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

The TRAPPC8/TRS85 subunit of the Arabidopsis TRAPPIII tethering complex regulates endoplasmic reticulum function and autophagy

Transport protein particle (TRAPP) tethering complexes are known for their function as Rab GTPase exchange factors. Two versions of the complex are considered functionally separate: TRAPPII, an activator of the Rab11 family (RabA in plants) GTPases that function in post-Golgi sorting, and TRAPPIII, activating Rab1 family (RabD in plants) members that regulate endoplasmic reticulum (ER)-to-Golgi trafficking and autophagy. In Arabidopsis (Arabidopsis thaliana), the TRAPPIII complex has been identified and its subunit composition established, but little is known about its functions. Here, we found that binary subunit interactions of the plant TRAPPIII complex are analogous to those of metazoan TRAPPIII, with the 2 large subunits TRAPPC8 and TRAPPC11 linking the TRAPP core and the small C12 to C13 dimer. To gain insight into the functions of TRAPPIII in plants, we characterized 2 A. thaliana trappc8 mutants. These mutants display abnormalities in plant morphology, particularly in flower and seed development. They also exhibit autophagic defects, a constitutive ER stress response, and elevated levels of the ER lipid dolichol (Dol), which is an indispensable cofactor in protein glycosylation. These results indicate that plant TRAPPC8 is involved in multiple cellular trafficking events and suggest a link between ER stress responses and Dol levels.

Fine mapping of stripe rust resistance gene YrAn1589 in common wheat using Wheat660K SNP array and BSR-Seq

KEY MESSAGE

A new stripe rust resistance gene YrAn1589 in Chinese wheat Annong1589 was mapped to a 160.9-166.6 kb interval on chromosome arm 3BL and co-segregated with a marker CAPS9 developed from candidate gene TraesCS3B03G1054600.  Stripe rust, caused by Puccinia. striiformis f. sp. tritici (Pst), is a devastating fungal disease that can significantly reduce wheat yield. The Chinese wheat cultivar Annong1589 demonstrates high resistance against the predominant Pst races in the Huang-Huai valley wheat region. The present study aimed to identify the stripe rust resistance gene in Annong1589. Genetic analysis indicated that the resistance in Annong1589 was conferred by a single dominant gene, provisionally designated YrAn1589. Using Wheat660K SNP array, bulked segregant RNA sequencing and new molecular markers developed, the resistance gene was mapped to a 160.9-166.6 kb region between CAPS8 and CAPS10 on chromosome 3BL based on IWGSC CS RefSeq v2.1 and eight other reference genome sequences, including eight high-confidence annotated genes. Transcriptome and qRT-PCR analyses revealed significantly upregulated expression of TraesCS3B03G1054600 in resistant plants following CYR32 inoculation, suggesting it is a potential candidate gene for YrAn1589. A functional marker CAPS9 developed from a A/G polymorphic SNP in the candidate co-segregated with YrAn1589 in the F2 population. Subcellular localization experiments showed that TraesCS3B03G1054600 protein was localized in the cytoplasm and nucleus, implying its role in immune response and resistance. Our findings establish YrAn1589 as a new stripe rust resistance gene, providing valuable gene resource and molecular markers for improvement of stripe rust resistance in wheat.

Pigment-dispersing factor neuropeptides act as multifunctional hormones and modulators in tardigrades

Pigment-dispersing factors (PDFs) are neuropeptides that play key roles in controlling the circadian rhythms in various insects, whereas their function remains elusive in other protostomes including tardigrades (water bears). Here we show that the three PDFs of the tardigrade Hypsibius exemplaris are co-localized in two pairs of inner lobe cells in the brain, whereas only one PDF occurs in four additional cerebral and two extracerebral cells. The axons of the inner lobe cells pass through the contralateral brain hemisphere, descend to the ventral nerve cord and terminate in two pairs of potential release sites in the posteriormost trunk ganglion. Using in vitro assays, we demonstrate that all three PDFs and their deorphanized receptor (PDFR) are functional. Widespread localization of PDFR suggests that tardigrade PDFs may act as multifunctional hormones and neuromodulators that control major functions including light detection, neural processing, locomotion, feeding, digestion, osmoregulation, growth, embryonic development and oogenesis/reproduction.

High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy

Nanopore sequencing is a third-generation technology known for its portability, real-time analysis and ability to generate long reads. It has great potential for use in clinical diagnostics, but thorough validation is required to address accuracy concerns and ensure reliable and reproducible results. In this study, we automated an open-source workflow (freely available at https://gitlab.com/FLI_Bioinfo/nanobacta) for the assembly of Oxford Nanopore sequencing data and used it to investigate the reproducibility of assembly results under consistent conditions. We used a benchmark dataset of five bacterial reference strains and generated eight technical sequencing replicates of the same DNA using the Ligation and Rapid Barcoding kits together with the Flongle and MinION flow cells. We assessed reproducibility by measuring discrepancies such as substitution and insertion/deletion errors, analysing plasmid recovery results and examining genetic markers and clustering information. We compared the results of genome assemblies with and without short-read polishing. Our results show an average reproducibility accuracy of 99.999955% for nanopore-only assemblies and 99.999996% when the short reads were used for polishing. The genomic analysis results were highly reproducible for the nanopore-only assemblies without short read in the following areas: identification of genetic markers for antimicrobial resistance and virulence, classical MLST, taxonomic classification, genome completeness and contamination analysis. Interestingly, the clustering information results from the core genome SNP and core genome MLST analyses were also highly reproducible for the nanopore-only assemblies, with pairwise differences of up to two allele differences in core genome MLST and two SNPs in core genome SNP across replicates. After polishing the assemblies with short reads, the pairwise differences for cgMLST were 0 and for cgSNP were 0-1 SNP across replicates. These results highlight the advances in sequencing accuracy of nanopore data without the use of short reads.

Overcoming cross-reactivity of antibodies against human lactate dehydrogenase

Lactate dehydrogenase subunit A (LD-A) plays an important role in cancer regulation and therapy. We attempted to develop an enzyme-linked immune-solvent assay (ELISA) for LD-A in human serum. However, commercial antibodies against LD-A exhibited cross-reactivity with an unknown protein. The unknown protein was purified and characterized by protein sequencing and Western blotting. In addition, we attempted to prepare a specific antibody for the ELISA using partially synthesized peptides of LD-A as immunogens. The epitope position in LD-A was carefully selected based on bioinformatics analysis. Peptide sequencer elucidated a ten amino acid sequence of the purified protein at the N-terminal. A BLAST search revealed that this sequence perfectly matched that at the N-terminus of the IgG heavy chain (H-chain). Furthermore, we demonstrated that twelve commercially available antibodies targeting LD-A or LD-B (subunit B) primarily cross-reacted with IgG or its H-chain, with only one specific antibody for each subunit. As the specific antibody against LD-A is no longer commercially accessible, we successfully produced two kinds of specific antibodies using partially synthesized LD-A peptides as immunogens. In conclusion, we have successfully produced specific antibodies against LD-A. Moreover, our findings underscore the utility of bioinformatics tools for determining the optimal positions of immunizing peptides.

Presence of polyketide synthases and nonribosomal peptide synthetase in culturable bacteria associated with Aplysina fulva and Aplysina caissara (Porifera)

Culture-dependent and -independent studies have provided access to symbiont genes and the functions they play for host sponges. Thus, this work investigates the diversity, presence of genes of pharmacological interest, biological activities and metabolome of the bacteria isolated from the sponges Aplysina caissara and Aplysina fulva collected on the southwestern Atlantic Coast. The genes for Polyketide Synthases types I and II and Nonribosomal Peptide Synthetases were screened in more than 200 bacterial strains obtained, from which around 40% were putatively novel. Twenty-two were positive for at least one of the genes screened. Among them, 12 exhibited antimicrobial activities and one inhibited the proliferation of cancer cells. The metabolic profiles of the 22 strains were analyzed by liquid chromatography with tandem mass spectrometry and molecular network. The Global Natural Products Social Molecular Networking MolNetEnhancer workflow provided a more comprehensive understanding of the metabolic profiles. The results revealed the existence of a wide range of metabolites, however more than half of the compounds could not be identified. It was further observed that the metabolic diversity among the strains varied primarily due to the cultivation medium used. Together the results obtained here revealed the pharmacological potential of the bacteria isolated from Aplysina species.

Differential Nasal Recolonization and Microbial Profiles in Chronic Rhinosinusitis With Nasal Polyps Patients After Endoscopic Sinus Surgery or Dupilumab Treatment: A Prospective Observational Study

INTRODUCTION

The role of microbial profiles in Chronic Rhinosinusitis with Nasal Polyps (CRSwNP) pathogenesis is increasingly recognised, with microbial imbalances perpetuating inflammation. We performed this study to associate the different nasal microbiological profile changes with the response to surgical or monoclonal treatment.

METHODS

This prospective observational study evaluated changes in the nasal microbial profiles of 44 patients (22 dupilumab, 22 surgery) over 6 months. Clinical assessments were performed at baseline and follow-ups, including Sino-Nasal Outcome Test-22 (SNOT-22) scores and Sniffin Sticks-Identification (SS-I) olfactory testing. Microbial profiling of nasal swabs was carried out by microbial culture and subsequent molecular identification by Polymerase chain reaction (PCR) and sequencing.

RESULTS

Baseline characteristics of 44 patients (22 dupilumab, 22 surgery) enrolled in this study were similar between groups. In the dupilumab group, Staphylococcus epidermidis prevalence rose from 37.03% to 59.25%, while Pseudomonas aeruginosa was eradicated. Moreover, dupilumab stabilised Staphylococcus aureus at 63.64%, while its prevalence increased in the surgery group (from 22.72% to 50%). When bacterial groups were associated with clinical scores, P. aeruginosa carriers had worse SNOT-22 (21.00 ± 1.41) and SS-I (5.50 ± 0.71) scores. Instead, S. epidermidis-colonised patients exhibited significantly lower mean SNOT-22 (15.39 ± 8.54) and greater SS-I scores (8.39 ± 3.77). The best outcomes were found in the subgroup of S. epidermidis carriers undergoing the dupilumab treatment.

CONCLUSION

The two treatments modulated the microbial profiles differently, and, most importantly, clinical responses might depend on the association between treatment and the dominant bacterial species colonising the nasal cavity. Further investigation into microbial-restorative strategies could enhance outcomes for better treatment of CRS.

Isolation of Toxoplasma gondii from the masseter muscles of equines destined for human consumption in a slaughterhouse in southern Brazil

The aim of this study was to isolate Toxoplasma gondii from equids destined for slaughter in a Brazilian slaughterhouse. A total of 354 equids were analyzed, with blood samples collected from all the animals and samples of masseter muscle and brain tissue collected from 319 animals. A serological test was conducted to detect equids with specific antibodies for T. gondii. Molecular detection of T. gondii by nested PCR was performed on the tissue samples collected. Tissue samples were tested by murine bioassay in an attempt to isolate either the parasite or the parasite DNA. Real-time PCR was performed on the brain samples from 11 mice which seroconverted after inoculation, to quantify the parasitic DNA. Genotyping was performed in masseter tissues samples from positive horses or from tissues of mice inoculated with masseter. The seroprevalence of T. gondii infection was 19.2%. Nested PCR showed that 5.3% of the equines and 28.8% of the mice from the bioassays were positive for T. gondii. Nine masseter muscle samples were positive (either on nested-PCR or in bioassay). Genotyping by PCR-RFLP was attempeted on all 12 isolates and was successful in seven, revealing six recombinant and one atypical genotype. The detection of T. gondii DNA in masseter muscle tissue of horses destined for consumption clearly indicates a risk to human health.

AnimalGWASAtlas: Annotation and prioritization of GWAS loci and quantitative trait loci for animal complex traits

Genome-wide association study (GWAS) and quantitative trait locus (QTL) mapping methods provide valuable insights and opportunities for identifying functional gene underlying phenotype formation. However, the majority of GWAS risk loci and QTLs located in noncoding regions poses significant challenges in pinpointing the protein-coding genes associated with specific traits. Moreover, growing evidence suggests not all GWAS risk loci and QTLs are functional, emphasizing the critical need for prioritizing causal sites-a task of paramount importance for biologists. The accumulation of publicly available multiomics data provides an unprecedented opportunity to annotate and prioritize GWAS risk loci and QTLs. Therefore, we developed a comprehensive multiomics database encompassing four major agricultural species-pig, sheep, cattle, and chicken. This database integrates publicly accessible datasets, including 140 GWAS studies (covering 471 traits), 2625 QTL datasets (spanning 1235 traits), 86 Hi-C datasets (from eight cells/tissue types), 95 epigenomic datasets (from four cells/tissue types), and 769 transcription factor motifs. The database aims to link GWAS-QTL loci located in the noncoding regions to the target genes they regulate and prioritize functional and causal regulatory elements. Ultimately, it provides a valuable resource and potential validation targets for elucidating the genes and molecular pathways underlying economically important traits in agricultural animals.

Integrons are anti-phage defence libraries in Vibrio parahaemolyticus

Bacterial genomes have regions known as defence islands that encode diverse systems to protect against phage infection. Although genetic elements that capture and store gene cassettes in Vibrio species, called integrons, are known to play an important role in bacterial adaptation, a role in phage defence had not been defined. Here we combine bioinformatic and molecular techniques to show that the chromosomal integron of Vibrio parahaemolyticus is a hotspot for anti-phage defence genes. Using bioinformatics, we discovered that previously characterized defences localize to integrons. Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence. Our work reveals that integrons are an important reservoir of defence systems in V. parahaemolyticus. As integrons are of ancient origin and are widely distributed among Proteobacteria, these results provide an approach for the discovery of anti-phage defence systems across a broad range of bacteria.

First identification of Brucella melitensis and Rickettsia monacensis in a red fox, Vulpes vulpes

Wild canids, in particular red foxes, serve as potential carriers of zoonotic pathogens. This study aimed to investigate the presence of somepathogenic bacteria relevant to veterinary public health concern. On November 15, 2023, we collected spleen and blood samples from a corpse of a red fox found randomly during a field trip in the El-Jouza district, Beja governorate, northern Tunisia. PCR amplification assays were conducted using specific primers to detect Brucella spp. and major vector-borne bacteria, including Rickettsia, Anaplasma, Borrelia, Bartonella, Coxiella, and hemotropic Mycoplasma. Species identification and genetic characterization were performed through BLAST analysis and phylogenetic studies following the sequencing of the obtained PCR products. DNA of both Brucella melitensis and Rickettsia monacensis was detected in the blood sample. Phylogenetic analysis revealed that the identified B. melitensis isolate was clustered with two strains isolated from humans in Mediterranean countries. The R. monacensis isolate was found to be genetically close to a human strain from a South Korea and several isolates infectingIxodes ticks primarily in Europe. This study revealed for the first time the potential infection of red foxes by B. melitensis and R. monacensis. Further research with larger sample sizes is needed to comprehensively understand the range of zoonotic bacteria in wildlife and to develop effective monitoring and control strategies.

Current state and future prospects of Horizontal Gene Transfer detection

Artificial intelligence (AI) has been shown to be beneficial in a wide range of bioinformatics applications. Horizontal Gene Transfer (HGT) is a driving force of evolutionary changes in prokaryotes. It is widely recognized that it contributes to the emergence of antimicrobial resistance (AMR), which poses a particularly serious threat to public health. Many computational approaches have been developed to study and detect HGT. However, the application of AI in this field has not been investigated. In this work, we conducted a review to provide information on the current trend of existing computational approaches for detecting HGT and to decipher the use of AI in this field. Here, we show a growing interest in HGT detection, characterized by a surge in the number of computational approaches, including AI-based approaches, in recent years. We organize existing computational approaches into a hierarchical structure of computational groups based on their computational methods and show how each computational group evolved. We make recommendations and discuss the challenges of HGT detection in general and the adoption of AI in particular. Moreover, we provide future directions for the field of HGT detection.

Exploring climate-related gut microbiome variation in bumble bees: An experimental and observational perspective

Rising temperatures negatively affect bumble bee fitness directly through physiological impacts and indirectly by disrupting mutualistic interactions between bees and other organisms, which are crucial in determining species-specific responses to climate change. Gut microbial symbionts, key regulators of host nutrition and health, may be the Achilles' heel of thermal responses in insects. They not only modulate biotic interactions with plants and pathogens but also exhibit varying thermal sensitivity themselves. Understanding how environmental changes disrupt microbiome communities is a crucial first step to determine potential consequences for host population responses. We analyzed gut bacterial communities of six bumble bee species inhabiting different climatic niches along an elevational gradient in the German Alps using 16S ribosomal DNA amplicon sequencing. We first investigated whether inter- and intraspecific differences in gut bacterial communities can be linked to species' elevational niches, which differ in temperature, flower resource composition, and likely pathogen pressure. A reciprocal translocation experiment between distinct climatic regions tested how the gut bacterial communities of Bombus terrestris and Bombus lucorum change short-term when exposed to new environments. Finally, we exposed these species to heat and cold wave scenarios within climate chambers to disentangle pure temperature-driven effects on the microbiome from other environmental effects. Interspecific variation in microbiome composition exceeded intraspecific variation. Species exhibit varying levels of gut microbiome stability, where stability is defined as the within-group variance: lower stability, indicated by greater within-group variance, is predominantly observed in species inhabiting higher elevations. Transplanted species showed subtle short-term gut microbiome adjustments, marked by an increase in Lactobacillaceae upon exposure to warmer regions; however, the gut microbiomes of these bumble bees did not change under laboratory temperature scenarios. We conclude that marked differences in the gut microbiomes of bumble bees could lead to species-specific responses to environmental change. For example, less stable microbiomes in bumble bees inhabiting higher elevations might indicate an increased sensitivity to pathogens. Short-term microbiome changes following translocation indicate that species with relatively stable microbiomes, such as B. lucorum and B. terrestris, can rapidly integrate new bacteria, which could increase their capacity to cope with new environments under climate change.

Long-read genome sequencing reveals the sequence characteristics of pear self-incompatibility locus

The S-RNase-based self-incompatibility locus (S-locus) in Petunia species contains 16-20 F-box genes, which collaboratively function in the recognition and subsequent degradation of non-self S-RNases, while distinguishing them from self S-RNase. However, the number of S-locus F-box genes (SFBBs) physically interacted with non-self S-RNases remains uncertain in Pyrus species. Utilizing Pacbio long-read sequencing, we successfully assembled the genome of pear cultivar 'Yali' (Pyrus bretschneideri), and identified 19 SFBBs from the Pyrus S17-locus spanning approximately 1.78 Mb. Additionally, we identified 17-21 SFBBs from other Pyrus and Malus S-loci spanning a range of 1.35 to 2.64 Mb. Based on the phylogenetic analysis, it was determined that Pyrus and Malus SFBBs could be classified into 22 groups, denoted as I to XXII. At amino acid level, SFBBs within a given group exhibited average identities ranged from 88.9% to 97.9%. Notably, all 19 SFBBs from the S17-locus co-segregated with S17-RNase, with 18 of them being specifically expressed in pollen. Consequently, these 18 pollen-specifically expressed SFBBs are considered potential candidates for the pollen-S determinant. Intriguingly, out of the 18 pollen-specifically expressed SFBBs, eight demonstrated interactions with at least one non-self S-RNase, while the remaining SFBBs failed to recognize any S-RNase. These findings provide compelling evidence supporting the existence of a collaborative non-self-recognition system governing self-incompatibility in pear species.

CROSS-SPECIES TRANSMISSION OF A GENOGROUP C FERLAVIRUS IN A ZOOLOGICAL COLLECTION IN THE UNITED STATES

Ferlaviruses have been associated with significant mortality events in squamates. Over a 5-month period in 2012, a mortality event at the Phoenix Zoo involved seven rattlesnakes (Crotalus spp.), a Sonoran gopher snake (Pituophis catenifer affinis), and a Gila monster (Heloderma suspectum). All individuals had been managed within the same group of enclosures at the zoo, and many of the affected individuals had previously been housed together. Clinical signs during the outbreak included sudden death, agonal behavior, anorexia, regurgitation, and loss of body condition. Histologic findings were similar in all animals, with lesions primarily in the respiratory tract and pancreas; these findings were consistent with viral infection, and in five of the seven cases for which samples were submitted, RT-PCR identified a genogroup C Ferlavirus. The findings in this outbreak support the possibility of cross-species viral transmission and clinical disease associated with genogroup C Ferlavirus infection and suggest persistence of paramyxoviral infection within captive reptile populations. These findings have widespread implications for the management of mixed reptile species habitats in zoological and private collections, and suggest a need to include all reptiles, not just snakes, in preshipment and quarantine investigation of potential ferlavirus infection.

Screening CYP450 genes from Gleditsia japonica Miq. and identifying CYP710A157 and CYP71D752 functions in the catalysis of echinocystic acid and betulin

The triterpenes and saponin compounds of Gleditsia japonica Miq. play a key role in the suppression of various human tumor cell lines. Cytochrome P450 monooxygenases (CYP450s) are critical for the triterpene skeleton diversification and functional modification. This study systematically analyzed 104 full-length GjCYP450 genes in G. japonica from northeast China, classifying them into nine clans using bioinformatics. Co-expression modules and response patterns of GjCYP450s with triterpene pathway genes were constructed. Four genes - CYP710A157, CYP714E97, CYP716A377, and CYP71D752 - were selected for functional studies based on their high expression in different tissues of G. japonica and their homology with triterpenoid-related CYP450s in Arabidopsis thaliana. Co-expression of the CYP710A157 gene with the BpY gene (encoding β-amyrin synthase), and CYP71D752 with the BpW gene (encoding lupeol synthase) in tobacco significantly enhanced the catalytic efficiency of echinocystic acid (EA) and betulin (BT) compared to the control, by achieving 10.22-fold and 3.73-fold increases, respectively. Overexpression of CYP710A157 and CYP71D752 in Saccharomyces cerevisiae JWy602 yielded EA and BT at 3.25 mg l-1 and 13.84 mg l-1, respectively, whereas no product accumulation was detected in the control. Additionally, CYP710A157 and CYP714E97 enhanced yeast alkaline tolerance (500 mmol l-1 Na2CO3), while CYP716A377 and CYP71D752 improved their salt tolerance (10% NaCl). We reported the catalytic activity of CYP450 genes responsible for EA and BT synthesis within the CYP710A and CYP71D subfamilies in G. japonica for the first time here. These findings provide valuable genetic resources for plants' triterpene biosynthesis, including ginsenosides, and betulinic acid, and insights into regulating the triterpene metabolic network in G. japonica.

A linkage map of Aegilops biuncialis reveals significant genomic rearrangements compared to bread wheat

Goatgrasses with U- and M-genomes are important sources of new alleles for wheat breeding to maintain yield and quality under extreme conditions. However, the introgression of beneficial traits from wild Aegilops species into wheat has been limited by poor knowledge of their genomes and scarcity of molecular tools. Here, we present the first linkage map of allotetraploid Aegilops biuncialis Vis., developed using 224 F2 individuals derived from a cross between MvGB382 and MvGB642 accessions. The map comprises 5663 DArTseq markers assigned to 15 linkage groups corresponding to 13 chromosomes. Chromosome 1Mb could not be constructed due to a lack of recombination caused by rearrangements in the MvGB382 accession. The genetic map spans 2518 cM with an average marker density of 2.79 cM. The skeleton map contains 920 segregating markers, divided between the Mb sub-genome (425 markers) and the Ub sub-genome (495 markers). Chromosomes of the Mb sub-genome, originating from Aegilops comosa Sm. in Sibth. et Sm., show well-preserved collinearity with Triticum aestivum L. chromosomes. In contrast, chromosomes of the Ub sub-genome, originating from Aegilops umbellulata Zhuk., exhibit a varying degree of collinearity, with 1Ub, 3Ub, and 5Ub retaining a substantial level of collinearity with Triticum aestivum, while 2Ub, 4Ub, 6Ub, and 7Ub show significant rearrangements. A quantitative trait locus affecting fertility was identified near the centromere on the long arm of chromosome 3Mb, explaining 23.5% of the variance. The genome structure of Aegilops biuncialis, highlighted by the genetic map, provides insights into the speciation within the species and will support alien gene transfer into wheat.

Genome and Tissue-Specific Transcriptome of the Tropical Milkweed (Asclepias curassavica)

Tropical milkweed (Asclepias curassavica) serves as a host plant for monarch butterflies (Danaus plexippus) and other insect herbivores that can tolerate the abundant cardiac glycosides that are characteristic of this species. Cardiac glycosides, along with additional specialized metabolites, also contribute to the ethnobotanical uses of A. curassavica. To facilitate further research on milkweed metabolism, we assembled the 197-Mbp genome of a fifth-generation inbred line of A. curassavica into 619 contigs, with an N50 of 10 Mbp. Scaffolding resulted in 98% of the assembly being anchored to 11 chromosomes, which are mostly colinear with the previously assembled common milkweed (A. syriaca) genome. Assembly completeness evaluations showed that 98% of the BUSCO gene set is present in the A. curassavica genome assembly. The transcriptomes of six tissue types (young leaves, mature leaves, stems, flowers, buds, and roots), with and without defense elicitation by methyl jasmonate treatment, showed both tissue-specific gene expression and induced expression of genes that may be involved in cardiac glycoside biosynthesis. Expression of a CYP87A gene, the predicted first gene in the cardiac glycoside biosynthesis pathway, was observed only in the stems and roots and was induced by methyl jasmonate. Together, this genome sequence and transcriptome analysis provide important resources for further investigation of the ecological and medicinal uses of A. curassavica.

Is Pseudomonas aeruginosa a possible aetiological agent of periodontitis in dogs?

Introduction

Periodontal diseases are the most frequently diagnosed problem in small animal veterinary medicine. Although their exact cause is not fully understood, bacteria play an important role in their development. Pseudomonas aeruginosa is a Gram-negative, rod-shaped, non-spore-forming bacterium. The living environment of this bacterium may be soil and water; however, it can also be found in humans and animals. Antibiotic treatment of periodontitis may be complicated by the carbapenem resistance of some P. aeruginosa strains, if these bacteria are found to be an aetiological agent. The aim of the study was to identify all bacterial strains isolated from dog with periodontitis.

Material and Methods

After a clinical examination of a Schnauzer dog in the Department and Clinic of Animal Surgery in the University of Life Sciences in Lublin Faculty of Veterinary Medicine, periodontitis was diagnosed. A swab was taken from the diseased tissue and submitted for microbiological tests. Microorganisms were initially identified by colony morphology, haemolytic pattern and Gram staining, and subsequently by sensitivity tests, VITEK 2 and matrix-assisted laser desorption/ionisation-time-of-flight.

Results

Pseudomonas aeruginosa was isolated and identified as a probable aetiological factor of periodontitis in dogs.

Conclusion

In our opinion, attention should be paid to Pseudomonas aeruginosa as a possible aetiological factor of periodontal diseases in dogs.

Exploring P450 superfamily diversity with P450Atlas - Online tool for automated subfamily assignment

Cytochrome P450 monooxygenases (CYPs/P450s) are heme-containing enzymes known to biology for more than six decades. Their stereo- and regio-specific enzymatic activities on various compounds led to exploring their potential in almost all areas of life. The P450 superfamily, encompassing nearly 10,000 known families, boasts a staggering diversity represented by numerous families, highlighting its immense scale within the realm of enzymes. In this contribution, we describe the P450Atlas website: the ultimate source of information about all named P450 families and subfamilies. The website's main functionality is the automated assignment of a query sequence to one of the known subfamilies. The new subfamily assignment algorithm relies on Hidden Markov Models (HMM) and has been extensively tested and compared to an approach based on the BLAST program. Extensive validation shows that the HMM approach is more sensitive than the latter one, offering almost perfect automated P450 sequence assignment to subfamilies. A user can also browse and search through the online list of families across the Tree of Life. We believe that the P450Atlas website (https://p450atlas.org) will become a comprehensive and unified source of information on cytochrome 450 nomenclature.

Rhodotorula tropicalis sp. nov., a novel red yeast of the order Sporidiobolales isolated from Thailand, Indonesia and Japan

Six yeast strains, representing a novel anamorphic species of the genus Rhodotorula, were investigated in this study. Among them, three strains, SU21, SU16 and SU14, were obtained from three different fruiting bodies of wild mushrooms in Thailand. One strain (ISM36-1) was isolated from soil in Japan, and two strains were isolated from soil (14Y315) and leaf litter (Y15Kr055) collected in Indonesia. Analysis of the sequences of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) regions showed that the six strains were identical or differed by only one nt substitution in both the D1/D2 domain of the LSU rRNA gene and the ITS regions. Rhodotorula paludigena CBS 6566T was the most closely related species but with 23-24 nt substitutions in the D1/D2 domain of the LSU rRNA gene and 38-39 nt substitutions in the ITS regions. Phylogenetic analysis based on the concatenated sequences of the ITS regions and D1/D2 domain showed that these strains represent a single species of the Rhodotorula clade that is distinct from other recognized species of the genus. Based on the phylogenetic analysis and phenotypic characteristics, these six strains were assigned to a novel species of the genus Rhodotorula, although sexual reproduction was not observed. The name, Rhodotorula tropicalis sp. nov., is proposed to accommodate the six strains. The holotype is TBRC 14874T and the ex-type culture is PYCC 8913 (=SU21). The MycoBank number of the novel species is MB 856795.

Birmingham-group IncP-1α plasmids revisited: RP4, RP1 and RK2 are identical and their remnants can be detected in environmental isolates

RP4, RP1, RK2 and R68 were isolated from the multidrug-resistant bacterial wound isolates in 1969 in the Birmingham Accident Hospital, Birmingham, England, and collectively called Birmingham-group IncP-1α plasmids. These plasmids have been widely used as models to study different aspects of plasmid biology, develop genetic delivery systems and design plasmid vectors. Early studies showed that these plasmids conferred the same antibiotic resistance profile, had a similar size and were undistinguishable from each other using DNA heteroduplex electron microscopy and restriction endonuclease analyses. These observations have led to the widely held assumption that they are identical, although there has been no conclusive supporting evidence. In this work, we sequenced the plasmids RP1 and RP4 from our laboratory strain collection and compared these new sequences with the plasmids RP4 and RK2 assembled from a publicly available sequencing database, showing that the RP1, RP4 and RK2 plasmids are 60 095 bp in length and identical at the nucleotide resolution. Noteworthily, the plasmid sequence is highly conserved despite having been distributed to different labs over 50 years and propagated in different bacterial hosts, strengthening the previous observation that the bacterial host adapts to the RP4/RP1/RK2 plasmid rather than the opposite. In the updated RP4/RP1/RK2 sequence, we found a fusion gene, called pecM-orf2, that was formed putatively by a genetic deletion event. By searching for pecM-orf2 in the National Center for Biotechnology Information database, we detected remnants of the RP4/RP1/RK2 plasmid that carry features of laboratory-engineered vectors in bacterial environmental isolates, either in their chromosome or as a plasmid. This suggests a leak of these plasmids from the laboratory into the environment, which may subsequently impact bacterial evolution and raises concerns about the biocontainment of engineered plasmids when being handled in laboratory settings.

Identification and purification of a novel bacteriophage T7 endonuclease from the Kogelberg Biosphere Reserve (KBR) biodiversity hotspot

The four-way (Holliday) DNA junction is a key intermediate in homologous recombination, a ubiquitous process that is important in DNA repair and generation of genetic diversity. The final stages of recombination require resolution of the junction into nicked-duplex species by the action of a junction-resolving enzyme. The enzymes involved are nucleases that are highly selective for the structure of branched DNA. Here we present the isolation, expression and purification of a novel T7 endonuclease from the Kogelberg Biosphere Reserve (KBR), which possesses junction resolving capabilities. An initial approach was employed where the process was scaled up to 3 L with IPTG concentration of 0.1 mM at 30 °C and purified via immobilised metal affinity chromatography (IMAC). Expression titres of 20 ± 0.003 µg.L-1 culture were achieved with the amount of KBR-T7 endonuclease required per reaction ranging from as low as 10 to 100 nanograms. The solubility of the enzyme was relatively poor; however, enzyme activity was not affected. A derivative for improved solubility and efficacy was then designed from this original wild-type version, MBP-KBR-T7 and was expressed under similar conditions at 20 °C yielding 1.63 ± 0.154 mg.L-1 of formulated enzyme. This novel high value enzyme derivative is a valuable asset within the molecular reagent space as a tool for confirming both in vivo and in vitro genome editing; therefore, a means to produce it recombinantly in a scalable and technoeconomicaly viable process is highly desirable.

mCNN-glucose: Identifying families of glucose transporters using a deep convolutional neural network based on multiple-scanning windows

Glucose transporters are essential carrier proteins that function on the phospholipid bilayer to facilitate glucose diffusion across cell membranes. The transporters play many physiological and pathological roles in addition to absorption and metabolism of fructose in food and the pathogenesis of gastrointestinal diseases. These carrier proteins play an important role in diseases of the nervous system, cardiovascular system, digestive system, and urinary system. These essential transporters have been extensively studied as potential therapeutic targets for cancers such as pancreatic, prostate, and hepatocellular carcinoma, which serve as diagnostic and prognostic indicators. The method uses position-specific scoring metrics (PSSM) with multiple-scanning windows-based convolutional neural networks to classify glucose transport proteins based on their functional significance and crucial role in therapy. Convolutional neural networks with multiple window scanning are employed to capture biologically meaningful, significant, and meaningful features from PSSM evolutionary profiles. Our proposed Method obtained Matthews correlation coefficients (MCC) of 0.99, Accuracy (AC) of 99.46, for Glucose facilitative transporters (GLUT), 0.99, 99.46, for Sodium Coupled glucose transporters (SGLT), and 0.92, and 97.3 for Sugars will eventually be exported transporters (SWEET) respectively. This study shows significantly higher performance than our previous study, which could be used to accurately classify novel glucose transporters.

Activation of prep expression by Tet2 promotes the proliferation of bipotential progenitor cells during liver regeneration

Biliary epithelial cell (BEC)-derived liver regeneration in zebrafish exhibits similarities to liver regeneration in chronic liver injury. However, the underlying mechanisms remain poorly understood. Here, we identified a serine peptidase called prolyl endopeptidase (Prep) as an indispensable factor during the BEC-derived liver regeneration process. prep was significantly upregulated and enriched in bipotential progenitor cells (BP-PCs). Through gain- and loss-of-function assays, prep was found to potently accelerate liver regeneration and drastically increase the proliferation of BP-PCs. Mechanistically, prep expression was directly regulated by ten-eleven translocation 2 (Tet2)-mediated DNA demethylation. More strikingly, Tet2 regulated prep expression by directly interacting and reducing the methylation of CpG sites in the prep promoter. Subsequently, Prep activated the PI3K-AKT-mTOR signaling pathway to regulate liver regeneration. Therefore, our study revealed the role and mechanism of Tet2-mediated DNA demethylation-associated upregulation of prep in the proliferation of BP-PCs during liver regeneration. These results identify promising targets for stimulating regeneration following chronic liver injury.

Phytotoxic and Antifungal Activity of (-)-Penienone Produced by Penicillium palitans (Ascomycota) Isolated from Deep Sea Sediments in the Southern Ocean, Maritime Antarctica

Metabolites isolated from Penicillium palitans, obtained from deep sea sediments in the maritime Antarctica, were investigated for phytotoxic and antifungal activities. The fungus was submitted to solid state fermentation, and its crude extract was produced. Chromatographic separations of the P. palitans methylene chloride crude extract led to the isolation of two analogous compounds: (-)-penienone (1) and (-)-palitantin (2). The phytotoxic activity of these compounds was assessed against seeds of Lactuca sativa and Agrostis stolonifera. Both compounds demonstrated activity exclusively in the monocotyledonous model, A. stolonifera. At a concentration of 1 mg mL-1, (-)-penienone caused 100 % inhibition of seed germination, while (-)-palitantin had only moderate activity on germination and growth of seedlings at this concentration after 7 days of treatment. Against Lemna paucicostata, at 57 μM, (-)-penienone inhibited growth by 50 % (IC50). (-)-Palitantin was much less active. When evaluated for their antifungal activity against Colletotrichum fragariae, only (-)-penienone had an IC50 value of 0.3 μM. The strain P. palitans was shown to be a promising source of phytotoxic and antifungal compounds, suggesting that extremophilic fungi, such as wild Penicillium strains from Antarctica, have the potential to yield novel prototype molecules for new pesticide development.

Performance of electro-assisted ecological floating bed in antibiotics and conventional pollutants degradation: Mechanisms and microbial response

Electro-assisted technology is promising for enhancing plant activity, optimizing functional microbial communities, and significantly strengthening pollutant removal efficiency. In this study, four reactors were designed as control group (CG), Hydrocotyle vulgaris L. ecological floating bed (PEFB), microbial fuel cell (MFC), and Hydrocotyle vulgaris L. ecological floating bed-microbial fuel cell (PEFB-MFC) to investigate the efficiency and mechanisms for the synchronous removal of conventional and antibiotic contaminants. Results showed that PEFB-MFC hold superior removal performance for sulfamethoxazole (61%), tetracycline (61%), CODCr (65%), NH4+-N (86%), TN (41%), and TP (51%). High-throughput sequencing indicated that Pseudomonadota and Actinomycetota were the predominant phyla in the different reactors. Metagenomic sequencing results showed that pollutant degradation-related metabolic functions, such as those involved in carbohydrate and amino acid metabolism in PEFB-MFC exhibited superior abundance compared to the other reactors. LC-MS analysis revealed sulfamethoxazole degradation occurred through active-site cleavage, and tetracycline underwent demethylation, aldehyde formation, dehydroxylation. This study offers a deeper insight into electro-enhanced PEFB on decontamination performance and functional microbial communities.

AtLEC2-Mediated Enhancement of Endoplasmic Reticulum-Targeted Foreign Protein Synthesis in Nicotiana benthamiana Leaves: Insights From Transcriptomic Analysis

Many proteins used in industrial and pharmaceutical applications are typically synthesized within the secretory pathway. While yeast and mammalian cells have been engineered to enhance the production of endomembrane-targeted proteins, similar strategies in plant cells remain underexplored. This study investigates the potential of arabidopsis leafy cotyledon 2 (AtLEC2), a key regulator of seed development, to enhance the production of proteins targeted to the endoplasmic reticulum (ER) in Nicotiana benthamiana leaves. Through transient expression experiments, we demonstrate that AtLEC2 selectively increases the production of ER-targeted GUS without affecting its cytosolic variant. Moreover, leaves agroinfiltrated with AtLEC2 show a significant increase in ER-GFP accumulation compared to controls lacking AtLEC2. Transcriptomic analysis reveals that AtLEC2 promotes ribosome and chloroplast biogenesis, along with the upregulation of genes involved in photosynthesis, translation, and membrane synthesis. Notably, seed-specific poly(A) binding proteins involved in RNA stability and translation initiation, as well as 3-hydroxy-3-methylglutaryl coenzyme A reductase-linked to ER hypertrophy-are highly upregulated. This study establishes a novel connection between AtLEC2 and the enhancement of ER-targeted foreign protein synthesis, paving the way for innovative strategies in plant cellular engineering.

Nitro-fatty acids-mediated nitroalkylation modulates fine-tuning catalase antioxidant function during salinity stress in plants

Nitro-fatty acids (NO2-FAs) are novel molecules resulting from the interaction of unsaturated fatty acids and nitric oxide (NO) or NO-related molecules. In plants, it has recently been described that NO2-FAs trigger a powerful antioxidant and defense response against stressful situations, the induction of the heat-shock response (HSR), and they exert their signaling function mainly through a reversible post-translational modification called nitroalkylation. Catalase (CAT) is a key antioxidant enzyme for the control of the hydrogen peroxide (H2O2) levels generated by environmental oxidative stress. The data presented in this study provide novel information on the role of NO2-FAs in modulating the antioxidant activity of catalase 2 (CAT2) during salinity stress in Arabidopsis thaliana. Initially, in vitro treatment with nitro-linolenic acid (NO2-Ln) down-regulated Arabidopsis CAT2 activity, as a consequence of the nitroalkylation of His 156 and His 248, evolutionarily conserved residues with key functional implications for the quaternary structure and hence CAT2 activity. Any effect of NO2-Ln on the heme group or S-nitrosylation of CAT2 was excluded. To further our knowledge of the regulatory mechanism of this antioxidant enzyme by nitroalkylation, the functional modulation of CAT by NO2-FAs was analyzed in 5-day-old Arabidopsis cell suspension cultures subjected to salinity stress. In this situation, the oxidative stress generated caused the nitroalkylation of these residues to disappear through the cleavage of NO2-Ln binding to CAT2, thus restoring CAT2 catalytic activity. Thus, during salinity stress, CAT2 enzymatic activity increased without changes in protein levels. These results highlight the amino acid targets that are susceptible to nitroalkylation and the modulatory effect of this post-translational modification on CAT2 enzymatic activity in vitro and in vivo. These findings underline the regulatory role of nitroalkylation in CAT2 functionality, which is strongly influenced by the redox state thus becoming a new key control mechanism of this antioxidant enzyme in abiotic stress cell response processes.

The evolution of the plastid genomes in the holoparasitic Balanophoraceae

The independent transition to a heterotrophic lifestyle in plants drove remarkably convergent evolutionary trajectories, characterized by morphological modifications and reductions in their plastomes. The characteristics of the minimum plastome required for survival, if they exist, remain a topic of debate. The holoparasitic family Balanophoraceae was initially presumed to have entirely lost their plastids, however, recent reports revealed the presence of reduced and aberrant plastids with odd genomes. Among the outstanding features of these genomes are the highest nucleotide composition bias across the tree of life and the only two genetic code changes ever recorded among plants. In this study, we assembled the plastomes from five genera, four of which had never been studied. Major common features include extremely high AT content, the lack of a typical quadripartite structure and extensive size reduction due to gene elimination and genome compaction. The family exhibits multiple gene and intron losses, and a broad range of scenarios regarding the evolution of the plastid trnE, a gene considered essential because of its dual function in tetrapyrrole biosynthesis and translation within the plastid. In addition, phylogenetic analyses suggest that the genus Scybalium is not monophyletic. An evolutionary model for the plastomes of the Balanophoraceae is proposed.

Sporophyte-directed gametogenesis in Arabidopsis

Plants alternate between diploid sporophyte and haploid gametophyte generations1. In mosses, which retain features of ancestral land plants, the gametophyte is dominant and has an independent existence. However, in flowering plants the gametophyte has undergone evolutionary reduction to just a few cells enclosed within the sporophyte. The gametophyte is thought to retain genetic control of its development even after reduction2. Here we show that male gametophyte development in Arabidopsis, long considered to be autonomous, is also under genetic control of the sporophyte via a repressive mechanism that includes large-scale regulation of protein turnover. We identify an Arabidopsis gene SHUKR as an inhibitor of male gametic gene expression. SHUKR is unrelated to proteins of known function and acts sporophytically in meiosis to control gametophyte development by negatively regulating expression of a large set of genes specific to postmeiotic gametogenesis. This control emerged late in evolution as SHUKR homologues are found only in eudicots. We show that SHUKR is rapidly evolving under positive selection, suggesting that variation in control of protein turnover during male gametogenesis has played an important role in evolution within eudicots.

QAFI: a novel method for quantitative estimation of missense variant impact using protein-specific predictors and ensemble learning

Next-generation sequencing (NGS) has revolutionized genetic diagnostics, yet its application in precision medicine remains incomplete, despite significant advances in computational tools for variant annotation. Many variants remain unannotated, and existing tools often fail to accurately predict the range of impacts that variants have on protein function. This limitation restricts their utility in relevant applications such as predicting disease severity and onset age. In response to these challenges, a new generation of computational models is emerging, aimed at producing quantitative predictions of genetic variant impacts. However, the field is still in its early stages, and several issues need to be addressed, including improved performance and better interpretability. This study introduces QAFI, a novel methodology that integrates protein-specific regression models within an ensemble learning framework, utilizing conservation-based and structure-related features derived from AlphaFold models. Our findings indicate that QAFI significantly enhances the accuracy of quantitative predictions across various proteins. The approach has been rigorously validated through its application in the CAGI6 contest, focusing on ARSA protein variants, and further tested on a comprehensive set of clinically labeled variants, demonstrating its generalizability and robust predictive power. The straightforward nature of our models may also contribute to better interpretability of the results.

A computational approach for MHC-restricted multi-epitope vaccine design targeting Oropouche virus structural proteins

In recent years, Brazil has recorded approximately 500,000 Oropouche virus (OROV) cases in the Amazon region, underscoring the growing global threat posed by emerging and reemerging viruses. Symptoms of OROV closely resemble those of Dengue virus and Zika virus, contributing to underreporting and underestimation of its true impact. In the absence of specific treatments, the development of vaccines becomes essential. This study aimed to identify immunogenic epitopes in three structural proteins of OROV and develop a multi-epitope vaccine candidate. RefSeq sequences of the nucleocapsid protein and the Gn and Gc glycoproteins were obtained from the National Center for Biotechnology Information Virus and submitted to epitope search in Immune Epitope Database. Antigenicity, allergenicity, stability, and toxicity analyses were conducted, and the approved epitopes were aligned to the global protein to remove transmembrane regions and N-glycosylation sites. Thirteen epitopes were selected and used to construct a multi-epitope vaccine candidate, with β-defensin and PADRE adjuvants. The protein demonstrated optimal antigenicity, low allergenicity, and satisfactory stability and solubility. Predictions of humoral and cellular immune responses were performed, indicating satisfactory results for three doses of the vaccine candidate. 3D modeling of the protein was performed, evaluating the molecular docking of the multi-epitope protein with TLR-2, TLR-3, TLR-6, and TLR-8 receptors. Our findings present a promising vaccine candidate against OROV, potentially protecting immunocompromised individuals and high-risk populations, and establishing a foundation for both in vitro and in vivo testing. The identified epitopes could also aid in immunodiagnostic test development, advancing surveillance and control strategies.

LGS-PPIS: A Local-Global Structural Information Aggregation Framework for Predicting Protein-Protein Interaction Sites

Exploring protein-protein interaction sites (PPIS) is of significance to elucidating the intrinsic mechanisms of diverse biological processes. On this basis, recent studies have applied deep learning-based technologies to overcome the high cost of wet experiments for PPIS determination. However, the existing methods still suffer from two limitations that remain to be solved. Firstly, the process of feature aggregation in most methods only took into account node features, but ignored the complex edge features of the target residue to its neighbor residues, resulting in insufficient local feature extraction. Secondly, such feature aggregation was limited to aggregating spatially adjacent residues, and could not capture the "remote" residues that played a critical role in determining PPIS, which can be summed up as the lack of global feature at the residue level. To break the above limitations, a local-global structural information aggregation framework, LGS-PPIS, was proposed in this study, including two modules of edge-aware graph convolutional network (EA-GCN) and self-attention integrated with initial residual and identity mapping (SA-RIM), which achieved the aggregation of local and global information for PPIS prediction. Evaluation results of LGS-PPIS showed that the proposed method outperformed state-of-the-art deep learning methods on three widely used PPIS prediction benchmarks. Besides, the results of ablation experiments demonstrated that the local features from spatially adjacent residues and global features from "remote" residues separately captured by EA-GCN and SA-RIM could benefit the model performance. Among them, the former was shown to have a more significant role in the PPIS prediction.

Impact of Alignments on the Accuracy of Protein Subcellular Localization Predictions

Alignments in bioinformatics refer to the arrangement of sequences to identify regions of similarity that can indicate functional, structural, or evolutionary relationships. They are crucial for bioinformaticians as they enable accurate predictions and analyses in various applications, including protein subcellular localization. The predictive model used in this article is based on a deep - convolutional architecture. We tested configurations of Deep N-to-1 convolutional neural networks of various depths and widths during experimentation for the evaluation of better-performing values across a diverse set of eight classes. For without alignment assessment, sequences are encoded using one-hot encoding, converting each character into a numerical representation, which is straightforward for non-numerical data and useful for machine learning models. For with alignments assessment, multiple sequence alignments (MSAs) are created using PSI-BLAST, capturing evolutionary information by calculating frequencies of residues and gaps. The average difference in peak performance between models with alignments and without alignments is approximately 15.82%. The average difference in the highest accuracy achieved with alignments compared with without alignments is approximately 15.16%. Thus, extensive experimentation indicates that higher alignment accuracy implies a more reliable model and improved prediction accuracy, which can be trusted to deliver consistent performance across different layers and classes of subcellular localization predictions. This research provides valuable insights into prediction accuracies with and without alignments, offering bioinformaticians an effective tool for better understanding while potentially reducing the need for extensive experimental validations. The source code and datasets are available at http://distilldeep.ucd.ie/SCL8/.

Atomically accurate de novo design of antibodies with RFdiffusion

Despite the central role that antibodies play in modern medicine, there is currently no method to design novel antibodies that bind a specific epitope entirely in silico. Instead, antibody discovery currently relies on animal immunization or random library screening approaches. Here, we demonstrate that combining computational protein design using a fine-tuned RFdiffusion network alongside yeast display screening enables the generation of antibody variable heavy chains (VHHs) and single chain variable fragments (scFvs) that bind user-specified epitopes with atomic-level precision. To verify this, we experimentally characterized VHH binders to four disease-relevant epitopes using multiple orthogonal biophysical methods, including cryo-EM, which confirmed the proper Ig fold and binding pose of designed VHHs targeting influenza hemagglutinin and Clostridium difficile toxin B (TcdB). For the influenza-targeting VHH, high-resolution structural data further confirmed the accuracy of CDR loop conformations. While initial computational designs exhibit modest affinity, affinity maturation using OrthoRep enables production of single-digit nanomolar binders that maintain the intended epitope selectivity. We further demonstrate the de novo design of single-chain variable fragments (scFvs), creating binders to TcdB and a Phox2b peptide-MHC complex by combining designed heavy and light chain CDRs. Cryo-EM structural data confirmed the proper Ig fold and binding pose for two distinct TcdB scFvs, with high-resolution data for one design additionally verifying the atomically accurate conformations of all six CDR loops. Our approach establishes a framework for the rational computational design, screening, isolation, and characterization of fully de novo antibodies with atomic-level precision in both structure and epitope targeting.

RNA anchoring of Upf1 facilitates recruitment of Dcp2 in the NMD decapping complex

Upf1 RNA helicase is a pivotal factor in the conserved nonsense-mediated mRNA decay (NMD) process. Upf1 is responsible for coordinating the recognition of premature termination codons (PTCs) in a translation-dependent manner and subsequently triggering mRNA degradation. Multiple factors assist Upf1 during these two consecutive steps. In Saccharomyces cerevisiae, Upf2 and Upf3 associated with Upf1 (Upf1-2/3) contribute to PTC recognition but are absent from the Upf1-decapping complex that includes Nmd4, Ebs1, Dcp1, and Dcp2. Despite their importance for NMD, the organization and dynamics of these Upf1-containing complexes remain unclear. Using recombinant proteins, here we show how distinct domains of Upf1 make direct contacts with Dcp1/Dcp2, Nmd4, and Ebs1. These proteins also bind to each other, forming an extended network of interactions within the Upf1-decapping complex. Dcp2 and Upf2 compete for the same binding site on the N-terminal CH domain of Upf1, which explains the presence of two mutually exclusive Upf1-containing complexes in cells. Our data demonstrate that Nmd4-assisted recruitment of Upf1 promotes anchoring of the decapping enzyme to NMD targets.

Pseudomonads coordinate innate defense against viruses and bacteria with a single regulatory system

Bacterial cells live under the constant existential threats imposed by other bacteria and viruses. Their mechanisms for contending with these threats are well documented; however, the regulation of these diverse defense elements remains poorly understood. Here we show that bacteria can mount a genome-wide, coordinated, and highly effective immune response against bacterial and viral threats using a single regulatory pathway. Bioinformatic analyses revealed that Pseudomonas species broadly possess a specialized form of the Gac/Rsm regulatory pathway (GRP), which our prior work in Pseudomonas aeruginosa implicated in activating interbacterial antagonism defense mechanisms in response to neighbor cell death. Proteomic studies comparing GRP-activated and -inactivated strains derived from diverse Pseudomonas species showed that the pathway regulates a large and variable suite of factors implicated in defense against both bacterial and phage threats. Focusing on P. protegens, we identify profound phenotypic consequences of these factors against multiple forms of bacterial antagonism and several phage. Together, our results reveal that bacteria, like more complex organisms, couple danger sensing to the activation of an immune system with antibacterial and antiviral arms.

Engineering human/simian rotavirus VP7 reassortants in the absence of UTR sequence information

Recently developed plasmid-based reverse genetics systems for rotavirus A (RVA) enable rapid engineering of reassortants carrying human RVA antigens. However, complete genome segment sequences are required for successful generation of such reassortants, and sequencing of the untranslated regions (UTRs) of field strains is often not accomplished. To address this problem, we established a system that permits the generation of reassortants using only the open reading frame (ORF) nucleotide sequence information. Plasmids containing the VP7-ORF nucleotide sequence of six human RVA field strains (genotypes G2, G5, G8, G9, G12 and G29) derived from GenBank and flanked by the UTR sequences of simian RVA strain SA11 were constructed. Using these plasmids, four VP7 (G2, G5, G9 and G12) reassortants in an SA11 backbone were successfully generated. In contrast, the G8 and G29 reassortants were not viable. BLASTp search of the G8 and G29 sequences revealed an unusual amino acid substitution in each sequence, which was not present in related field strains. Site-directed reversion of the corresponding C656T mutation in G8 led to effective rescue of reassortant virus. However, reverting the G84C mutation in G29 did not result in replicating virus. The results suggest that most human RVA VP7 UTRs can be substituted with simian RVA UTRs. However, generation of reassortants might be impeded by potential sequencing errors or intrinsic reassortment limitations. The established system could help to broaden the antigenic repertoire for rapid engineering of potential novel RVA vaccine strains. KEY POINTS: • Generation of diverse rotavirus vaccine strains is impeded by missing UTR sequences. • UTRs from SA11 can be used instead of missing UTR sequences from field strains. • Human RVA reassortants of genotypes G2, G5, G8, G9, G12 were successfully rescued.

First report of Sarcocystis halieti in Asia: the genetic confirmation in muscles of the Eurasian sparrowhawk (Accipiter nisus) from Iran

Previous studies showed that the Eurasian sparrowhawk Accipiter nisus (Linnaeus, 1758) acts as the definitive host of the Sarcocystis halieti (Apicomplexa: Sarcocystidae) Gjerde, Vikøren et Hamnes, 2017. Herein, we report macrocysts of S. halieti in the pectoral muscle of a Sparrowhawk in the west of Iran. Between September 2019 and December 2023, a total of 55 wild birds belonging to 8 orders, 9 families, 18 genera, and 21 species were examined in Hamedan province, western Iran. In one Eurasian sparrowhawk, macroscopic cysts resembling rice grains were observed in the breast muscle of the bird. None of the other examined birds were infested with macrosarcocysts. DNA extracted from sarcocysts was molecularly characterized at four nuclear and mitochondrial DNA markers (the 18 S rRNA, 28 S rRNA, cox1 genes, and the ITS1 region). Sequence analysis confirmed the identity of the macrosarcocysts as Sarcocystis halieti. This is the first report of S. halieti in Asia. Sparrowhawk proved to act as both the definitive and intermediate host of Sarcocystis halieti. The phenomenon of the same species of Sarcocystis serving as both hosts is extremely rare among birds and needs to be studied further.

Transcriptomic analysis of Virescentia guangxiensis (Rhodophyta: Batrachospermales) revealed differential expression of genes in gametophyte and chantransia life phases

BACKGROUND

The genus Virescentia is a significant member of the Batrachospermaceae, exhibiting distinctive life history characteristics defined by alternating generations. This group of taxa has specific environmental requirements for growth. This paper investigates Virescentia, which primarily thrives in freshwater environments, such as streams and springs, characterized by low light, low temperatures, and high dissolved oxygen levels. Currently, no laboratory simulations of their growth conditions have been reported in culture studies. Additionally, previous studies indicate that comparisons of photosynthetic strength across different life-history stages of the same species have not been conducted, mainly due to the challenges of simultaneously collecting algal strains at both life-history stages.

RESULTS

During the gametophyte stage, the chloroplast and mitochondrial genomes were measured at 184,899 bp and 26,867 bp, respectively. In the chantransia stage, the lengths of these genomes were 184,887 bp and 27,014 bp, respectively. A comparison of organellar genome covariation and phylogenetic reconstruction revealed that the chloroplast and mitochondrial genomes across different life history stages were highly conserved, with genetic distances of 0 and nucleotide variants of only 9-15 bp. The mitochondrial genome of gametophyte SXU-YN24005 was found to lack two tRNA-Leu (tag) genes compared to that of the chantransia strain. Additionally, a comparative analysis of KEGG pathway transcriptome data from the two life history stages showed that 33 genes related to the ribosomal pathway and 53 genes associated with the photosynthesis pathway exhibited a significant decline in expression during the gametophyte stage compared to the chantransia stage.

CONCLUSION

In this study, two samples of the same species at different life-history stages were collected from the same location for the first time. The analysis revealed a high degree of conservation between their organelle genomes. Additionally, transcriptome sequencing results indicated substantial differences in gene expression patterns between the two life-history stages. This research will provide reliable data to support the future histological database of freshwater red algae and will establish a theoretical basis for conserving rare and endangered species.

Structural Determination and Functional Residues Analysis of a CBM99 Family Carbohydrate-Binding Module Targeting Porphyran

Porphyran is a bioactive polysaccharide extensively distributed in algae of the genus Porphyra. Carbohydrate-binding modules (CBMs) are independent domains often found in carbohydrate-active enzymes that function to bind carbohydrates and have various applications. Only one porphyran-binding CBM has been hitherto structurally characterized. The founding member (FvCBM99) of the CBM99 family was previously shown to exhibit a specific binding capacity to the primary constituent units of porphyran. In this study, the structure of FvCBM99 was determined at 1.75 Å resolution by X-ray crystallography. The protein adopts an overall β-sandwich fold with two antiparallel β-sheets comprising 7 β-strands. Site-directed mutagenesis analysis confirmed that residues W44, W49, K83, R87, and W93 are indispensable for the interaction of FvCBM99 with porphyran. The work delivers the first structural insights into the CBM99 family, which can guide the practical applications of FvCBM99 and promote the future discovery and characterization of porphyran-binding proteins.

First molecular evidence of Candidatus Anaplasma camelii in two dromedary camels from Qatar

Anaplasma species are intracellular pathogens that impact human and animal health. Despite Qatar having the highest density of dromedary camel (Camelus dromedarius) population, there have been no previous reports of anaplasmosis in dromedary camels in the country. Here, two cases of 5-year-old female dromedary camels presented symptoms like fever, reduced appetite, edema, and respiratory distress. These camels had a history of unsuccessful treatment for trypanosomiasis, on that basis diagnosis of possible anaplasmosis was made. DNA was extracted from the whole blood and then subjected to PCR testing and sequencing targeting 16S rRNA and groEL genes which confirmed both cases to be positive for Anaplasma. Phylogenetic analysis using 16S rRNA exhibited a 100% similarity with Candidatus Anaplasma camelii, while groEL gene showed a 100% match with A. platys-like. Phylogenetic analysis indicated that Candidatus Anaplasma camelii and A. platys-like sequences were grouped in the same cluster either in 16S RNA or groEL and were closely related to A. platys. The Infected cases highlight the need for a large-scale molecular diagnostic effort to monitor the clinical health of animals with a particular focus on camels in Qatar. Additionally, this report points to the role of dromedary camels in supporting the enzootic cycle of Anaplasma transmission within the region. This report marks the first instance of camel anaplasmosis in Qatar. Surveillance of Anaplasma among susceptible hosts (animals and human) in Qatar is required for assessing the zoonotic potential.

PON-P3: Accurate Prediction of Pathogenicity of Amino Acid Substitutions

Different types of information are combined during variation interpretation. Computational predictors, most often pathogenicity predictors, provide one type of information for this purpose. These tools are based on various kinds of algorithms. Although the American College of Genetics and the Association for Molecular Pathology guidelines classify variants into five categories, practically all pathogenicity predictors provide binary pathogenic/benign predictions. We developed a novel artificial intelligence-based tool, PON-P3, on the basis of a carefully selected training dataset, meticulous feature selection, and optimization. We started with 1526 features describing variations, their sequence and structural context, and parameters for the affected genes and proteins. The final random boosting method was tested and compared with a total of 23 predictors. PON-P3 performed better than recently introduced predictors, which utilize large language models or structural predictions. PON-P3 was better than methods that use evolutionary data alone or in combination with different gene and protein properties. PON-P3 classifies cases into three categories as benign, pathogenic, and variants of uncertain significance (VUSs). When binary test data were used, some metapredictors performed slightly better than PON-P3; however, in real-life situations, with patient data, those methods overpredict both pathogenic and benign cases. We predicted with PON-P3 all possible amino acid substitutions in all human proteins encoded from MANE transcripts. The method was also used to predict all unambiguous VUSs (i.e., without conflicts) in ClinVar. A total of 12.9% were predicted to be pathogenic, and 49.9% were benign.

Molecular epidemiology and characterization of antibiotic resistance of Pasteurella multocida isolated from livestock population of Punjab, Pakistan

Haemorrhagic septicaemia (HS) is an acute and life-threatening infection of livestock population caused by Pasteurella multocida (P. multocida), responsible for huge mortality, morbidity and production losses. The increase in antibiotic resistance is a growing concern, posing a significant threat to animals and public health. There is limited data on P. multocida disease burden, serotypes, antibiotic susceptibility, and resistance gene profiles in Pakistan. In the current study, 1017 nasal swabs from haemorrhagic septicaemic cattle and buffaloes were collected to isolate P. multocida through microbiological and molecular methods. Susceptibility against commonly used antibiotics was performed and antibiotic resistance genes were evaluated. A prevalence rate of 7.57% was found, where buffaloes were more prone to infection (8.3%) as compared to cows (6.7%). Molecular and sequence analysis confirmed P. multocida isolates in 94.8% (73/77) of samples. Capsular typing revealed all isolates belong to serotype B. Antibiogram analysis showed that enrofloxacin 85.7% (66/77) and ceftiofur 56/77 (72.7%) were the most effective antibiotics. The highest resistance was observed against trimethoprim/sulfamethoxazole 54/77 (70.1%), followed by erythromycin 52/77 (67.5%). Most of the isolates (31.5% (23/73)) carried β-lactamase resistance genes (bla TEM n = 10, bla ROB-1 n = 6, bla OXA-2 n = 5, bla NDM n = 2) followed by trimethoprim/sulfamethoxazole (sul2) resistance genes (26% (19/73)). The current study indicates that HS is consistently circulating among the animal population in Punjab, Pakistan. The current scenario of higher resistance in P. multocida needs continuous surveillance of the infection and mass awareness programs about the non-prescribed and excessive use of antibiotics in the animal sector.

Breastfeeding patterns and total volume of human milk consumed influence the development of the infant oral microbiome

Background

The oral microbiome of breastfed infants is distinct from that of formula-fed infants. However, breastfeeding characteristics, such as time spent breastfeeding (min/24 h), breastfeeding frequency (number of breastfeeds per day), and human milk intake (ml/day) vary significantly between breastfeeding dyads.

Objectives

Given that human milk and breastfeeding exposures likely influence early colonisation of the infant oral microbiome, this study aimed to elucidate the impact of breastfeeding characteristics on the development of the infant oral microbiome.

Materials and methods

Oral swabs (n = 55) were collected from infants at three months of age, alongside breastfeeding data collected over a 24-hour period. Bacterial DNA profiles were analysed using full-length 16S rRNA gene sequencing.

Results

Variations in breastfeeding characteristics contributed to differences in microbial community structure. Total breastfeeding duration (min/24 h) was positively associated with Bifidobacterium longum and Lactobacillus gasseri, while breastfeeding frequency was negatively associated with Veillonella sp. Additionally, human milk intake (ml/24 h) was negatively associated with Streptococcus parasanguinis.

Conclusion

These findings underscore the significant influence of early life feeding practices on oral microbial communities and emphasise the importance role of breastfeeding in shaping the oral microbiome during early life.

Full-Length Transcriptome Sequencing and Comparative Transcriptomics Reveal the Molecular Mechanisms Underlying Gonadal Development in Sleepy Cod (Oxyeleotris lineolata)

Sleepy cod (Oxyeleotris lineolata) is native to Australia and is now an economically valuable fish cultured in China and Southern Asian countries. Its growth rate exhibits as sexually dimorphic, with males generally growing more rapidly and attaining a larger body size compared to females. Thus, the effective development of sex control breeding can significantly contribute to increased yields and output value. Nevertheless, due to the lack of genomic and transcriptomic data, the molecular mechanisms underlying sex determination and gonadal differentiation in sleepy cod remain poorly understood. In this study, long-read PacBio isoform sequencing (Iso-Seq) was performed to obtain a full-length transcriptome from a pooled sample of eight tissues (kidney, brain, liver, muscle, heart, spleen, ovary and testis). A total of 30.41 G subread bases were generated and 49,113 non-redundant full-length transcripts with an average length of 2948 bp were produced. Using the full-length transcriptome as a reference, short-read Illumina sequencing was performed to investigate the differences in gene expression at the transcriptome level between ovaries and testes from 12-month-old individuals. A total of 19,102 differentially expressed transcripts (DETs) were identified, of which 8510 (44.55%) were up-regulated in the ovary and 10,592 (55.45%) were up-regulated in the testis. The DETs were mainly clustered into 241 KEGG pathways, in which oocyte meiosis and arachidonic acid metabolism were the most relevant pathways involved in gonadal differentiation. To verify the validity of the transcriptomic data, 20 DETs were selected to investigate the gonad expression profiles based on qPCR. The expression levels of all 20 screened genes were consistent with the transcriptome sequencing results. The present study provides new genetic resources-including full-length transcriptome sequences and annotation information-as a coding genomic-level reference for sleepy cod-yielding valuable insights into the genetic mechanisms of sex determination and gonadal differentiation in this economically important species.

Deep Learning for Antimicrobial Peptides: Computational Models and Databases

Antimicrobial peptides are a promising strategy to combat antimicrobial resistance. However, the experimental discovery of antimicrobial peptides is both time-consuming and laborious. In recent years, the development of computational technologies (especially deep learning) has provided new opportunities for antimicrobial peptide prediction. Various computational models have been proposed to predict antimicrobial peptide. In this review, we focus on deep learning models for antimicrobial peptide prediction. We first collected and summarized available data resources for antimicrobial peptides. Subsequently, we summarized existing deep learning models for antimicrobial peptides and discussed their limitations and challenges. This study aims to help computational biologists design better deep learning models for antimicrobial peptide prediction.

Activation of CAMK2 by pseudokinase PEAK1 represents a targetable pathway in triple negative breast cancer

The PEAK family of pseudokinases, comprising PEAK1-3, play oncogenic roles in several poor prognosis human cancers, including triple negative breast cancer (TNBC). However, therapeutic targeting of pseudokinases is challenging due to their lack of catalytic activity. To address this, we screen for PEAK1 effectors and identify calcium/calmodulin-dependent protein kinase 2 (CAMK2)D and CAMK2G. PEAK1 promotes CAMK2 activation in TNBC cells via PLCγ1/Ca2+ signalling and direct binding to CAMK2. In turn, CAMK2 phosphorylates PEAK1 to enhance association with PEAK2, which is critical for PEAK1 oncogenic signalling. To achieve pharmacologic targeting of PEAK1/CAMK2, we repurpose RA306, a second generation CAMK2 inhibitor. RA306 inhibits PEAK1-enhanced migration and invasion of TNBC cells in vitro and significantly attenuates TNBC xenograft growth and metastasis in a manner mirrored by PEAK1 ablation. Overall, these studies establish PEAK1 as a critical cell signalling nexus that integrates Ca2+ and tyrosine kinase signals and identify CAMK2 as a therapeutically 'actionable' target downstream of PEAK1.

Radical SAM Enzyme WprB Catalyzes Uniform Cross-Link Topology between Trp-C5 and Arg-Cγ on the Precursor Peptide

Cross-link containing products from ribosomally synthesized and post-translationally modified peptides (RiPPs) are generated by radical SAM enzymes (rSAM). Here, we bioinformatically expanded rSAM enzymes based on the known families StrB, NxxcB, WgkB, RrrB, TqqB and GggB. Through in vivo functional studies in E. coli, the newly identified enzyme WprB from Xenorhabdus sp. psl was found to catalyze formation of a cross-link between Trp-C5 and Arg-Cγ at three WPR motifs on the precursor peptide WprA. This represents the first report of this type of cross-link by rSAM enzymes.