Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Chromosome-level genome assembly and annotation of Gypsophila vaccaria

Gypsophila vaccaria Sm., a member of the Caryophyllaceae family, is known for its dry mature seeds, which are widely used in traditional Chinese medicine as "Wang Bu Liu Xing". This study presents a high-quality, chromosome-scale genome assembly of G. vaccaria, integrating Hi-C technology with PacBio and Illumina sequencing data. The final assembled genome measures 1.09 Gb in total length, with a contig N50 of 9.73 Mb and a scaffold N50 of 73.3 Mb, and complete benchmarking universal single-copy orthologs (BUSCO) for the genome and protein modes were 95.9% and 94.9%. Notably, 99.93% of the sequences are anchored to 15 pseudo-chromosomes. A total of 21,795 protein-coding genes were predicted, and repetitive elements were found to constitute 80.43% of the assembled genome. This chromosome-level genome assembly serves as an invaluable resource for future research, including functional genomics and molecular breeding of G. vaccaria.

Effect of Pyrethroids on the Colony Growth and Metabolic Activity of Entomopathogenic Fungi of the Beauveria Genus

Pyrethroids are chemical insecticides used on a large scale in agriculture, horticulture, and forest protection. In order to reduce their use in IPM, alternative methods of controlling insect pests are introduced, such as the use of biopesticides based on entomopathogenic fungi (EPF). Species of the Beauveria genus are characterized by a very broad spectrum of action, which is why they are often used to produce preparations based on EPF. The aim of the study was to determine the effect of different doses of tested pyrethroids on the colony growth and metabolic activity of EPF from the Beauveria genus. In vitro, the effect of three pyrethroids (deltamethrin, λ-cyhalothrin, and α-cypermethrin) added to SDA medium at a dose 10 times lower than the recommended field dose (A), the recommended field dose (B), and 10 times higher than the recommended field dose (C) on colony growth and metabolic activity of B. bassiana and B. brongniartii was tested. The research carried out showed that pyrethroid insecticides used in the experiment showed various toxic effects towards the tested EPF of the genus Beauveria. The studies conducted showed that on the 20th day of the observation, λ-cyhalothrin used in the recommended field dose limited the growth of B. bassiana to the least extent in relation to the other tested pyrethroids. However, with respect to the fungus B. brongniartii, no toxic effect of this pyrethroid was found. Based on the results obtained, it was found that λ-cyhalothrin used in the recommended field dose and 10 times lower than recommended significantly increased the metabolic activity of B. bassiana. In relation to the B. brongniartii strain, detlamethrin used in each of the tested concentrations significantly affected its viability.

Transcriptome analysis reveals candidate genes involved in quercetin biosynthesis in Euphorbia maculata

An investigation was conducted through transcriptome sequencing in various tissues at different stages to explore the quercetin biosynthesis pathway in Euphorbia maculata. A total of 83,028 unigenes was assembled utilizing Trinity software, with an N50 length of 1721 bp and a mean length of 1004 bp. Among these unigenes, 51,822 were annotated in six public databases. The transcriptome analysis revealed 45,727 CDS sequences and 56 TF families. Candidate genes involved in quercetin biosynthesis were also revealed, including phenylalanine ammonia-lyase (17 unigenes), cinnamate 4-hydroxylase (3 unigenes), 4-coumarate-CoA ligase (16 unigenes), chalcone synthase (5 unigenes), chalcone isomerase (4 unigenes), flavanone 3-hydroxylase (1 unigene), flavonoid 3'-hydroxylase (4 unigenes), and flavonol synthase (9 unigenes). Additionally, 42 key differentially expressed genes (DEGs) related to quercetin biosynthesis were identified in the same tissues at different stages, with 35 DEGs exhibiting down-regulated expression and 7 DEGs displaying up-regulated expression. These findings not only enhance the genetic knowledge of E. maculata, but also establish a basis for further investigating the mechanism of quercetin biosynthesis, and improving the quality of E. maculata.

Morphological, Physiological, Biochemical, and Molecular Characterization of Fungal Species Associated with Papaya Rot in Cameroon

Post-harvest decay of Carica papaya L. is the primary cause of deterioration in papaya quality and the low economic impact of this sector in Cameroon. Field surveys conducted by teams from the Ministry of Agriculture and Rural Development (MINADER) in Cameroon have primarily associated these decays with fungal attacks. However, to date, no methodological analysis has been conducted on the identification of these fungal agents. To reduce post-harvest losses, rapid detection of diseases is crucial for the application of effective management strategies. This study sought to identify the fungal agents associated with post-harvest decay of papaya cv Sunrise solo in Cameroon and to determine their physiological and biochemical growth characteristics. Isolation and pathogenicity tests were performed according to Koch's postulate. Molecular identification of isolates was achieved by amplification and sequencing of the ITS1 and ITS4 regions. Phylogenetic analysis was based on the substitution models corresponding to each fungal genus determined by jModeltest, according to the Akaike information criterion (AIC). Fungal explants of each identified species were subjected to variations in temperature, pH, water activity, and NaCl concentration. The ability to secrete hydrolytic enzymes was determined on specific media such as skimmed milk agar for protease, peptone agar for lipase, and carboxymethylcellulose for cellulase. These experiments allowed the identification of three fungi responsible for papaya fruit decay, namely Colletotrichum gloeosporioides, Fusarium equiseti, and Lasiodiplodia theobromae. All three pathogens had maximum mycelial growth at a temperature of 25 ± 2 °C, pH 6.5, NaCl concentration of 100 µM, and water activity (aw) equal to 0.98. The three fungal agents demonstrated a strong potential for secreting cellulases, lipases, and proteases, which they use as lytic enzymes to degrade papaya tissues. The relative enzymatic activity varied depending on the fungal pathogen as well as the type of enzyme secreted. This study is the first report of F. equiseti as a causal agent of papaya fruit decay in Cameroon.

In silico report on five high-risk protein C pathogenic variants: G403R, P405S, S421N, C238S, and I243T

In this study, we propose reclassification of 5 out of 16 PROC VUS (variants of uncertain significance): C238S, I243T, G403R, P405S, and S421N, as pathogenic variants, associated with thrombophilia due to PROC deficiency. The obtained results are based on in silico analysis, which enables a detailed assessment of variants' impact, despite limited clinical evidence. In particular, the G403R substitution, next to the S402-active site, is expected to reduce the flexibility of the local coil domain, affecting the catalytic activity of serine protease. The P405S substitution may imply B-factor gain (P = 0.24; p-value=0.040). On the other hand, the S421N variant causes phosphorylation site disruption at S421, which serves as a target for CK2 phosphorylation. C238S substitution alters metal binding, while the I243T variant may alter transmembrane properties (P = 0.27, P-value=0.00071). All five PROC variants hold promise as diagnostic markers for protein C deficiency and may also serve as potential drug targets for therapeutic intervention.

Characterization of microbial type terpene synthases from two liverworts Lophocolea bidentata and Nardia scalaris

Microbial terpene synthase-like (MTPSL) enzymes from the two liverworts Nardia scalaris (Gymnomitriaceae) and Lopcholea bidentata (Lophocoleaceae) were characterized in yeast. The hexane extract of the fresh plant material was also analyzed for its terpenoid content. Following the expression of the enzymes in yeast (WAT11), the volatile terpenoid products were analyzed using GC-MS, and their scent was qualitatively evaluated. Four full lengths MTPSLs from L. bidentata and four from N. scalaris were identified in the transcriptome data and expressed in yeast. Three MTPSLs from L. bidentata and two from N. scalaris were found to be biochemically active in yeast, and all of these were found to be sesquiterpene synthases without any monoterpenoid products. These represent the first terpene synthases characterized from these two plants. LbMTPSL1 was found to be a murolene synthase, LbMTPSL3 was a cubenene synthase, and LbMTPSL5 had α-selinene and β-elemene as the major products. For N. scalaris it was found that NsMTPSL3 was a viridiflorol synthase and NsMTPSL4 was a α/β-chamigrene synthase with at least five other minor products. The 3D structure of the enzymes was modelled using CPH-models, in order to enhance the understanding of the biochemical differences of the enzymes. The models clearly show that these MTPSL only contain one α-domain, which is characteristic of MTPSLs and is previously described for similar enzymes. The bioactivities of the enzymes align with compounds identified in the two liverworts, and this study represents the first onset of further investigations into terpenoid biochemistry of Lopcholea and Nardia species.

Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut

Faecalibacterium is one of the most abundant bacteria of the human gut microbiota of healthy adults and is recognized to have positive effects on health. Here, we precisely and comprehensively analyzed the conjugative mobilome of four complete Faecalibacterium genomes. Despite lacking any plasmid, these bacteria harbor a vast arsenal of 130 elements, including 17 integrative and conjugative elements (ICEs) and 83 integrative and mobilizable elements (IMEs), collectively comprising 14-23% of the genome. Genome comparison of two strains isolated from the same fecal sample (Faecalibacterium and Roseburia strains) revealed almost identical elements indicating that transfer of ICEs and IMEs shape gut microbiome. ICEs and IMEs from Faecalibacterium encode many and diverse predicted functions such as defense and stress response (phages, multidrug, antibiotics, oxidative stress, biliar salts, antimicrobial peptides), nutrient import and metabolisms (Fe3+, carbohydrates) and riboflavin synthesis. This hints at their important role in the survival and adaptation of Faecalibacterium strains to the gut ecosystem. A rapid survey of 29 additional Faecalibacterium genomes uncovered many putative ICEs and IMEs, reinforcing their role in the rapid and massive evolution of Faecalibacterium genomes.

The virulent bacteriophage Henu8 as an antimicrobial synergist against Escherichia coli

As the overuse of antibiotics has not yet been strictly limited in urban areas, drug-resistant Escherichia coli has become a fatal pressure for bacteremia treatment. Considering the outstanding performance of bacteriophages in vitro, bacteriophages may serve as an alternative to heal chronic refractory infections. In this study, a 49,890 bp double-stranded circular DNA phage, Henu8, was isolated and was able to lyse the group of E. coli strains tested in this study. Prominent biological characterization revealed that the highly adsorbed bacteriophage Henu8 could form a fully transparent plaque with a narrow translucent halo. The optimal multiplicity of infection of the bacteriophage Henu8 was 0.01, with a burst size of 275 PFU/cell. Genomic analysis revealed a G + C content of 44.17% Henu8, in which 65 open reading frames were located, which could be assigned as a new species in the genus Hanrivervirus of the subfamily Tempevirinae. The effective antibacterial ability and the obvious biofilm destruction and inhibition capability of phage Henu8 were observed. The time-killing assay demonstrated the synergetic potential of Henu8 with antibiotics in vitro for E. coli eradication. Henu8 has profound medicinal potential in a mouse bacteremia model. These studies indicate that Henu8 is a novel bacteriophage with therapeutic potential alone or in combination with antibiotics for clinical treatment.IMPORTANCEThe findings described in this study constitute concrete evidence that it is possible to significantly synergize the antimicrobial activity of bacteriophages and antibiotics. We showed that the newly isolated potent bacteriophage Henu8 lyses Escherichia coli rapidly but tends to produce resistant bacteria. The bacteriophage Henu8 has synergistic antimicrobial effects with several antibiotics and is not susceptible to developing resistance. These results provide further evidence that bacterial resistance to phages arises, possibly at an adaptive cost to sensitivity to antibiotics. Therefore, the findings of this study are important for increasing the potential of phages for clinical applications and developing new approaches to improve their therapeutic efficacy against bacterial drug resistance.

Design of a Continuous GAA-Producing Probiotic as a Potential Mitigator of the Effects of Sleep Deprivation

Creatine is a popular athletic supplement that has also been shown to improve cognitive performance upon sleep deprivation. However, it is rapidly cleared from the gastrointestinal tract a few hours after consumption. Toward providing a persistent creatine dose, we engineered the human probiotic Escherichia coli Nissle (EcN) to produce guanidinoacetic acid (GAA), which is converted to creatine in the liver. We find GAA-producing enzymes present in the human microbiome and compare their activities to known enzymes. Three copies of arginine:glycine amidinotransferase (AGAT) from Actinokineospora terrae are expressed from the genome, and native gcvP, argR, and argA are edited or deleted to improve substrate availability without negatively impacting cell viability. A standard EcN dose (1012 cells) produces 41 ± 7 mg GAA per hour under laboratory conditions. This work demonstrates that a probiotic bacterium can be engineered to produce sustained GAA titers known to impact cognitive performance.

Chromosome-level assembly of Pseudopodoces humilis genome: A resource for avian evolutionary studies

Pseudopodoces humilis is a small passerine bird predominantly found in the mid-latitude regions of the Tibetan Plateau in Asia. A chromosome-level reference genome assembly for P. humilis was generated using PacBio CLR with Hi-C. The final genome assembly spans approximately 1.096 Gb, consisting of 1,968 contigs with a Contig N50 of 32.246 Mb, and was evaluated to be 95.60% complete using BUSCO. Hi-C chromosome mapping resulted in 33 chromosome sequences, which enabled the ordering and orientation of 329 contigs, with chromosome lengths ranging from 2.08 Mb to 152.13 Mb, covering 95.85% of the total genome sequence. Repetitive sequences comprised 144.91 Mb of the genome. A total of 381 tRNA, 507 non-coding RNA (ncRNA), and 205 rRNA were identified. In addition, we identified 17,108 protein-coding genes and 29,473 proteins, comprising a total of 17,236,726 amino acids. This high-quality genome assembly provides a strong genomic foundation for exploring critical questions in evolutionary genetics, phylogenomics, and the molecular mechanisms of adaptation - key areas for understanding biodiversity and species resilience amidst changing environments.

Ultrafast and accurate sequence alignment and clustering of viral genomes

Viromics produces millions of viral genomes and fragments annually, overwhelming traditional sequence comparison methods. Here we introduce Vclust, an approach that determines average nucleotide identity by Lempel-Ziv parsing and clusters viral genomes with thresholds endorsed by authoritative viral genomics and taxonomy consortia. Vclust demonstrates superior accuracy and efficiency compared to existing tools, clustering millions of genomes in a few hours on a mid-range workstation.

Non-Catalytic Domains of Glycoside Hydrolase Family 5 from Paenibacillus curdlanolyticus are Important for Promoting Multifunctional Enzyme Activities and Degradation of Agricultural Residues

PcGH5 from Paenibacillus curdlanolyticus strain B-6 is a modular protein consisting of a catalytic domain of glycoside hydrolase family 5 (GH5), and three non-catalytic domains (a family 11 carbohydrate-binding module (CBM11), a fibronectin type 3 (Fn3), and a family 3 carbohydrate-binding module (CBM3). In this study, the recombinants full-length PcGH5 and the catalytic domain (PcGH5_CD) were expressed in Escherichia coli and purified. Most GH5 members exhibit endo-cellulase activity. However, the catalytic domain enzyme of strain B-6 exhibited unique properties, showing multifunctional enzyme activities of endo-cellulase, endo-xylanase, endo-mannanase, and endo-1,3-1,4-β-glucanase. The sequence alignment of PcGH5_CD compared to other characterized GH5 enzymes suggests that the two catalytic residues and the six substrate-binding subsites of endo-cellulases were conserved with other different GH5 enzyme properties. Whereas a few conserved amino acid residues and/or short peptides located outside the active site of the GH5 endo-cellulases may be involved in broad substrate specificity of PcGH5_CD enzyme on xylan, mannan and 1,3-1,4-β-glucan. Moreover, the non-catalytic domains (CBM11-Fn3-CBM3) linked to the GH5 catalytic domain are important for promoting the multifunctional enzyme activities of PcGH5 on the β-1,4 glycosidic linkages of crystalline cellulose, highly branched polysaccharides, and β-1,4-1,6 and β-1,3-1,4 glycosidic linkages of polysaccharides, especially for the polysaccharides complex contained in agricultural residues. The full-length PcGH5 is effective in producing oligosaccharides from agricultural residues without pretreatment. Therefore, it is interesting to use it as a source of prebiotics producer for use in various food products.

Evaluating allergenicity of protein fragments and peptides in partially hydrolysed infant formulas available in Hong Kong

Partially hydrolysed infant formula (pHF) is designed as a cow's milk substitute for the infants with cow's milk protein allergy (CMPA) and consuming pHFs for preventing allergenic diseases is still under debate. Possibly, differences in protein fragment and peptide profiles among different brands of pHFs are the key confounder in the cohort studies. Thus, top-down and bottom-up proteomic analysis were conducted to identify the profiles of 4 brands of pHFs available in Hong Kong. Subsequently, allergenicities of the profiles were evaluated in silico. The analysis revealed that pHF-A and pHF-B contains large allergenic fragments of β-lactoglobulin and α-lactalbumin with molecular weights over 14 kDa. Most of peptides in pHF-D were less than 2 kDa and considered as non-allergenic. As the allergenicities varies a lot among different brands of pHFs in Hong Kong, so people need to be well informed before consuming for better managements of CMPA.

DNA methyltransferase 1 modulates mitochondrial function through bridging m5C RNA methylation

DNA methyltransferase 1 (DNMT1) is an enzyme known for DNA methylation maintenance. Point mutations in its replication focus targeting sequence (RFTS) domain lead to late-onset neurodegeneration, such as autosomal dominant cerebellar ataxia-deafness and narcolepsy (ADCA-DN) disorder. Here, we demonstrated that DNMT1 has the capability to bind to mRNA transcripts and facilitate 5-methylcytosine (m5C) RNA methylation by recruiting NOP2/Sun RNA methyltransferase 2 (NSUN2). RNA m5C methylation, in turn, promotes RNA stability for those genes modulating mitochondrial function. When the DNMT1 RFTS domain is mutated in mice, it triggers aberrant DNMT1-RNA interaction and significantly elevated m5C RNA methylation and RNA stability for a portion of metabolic genes. Consequently, increased levels of metabolic RNA transcripts contribute to cumulative oxidative stress, mitochondrial dysfunction, and neurological symptoms. Collectively, our results reveal a dual role of DNMT1 in regulating both DNA and RNA methylation, which further modulates mitochondrial function, shedding light on the pathogenic mechanism of DNMT1 mutation-induced neurodegeneration.

Biochemical mapping reveals a conserved heme transport mechanism via CcmCD in System I bacterial cytochrome c biogenesis

Heme is a redox-active cofactor for essential processes across all domains of life. Heme's redox capabilities are responsible for its biological significance but also make it highly cytotoxic, requiring tight intracellular regulation. Thus, the mechanisms of heme trafficking are still not well understood. To address this, the bacterial cytochrome c biogenesis pathways are being developed into model systems to elucidate mechanisms of heme trafficking. These pathways function to attach heme to apocytochrome c, which requires the transport of heme from inside to outside of the cell. Here, we focus on the System I pathway (CcmABCDEFGH) which is proposed to function in two steps: CcmABCD transports heme across the membrane and attaches it to CcmE. HoloCcmE then transports heme to the holocytochrome c synthase, CcmFH, for attachment to apocytochrome c. To interrogate heme transport across the membrane, we focus on CcmCD, which can form holoCcmE independent of CcmAB, leading to the hypothesis that CcmCD is a heme transporter. A structure-function analysis via cysteine/heme crosslinking identified a heme acceptance domain and heme transport channel in CcmCD. Bioinformatic analysis and structural predictions across prokaryotic organisms determined that the heme acceptance domains are structurally variable, potentially to interact with diverse heme delivery proteins. In contrast, the CcmC transmembrane heme channel is structurally conserved, indicating a common mechanism for transmembrane heme transport. We provide direct biochemical evidence mapping the CcmCD heme channel and providing insights into general mechanisms of heme trafficking by other putative heme transporters.

IMPORTANCE

Heme is a biologically important cofactor for proteins involved with essential cellular functions, such as oxygen transport and energy production. Heme can also be toxic to cells and thus requires tight regulation and specific trafficking pathways. As a result, much effort has been devoted to understanding how this important, yet cytotoxic, molecule is transported. While several heme transporters/importers/exporters have been identified, the biochemical mechanisms of transport are not well understood, representing a major knowledge gap. Here, the bacterial cytochrome c biogenesis pathway, System I (CcmABCDEFGH), is used to elucidate the transmembrane transport of heme via CcmCD. We utilize a cysteine/heme crosslinking approach, which can trap endogenous heme in specific domains, to biochemically map the heme transport channel in CcmCD, demonstrating that CcmCD is a heme transporter. These results suggest a model for heme trafficking by other heme transporters in both prokaryotes and eukaryotes.

Coevolutionary dynamics of 53BP1 and its impact on TP53 interaction for DNA damage repair

The p53-binding protein 1 (53BP1) is essential for DNA damage repair via non-homologous end joining (NHEJ) and plays a crucial role in maintaining genomic stability by interacting with the tumor suppressor protein p53, a key regulator of the DNA damage response (DDR). This study investigates the role of coevolution within 53BP1 and its impact on structural integrity and binding affinity with p53. Through multiple sequence alignment and phylogenetic analysis, we identified 72 coevolving groups of amino acid residues, five of which were mapped to the BRCT domain of 53BP1. Mutational effects on these residues were assessed using point mutation mapping and stability analysis via DynaMut, with a detailed evaluation of groups 12 and 16. Docking studies revealed that coevolution-induced modifications enhanced 53BP1-p53 interactions, with group 12 exhibiting the highest binding affinity (-9.9 kcal/mol), followed by group 16 (-9 kcal/mol), both outperforming the wild-type (-8.9 kcal/mol). These modifications resulted in novel interactions that contributed to overall structural stability. Our findings highlight the significance of coevolution in shaping protein-protein interactions and maintaining the structural and functional integrity of 53BP1 protein.

New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis

BACKGROUND

Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance compared to the lowland ecotype, but the underlying molecular mechanisms remain unclear.

RESULTS

Here, we present a high-quality haplotype-resolved genome of the upland ecotype "Jingji31." We then conduct multi-omics analysis to explore the mechanism underlying its cold tolerance. By comparative transcriptome analysis of the upland and lowland ecotypes, we identify many genes with ecotype-specific differential expression, particularly members of the cold-responsive (COR) gene family, under cold stress. Notably, AFB1, ATL80, HOS10, and STRS2 gene families show opposite expression changes between the two ecotypes. Based on the haplotype-resolved genome of "Jingji31," we detect more cold-induced allele-specific expression genes in the upland ecotype than in the lowland ecotype, and these genes are significantly enriched in the COR gene family. By genome-wide association study, we detect an association signal related to the overwintering rate, which overlaps with a selective sweep region containing a cytochrome P450 gene highly expressed under cold stress. Heterologous overexpression of this gene in rice alleviates leaf chlorosis and wilting under cold stress. We also verify that expression of this gene is suppressed by a structural variation in the promoter region.

CONCLUSIONS

Based on the high-quality haplotype-resolved genome and multi-omics analysis of upland switchgrass, we characterize candidate genes responsible for cold tolerance. This study advances our understanding of plant cold tolerance, which provides crop breeding for improved cold tolerance.

Comparison of Anti-Biofilm Potential of Rhamnolipid Biosurfactant, Chemical Agents, and Coliphage Against E. coli Biofilm

Biosurfactants are amphipathic microbial products that are released extracellularly or remain attached to the cell surface. The strong biofilm anti-adhesive and anti-biofilm properties of biosurfactants make them suitable candidates for application aimed at destroying troublesome bacterial biofilm. To investigate the anti-adhesion and biofilm disruptive properties of natural rhamnolipid biosurfactant, targeted isolation of a hydrocarbonoclastic bacteria from hydrocarbon-contaminated soil of Dakor, Gujarat, India, led to the isolation of bacteria producing biosurfactant, identified as Pseudomonas aeruginosa. DKR. The orcinol test preliminarily indicated that the biosurfactant was indeed rhamnolipid. The Fourier transform infrared spectroscopy and nuclear magnetic resonance further confirmed the biosurfactant as rhamnolipid. Pseudomonas aeruginosa DKR produced 25 mg/ml rhamnolipid that reduced the surface tension to 22.4 mN/m and possessed CMC (critical micellar concentration) of 130 mg/L. Sub-inhibitory dilution (0.25 mg/ml) of purified rhamnolipid DKR demonstrated superior antiadhesive and antibiofilm properties against biofilm-forming E. coli strains isolated from drinking water coolers in comparison to subinhibitory concentrations of common chemical surfactants, chelating agents, and weak acids used. Coliphage AM isolated on selected E. coli strains as hosts also demonstrated an appreciable biofilm anti-adhesive and anti-biofilm effect at 106 Pfu/ml. This study emphasizes the utility of rhamnolipid biosurfactant DKR and Coliphage AM in lieu of chemicals as natural and eco-friendly agents in applications to eradicate biofilm from drinking water cooling containers, etc.

The assessment of Oreochromis mossambicus muscle tissue and the yield performance of Solanum tuberosum in a small-scale sandponics system

Aquaponics, integrating hydroponics and aquaculture in a circular system, offers a promising approach to addressing food and nutrition security while promoting water conservation in South Africa. This technology is a sustainable means of food production that minimizes environmental waste by simultaneously cultivating plants and rearing fish. This study aimed to evaluate the histology of muscle tissue in Mozambique tilapia (Oreochromis mossambicus) and the performance of Irish potato (Solanum tuberosum) in a small-scale sandponics system. Two potato cultivars (Moonlight and Taurus) were planted in a system linked to a 1000-L water tank containing 25 sexually mature Mozambique tilapia from January to June 2023. Fish histology and potato yield performance were assessed to gauge the efficiency of the system and to generate baseline data for future studies. Results showed that tuber production in the sandponics system was comparable to field conditions, with the Moonlight cultivar yielding the heaviest tubers (293-307 g per plant) with a short-oval shape, demonstrating its superior adaptability to this system. Taurus yielded lighter tubers (139-168 g per plant) that were either round or short oval depending on the grow beds used for production. Fish histological analysis revealed a higher prevalence of muscle tissue alterations in the control group compared to the experimental group. However, both groups displayed a similar condition factor (p < 0.05), indicating good overall health. Despite the promising results, the significantly high levels (p < 0.05) of metal accumulation (As, Cu, Mn, and Zn) in the fish were observed, raising concerns about their suitability for human consumption. This study demonstrates that sandponics systems can effectively support potato production with fish maintaining good general health. However, further investigation is needed to mitigate metal accumulation to ensure the safety of fish for consumption.

Identification and Characterization of a Novel Alginate Lyase VSAly7C with Potential Application for Alginate Di- and Tri-Saccharide Preparation

Brown algae are the largest-producing macroalgae, and alginate lyase plays a key role in the green degradation and high-value conversion of brown algae. This study characterized a novel alginate lyase, VSAly7C, from the marine bacterium Vibrio sp. 8-14, which belongs to the PL7_5 subfamily. Biochemical analysis suggested that VSAly7C is medium-temperature, neutral, and polyG-preferred, with enzyme activities of 2608.3 ± 27.3, 1453.2 ± 50.2, and 2545.2 ± 13.2 U/mg toward polyG, polyM, and sodium alginate, respectively. The minimal oligosaccharides VSAly7C could degrade were tetrasaccharides, and its major products were disaccharides and trisaccharides. Structural bioinformatic analysis of the VSAly7C active groove showed that the -1 to +3 subsite interaction network is crucial for determining the minimal oligosaccharides it can degrade. This study elucidates the catalytic properties, modes of action, and substrate recognition mechanisms of a novel alginate lyase, VSAly7C, which may be potentially applicable in alginate disaccharide and trisaccharide preparation.

A remarkable new blue Ranitomeya species (Anura: Dendrobatidae) with copper metallic legs from open forests of Juruá River Basin, Amazonia

Poison dart frogs (Dendrobatidae) are known for their aposematic coloration and toxic skin, making them a frequent subject of interest and research. However, descriptions of new species of Ranitomeya were interrupted for more than a decade. The implementation of a RAPELD (Rapid Assessment surveys of Long-Term Ecological Research) module in the Juruá River basin, a highly biodiverse and underexplored region, led to the record of a Ranitomeya species with blue dorsal stripes and coppery limbs. Herein we use morphological, morphometric, advertisement call, natural history, tadpole data and genetic data to describe the new species. Our phylogenetic analysis places the species within the Ranitomeya vanzolinii clade, and all delimitation methods confirmed its status as a new species. The species is characterized by its (i) small size (snout-vent length: males 15.2-17.0 mm, females 14.4-16.9 mm), (ii) dorsum with light sky-blue stripes on a reddish-brown ground, and metallic copper limbs with reddish-brown spots, (iii) ring-shaped granular region on the belly, (iv) toes with poorly developed lateral fringes, (v) later tadpole stages with tooth rows P1 = P2 > P3, P3 of 83-87% of P1, and conspicuous light sky-blue dorsal stripes, and (vi) cricket-like advertisement call consisting of 16-35 notes, call duration of 490-1,005 ms, note duration of 8.2-16.9 ms and dominant frequency of 5,168-6,029 Hz. The discovery of the new species emphasizes the significance of researching under-sampled regions like the Juruá River basin, and the usefulness of using a multidisciplinary approach to reveal new dendrobatid species.

Taxonomy and molecular phylogeny of a new species of black fly (Diptera: Simuliidae) in the Simulium striatum species-group from central Thailand

Generally, the DNA barcode relying on a short fragment of the cytochrome c oxidase I (COI) gene is a powerful tool for facilitating species discovery and taxonomic resolution in Diptera, including black flies. However, the COI barcode lacks sufficient resolution to identify several species or infer phylogenetic relationships of black flies in the Simulium striatum species-group, whereas the fast-evolving nuclear big zinc finger (BZF) gene has been suggested as a key marker for identifying the species. In this study, a new species of black fly in the S. striatum species-group from Kamphaeng Phet province, central Thailand, was discovered and characterized through an integrated method combining morphological analysis and molecular data based on the BZF gene. The new species, Simulium (Simulium) concitatum sp. nov., was morphologically described for all life stages, excluding the egg. It shares many morphological similarities with other species of the S. striatum species-group, particularly S. thilorsuense Takaoka, Srisuka & Saeung, 2022 described from Tak province, western Thailand. Sequence analysis and phylogeny inferred from the BZF gene further confirmed that S. concitatum sp. nov. is a distinct species of the S. striatum species-group and revealed its close genetic relationship to S. wangkwaiense Takaoka, Srisuka & Saeung, 2020. The morphological differences between the new species and all known species of the S. striatum species-group documented in Thailand and other countries are provided to assist in species identification. Furthermore, this study underscores the BZF gene as an effective genetic marker to differentiate the species.

Genome-wide identification and expression analysis of TCP transcription factors in Chrysanthemum indicum reveals their critical role in the response to various abiotic stresses

Chrysanthemum indicum is an important medicinal plant that has a particularly strong effect on bacteria and viruses and has antioxidant, anti-inflammatory, and immunomodulatory properties. The genes of the TCP family, a group of plant-specific transcription factors (TFs), have been found to play a crucial role in the regulation of plant growth and development as well as resistance to abiotic stress. Nevertheless, no systematic analysis of the TCP family genes in C. indicum has been performed so far. In the present study, a total of 26 non-redundant CiTCP genes were identified in the genome of C. indicum. The TCP genes were categorized into three subgroups on the basis of the phylogenetic analysis: 7, 9, and 10 genes belonged to the CIN subgroup, CYC/TB1 subgroup, and PCF subgroup, respectively. All CiTCPs were unevenly distributed across the 9 chromosomes. TCP genes in the same subgroup showed similar gene structures and conserved motifs. Gene duplication analysis revealed that segmental duplications had a significant effect on the expansion of CiTCP genes. The analysis of cis-elements revealed that CiTCP genes may be involved in the regulation of plant development, hormone response and response to abiotic stress. Expression profile analysis of the transcriptome data indicated that CiTCP genes exhibited similar or distinct expressions within different tissues and under different abiotic stresses. According to the results of quantitative RT-PCR (qRT-PCR), the expression of 15 selected genes responded strongly to various abiotic stress factors. The results of our studies could provide comprehensive insights into the TCP family genes of C. indicum for further functional investigations.

Structural insights of WBmDapE and deciphering of potent anti-filarial inhibitors: a state-of-art computational approach

Lymphatic filariasis (LF) stands as a debilitating tropical ailment, impacting a considerable global populace. Existing drug therapies for LF exhibit limited effectiveness across all parasite stages, thereby accentuating the imperative for novel anti-filarial medications characterized by enhanced prognostic attributes and minimized adverse reactions. A promising avenue involves targeting the microbial enzyme WBmDapE, pivotal in worm survival and intricately linked to the lysine biosynthetic pathway and peptidoglycan cell wall construction. This investigation employs in silico methodologies encompassing molecular docking, Molecular Dynamics Simulation (MDS), conformational analysis, Shape-Based Virtual Screening (SBVS), ADMETox, MMGBSA, and Density Functional Theory (DFT) calculations to discern potential inhibitors of WBmDapE. Through discerning the conformational shifts of the WBmDapE-bound substrate and product, key amino acids implicated in substrate binding (Arg182 and Asp248) are unveiled. While the apo and substrate-bound structures exhibit an open conformation, the product-bound structure displays marked conformational alterations, including shifts within the catalytic domain and the cofactor in the dimerization domain, suggestive of an active and closed conformation. From the prism of shape-based virtual screening, two preeminent compounds (ZINC42784280 and ZINC84308049) have surfaced as potential hits. These compounds evince heightened binding affinity, optimal binding free energy, pivotal hydrogen bond interactions, and akin attributes to the product-bound complex. Subsequently, these compounds emerge as prospective candidates for filariasis treatment. In summation, our study furnishes invaluable insights into the fabrication of innovative WBmDapE inhibitors, potentially serving as anti-filarial agents. Rigorous experimental substantiation and fine-tuning of these compounds are requisite for prospective therapeutic interventions against LF.

Unveiling the multifaceted domain polymorphism of the Menshen antiphage system

Recent advances have significantly enriched our understanding of complex bacteria-phage interactions. To date, over one hundred bacterial antiphage systems have been identified, yet the mechanisms of many, including the recently discovered Menshen system, remain elusive. We employed comparative genomics and protein bioinformatics for a systematic investigation of the Menshen system, focusing on its organization, structure, function, and evolution. By delineating six primary domain determinants and predicting their functions, we propose that the three components (NsnA-B-C) of Menshen likely act as sensor, transducer, and effector modules, respectively. Notably, we unveil remarkable polymorphism in domain composition within both NsnA and NsnC. NsnA proteins universally share ParB-DUF262 and DNA-binding ParBDB domains, and often include additional DNA-binding modules at their N-termini. NsnC effectors exhibit diverse inactive PIN (inPIN)-like domains for target recognition in their N-termini, and multiple nuclease domains for toxicity in their C-termini. We demonstrate that this multifaceted polymorphism results from the independent integration of various sensor domains into NsnA, alongside constant shuffling and diversification of the inPIN and effector domains in NsnC. These findings not only elucidate the functional diversity and inter-subunit interactions of the Menshen system, but also underscore its exceptional capacity for adaptability and versatility in the ongoing arms race between bacteria and phages.

GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database

Despite the vast amount of sequence data available, a significant disparity exists between the number of protein sequences identified and the relatively few structures that have been resolved. This disparity highlights the challenge in structural biology to bridge the gap between sequence information and 3D structural data, and the necessity for robust databases capable of linking distant homologs to known structures. Studies have indicated that there are a limited number of structural folds, despite the vast diversity of proteins. Hence, computational tools can enhance our ability to classify protein sequences, much before their structures are determined or their functions are characterized, thereby bridging the gap between sequence and structural data. GenDiS (Genomic Distribution of Superfamilies) is a repository with information on the genomic distribution of protein domain superfamilies, involving a one-time computational exercise to search for trusted homologs of protein domains of known structures against the vast sequence database. We have updated this database employing advanced bioinformatics tools, including DELTA-BLAST (domain enhanced lookup time accelerated BLAST) for initial detection of hits and HMMSCAN for validation, significantly improving the accuracy of domain identification. Using these tools, over 151 million sequence homologs for 2060 superfamilies [SCOPe (Structural Classification of Proteins extended)] were identified and 116 million out of them were validated as true positives. Through a case study on glycolysis-related enzymes, variations in domain architectures of these enzymes are explored, revealing evolutionary changes and functional diversity among these essential proteins. We present another case, LOG gene, where one can tune in and find significant mutations across the evolutionary lineage. The GenDiS database, GenDiS3, and the associated tools made available at https://caps.ncbs.res.in/gendis3/ offer a powerful resource for researchers in functional annotation and evolutionary studies. Database URL: https://caps.ncbs.res.in/gendis3/.

Titin-dependent biomechanical feedback tailors sarcomeres to specialized muscle functions in insects

Sarcomeres are the universal contractile units of muscles that enable animals to move. Insect muscles display a remarkable functional diversity: they operate at extremely different contraction frequencies (ranging from ~1 to 1000 hertz) and amplitudes during flying, walking, and crawling. This is puzzling because sarcomeres are built from essentially the same actin-myosin components. Here, we address how functionally different sarcomeres are made. We show that the giant protein titin and the regulation of developmental contractility are key for the sarcomere specializations. I-band titin spans and determines the length of the sarcomeric I-band in a muscle type-specific manner. Unexpectedly, I-band titin also rules the length of the force-generating myosin filament using a feedback mechanism that is modulated by myosin contractility. We propose a model of how sarcomere specializations in insects are tuned, provide evidence for this model, and discuss its validity beyond insects.

Investigating a role for piRNA-associated piwi genes in overcoming host-plant resistance in the soybean aphid, Aphis glycines

Natural host-plant resistance provides a sustainable solution to control insect outbreaks but can be limited due to insect counter-adaptation. The exact mechanisms of insect adaptation to host-plant resistance remain unclear in most systems. Some insect adaptations are controlled by epigenetic mechanisms, such as through noncoding RNA. PIWI-interacting RNAs are specific noncoding RNAs that bind with PIWI proteins to control a diverse range of gene regulatory functions, particularly in insects. Previous investigation into aphid PIWI gene copies showed expansion in their abundance compared to other insects, which may suggest PIWI genes have additional functions among aphids. We first characterized PIWI gene evolution through a phylogenetic analysis, then investigated the role of PIWIs by examining gene expression in the soybean aphid (Aphis glycines), a significant insect pest of soybean which has adapted to overcome aphid-resistance in host plants. Our data indicated the presence of three PIWI ortholog groups, as well as taxon-specific gene expansions, with gene copy numbers ranging from 3 to 17 across species. To evaluate a potential role of PIWIs in overcoming host-plant resistance, we measured their gene expression in Ap. glycines with (virulent) and without (avirulent) the ability to survive on aphid-resistant soybean. We found that virulent Ap. glycines have significantly higher expression of 2 PIWI genes (Agl1.1 and Agl1.3) compared to the avirulent biotype. These data suggest that gene regulatory mechanisms related to the PIWI pathway, potentially including piRNAs, are important in aphid systems and may enable adaptation to host-plant resistance.

HsGA20ox1, HsGA3ox1, and HsGA2ox1 Are Involved in Endogenous Gibberellin Regulation Within Heracleum sosnowskyi Ovaries After Gibberellin A3 Treatment

This study aims to investigate the endogenous gibberellin levels and related genes analysis of noxious invasive weed Heracleum sosnowskyi. Genome-wide identification, phylogenetic analysis, conserved motif analysis, and gene structure characterization of GA-oxidases were performed. We analysed endogenous GAs levels and the expression of target HsGAoxs in response to GA3 within H. sosnowskyi developing ovaries. Twenty-seven HsGAoxs genes were identified, distributed across eleven chromosomes. Phylogenetic analysis classified proteins into the HsGA20ox, C19-HsGA2ox, and HsGA3ox subfamilies, facilitating functional predictions. Among the thirteen HsGA2ox protein members, there were no C20-GA2ox subfamily that distinguish H. sosnowskyi from other model plant species. The analysis of gene structure and conserved motifs confirmed the phylogenetic grouping and suggested that the evolutionary pattern was maintained within these subfamilies. The observed increase in precursor and bioactive GA levels provides evidence that they play a crucial role in promoting fruit growth. Ovary phenotypes reflected the timing of peak gibberellin levels, specifically during the cell expansion period. Exogenous GA3 treatment promoted HsGA3ox1 expression within both the central and lateral regions of the umbel ovaries. Overall, the results show that GA levels are precisely regulated by multiple HsGAox genes for stable early fruit development, and that disturbances in this stability affect fruit development. This opens up the possibility of investigating the role of GA in H. sosnowskyi fruit formation and developing measures for invasion control.

AFP-MCDF: Multi and cross-dimensional feature fusion methods for antifreeze protein prediction

Antifreeze proteins can effectively inhibit the formation of ice crystals and enhance cell survival in low-temperature environments. They protect the texture prolong the shelf life of food and maintain cell and tissue integrity in medical treatments, thereby improving the success rate of surgery and transplantation. Accurate prediction of Antifreeze proteins is important to advance these fields. Traditional wet-experiment methods, while providing reliable validation results, are usually time-consuming and costly. And existing computational methods still have room for improvement in predicting performance. In this study, a novel antifreeze protein prediction method, AFP-MCDF, is proposed. The AFP-MCDF method first extracts one- and two-dimensional feature representations of Antifreeze protein sequences using the pre-trained protein language models ProtBERT and ESM-2. Subsequently, these features are fused multidimensionally via BiLSTM and TextCNN to capture long-term dependencies and local features. Finally, the method predicts the frost resistance of Antifreeze protein sequences by cross-dimensional fusion and linear mapping from N to 2 dimensions. Experimental results show that AFP-MCDF performs well in the antifreeze protein prediction task, outperforming traditional computational methods and reaching the current state-of-the-art.

Complete genome sequence of Desulfovibrio sp. GTC20076 isolated from a clinical specimen in Japan

Desulfovibrio is a genus of sulfate-reducing, anaerobic bacteria ubiquitously present in the environment. Herein, we report the complete genome sequence of an isolate of a new Desulfovibrio species obtained from a human clinical specimen in Japan. The genome comprised a circular chromosome with a length of 3,213,183 bp.

Testis-specific serine/threonine kinase dTSSK2 regulates sperm motility and male fertility in Drosophila

Serine/threonine kinases of the TSSK (Testis-Specific Serine/Threonine Kinase) family play crucial roles in spermatogenesis and male fertility across species, but the underlying regulatory mechanism remains incompletely understood. In this study, we identified and characterized a novel TSSK homolog in Drosophila, named dTSSK2 (CG9222), which functions as the ortholog of human TSSK4. dTSSK2 is specifically expressed in the testis and localizes to individualization complexes during spermiogenesis. Disruption of dTSSK2 severely compromises sperm motility, leading to failed sperm transit into the seminal vesicle and male infertility. Phosphoproteomic analyses reveal that dTSSK2 coordinates sperm flagella assembly and motility by phosphorylating proteins involved in microtubule organization, organelle assembly, and flagella structure. Notably, dTSSK2 phosphorylates the substrate Gudu at Ser9, which partially contributes to individualization complex integrity and sperm motility. These findings elucidate the critical role of dTSSK2-mediated phosphorylation in regulating Drosophila male fertility.

Complete genome sequence of Planococcus koreensis isolated from soil in Fort Collins, Colorado

The complete genome of Planococcus koreensis was obtained using Nanopore MinION sequencing after isolation from soil in Colorado. The assembled genome contains one circular contig with 3,519,105 bp, 3,606 genes, 419 pseudogenes, and 47.62% guanine-cytosine content. This discovery provides a fully assembled P. koreensis genome available at the National Center for Biotechnology Information.

Genetic Variation and Gene Expression of the Antimicrobial Peptide Macins in Asian Buffalo Leech (Hirudinaria manillensis)

With the growing severity of antibiotic resistance, antimicrobial peptides demonstrate significant potential for medical applications. Here, we performed genome and transcriptome sequencing of 30 Asian buffalo leech (Hirudinaria manillensis) individuals and integrated data from three other leech species (Whitmania pigra, Hirudo nipponia, and Hirudo medicinalis) to investigate genetic variation and gene expression of H. manillensis macins. Three macins (Hman1, Hman2, and Hman3), along with their encoding genes (Hman1, Hman2, and Hman3), were identified in H. manillensis. Hman1 exhibited the highest similarity (63.5 ± 12.0%) to macins from other leeches, followed by Hman2 (57.8 ± 7.4%) and Hman3 (30.0 ± 3.5%). Both amino acid and codon sequences of Hman1 were conserved within the species, whereas Hman2 and Hman3 exhibited markedly higher variability. All Hman1 sequences were translatable, while four Hman2 and 28 Hman3 sequences had degenerated into pseudogenes. Transcripts per million (TPM) values for Hman1, Hman2, and Hman3 were 2196.63, 242.35, and 1.22, respectively. Total macin expression in H. manillensis was less than 1/20 of that in W. pigra. Based on sequence variation and expression patterns, we propose that Hman1 retains functionality while Hman2 and Hman3 have lost or are losing their antibacterial functions.

The expanded Bostrychia moritziana genome unveils evolution in the most diverse and complex order of red algae

Red algae are an ancient eukaryotic lineage that were among the first to evolve multicellularity. Although they share a common origin with modern-day plants and display complex multicellular development, comprehensive genome data from the most highly evolved red algal groups remain scarce. Here, we present a chromosome-level genome assembly of Bostrychia moritziana, a complex red seaweed in the Rhodomelaceae family of the Ceramiales-the largest and most diverse order of red algae. Contrary to the view that red algal genomes are typically small, we report significant genome size expansion in Bostrychia and other Ceramiales, which represents one of at least three independent expansion events in red algal evolution. Our analyses suggest that these expansions do not involve polyploidy or ancient whole-genome duplications, but in Bostrychia rather stem from the proliferation of a single lineage of giant Plavaka DNA transposons. Consistent with its enlarged genome, Bostrychia has an increased gene content shaped by de novo gene emergence and amplified gene families in common with other Ceramiales, providing insight into the genetic adaptations underpinning this successful and species-rich order. Finally, our sex-specific assemblies resolve the UV sex chromosomes in Bostrychia, which feature expanded gene-rich sex-linked regions. Notably, each sex chromosome harbors a three amino acid loop extension homeodomain (TALE-HD) transcription factor orthologous to ancient regulators of haploid-diploid transitions in other multicellular lineages. Together, our findings offer a unique perspective of the genomic adaptations driving red algal diversity and demonstrate how this red seaweed lineage can provide insight into the evolutionary origins and universal principles underpinning complex multicellularity.

A new strategy for the fermentation of Massa Medicata Fermentata by combining multiple strains of fermentation and their fermentation mechanisms

To address the quality instability of the traditional fermentation process of Massa Medicata Fermentata (LSQ), we designed an innovation strategy for dual-strain co-fermentation LSQ. Rhizopus arrhizus, Bacillus velezensis, Bacillus subtills, and Bacillus cereus were selected as the fermentation strains for the LSQ. After dual-strain co-fermentation, its pro-digestive enzymes and anti-inflammatory activities were significantly enhanced. Particularly, R. arrhizus/B. subtills fermentation group showed the prominent promotion of the enzymatic activities of amyloglucosidase, cellulase and trypsin, with AC200 values < 1.00 and Max fold increase values of 27.39 ± 0.22, 25.39 ± 0.87 and 48.07 ± 1.84, respectively, and anti-inflammatory activity with an IC50 value of 2.35 ± 0.18 mg/mL. Based on the correlation analysis of differential metabolic profiles and activities, the key pharmacodynamic metabolites were analyzed and validated, such as levomycetin succinatea, β-citrylglutamate, D-glucosaminic acid, nikkomycin and fucose 1-phosphate. Among them, D-glucosaminic acid was positively correlated with the promoting activity of amyloglucosidase, cellulose, enzyme trypsin, pepsin, and the inhibitory activity of NO production, and fucose 1-phosphate and nikkomycin had the prominently positive correlation with the promoting activity of pepsin (p < 0.01). In addition, the docking scores between them and digestive enzyme proteins were all < - 5. A new strategy involving the dual-strain fermentation of LSQ was investigated, and clarified the LSQ fermentation strain-constituent-pharmacological activity correlations, which provides a valuable reference for delving into the LSQ fermentation mechanism.

Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota

Research on the morphology, physiology and genomics of Asgard archaea has provided valuable insights into the evolutionary history of eukaryotes1-3. A previous study suggested that eukaryotes are nested within Heimdallarchaeia4, but their exact phylogenetic placement within Asgard archaea remains controversial4,5. This debate complicates understanding of the metabolic features and timescales of early eukaryotic ancestors. Here we generated 223 metagenome-assembled nearly complete genomes of Asgard archaea that have not previously been documented. We identify 16 new lineages at the genus level or higher, which substantially expands the known phylogenetic diversity of Asgard archaea. Through sophisticated phylogenomic analysis of this expanded genomic dataset involving several marker sets we infer that eukaryotes evolved before the diversification of all sampled Heimdallarchaeia, rather than branching with Hodarchaeales within the Heimdallarchaeia. This difference in the placement of eukaryotes is probably caused by the previously underappreciated chimeric nature of Njordarchaeales genomes, which we find are composed of sequences of both Asgard and TACK archaea (Asgard's sister phylum). Using ancestral reconstruction and molecular dating, we infer that the last Asgard archaea and eukaryote common ancestor emerged before the Great Oxidation Event and was probably an anaerobic H2-dependent acetogen. Our findings support the hydrogen hypothesis of eukaryogenesis, which posits that eukaryotes arose from the fusion of a H2-consuming archaeal host and a H2-producing protomitochondrion.

PRESCOTT: a population aware, epistatic, and structural model accurately predicts missense effects

Predicting the functional impact of point mutations is a critical challenge in genomics. PRESCOTT reconstructs complete mutational landscapes, identifies mutation-sensitive regions, and categorizes missense variants as benign, pathogenic, or variants of uncertain significance. Leveraging protein sequences, structural models, and population-specific allele frequencies, PRESCOTT surpasses existing methods in classifying ClinVar variants, the ACMG dataset, and over 1800 proteins from the Human Protein Dataset. Its online server facilitates mutation effect predictions for any protein and variant, and includes a database of over 19,000 human proteins, ready for population-specific analyses. Open access to residue-specific scores offers transparency and valuable insights for genomic medicine.

Genome Announcement of Four Parechovirus A3 Isolates from the United States of America

We report the complete genome sequences of four parechovirus-A3 (PeV-A3) isolates from Children's Mercy Kansas City (CMKC), United States of America (USA): PeV-A3-MO-12-CMKC/CSF/MO/USA/2012 (isolated in 2012 from cerebrospinal fluid), PeV-A3-8C-CMKC/CSF/MO/USA/2022/ (isolated in 2022 from cerebrospinal fluid), PeV-A3-9C-CMKC/CSF/MO/USA/2022 (isolated in 2022 from cerebrospinal fluid), and PeV-A3-11B-CMKC/Blood/MO/USA/2022 (isolated in 2022 from blood). Sequence analysis revealed multiple mutations throughout the genome of the PeV-A3 isolates in comparison to the prototypic PeV-A3 A308/99 reference sequence (AB084913). Several unique amino acid changes were observed in the PeV-A3 isolates from 2022 that were absent in the PeV-A3 isolate from 2012. Phylogenetic analysis comparison determined that the sequenced PeV-A3 isolates from 2022 cluster together as a separate clade.

Near-complete assembly and comprehensive annotation of the wheat Chinese Spring genome

A complete reference genome assembly is crucial for biological research and genetic improvement. Owing to its large size and highly repetitive nature, there are numerous gaps in the globally used wheat Chinese Spring (CS) genome assembly. In this study, we generated a 14.46 Gb near-complete assembly of the CS genome, with a contig N50 of over 266 Mb and an overall base accuracy of 99.9963%. Among the 290 gaps that remained (26, 257, and 7 gaps from the A, B, and D subgenomes, respectively), 278 were extremely high-copy tandem repeats, whereas the remaining 12 were transposable-element-associated gaps. Four chromosome assemblies were completely gap-free, including chr1D, chr3D, chr4D, and chr5D. Extensive annotation of the near-complete genome revealed 151 405 high-confidence genes, of which 59 180 were newly annotated, including 7602 newly assembled genes. Except for the centromere of chr1B, which has a gap associated with superlong GAA repeat arrays, the centromeric sequences of all of the remaining 20 chromosomes were completely assembled. Our near-complete assembly revealed that the extent of tandem repeats, such as simple-sequence repeats, was highly uneven among different subgenomes. Similarly, the repeat compositions of the centromeres also varied among the three subgenomes. With the genome sequences of all six types of seed storage proteins (SSPs) fully assembled, the expression of ω-gliadin was found to be contributed entirely by the B subgenome, whereas the expression of the other five types of SSPs was most abundant from the D subgenome. The near-complete CS genome will serve as a valuable resource for genomic and functional genomic research and breeding of wheat as well as its related species.

High-Throughput Sequencing Detects a Viral Complex in Agave Tequilana Plants

Agave tequilana Weber var. Azul is one of the most economically important species in Mexico because of its use in the production of tequila. Recently, young agave plants in commercial plantations in the state of Jalisco and agave ornamental plants have been observed to have symptoms of yellow streaks and mottle like those caused by viruses. The diversity of symptoms observed in agave and the negative results of the different diagnostic tests indicated the possible presence of different unknown viruses, and so we conducted high-throughput sequencing (HTS) analyses of viral RNA. The bioinformatics analyses showed the complete genomes of isolates of Vitivirus genus, Potexvirus genus, Tepovirus genus, and the partial genome of a Badnavirus genus in mixed infections in agave samples from commercial plots and in ornamental plants. The presence of each virus was confirmed by sequencing and cloning of the RT-PCR products of the capsid protein (CP), using specific oligonucleotides designed from the sequences obtained by HTS. This is the first time to our knowledge that mixed infections of potential novel Vitivirus, Potexvirus, Tepovirus, and Badnavirus genomes have been identified in A. tequilana plants.

BrCNGC12 and BrCNGC16 mediate Ca2+ absorption and transport to enhance resistance to tipburn in Chinese cabbage

Tipburn is a common physiological disorder in leafy vegetables, significantly impairing crop growth and commercial value. It is widely recognized that Ca2+ deficiency is a key factor triggering tipburn; however, the functions and regulatory mechanisms of genes conferring resistance remain largely unexplored. Through transcriptomic analysis of Chinese cabbage under normal (medium calcium, MCa) and Ca2+-deficient (low calcium, LCa) conditions, we observed that genes in the hormone and calcium signalling pathways exhibited significant responses to LCa stress. Among these, the cyclic nucleotide-gated ion channel (CNGC) genes BrCNGC12 and BrCNGC16, part of the calcium signalling pathway, were notably up-regulated and down-regulated, respectively, under LCa stress. Silencing BrCNGC12 in Chinese cabbage improves Ca2+ absorption and distribution, which strengthens tipburn resistance. Conversely, under LCa stress, heterologous expression of BrCNGC16 in Arabidopsis thaliana increases resistance to tipburn, whereas partial silencing of BrCNGC16 in Chinese cabbage diminishes resistance, with both outcomes linked to altered Ca2+ uptake and translocation. Additionally, overexpression of BrCNGC16 in Chinese cabbage promotes Ca2+ uptake and translocation, thereby enhancing resistance to tipburn and mitigating oxidative damage induced by Ca2+ deficiency. In conclusion, BrCNGC12 and BrCNGC16 play pivotal roles in tipburn resistance in Chinese cabbage, offering novel insights into the interplay between the calcium signalling pathway and tipburn resistance.

NA_mCNN: Classification of Sodium Transporters in Membrane Proteins by Integrating Multi-Window Deep Learning and ProtTrans for Their Therapeutic Potential

Sodium transporters maintain cellular homeostasis by transporting ions, minerals, and nutrients across the membrane, and Na+/K+ ATPases facilitate the cotransport of solutes in neurons, muscle cells, and epithelial cells. Sodium transporters are important for many physiological processes, and their dysfunction leads to diseases such as hypertension, diabetes, neurological disorders, and cancer. The NA_mCNN computational method highlights the functional diversity and significance of sodium transporters in membrane proteins using protein language model embeddings (PLMs) and multiple-window scanning deep learning models. This work investigates PLMs that include Tape, ProtTrans, ESM-1b-1280, and ESM-2-128 to achieve more accuracy in sodium transporter classification. Five-fold cross-validation and independent testing demonstrate ProtTrans embedding robustness. In cross-validation, ProtTrans achieved an AUC of 0.9939, a sensitivity of 0.9829, and a specificity of 0.9889, demonstrating its ability to distinguish positive and negative samples. In independent testing, ProtTrans maintained a sensitivity of 0.9765, a specificity of 0.9991, and an AUC of 0.9975, which indicates its high level of discrimination. This study advances the understanding of sodium transporter diversity and function, as well as their role in human pathophysiology. Our goal is to use deep learning techniques and protein language models for identifying sodium transporters to accelerate identification and develop new therapeutic interventions.

Secalonic acid F1 derived from an endophytic fungus Periconia verrucosa as a potential antimicrobial agent against Staphylococcus aureus

AIM

To investigate the antimicrobial potential of a secalonic acid F1 derivative produced by an endophytic Periconia verrucosa.

METHODS AND RESULTS

The endophyte RDE85 was characterized as P. verrucosa by morphological and phylogenetic analysis. We characterized a major compound from RDE85 as Secalonic acid F1 (SF1) with a 2,4'-linkage. SF1 demonstrated antimicrobial activity with an IC50 of 7.6 µg mL-1 against Staphylococcus aureus. It inhibited the biofilm formation, causing morphological changes and disruption of cell membrane integrity in the pathogen, confirmed by scanning electron microscopy (SEM). The compound depicted strong synergistic potential with ciprofloxacin and reduced DNA and RNA synthesis. The time-kill kinetics demonstrate that SF1 is an effective concentration-dependent bactericidal agent. Further, SF1 severely affected the respiratory chain dehydrogenase activity, confirmed by in-silico studies, revealing its interaction with respiratory chain succinate dehydrogenase. The treatment with this compound downregulated the staphylococcal accessory gene regulator and enterotoxin gene, two important virulence factors of the organism, and reduced the staphyloxanthin production, which is also an important virulence trait.

CONCLUSION

SF1 is a potential antimicrobial agent against S. aureus.

Molecular detection, epidemiology and phylogenetic evaluation of Babesia ovis in apparently healthy goats

Babesia (B.) ovis is an intra-erythrocytic protozoan parasite that infects small ruminants globally, causing economic losses. This study aimed to investigate the molecular prevalence of B. ovis in 1200 asymptomatic goats of various breeds across four districts in Punjab, Pakistan: Layyah, Lohdran, Dera Ghazi Khan, and Rajanpur. The enrolled goats represented ten breeds, including Daira Din Pannah (n = 890), Pahari goat (n = 68), Nukri (n = 44), Teddy (n = 37), Lail Puri (n = 36), Beetal (n = 36), Dessi (n = 32), Makhi Cheena (n = 27), Muhammad Puri (n = 19) and Fazil Puri (n = 11). The hematological and biochemical profiles of the goats, risk factors associated with the infection, and the phylogenetic relationship of the detected isolates were also evaluated. In total, 105 blood samples (9.6 %) tested positive by PCR. Sanger sequencing of a partial fragment of the 18S rRNA gene confirmed B. ovis. Phylogenetic analysis of the 18S rRNA gene sequences revealed 99-100 % similarity with isolates previously reported from Iran, Iraq, Turkey, and Spain. The infection rate varied across districts, with the highest prevalence observed in goats from Rajanpur (13 %), followed by Dera Ghazi Khan (11 %), Layyah (7 %), and Lohdran (5 %) (P = 0.003). The susceptibility to infection varied among goat breeds, with Lail Puri breed showing the highest susceptibility (P = 0.03). Risk factor analysis revealed that goats under one year of age and those kept on farms where other animals and dogs were also present had higher B. ovis infection rates. Babesia ovis-infected goats showed reductions in white and red blood cells, hemoglobin concentration, and alterations in serum aspartate aminotransferase and creatinine levels. This study provides updated data on the prevalence of B. ovis in local Pakistani goat populations, emphasizing the need for integrated control strategies against this tick-borne pathogen.

PredIDR2: Improving accuracy of protein intrinsic disorder prediction by updating deep convolutional neural network and supplementing DisProt data

Intrinsically disordered proteins (IDPs) or regions (IDRs) are widespread in proteomes, and involved in several important biological processes and implicated in many diseases. Many computational methods for IDR prediction are being developed to decrease the gap between the low speed of experimental determination of annotated proteins and the rapid increase of non-annotated proteins, and their performances are blindly tested by the community-driven experiment, the Critical Assessment of protein Intrinsic Disorder (CAID). In this paper, we developed PredIDR2 series, an updated version of PredIDR tested in CAID2 in order to accurately predict intrinsically disordered regions from protein sequence. It includes four methods depending on the input features and the producing mode of the negative samples of the training set. PredIDR2 series (AUC_ROC = 0.952) perform remarkably better than our previous PredIDR (AUC_ROC = 0.933) for Disorder-PDB dataset of CAID2, which seems to be mainly attributed to the introduction of a new deep convolutional neural network and the augmentation of the training data, especially from DisProt database. PredIDR2 series outperform the state-of-the-art IDR prediction methods participated in CAID2 in terms of AUC_ROC, AUC_PR and DC_mae and belong to the seven top-performing methods in terms of MCC. PredIDR2 series can be freely used through the CAID Prediction Portal available at https://caid.idpcentral.org/portal or downloaded as a Singularity container from https://biocomputingup.it/shared/caid-predictors/.

Complete Mitochondrial Genome of Chlorogomphus papilio (Odonata: Anisoptera: Chlorogomphidae) and Phylogenetic Analyses

This study aimed to elucidate the mitochondrial genome organization of Chlorogomphus papilio and the phylogenetic relationships of Chlorogomphidae. We used the Illumina MiSeq sequencing platform to sequence the mitochondrial genome of C. papilio, which was subsequently assembled, annotated, and analyzed. Bayesian inference, maximum likelihood, and maximum parsimony methods were employed to construct the mitochondrial phylogenetic tree of 25 species of Chlorogomphidae based on 16S rRNA and cox1 genes. We observed that the mitochondrial genome of C. papilio is 15,251 bp in length and includes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region. All PCGs start with a typical ATN codon. While cox1, cox2, cox3, and nad5 end with an incomplete termination codon (T), the remaining PCGs terminate with TAG. The secondary structure of the 22 tRNAs showed that only the trnS1 gene lacked the dihydrouracil arm (DHU arm), whereas the rest formed a typical cloverleaf structure. Additionally, 32 G-U mismatches were observed in the secondary structure. Phylogenetic analyses indicated that C. papilio and C. magnificus are sister species. Divergence time analyses indicated that Chlorogomphidae originated around 111.04 Ma, with C. papilio diverging from the common ancestor shared with C. magnificus approximately 58.51 Ma. This divergence is likely linked to the Paleocene-Eocene Thermal Maximum (PETM) and the tectonic uplift of the Himalayas, which created warm, humid habitats and contributed to geographic isolation. This study contributes to a better understanding of the mitochondrial genome and phylogeny of C. papilio, providing valuable molecular markers for further genetic studies.

Bioprospecting amylase from Samiti Lake, situated in the eastern Himalayas

Enzymes, especially amylases, have been an economic boon to the industrial sector, their bioprospective and biotechnological use is an added advantage. Our primary focus of the study was to isolate the most potent amylase producer and to optimize its production parameters through One Factor At A Time (OFAT), Central Composite Rotatable Design Response Surface Methodology (CCRD RSM) and Artificial Neural Network (ANN). Based on the qualitative and quantitative analysis, SLAB1 was selected as the most potent amylase producer out of the potential isolates. Further SLAB1 was identified as Priestia flexa via 16SrRNA identification. Optimization of the production parameters showed the best carbon, nitrogen sources, temperature and pH to be fructose, peptone, 20 °C and pH 8.0 respectively. Further, the enzyme was purified using ammonium sulphate precipitation followed by dialysis. Later, DEAE Sepharose (Sigma) resin was used for ion exchange chromatography and the protein was eluted using NaCl gradients from 0.1 M - 0.6 M. Enzyme kinetics assessment of the purified amylase with the Lineweaver Burk plot showed values of maximum rate; Vmax (10.869 μmoL/min), and Michaelis-Menten constant Km to be around (14.91 mg/ml). To determine its potential application, analysis of this purified amylase in cleaning the tomato and chocolate stained cotton fabrics after comparing its compatibility with different detergents were executed. Further analysis of the washed stained fabrics via Scanning Electron Microscopy was carried out.

AMPCliff: Quantitative definition and benchmarking of activity cliffs in antimicrobial peptides

INTRODUCTION

Activity cliff (AC) is a phenomenon that a pair of similar molecules differ by a small structural alternation but exhibit a large difference in their biochemical activities. This phenomenon affects various tasks ranging from virtual screening to lead optimization in drug development. The AC of small molecules has been extensively investigated but limited knowledge is accumulated about the AC phenomenon in pharmaceutical peptides with canonical amino acids.

OBJECTIVES

This study introduces a quantitative definition and benchmarking framework AMPCliff for the AC phenomenon in antimicrobial peptides (AMPs) composed by canonical amino acids.

METHODS

This study establishes a benchmark dataset of paired AMPs in Staphylococcus aureus from the publicly available AMP dataset GRAMPA, and conducts a rigorous procedure to evaluate various AMP AC prediction models, including nine machine learning, four deep learning algorithms, four masked language models, and four generative language models.

RESULTS

A comprehensive analysis of the existing AMP dataset reveals a significant prevalence of AC within AMPs. AMPCliff quantifies the activities of AMPs by the metric minimum inhibitory concentration (MIC), and defines 0.9 as the minimum threshold for the normalized BLOSUM62 similarity score between a pair of aligned peptides with at least two-fold MIC changes. Our analysis reveals that these models are capable of detecting AMP AC events and the pre-trained protein language model ESM2 demonstrates superior performance across the evaluations. The predictive performance of AMP activity cliffs remains to be further improved, considering that ESM2 with 33 layers only achieves the Spearman correlation coefficient 0.4669 for the regression task of the -log(MIC) values on the benchmark dataset.

CONCLUSION

Our findings highlight limitations in current deep learning-based representation models. To more accurately capture the properties of antimicrobial peptides (AMPs), it is essential to integrate atomic-level dynamic information that reflects their underlying mechanisms of action.

Characterization of Streptomyces species with poly(3-hydroxybutyrate) degradation capabilities isolated from rice field soil

The shift towards sustainable alternatives to petroleum-based polymers has become essential for addressing environmental challenges. Among these alternatives, bio-plastics such as poly(3-hydroxybutyrate) (PHB) have gained considerable attention due to their biodegradability into water and carbon dioxide through microbial activity. PHB is one of the most widely commercialized bio-plastics. However, its excessive accumulation in the environment due to insufficient degradation remains a significant ecological concern. This study focused on isolating and characterizing PHB-degrading bacteria from soil samples collected from rice fields. Screening led to the identification of five PHB-degrading bacterial strains belonging to different genera. Among these, Streptomyces sp. AG7 and Streptomyces sp. RG41 were identified as the most effective PHB degraders. Their PHB-degrading abilities were evaluated in shake-flask cultures using PHB films as substrates. After 20 days of incubation at 37 °C, Streptomyces sp. AG7 and Streptomyces sp. RG41 achieved PHB degradation rates of approximately 74.7 % and 68.5 %, respectively. Additionally, both strains demonstrated the ability to produce indole-3-acetic acid (IAA), a key phytohormone that promotes plant growth, and exhibited phosphate-solubilizing activity, which enhances nutrient availability. Further analysis using scanning electron microscopy (SEM) revealed structural changes in the PHB films, while gel permeation chromatography (GPC) confirmed significant alterations in the polymer's molecular properties. These findings highlight the potential of utilizing soil-derived Streptomyces species for sustainable PHB waste management, in order to promote plant growth, improve soil fertility through phosphate solubilization, and contribute to agricultural sustainability.