneously forming two H-hydrogen bonds, seems to plays a key role in improvement of binding affinity.

Apart from docking results the synthesized set of AVPI-mimetics was tested in vitro using cell biology (MTT assay) and parallel artificial membrane permeability assay (PAMPA). The results showed that the double modification of AVPI via substitution of Pro³ with Hyp³, as well as elongation of AVPI’s C-terminus by its conjugation with RGD-analogs, significantly increase the antiproliferative effects of AVPI-conjugates on all tested cancer cell lines (MDA-MB-231, MCF-7, HepG2 and HT-29 cells) compared to the parent AVPI peptide. SARs analysis defined this modification beneficial for the overall biological activity of the AVPI-mimetics and pointed out AVHypI-AgbGD as the most active conjugate with an IC₅₀ of 348 µM for MDA-MB-231, 457 µM for MCF-7, 399 µM for HepG2, and 578 µM for HT-29 cells. Though the calculated IC₅₀ values were still high, we consider AVHypI-AgbGD peptide as a good basis for further modifications. In addition, PAMPA results showed that substitution of Pro with Hyp improved the BBB permeability of AVHypI peptide compared to its parent molecule.