MEGA11: Molecular Evolutionary Genetics Analysis Version 11

ClaPEPCK4: target gene for breeding innovative watermelon germplasm with low malic acid and high sweetness

Malic acid markedly affects watermelon flavor. Reducing the malic acid content can significantly increase the sweetness of watermelon. An effective solution strategy is to reduce watermelon malic acid content through molecular breeding technology. In this study, we measured the TSS and pH of six watermelon varieties at four growth nodes. The TSS content was very low at 10 DAP and accumulated rapidly at 18, 26, and 34 DAP. Three phosphoenolpyruvate carboxykinase (PEPCK) genes of watermelon were identified and analyzed. The ClaPEPCK4 expression was inversely proportional to malate content variations in fruits. In transgenic watermelon plants, overexpressing the ClaPEPCK4 gene, malic acid content markedly decreased. In the knockout transgenic watermelon plants, two SNP mutations and one base deletion occurred in the ClaPEPCK4 gene, with the malic acid content in the leaves increasing considerably and the PEPCK enzyme activity reduced to half of the wild-type. It is interesting that the ClaPEPCK4 gene triggered the closure of leaf stomata under dark conditions in the knockout transgenic plants, which indicated its involvement in stomatal movement. In conclusion, this study provides a gene target ClaPEPCK4 for creating innovative new high-sweetness watermelon varieties.

West Nile Virus in a changing climate: epidemiology, pathology, advances in diagnosis and treatment, vaccine designing and control strategies, emerging public health challenges - a comprehensive review

ABSTRACTWest Nile Virus (WNV), first identified in Uganda in 1937, remains a significant global health threat, adapting across diverse ecosystems and expanding geographically, particularly into temperate regions of Europe and North America. This review provides a comprehensive exploration of the latest insights and challenges in WNV management, focusing on epidemiological trends, molecular advancements, and public health implications. Recent data highlight WNV's expansion, driven by climate changes such as milder winters and longer warm seasons that increase mosquito activity and enable the virus to overwinter within mosquito populations. This facilitates year-round transmission and challenges current control strategies. Molecularly, advancements in genomic and proteomic technologies have deepened our understanding of WNV's replication and pathogenesis, identifying new therapeutic targets and improving diagnostic methods. However, the absence of an approved human vaccine leaves management dependent on supportive care, particularly for severe neurological cases. Effective vector control remains crucial, with innovative strategies including genetically modified mosquitoes and novel insecticides being pivotal. Furthermore, environmental factors like climate change and urbanization are altering vector behaviors and WNV transmission dynamics, necessitating adaptive public health strategies to manage these evolving threats. The review underscores the need for ongoing research, vaccine and therapeutic development, and enhanced public health infrastructures to better respond to WNV challenges. It stresses the critical role of integrating scientific research, public health policy, and community engagement to effectively address the persistent threat of WNV.

First isolation of the Sindbis virus in mosquitoes from southwestern Spain reveals a new recent introduction from Africa

Sindbis virus (SINV), is an Alphavirus of the family Togaviridae. This zoonotic arbovirus is transmitted by mosquitoes, primarily from the Culex genus, with bird species acting as amplifying vertebrate hosts. Occasionally it can also affect humans that are accidental hosts. SINV genotype I (SINV-I) has been isolated in mosquitoes and birds in South Africa and Northern Europe, producing fever outbreaks. In the last decades, there were several detections of SINV in Europe. In 2022, during the West Nile virus (WNV) mosquito surveillance program in Andalucía (Spain) implemented by the regional health administration, we detected the presence of both SINV and WNV in a Culex perexiguus pool, representing the first detection of SINV in Spain. After this finding, we screened 1149 mosquito pools to determine the status of SINV circulation in western Andalucía. We identified for the first time the presence of SINV in five different mosquito species. Culex perexiguus presented the highest infection rate by SINV. In addition, SINV was geographically widespread and distributed in four out of the five Andalucía's provinces studied, with Cadiz presenting the highest infection rate. All SINV genomes from Southwestern Spain characterised in this study belonged to SINV-I, previously detected in Europe and Africa. These isolated SINV-I strains presented low molecular variation among them and in the phylogenomic analyses they formed a monophyletic group that clustered with strains from Algeria and Kenya. These results suggest that, around 2017, a single new SINV introduction into the European continent occurred, probably from Northern (Algeria) or Central Africa.

Leishmania donovani homoserine dehydrogenase: Biochemical and structural characterization of a novel parasite specific enzyme of aspartate pathway

Visceral leishmaniasis is a neglected tropical disease. Drug resistance and toxicity are the critical issues with the currently available antileishmanial drugs. Therefore, research efforts are underway to identify and validate new drug targets specific to Leishmania parasite. The enzyme homoserine dehydrogenase (HSD) functions in the third step of aspartate pathway. The present study focuses on the biophysical and biochemical characterization of HSD enzyme from Leishmania donovani (LdHSD) which is unique to the parasite with no homologous enzyme in the host. LdHSD gene was cloned in pET28c(+) vector and transformed in E. coli BL21 (DE3) strain. LdHSD recombinant enzyme of molecular weight 46.6 kDa with 6X-His tag at the C-terminal end was expressed, purified by nickel affinity chromatography and confirmed by western blot analysis using anti-His antibody. Effect of pH, temperature, salts, metal ions and amino acids on the recombinant enzyme were evaluated. Kinetic parameters of LdHSD were evaluated for substrates L-homoserine and NADP+. Biophysical analysis revealed that the enzyme is rich in β-sheets. Thermal denaturation study revealed that the protein is stable up to 45 °C. Furthermore, comprehensive comparative sequence analysis and structural modeling revealed the structural and functionally important residues, which are involved in the catalytic mechanisms. The putative binding mode of the natural substrate L-homoserine into the active site of LdHSD was also elucidated. These findings provide a foundation for the development of selective, target-based inhibitors against the HSD enzyme of the parasite.

Cloning, expression, and characterization of collagen galactosyltransferases from human, sponge, and sea walnut

Collagen is an extracellular matrix protein conserved across animals and viruses, with its function regulated by post-translational modifications of lysine residues. Specifically, certain lysine residues in collagen are hydroxylated to form hydroxylysine, which serves as an attachment site for hydroxylysine-linked glycosylation. This glycosylation process is initiated by collagen galactosyltransferases from the GT25 family, also known as GLT25D or COLGALT proteins. Despite their biological importance, efficient methods for expressing and isolating GLT25Ds have yet to be fully developed, and the biochemical mechanisms underlying their function still need to be better understood. To address this, we performed sequence alignment and phylogenetic analyses of GLT25Ds across vertebrates, invertebrates, and viruses. Using sponge (amphimedon queenslandica) GLT25D as a model, we established a bacterial expression, purification, and assay protocol. Sponge GLT25D expressed robustly in E. coli strain BL21 and demonstrated enzymatic activity comparable to human GLT25D1 from mammalian cells. Kinetic parameters and the effects of time, temperature and pH on enzymatic activity were characterized for both enzymes. AlphaFold structural modeling and sequence alignment revealed an EXD motif and a conserved leucine in a pocket of the second Rossmann-fold domain of sponge GLT25D, suggesting this pocket as the active site. Using the standardized bacterial expression, purification, and assay protocol, we screened GLT25Ds from various vertebrate and invertebrate species. Notably, the sea walnut (mnemiopsis leidyi) GLT25D exhibited superior expression levels and robust enzymatic activity. This established method provides a strong foundation for future bioengineering efforts, structure-function analyses, and the development of GLT25D inhibitors.

Quaking RNA-Binding protein (QKI) mediates circular RNA biogenesis in Litopenaeus vannamei during WSSV infection

The Quaking RNA-binding protein (QKI), a member of the STAR family, is considered critical in the formation of circular RNAs (circRNAs), as it aids in catalyzing a back-splicing phenomenon by interacting with RNA precursors. CircRNAs have progressively been revealed to play central roles in the regulation of various biological processes, such as antiviral defense mechanisms. This study identifies a QKI in L. vannamei, referred to as LvQKI, comprised of conserved STAR and KH RNA-binding domains. Analysis through tissue-specific expression using qRT-PCR has revealed a high expression level of LvQKI in the gill - one of the primary regions heavily populated by the white spot syndrome virus (WSSV) - and its activation was triggered during WSSV infection. From an RNA interference-mediated suppression targeting LvQKI, a decrease and increase in survival rates and WSSV copy number were observed, respectively. Notably, circRNA levels were significantly lowered in LvQKI-silenced shrimp, whereas linear RNAs remained stable. Conversely, administration of recombinant LvQKI (rLvQKI) protein before a WSSV challenge not only enhanced survival rates but also reduced viral load, wherein both circRNAs and linear RNAs underwent up-regulation in rLvQKI-treated shrimp. Our results introduce LvQKI as a crucial factor in circRNA biogenesis and immune defense in shrimp, emphasizing the interplay between LvQKI's and circRNAs' roles in fighting viral invasion.

Prevalence, genotype distribution, and risk factors of Hepatitis E virus in blood donors, HIV patients, and pregnant women in Southwest Cameroon

Most HEV infections are self-limiting, but pregnant women in their third trimester and immunocompromised individuals, such as those with HIV, face risks, including fatal liver failure and chronic infection. This study investigates HEV prevalence and genotypes in healthy blood donors and high-risk groups, such as HIV patients and pregnant women, in Southwest Cameroon, where surveillance is limited. A cross-sectional study conducted between March and June 2023 recruited 712 participants: 289 blood donors, 233 HIV patients, and 190 pregnant women. Serum and stool samples were tested for anti-HEV IgG and IgM antibodies using ELISA, and HEV RNA was detected by nested PCR targeting the ORF1 and ORF2 regions. HEV RNA-positive samples were sequenced, and genotypes identified. Among the 712 participants, 7 % tested positive for anti-HEV IgG and 2 % for anti-HEV IgM. Blood donors had the highest anti-HEV IgG prevalence (9 %). No significant associations were found between HEV seropositivity and demographic or dietary risk factors. The overall HEV RNA positivity rate was 1 %, with the highest rates in blood donors (2 %) and pregnant women (1 %), while no cases were found in HIV patients. Phylogenetic analysis revealed that 75 % of HEV RNA-positive samples belonged to genotype 3a, and 25 % to genotype 3e. The nucleotide diversity between human and pig HEV genotype 3 suggests the involvement of environmental or other indirect transmission routes, rather than direct pig-to-human transmission. This study highlights HEV risk in Cameroon, especially among blood donors and pregnant women, underscoring the need for enhanced surveillance in HBV-endemic regions.

Processivity and enzymatic mechanism of a non-modular family 5 endoglucanase from Sporocytophaga sp. CX11 with potential applications in cellulose saccharification

In this study, a novel GH5 processive endoglucanase SmCel5A from Sporocytophaga sp. CX11 was functionally expressed in E. coli. It could rapidly decrease the viscosity of carboxymethyl cellulose (CMC-Na) solution by nearly 50 % within the initial 8 min of incubation and exhibited a significantly high specific activity towards CMC-Na of 9940 U/µmol. SmCel5A could also hydrolyze other cellulosic substrates such as RAC, Avicel, filter paper, β-glucan and the chromogenic substrate pNPC. When hydrolyzing filter paper, about 89.1 % of soluble reducing sugars were generated after 180 min of incubation, and the main products were cellobiose followed by cellotriose and glucose. The processive ratio of SmCel5A increased from 2.32 to 11.22 as the reaction time was extended from 5 min to 180 min, which is significantly higher than those of other known processive endoglucanases. Moreover, SmCel5A could hydrolyze cellodextrins with the degree of polymerization (DP) ≥ 3, but it was not active on cellobiose. In combination reaction with β-glucosidase, the maximum substrate conversion rate reached 73.2 %, showing that the synergistic reaction of the two enzymes could efficiently reduce the accumulation of cellobiose and greatly improve the hydrolysis efficiency of cellulose. The three-dimensional structure of SmCel5A was predicted by AlphaFold2 and showed to feature a classic GH5 family (β/α)8-barrel structure, with a deep substrate-binding cleft formed by the amino acids at the C-terminus. Molecular docking results indicated that when hydrolyzing cellulosic substrates, SmCel5A exhibits a preference for the exo-type mechanism of action over the endo-type mechanism of action.

Genome skimming for improved phylogenetics of Taiwanese phasmids (Insecta: Phasmatodea)

Taiwan, a relatively young continental island, harbors a high proportion of endemic phasmids, reflecting its unique evolutionary history. However, a comprehensive phylogenetic framework to clarify these phasmids is still lacking. In this study, we sequenced ten of eleven valid genera and two undescribed species of Taiwanese phasmids (total 16 species) using the genome-skimming approach. We also integrated these sequences with public databases to create two aligned datasets: one comprising 92 taxa (mitogenomes) and the other 606 taxa (seven nuclear and mitochondrial genes), enabling us to examine their phylogenetic relationships using longer sequences and more samples. Our analyses show that Taiwanese phasmids should be categorized into six families, with a revised number of genera to 13. Furthermore, four species require taxonomic treatments: namely Micadina honei (Günther, 1940) comb. nov., Micadina truncatum (Shiraki, 1935) comb. nov., Otraleus okunii (Shiraki, 1935) comb. nov., and Ramulus granulatus (Shiraki, 1935) syn. nov. now recognized as Ramulus artemis (Westwood, 1859). While some Taiwanese genera exhibit polyphyletic relationships, our findings highlight the importance of taxon sampling, particularly for type species in resolving these systematic issues. The genome-skimming approach has proven to be an excellent method for producing comparable sequence datasets, facilitating the investigation of highly diverse insects, even when samples are old, small, or have highly fragmented DNAs.

First record of Angiostrongylus cantonensis infection in Diplothrix legata (Rodentia: Muridae) in Tokunoshima Island, Japan

The Ryukyu long-furred rat, Diplothrix legata (Rodentia: Muridae), is an endangered species endemic to the Tokunoshima, Amami-Oshima, and Okinawajima Islands, which are part of Japan's southwestern islands. During the pathological examination of a deceased wild individual from Tokunoshima Island, lymphoma and infection with three nonnative parasites, Angiostrongylus cantonensis (Nematoda: Angiostrongylidae), Trichosomoides crassicauda (Nematoda: Trichosomoididae), and Hydatigera taeniaeformis (Cestoda: Taeniidae), were identified. Among these, A. cantonensis is a zoonotic species, with invasive rats as the final hosts and mollusks as intermediate hosts. Although the presence of A. cantonensis has been widely reported across the southwestern islands of Japan, this is the first record of this species on the Tokunoshima Island. With this study, A. cantonensis infection in wild D. legata is now confirmed in populations from all three islands where this species is found.

A new genus and species of isosporoid coccidium from captive green tree frogs, Ranoidea caerulea (Anura: Hylidae)

A new genus and a new species of isosporoid coccidium (Apicomplexa: Conoidasida: Eimeriorina) are described and illustrated from green tree frogs (Ranoidea caerulea) (Anura: Hylidae) imported from Papua New Guinea and Indonesia. The described species has disporocystic and tetrasporozoic oocysts without a Stieda body. Nine species originally belonging to the genus Isospora Schneider, 1881 in the family Eimeriidae Minchin, 1903 described from Anura are recognized as members of the new genus and new combinations of the species names are proposed. The phylogenetic analyses of partial gene fragments of 18S rRNA and mitochondrial cytochrome c oxidase subunit 1 genes from isosporoid oocysts from green tree frogs suggested that isosporoid oocysts without Stieda bodies from anurans should be placed in the Sarcocystidae and no longer belong in the Eimeriidae.

Primarily molecular detection and phylogenetic analyses of spotted fever group Rickettsia species in cats in Türkiye: With new host reports of Rickettsia aeschlimannii, Rickettsia slovaca, and Candidatus Rickettsia barbariae

Domestic cats are companion animals that live with people in their households or outdoors, and strong relationships exist between cats and humans. However, this animal is also a host/reservoir of zoonotic pathogens, including Rickettsia species. In Türkiye, cat ownership has increased over the years, but there is a lack of data on the pathogens in cats. In this study, 396 cat blood samples were collected from different parts of Türkiye, and these samples were investigated for Rickettsia species with PCR assay. In addition, DNA sequences were performed for species identification and phylogenetic analyses of detected Rickettsia species. 24 out of 396 cat blood samples (6.06 %) were found to be infected with Rickettsia species. The DNA sequence analyses of all PCR-positive samples were done, and Ri. aeschlimannii was identified in 17 samples, Ri. slovaca in four, Candidatus Rickettsia barbariae in two, and Ri. raoultii in one sample. The phylogenetic analyses of obtained DNA from the above-mentioned species were performed. The sequence data belonging to the species were uploaded to the GenBank, and accession numbers for Rickettsia aeschlimannii (PP998242-PP998258), Ri. slovaca (PP998259-PP998262), Candidatus Rickettsia barbariae (PP998263-PP998264), and Ri. raoultii (PP998265) were taken. This result provides the first molecular detection of Ri. aeschlimannii, Ri. slovaca, Candidatus Rickettsia barbariae, and Ri. raoultii in Türkiye. Moreover, the DNA of Ri. aeschlimannii, Ri. slovaca, and Candidatus Rickettsia barbariae were identified in cat blood samples for the first time in the world, and the cats were a new host for these Rickettsia species. Detailed studies are, however, needed to determine the pathogenicity, biological characteristics, and vectors of these Rickettsia species in this new host.

Deleted in malignant brain tumors 1 (DMBT1) gene relate to immune priming and phagocytosis modulation in the small abalone Haliotis diversicolor

The small abalone (Haliotis diversicolor) is an economic shellfish cultured in the south coast of China. In recent years, the frequent occurrence of the disease has led to significant mortality in abalone farms. Deleted in malignant brain tumors 1 (DMBT1), a member of the scavenger receptor cysteine-rich (SRCR) protein family, plays an important role in host defense. However, its function in H. diversicolor remains unknown. In order to evaluate the immune priming effect after secondary infection and elucidate possible regulatory mechanism, a novel DMBT1 from the small abalone H. diversicolor (designated as HdDMBT1) was cloned and characterized in this study. The open reading frame of HdDMBT1 was 2331 bp encoding 776 amino acids with a molecular weight of 84.73 kDa. HdDMBT1 contained conserved active sites with DMBT1 from other species, detected in all tested tissues and had higher expression levels in hepatopancreas. The temporal expression profiles of HdDMBT1 after two challenges of Vibrio harveyi were examined to evaluate priming response in the small abalone. The expression level of HdDMBT1 mRNA in hepatopancreas increased significantly after V. harveyi challenge. Meanwhile, the expression level of HdDMBT1 after the second challenge was significantly higher than that after the first challenge (4.23-fold). RNA interference (RNAi) experiments were conducted to examine the role of HdDMBT1 in response to V. harveyi infection. Knocking down HdDMBT1 decreased the hemocytes phagocytosis (0.48-fold). In addition, the bacterial density in hemolymph and the mortality of abalone raised, when infected with V. harveyi after dsHdDMBT1 injection. These results indicated that HdDMBT1 might play an important role in tolerance to bacterial infection.

Genome-wide characterization of the AlkB homolog (ALKBH) gene family in Litopenaeus vannamei identifies LvALKBH1 and LvALKBH8 as promising crustacean m6A demethylases involved in molting regulation and ammonia stress response

N6-methyladenosine (m6A) is the most abundant chemical modification on eukaryotic mRNAs. In crustaceans, the absence of canonical m6A demethylases, namely fat mass and obesity-associated protein (FTO) and AlkB Homolog 5 (ALKBH5), poses an unresolved puzzle about the m6A demethylation machinery of these invertebrates. Here, a genome-wide search for potential ALKBH gene family members in the whiteleg shrimp Litopenaeus vannamei was conducted. Six homologues of the ALKBH family were identified from the genome of L. vannamei, and comparative genomics analysis indicated that ALKBH3 and ALKBH5 are likely to exist in the common ancestor of arthropods and molluscs but are then lost in arthropods. Except for LvALKBH4 and LvALKBH7, all LvALKBH proteins possessed a typical 2OG-Fe(II)_Oxy_2 functional domain. Functional experiments revealed that LvALKBH1 and LvALKBH8 possessed significant m6A demethylation activity. Moreover, LvALKBH1 and LvALKBH8 significantly affected the m6A methylation and expression levels of the ecdysone receptor (EcR), retinoid X receptor (RXR), aspartate aminotransferase (AST), and glutamine synthetase (GS), implying their potential roles in regulating shrimp molting and ammonia toxicity resistance. The study provides important baseline information on the molecular characteristics of the ALKBH gene family in shrimp, and fills a current research gap concerning the m6A demethylation toolkit of crustaceans.

Evaluation of the safety and probiotic properties of Limosilactobacillus fermentum BGI-AF16, a uric acid-lowering probiotic strain

Some beneficial microorganisms in the intestine have the potential to degrade uric acid, offering a novel strategy for the prevention of hyperuricemia. In this study, the safety and probiotic potentials of Limosilactobacillus fermentum BGI-AF16 were evaluated by whole genome sequence analysis and in vitro experiments. Based on the gene analysis of antibiotic resistance and virulence factors, L. fermentum BGI-AF16 has been shown to be safe. We identified probiotic-related genes by genome annotation tools and conducted in vitro experiments to evaluate the ability of L. fermentum BGI-AF16 to inhibit pathogenic bacteria, tolerate a simulated gastrointestinal environment, and degrade uric acid. The results from in vitro experiments showed that L. fermentum BGI-AF16 had inhibitory effects on four clinically relevant pathogens and was highly tolerant to the gastrointestinal environment. In addition, L. fermentum BGI-AF16 was able to rapidly degrade uric acid within the first hour, and the strain could degrade 56.36 ± 2.32 % of uric acid by the third hour. The genome of the strain contains genes encoding flavin adenine dinucleotide (FAD)-dependent urate hydroxylase (EC.1.14.13.113), an enzyme that directly metabolizes uric acid. And the strain has a complete uric acid metabolic pathway. These results suggest that L. fermentum BGI-AF16 is a probiotic candidate with significant potential for reducing uric acid level.

Phylogenetic and lipid metabolic differences between migratory and Egyptian-domesticated Mallard ducks (Anas platyrhynchos)

Although a giant Egyptian domestic non-migratory duck breed is phenotypically identical to the migratory Mallard, yet it is three times larger. The current study sought to determine the genetic and metabolic differences between this duck and Mallard, which arrives in Egypt in September for wintering and departs in March. Mitochondrial DNA control region (D-loop) was extracted, amplified, sequenced, and analyzed in both ducks. Both ducks were given a high-fat diet (HFD) for 6 weeks to assess their metabolic response to this diet. Polymorphism results indicated that the D-loop is highly variable and both populations expansion is balanced. The hierarchical analysis of molecular variants (AMOVA) and interpopulation difference parameters revealed significant genetic differentiation and minimal gene flow between migrant and resident populations. Phylogeny and Network analyses revealed that domestic ducks are a distinct group that separated from mallards. Physiologically, domestic duck blood and adipose tissue had a higher level of triglycerides and adipocyte volume than that of the depleting arriving migratory Mallard ducks, while leaving Mallard parameters were the highest, suggesting a high level of preparatory fat deposition and utilization before starting the trip. In response to HFD, the expression of FA uptake genes cd36, fabp1 was upregulated similarly in livers of domestic and migratory Mallard ducks, while the expression of lipid accumulation genes dgat2 and plin2 was higher in domestic than in migratory Mallards. However, the highest body mass and adipocytes volume gain was observed in the arriving migratory Mallards. In pectoral muscle, the expression of cd36 and fabp3 was higher in domestic than in leaving ducks, while in arriving Mallards, both genes were not upregulated in response to HFD. Dgat2 was upregulated only in domestic muscle, while lipid oxidation genes cpt1, lpl, and the controlling ppara were more upregulated in leaving Mallard. In conclusion, both ducks can be genetically and metabolically differentiated. Migratory mallards are more flexible and efficient in lipid metabolism than domestic ducks.

Induced antibiotic production against pathogenic Klebsiella pneumoniae by bacterial coculture

The world is running short of effective antibiotics due to rapid development of antibiotic resistance against currently available antibiotics. The frequency of new antibiotic discovery from conventional axenic cultures has decreased significantly. In current study, azithromycin and ciprofloxacin supplemented plates were used as selection filter for isolation of antibiotic-producing bacteria from Gomti river sediments. All bacterial isolates grown on antibiotic supplemented plates are antibiotic-resistant. Some of these, antibiotic-resistant isolates have ability to produce antibiotics of same scaffold for which they are resistant. Replica-plating technique have been successfully used to screen antibiotic producing among the antibiotic-resistant bacteria by modification of traditional resistance-guided approach. Seven antibiotic-producing bacterial isolates were isolated based on modified resistance-guided approach. All possible 21 two-membered combinations of these seven isolates were used to make bacterial consortia. Effectiveness of bacterial coculture has been evaluated based on antimicrobial potential of extracted antibiotics against pathogenic strains of Klebsiella pneumoniae by using well diffusion method. Significantly increased antibiotic production was observed in cocultures, namely RS2-RS6 and RS2-RS7. As azithromycin and ciprofloxacin were used as selection filter, the produced antibiotic will be either a macrolide or a fluoroquinolone. Highest antimicrobial activity was observed in RS2-RS6 coculture. Molecular characterization revealed that bacterial partners involved in RS2-RS6 coculture were strains of Bacillus cereus and K. pneumoniae which were shown significantly enhanced antibiotic production against pathogenic strains of Klebsiella pneumoniae. Presence of K. pneumoniae vbspurs6 in RS2-RS6 coculture indicates towards the possible use of pathogen related strains to induce antibiotic production against several other antibiotic resistance pathogens.

Single-cell transcriptional footprint for pseudogene SsCLEC9A is associated with antigen processing and presentation in Sus scrofa

The C-type lectin domain family 9 member A (CLEC9A) is widely recognized as the most critical receptor protein for cross presentation of dead cell associated antigens in animal dendritic cells (DCs). Surprisingly, we revealed for the first time that the sole CLEC9A (SsCLEC9A) in pigs becomes a pseudogene due to three causal mutations that occurred approximately 29.8-44.7 million years ago, challenging the significance of CLEC9A in immune cross-presentation across mammals. Interestingly, we found that SsCLEC9A can transcribe a mutated transcript encoding a truncated protein. Through fluorescence-activated cell sorting and single-cell RNA sequencing, we observed that SsCLEC9A mutant transcript is mainly expressed in DCs and correlated with the expression of its homolog CLEC7A. Further data showed that DCs with SsCLEC9A mutant transcripts exhibited reduced cellular interaction ability and downregulation of antigen presentation function, displaying the characteristics of mature DCs. In addition, introducing the conserved sequence of CLEC9A gene into FLT3L-induced bone marrow hematopoietic cells significantly increased the expression of genes involved in antigen processing and presentation. This study presents a natural mutation model of pseudogenes to understand its transcriptional adation, and provides a fundamental basis for rescuing SsCLEC9A to promote immunity in pigs in the future.

Natural life cycle and molecular characterization of Taenia talicei Dollfus, 1960 (Cestoda: Taeniidae) from northwestern Patagonia, Argentina

Through morphological and molecular studies, the natural life cycle of Taenia talicei Dollfus, 1960 (Cestoda: Taeniidae) from Argentine Patagonia is elucidated, involving subterranean rodents (Ctenomyidae) as intermediate hosts, and the Andean fox Lycalopex culpaeus (Canidae) as definitive host. Metacestodes (mono- and polycephalic fimbriocerci) were found mainly in the peritoneal cavity of Ctenomys terraplen, and the strobilate adult in the intestine of L. culpaeus. Correspondence between metacestodes and strobilate adults was based primarily on number, size and shape of rostellar hooks: 45-53 hooks alternated in two rows, small hooks 88-180 μm long and large hooks 230-280 μm long, with the characteristic shape described in the two main description of the species, both that of the metacestode (original description) and that of the strobilate adult (obtained experimentally). Further genetic analysis (cox1 gene mtDNA) corroborated the conspecificity between the metacestodes and the strobilate adults found in the Andean fox in the same study area. Genetic analysis also revealed conspecificity of the taxon found in Patagonia with the species registered in GenBank as T. talicei, obtained from different intermediate and definitive hosts from Peru and Argentina. Taenia talicei was previously reported from Argentina in the form of metacestodes naturally infecting two other species of Ctenomys. However, the strobilate adult was only described from the experimental infection of a domestic dog. Hence, this is the first report of the natural life cycle of T. talicei and of a species of Taenia endemic from South America.

Making the most of mortalities: Novel host-parasite records in a sandy inland mouse (Pseudomys hermannsburgensis)

From 2020 to 2022, systematic investigation of wildlife mortalities on Dirk Hartog Island, Western Australia was initiated to inform wildlife disease risk analyses for translocation purposes. As part of this monitoring, in November 2020, a sandy inland mouse (Pseudomys hermannsburgensis) was found deceased with multiple comorbidities. Gross necropsy, histopathology and ancillary molecular testing identified several novel host-parasite associations. Sarcoptes scabiei was identified via molecular methods in association with consistent cutaneous pathology, representing the first known detection of this parasite in an Australian native rodent. A putative novel virus belonging to the subfamily Gammaherpesvirinae was also identified, representing the first known detection of a herpesvirus (Orthoherpesviridae) from this species, although it was not clearly associated with other disease processes. A heavy burden of the cestode Hymenolepis microstoma was also present in the gastrointestinal tract, representing a new host record for this species, whilst a pancreatic adenocarcinoma was also found. Beyond the novelty of these host records, these findings contribute to important health baselines of rodent populations on Dirk Hartog Island and highlight the value of investigating mortalities and implementing health surveillance as part of ecological monitoring and wildlife translocation projects.

Ascorbic acid transporter MmSLC23A2 functions to inhibit apoptosis via ROS scavenging in hard clam (Mercenaria mercenaria) under acute hypo-salinity stress

Solute carrier family 23 (SLC23) mediates cellular uptake of ascorbic acid, a crucial antioxidant protecting organisms against oxidative stress. Despite advances in understanding SLC23 in mammals, its physiological roles in bivalves remain poorly understood. Notably, euryhaline bivalves exhibit a significant expansion and positive selection of SLC23, highlighting the need for deeper investigation. Here, we identified 25 MmSLC23 in the hard clam genome. These genes predominantly cluster on chromosomes 3 and 14, with tandem duplications driving their expansion. All MmSLC23 localize to the plasma membrane, containing 9-14 transmembrane domains. Syntenic conservation of SLC23 was limited across order Venerida, with most expanded members being lineage-specific paralogs. Transcriptome analysis and fluorescence in situ hybridization revealed that MmSLC23 exhibited divergent expression patterns under acute and chronic salinity stress. Notably, RNA interference of MmSLC23A2 led to a significant reduction in intracellular ascorbic acid levels. Under acute hypo-salinity stress, increased ROS levels and elevated apoptosis rate were observed in MmSLC23A2 knockdown clams, as assessed by flow cytometry and transmission electron microscopy. These findings underscore the crucial role of SLC23 in mitigating oxidative damage and preventing premature apoptosis under acute salinity stress, offering new insights into the molecular mechanisms underlying the remarkable salinity adaptability of euryhaline bivalves.

Corrosion of carbon steel by Pseudomonas stutzeri CQ-Z5 in simulated oilfield water

Carbon steel, an important infrastructure material in the petroleum industry, experiences serious damage due to Microbially Influenced Corrosion (MIC) with untold economic impact. Pseudomonas stutzeri CQ-Z5 with solid biofilm formation and organic acid-producing ability was isolated from Changqing oilfield produced water. The corrosion behavior and mechanism of 20# carbon steel by P. stutzeri CQ-Z5 were explored in a simulated oilfield product water circulating device. Bacteria inoculation can hasten steel corrosion, the maximum corrosion rate reached 1.84 mm y-1. Pitting corrosion on rust layer was observed using SEM, and CLSM monitored the change in biofilm thickness. XRD displayed that oxides were the primary corrosion products, including Fe2O3, Fe3O4, and FeOOH. Analysis of contributions of corrosion types indicated that biofilm corrosion contributes 72 % to total corrosion, far higher than those of ion erosion and organic acid decay. Many genes involved in iron metabolism, biofilm synthesis, and organic acid production were annotated in the genome of P. stutzeri CQ-Z5. Accordingly, a hypothetical corrosion mechanism model of P. stutzeri CQ-Z5 for carbon steel involvement of initial ion erosion, then biofilm corrosion and organic acid decay was proposed. The work helped prevent carbon steel corrosion and improve corrosion mitigation strategies.

Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis)

Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.

Cloning and functional characterization of the caffeine oxidase gene CsCDH from Camellia sinensis

Theacrine, a purine alkaloid with pharmacological effects such as calming and anti-depressive activities, is biosynthesized through a key rate-limiting enzyme, caffeine oxidase. Despite its importance, the caffeine oxidase gene (CsCDH) in Camellia sinensis has not been cloned to date. We successfully isolated the full-length CsCDH cDNA, which contains a 501-bp open reading frame (ORF) encoding a 166-amino-acid protein with a calculated molecular weight of 18.7 kDa. Molecular docking and dynamics simulations showed that CsCDH binds tightly and stably to caffeine, indicating its catalytic potential in converting caffeine to 1,3,7-trimethyluric acid. The CsCDH fusion protein was expressed in Escherichia coli and purified through affinity chromatography. In vitro enzymatic assays verified that CsCDH catalyzes the conversion of caffeine into 1,3,7-trimethyluric acid. Furthermore, transient expression in tobacco confirmed its caffeine oxidase activity in planta. Finally, antisense oligonucleotide (asODN) interference experiments confirmed that CsCDH exhibits caffeine oxidase activity in tea plants. This study lays the groundwork for unraveling the theacrine biosynthesis pathway and offers new insights into breeding low-caffeine or high-theacrine tea cultivars.

Chitin-binding mechanism of a CBM73 module derived from a lytic polysaccharide monooxygenase from Vibrio campbellii

A lytic polysaccharide monooxygenase from Vibrio campbellii (VhLPMO10A) consists of four functional domains including an N-terminal AA10 catalytic domain (CatD) and a C-terminal CBM73 carbohydrate-binding domain. Phylogenetic analysis of CBM73s from AA10 LPMO and GH18/GH19 chitinases revealed that CBM73 from VhLPMO10A (VhCBM73) belongs a clade different from that of a well-studied CBM73 from Cellvibrio japonicus AA10 LPMO (CjCBM73, Madland et al., J. Biol. Chem. 297 (2021) 101084). A recombinant VhCBM73 protein did not bind chitooligosaccharides, but it almost equally bound colloidal chitins prepared from squid pen/crab shell. Mutations of Tyr437, Trp441, and Trp456 of VhCBM73 to alanine (Y437A, W441A, and W456A) revealed that the effects were most intensive in Y437A, moderate in W441A, but insignificant in W456A. We concluded that a single chitin chain more hydrated interact with the binding path spanning from Tyr437 to Trp441 of VhCBM73, while multiple chitin chains (chitin surface) interact with a wider binding surface of CjCBM73. VhCBM73 and CjCBM73 may have differently evolved to acquire different binding strategies for enhancing the LPMO function.

Amino Acid Properties, Substitution Rates, and the Nearly Neutral Theory

Do the properties of amino acids affect their rates of substitution? The neutral theory predicts that greater selective constraint leads to slower rates of evolution; similarly, we expect amino acids that are more different from each other to have lower rates of exchange because such changes are most likely to affect protein structure and function. Here, we test these predictions, using substitution rates estimated from empirical amino acid exchangeability matrices. To measure degree of amino acid difference, we focused on two physicochemical properties, charge and size, uncorrelated metrics that are known to have important implications for protein structure and function. We find that for both charge and size, amino acid pairs with large differences had lower rates of substitution. We also found that amino acids that differed in both properties had the lowest rates of substitution, suggesting that both physicochemical properties are under selective constraint. Mutation properties, such as the number of mutations or the number of transitions as opposed to transversions separating amino acid pairs, were also important predictors of substitution rates. The relationship between amino acid substitution rates and differences in their physiochemical properties holds across several taxonomically restricted datasets. This finding suggests that purifying selection affects amino acid substitution rates in a similar manner across taxonomic groups with different effective population sizes.

Diversity of Ticks and Rickettsiae in the Southwestern United States: Implications for Public Health

Background: Surveillance is important in addressing the significant public health concerns posed by tick-borne diseases. However, the southwestern U.S. presents particular challenges due to diverse tick fauna and varied ecologies. Methods: From 2021 to 2022, we conducted a partner-based tick surveillance program in Arizona and California to assess the presence of Rickettsia spp. pathogens and species composition of tick vectors. Results: A total of 913 ticks was collected, comprising in descending abundance Rhipicephalus sanguineus, Dermacentor similis, Ixodes pacificus (I. pacificus), Argas sp., Otobius megnini, and Haemaphysalis leporispalustris. Arizona submitted predominantly brown dog ticks (90.05% of all ticks from Arizona), while California showed greater tick species richness with five species identified. No Rickettsia rickettsii was detected, but a variety of other Rickettsia spp. was found in ticks from both Arizona and California and included Rickettsia rhipicephali (R. rhipicephali), Rickettsia massiliae, and Rickettsia monacensis-like rickettsial agents of I. pacificus, and two rickettsial organisms that were not identified to species: one Rickettsia montanensis or Rickettsia raoultii-like, and the other most similar to Candidatus Rickettsia tarasevichiae (R. tarasevichiae). Conclusion: This research contributes to our understanding of tickborne diseases in the southwestern U.S., and emphasizes the need for targeted surveillance and intervention initiatives in a region with complex relationships among ticks, hosts, and Rickettsia species. In particular, the finding of an apparently novel pairing of an unknown Argas sp. tick and R. tarasevichiae-like organism suggests that argasid species are an important target for future research. In addition, the results-both tick species submitted and resulting Rickettsia spp. identified-highlights the strengths and potential biases associated with a partner-based sampling method for tick surveillance.

Phenazine-1-carboxylic Acid Has a Broad-Spectrum Antifungal Effect by Targeting Isocitrate Lyase

Phenazine-1-carboxylic acid (PCA), as a broad-spectrum antifungal agent, showed significant resistance against the Apple Valsa canker caused by Valsa mali (V. mali). Therefore, it is of great importance to reveal the functions and mechanisms of PCA in plant pathogens, which would provide potential targets for crop disease control. In this study, we identified the major contribution of PCA in the resistance of Pseudomonas chlororaphis subsp. aureofaciens W9-1 to V. mali by gene knockout and high-performance liquid chromatography. Subsequently, we demonstrated that PCA could target isocitrate lyase (ICL) to exert a broad-spectrum antifungal effect by molecular docking, microscale thermophoresis, and isothermal titration calorimetry. Furthermore, lipidomics analysis shows that PCA alters the lipid balance at the cell membrane of V. mali. In summary, this study demonstrates that PCA has a broad-spectrum antifungal effect by targeting the ICL, which may be a potential target for the development and utilization of fungicides.

Functional Characterization of a Highly Efficient UDP-Glucosyltransferase CitUGT72AZ4 Involved in the Biosynthesis of Flavonoid Glycosides in Citrus

Citrus is an important dietary source of flavonoid glycosides, and UDP-glycosyltransferases (UGTs) are the key enzymes responsible for their glycosylation. In this study, a genome-wide analysis of the CitUGT gene family was conducted to identify CitUGTs that contribute to flavonoid 4'-O-glucosides biosynthesis. Our analysis identified 136 CitUGTs in the Citrus clementina genome, classifying them into 18 phylogenetic groups (A-R) and 25 families. This classification was strongly supported by consistent gene structures and motif patterns. Moreover, we identified a CitUGT gene (Ciclev10025462m, designated CitUGT72AZ4) that encodes flavonoid 4'-O-glucosyltransferase for the first time in citrus. This enzyme preferentially glycosylated the 4'-OH group of multiple flavonoids, exhibiting higher catalytic efficiency toward quercetin and three flavones in vitro. Virus-induced gene silencing of CitUGT72AZ4 significantly decreased the accumulation of flavonoid 4'-O-glucosides. These results indicated that CitUGT72AZ4 participated in the biosynthesis of flavonoid 4'-O-glucoside in citrus. Overall, our findings provide valuable insights into the CitUGT gene family and contribute to its functional characterization.

Epidemiological and Molecular Surveillance of Leishmania Species among Humans, Vectors, and Dogs in a Wildland-Urban Interface of Cartagena, Colombia

In Colombia, human leishmaniasis is endemic in rural areas, with increasing reports of outbreaks and cases in urban areas. Cartagena, an urban city in the Colombian Caribbean with a wildland-urban interface, faced its first local cases between 2011 and 2015. Despite reports, visceral leishmaniasis (VL) remains neglected and understudied and almost devoid of active surveillance. Here we report the epidemiological and molecular surveillance of Leishmania species in humans, domestic dogs, and sandflies at the wildland interface in two poverty-stricken neighborhoods of Cartagena. In October 2021, we conducted a surveillance study in the El Toril and La Quinta neighborhoods. Blood samples were collected from 150 healthy humans and 77 domestic dogs for Leishmania species testing by using molecular tools. Five human samples (3.3%) tested positive for Leishmania, one case in El Toril and four cases in La Quinta. The Leishmania donovani complex was detected in three human samples, and all dog samples tested negative for Leishmania. CDC light traps placed for three consecutive days in peridomiciliary areas of the Leishmania-positive case in El Toril allowed the capture of seven females of Lutzomyia dubitans, but none tested positive for Leishmania. Multiple attempts to conduct entomological surveillance in La Quinta were unsuccessful because of non-study-related issues. Our findings contribute to the characterization of the epidemiology of VL in Cartagena, revealing possible neglected cryptic infections in two neighborhoods with an urban-wildland interface.

Comparative in silico and in vivo study of the antioxidant activity of lactoferrin, Geobacillus stearothermophilus, and Lactobacillus delbrueckii subsp. lactis against Rotavirus infection in male mice

Rotavirus is a major cause of pediatric gastroenteritis, for which effective treatments are limited. This study investigates the antioxidant and antiviral potential of lactoferrin, Geobacillus stearothermophilus, and Lactobacillus delbrueckii subsp. lactis against Rotavirus infection. In this study, Geobacillus stearothermophilus and Lactobacillus delbrueckii subsp. lactis were isolated from Hammam Pharon soil and milk cheese, respectively, and identified using molecular techniques with accession numbers PP758390 and PP758383. The antioxidant effect against DPPH showed that lactoferrin exhibited the strongest scavenging ability, followed by Geobacillus stearothermophilus and Lactobacillus delbrueckii subsp. lactis. In vivo experiments involved administering lactoferrin, Geobacillus stearothermophilus, and Lactobacillus delbrueckii subsp. lactis in the drinking water of young mice for three days, followed by Rotavirus infection on the fourth day and sacrifice on the fifth day. The results demonstrated that lactoferrin significantly reduced the pathogenic effects of Rotavirus, as indicated by the normalization of inflammatory cytokines (TNF-α and IL-6) in the serum (p ≤ 0.001). Histological examination of small intestinal sections from Rotavirus-infected mice revealed extensive destruction of villus structures, while mice treated with lactoferrin showed no pathological changes compared to the control group. Geobacillus stearothermophilus-treated mice exhibited less pathological alteration and Lactobacillus delbrueckii subsp. lactis-treated mice showed mild pathological changes. Additionally, molecular docking studies indicated that bacteriocin (a bacterial protein) exhibited the highest binding affinity for the Rotavirus outer membrane protein (VP6) at -261.92 kcal/mol, outperforming lactoferrin (-229.32 kcal/mol). Additionally, bacteriocin's active compounds, turimicin (-7.9 kcal/mol) and lactin (-6.5 kcal/mol), also showed strong binding to VP6, suggesting their potential as therapeutic agents against Rotavirus. In conclusion, this study highlights the significant antiviral potential of lactoferrin against Rotavirus, demonstrating its ability to mitigate pathological changes and normalize inflammatory responses in infected mice. The findings also suggest that bacteriocins, particularly those with high binding affinities to Rotavirus proteins, could serve as promising candidates for therapeutic interventions against Rotavirus infections.

Carp edema virus surveillance in the koi trade: early detection through shipping environment sampling and longitudinal monitoring of CEV outbreaks in a wholesaler facility

Carp edema virus (CEV), a member of the Poxviridae family, has been a significant pathogen in koi and common carp since its initial identification in Japan during the 1970s. CEV, the causative agent of Koi Sleepy Disease (KSD), can cause high mortality rates and has been reported in many countries and is often linked to the fish trade. The virus is typically detected through DNA analysis of gill tissues, where the highest viral loads are found. However, traditional sampling methods, such as gill sampling, are lethal, complicating routine surveillance, particularly in asymptomatic or high-value koi. This study aimed to evaluate nonlethal sampling methods for CEV surveillance in the koi trade. We analysed various shipping environment samples, such as shipping water and fish bag swabs, alongside gill swabs from anaesthetised fish and gills from naturally deceased fish. Using qPCR, we found that the sensitivity of environmental samples, particularly shipping water, was greater than that of direct fish samples. Latent class modelling estimated that the sensitivity associated with 1.5 mL shipping water samples was greater than 89%, making them a reliable alternative for early detection. All detected variants belonged to genogroup II. Some post-import outbreaks shared variants with earlier outbreaks or shipping environment samples, suggesting that the detected DNA generally reflected infectious particles rather than just free environmental DNA and indicating that CEV can go unnoticed for several months after importation. These findings highlight the utility of environmental samples for effective, non-invasive surveillance and improved biosecurity management in the koi trade.

Bayesian phylogeographic analysis infers cross-border transmission dynamics of drug-resistant Salmonella Enteritidis

Salmonella Enteritidis (S. Enteritidis) stands as a leading cause of human salmonellosis worldwide with a tendency to spread through contaminated foodstuffs and animals. In Hong Kong, a significant proportion of food products are imported, and many cases are often caused by the consumption of contaminated food, hence making the geographical surveillance of drug-resistant S. Enteritidis important for strong public health and food safety measures. We analyzed the whole genomes of 207 S. Enteritidis from Hong Kong, Australia, Canada, mainland China, the United States of America, South Africa, Taiwan, and the United Kingdom to examine associated antimicrobial resistance and the transmission dynamics between continents. Phylogenetic cluster inferences and Bayesian phylogeographical analysis were performed. Overall, sequence type ST11 strains were dominant (92.8%, 192/207). Five phylogenomic clusters A to E were identified, where most isolates from mainland China and Hong Kong were in Cluster E. Among the 22 plasmid types identified, IncX1 was dominant in the Asian isolates. Most of the virulence genes were distributed in Salmonella pathogenicity islands -1 and -2, with two universal virulence operons responsible for the effector delivery system and bacterial cell adhesion. The phylogeographic inference analysis showed a statistically significant link between mainland China and Hong Kong with the highest relative migration rate (relativeGeoRates mean ± standard error = 2.93 ± .07, Bayes Factor [BF] = 1285.5], with some traceable to Canada (0.61 ± 0.03, BF = 6.9) and Australia (1.02 ± 0.04, BF = 4.2). Our analysis suggests hypothetical transmission of S. Enteritidis and its associated antimicrobial resistance across borders.

IMPORTANCE

Antimicrobial resistance and disease severity in nontyphoidal Salmonella have constituted a serious public health challenge worldwide. Drug-resistant Salmonella Enteritidis is a leading pathogen that causes human infections primarily through the consumption of contaminated food products. Previous research focuses on the whole-genome analysis of antimicrobial resistance and virulence factors in S. Enteritidis; however, details on how this bacterium localized, expanded, and diversified from location to location remain unknown. Our study for the first time addresses this gap by investigating the phylogeographic transmission to estimate the frequency and location of cross-border spread. By evidence-based inferred transmission, we aim to uncover novel insights into the dynamic spread of S. Enteritidis, revealing the route of emergence and migration. This research is crucial for enhancing our understanding of the control strategies to safeguard human health.

Revisiting Phryma leptostachya L.: phylogenetic relationships and biogeographical patterns from complete plastome

BACKGROUND

Phryma leptostachya L. is a notable example of a species with a disjunct distribution, found in both East Asia and Eastern North America. Despite the striking morphological similarities between these geographically isolated populations, molecular evidence suggests that they may have diverged sufficiently to be considered distinct taxa.

RESULTS

To clarify this, we analyzed the plastomes of P. leptostachya from Korea, Russia, and the USA. Their sizes ranged from 152,974 to 153,325 bp, each containing 113 genes. Differences were observed in the boundaries between large single copy (LSC)/IRa and IRb/LSC. In P. leptostachya_USA, the rps19 gene extended 30-31 bp into the IRa, and the rpl2 gene contracted 51-53 bp at the IRa/b compared to those of P. leptostachya_Korea and P. leptostachya_Russia, suggesting that expansion of the inverted repeat (IR) region occurred in P. leptostachya_USA. Regions such as psbZ-trnG, ccsA-ndhD, petA-psbJ, and psbC-trnS were identified as hotspots with sequence differences in the plastome, indicating differences among P. leptostachya variants. Phylogenetic analysis showed that P. leptostachya from Korea and Russia formed monophyletic groups, while the variety from the USA was paraphyletic. The divergence of P. leptostachya_USA occurred during the Pliocene, about 5.25 million years ago (MYA), whereas the split between P. leptostachya_Korea and P. leptostachya_Russia is estimated to have occurred approximately 0.87 MYA during the Pleistocene. The results also reveal that the family Phrymaceae underwent multiple dispersal and vicariance events from North America to East Asia, offering key insights into the phylogenetic relationships between P. leptostachya populations from Korea, Russia, and the USA. Based on the evidence, it is likely that P. leptostachya originated in North America and later migrated to East Asia via the Russian Far East and the Bering Land Bridge.

CONCLUSIONS

In conclusion, our study demonstrates clear molecular differences among P. leptostachya populations from various geographic locations, suggesting that these populations should be recognized as distinct species rather than conspecifics.

Fine mapping of the unique Ur-11 gene conferring broad resistance to the rust pathogen of common bean

KEY MESSAGE

Fine mapping positioned the Ur-11 rust resistance gene in common bean to a narrow 9 kb genomic region and enabled the development of a KASP marker tightly linked to Ur-11 for use in gene pyramiding to achieve durable rust resistance. The extensive virulence diversity of the fungal pathogen Uromyces appendiculatus threatens common bean (Phaseolus vulgaris) production. The Ur-11 gene present in the Guatemalan common bean accession PI 181996 conferred resistance to 89 of 90 virulent races of U. appendiculatus. We describe here the fine mapping of Ur-11 and the development and validation of a DNA marker tightly linked to Ur-11. An F2 population from the cross between the susceptible Pinto 114 with the resistant PI 181996 was inoculated with four races of U. appendiculatus. This study established that the rust resistance in PI 181996 was conferred by Ur-11. We then fine mapped Ur-11 using F2 plants and F2:3 families, high-throughput SNP genotyping, SSRs and KASPs marker development, whole-genome sequencing, and local haplotype analysis. Ur-11 was positioned in a narrow 9.01 Kb genomic region on chromosome Pv11 flanked by KASP markers SS322 and SS375. This genomic region included a candidate gene encoding a nucleotide-binding site and leucine rich-repeat domain with pathogen resistance functions. The validation of the SS322 KASP marker was performed on a panel of 206 diverse common bean cultivars that were inoculated with four races of U. appendiculatus. The SS322 marker was 97.5% accurate in identifying the presence of Ur-11 in common bean plants. These results suggest that S322 will be a highly effective molecular marker for the development of common bean cultivars with Ur-11 alone and combining Ur-11 with other rust resistance genes that would confer broad and durable resistance to the hypervirulent bean rust pathogen.

Interspecies signaling modulates the biosynthesis of antimicrobial secondary metabolites related to biological control activities of Pseudomonas fluorescens 2P24

Signaling between rhizosphere microorganisms is crucial in bacteria interaction and communication, shaping the rhizomicrobiome. Plant growth-promoting bacterium Pseudomonas produces a spectrum of important antibiotics to inhibit plant pathogens, albeit with an associated metabolic burden. Antibiotics could function as intra- and interspecies signals at subinhibitory concentrations to coordinate gene expression and microbial behaviors. In this work, we characterized pyoluteorin as an interspecies signal that modulates the biosynthesis of 2,4-diacetylphloroglucinol (2,4-DAPG), a broad-spectrum biocontrol agent, in non-pyoluteorin-producing Pseudomonas fluorescens 2P24. We demonstrated that the key transcriptional repressor PhlF from the 2,4-DAPG biosynthetic gene cluster spontaneously senses pyoluteorin, enhancing repression of the phlA promoter activity and inhibiting 2,4-DAPG synthesis in P. fluorescens 2P24. Pyoluteorin also binds to another transcriptional repressor, PhlH, from the 2,4-DAPG biosynthetic gene cluster, subsequently releasing the transcription of phlG, which facilitates the hydrolysis of 2,4-DAPG. Both PhlF and PhlH are simultaneously involved in sensing exogenous pyoluteorin to regulate the 2,4-DAPG biosynthetic operon, playing a crucial role in controlling antibiotic metabolites in response to environmental changes. Further phylogenetic and structural analyses demonstrated that PhlH and PhlF are widely distributed across Pseudomonas spp. with conserved ligand-binding domains. The findings shed new light on the regulatory mechanism of 2,4-DAPG biosynthesis underlying interspecies signaling by pyoluteorin and provide invaluable clues for the rational design of co-inhabiting Pseudomonas spp. as biocontrol agents.

IMPORTANCE

Rhizosphere microorganisms release vital signals that shape microbial communities, with antibiotics at low concentrations acting as intra- and interspecies signals. However, the mechanisms of these signals in coordinating gene expression are unclear. In non-pyoluteorin-producing Pseudomonas fluorescens 2P24, pyoluteorin was identified as an interspecies signal that regulates the phl biosynthesis gene cluster for 2,4-DAPG production. TetR family repressors PhlH and PhlF were found to positively regulate 2,4-DAPG hydrolysis and negatively regulate its synthesis in response to pyoluteorin. Structural modeling and docking analyses revealed the interactions between pyoluteorin and both PhlH and PhlF, modulating gene expression. Phylogenetic analyses showed a wide distribution of PhlH and PhlF across Pseudomonas spp. with conserved ligand-binding domains. These findings deepen our understanding of interspecies signaling mechanisms and highlight the potential for designing co-inhabiting Pseudomonas spp. as effective biocontrol agents.

Study of the probability of resistance to phage infection in a collection of clinical isolates of Pseudomonas aeruginosa in relation to the presence of Pf phages

Pseudomonas aeruginosa is a bacterial pathogen that is a major cause of lung infections in cystic fibrosis (CF) and other patients. Isolates of P. aeruginosa from CF patients commonly carry filamentous phages (Pf phages), which constitute a family of temperate phages known to be related to biofilm production and antibiotic sequestration. In this study, we identified 12 new Pf phage genomes in a collection of clinical isolates of P. aeruginosa from CF patients. Study of the anti-phage defense systems in the bacterial isolates revealed the presence of 89 such systems, of which eight were encoded in the Pf phage genomes. Finally, although a weak relation between resistance to phage infection and the number of anti-phage defense systems was detected, it was observed that the phage resistance was related to the presence of Pf phages and the anti-phage defense systems encoded in these phages.IMPORTANCEBacteria harbor a wide range of defense mechanisms to avoid phage infections that hamper the application of phage therapy because they can lead to the rapid acquisition of phage resistance. In this study, eight anti-phage defense systems were found in the genome of 12 Pf phages that were presents in 56% of the CF isolates of P. aeruginosa. The high prevalence of these phages underlines the importance of our findings about newly discovered filamentous phages and the role of these phages in resistance to phage infections. Thus, the knowledge of the anti-defense system in the Pf phage genomes could be useful in assessing the possible application of phage therapy to treat an infectious disease.

Essential oils and Lactobacillus metabolites as alternative antibiofilm agents against foodborne bacteria and molecular analysis of biofilm regulatory genes

The formation of biofilm by foodborne pathogens increases the risk of foodborne diseases, resulting in major health risks. Research on strategies for eliminating biofilm formation by foodborne pathogens is urgently needed. Therefore, the objective of this study was to construct a new technique for controlling foodborne bacteria and inhibiting the biosynthesis of biofilm via using natural products. The essential orange oil (EOO) and cell-free filtrate of Lactobacillus pentosus RS2 were used as antibacterial and antibiofilm agents against B. cereus RS1, the strongest biofilm-forming strain. The mixture of cell-free filtrate (CFF) and EOO (CFF/EOO) was the best antibiofilm agent under all tested conditions. The minimal inhibitory concentration (MIC) test revealed that 400 μl ml-1 CFF and 16 μl ml-1 EOO completely inhibited the growth of B. cereus. The treatment of three commercial surfaces with CFF/EOO resulted in a high reduction in biofilm synthesis, with adhesion percentages of 33.3, 36.3, and 40.8% on stainless steel, aluminum foil, and aluminum, respectively. The aluminum surface had the greatest adhesion with B. cereus RS1 among the three tested surfaces. These results were confirmed by expression analysis of three essential coding genes, sinR, calY, and spo0A, participating in biofilm formation in B. cereus. The biofilm-negative regulator gene sinR was overexpressed, whereas the biofilm-positive regulator genes calY and spo0A were down-expressed in B. cereus RS1 after treatment with antibiofilm agents, compared with those in the untreated sample. This study revealed that CFF/EOO was more effective at activating sinR (2.099 ± 0.167-fold increase) and suppressing calY and spo0A (0.314 ± 0.058 and0.238 ± 0.04-fold decrease, respectively) compared to control. This result confirmed the biochemical estimation of biofilm formation in B. cereus after treatment with all the experimental agents. The EOO and CFF of L. pentosus RS2 can be used as strong antibacterial and antibiofilm agents against foodborne bacteria. These products reduced the biofilm formation on trade surfaces affecting the expression of three essential biofilm regulatory genes. This study considered novel research concerning the potential antibiofilm activity of EOO combined with CFF of L. pentosus and the molecular analysis of genes regulating biofilm production under stress of CFF/EOO.

TccP4: a novel effector identified in the Escherichia albertii strain 1551-2 required for attaching and effacing lesion formation on infected Nck-null cells

Escherichia albertii is a pathogen that causes sporadic cases and outbreaks of diarrhea. The main virulence feature of this bacterium is the attaching and effacing (AE) lesion formation on infected intestinal epithelial cells, which is characterized by the formation of pedestal-like structures that are rich in F-actin. The Brazilian E. albertii 1551-2 strain can recruit F-actin using both the Nck-dependent and the Nck-independent pathways, the latter of which uses an adaptor protein named Tir-cytoskeleton coupling protein (TccP/EspFU). Genome analyses of the 1551-2 strain unveiled the existence of a gene encoding a putative novel TccP subtype in addition to a gene encoding for the TccP3 subtype. Amino-acid sequence comparison with known TccP subtypes (TccP/EspFU, TccP2, and TccP3) confirmed that the protein represents a novel TccP subtype-named here TccP4. Lack of TccP4 led to an approximately 96% reduction in the ability of the tccP3 deletion mutant of strain 1551-2 to induce the F-actin-rich pedestals formation in the infected Nck-null mouse embryonic fibroblasts (MEF) cells. The tccP4 gene was distributed widely in E. albertii, including the strains first separated from other E. albertii strains, suggesting that this gene was acquired at a very early stage during the diversification of E. albertii. The highly variable genetic organization of the tccP4-containing regions and the presence of various mobile genetic elements in this region may explain the lack of tccP4 in E. albertii strains belonging to various lineages.IMPORTANCEE. albertii, one of the new members of the genus Escherichia, is a diarrheagenic pathogen. The main characteristic of its pathogenicity is the formation of attaching and effacing (AE) lesions on the surface of infected epithelial cells. Here we identified a novel subtype of the TccP type 3 secretion system (T3SS) effector family (termed TccP4), which is required for the recruitment of F-actin during the AE lesion formation in infected host cells by the E. albertii 1551-2 strain. We also revealed that TccP4 is unique to E. albertii and widely distributed in this species, suggesting that the tccP4 gene was acquired at a very early stage during the diversification process of E. albertii. These findings expand our understanding of the function and diversity of this important T3SS effector family.

Deorphanization of Pheromone Receptors and Discovery of a Novel Agonist for Sex Pheromone Communication in Diamondback Moths

Sex pheromone communication is an essential component of mate recognition in moths. In this study, we heterologously expressed male-biased pheromone receptors (PRs) of diamondback moths, Plutella xylostella, in Drosophila OR67d neurons and determined their responses toward sex pheromonal compounds. The neurons expressing PxylOR59, PxylOR13, and PxylOR46 specifically responded to three sex pheromone components, Z11-16:Ald, Z11-16:Ac, and Z11-16:OH, respectively. The most effective ligands of other three PRs, PxylOR47, PxylOR49, and PxylOR73 were Z11-14:Ac, Z9,E12-14:Ac, and Z9,E11-14:Ac, respectively. Interestingly, the last two PRs were also tuned to Z11-14:Ac, which was not present in the pheromone glandular extract of P. xylostella in previous studies. Y-tube olfactometer assays revealed that the sex pheromone blend mixed with Z11-14:Ac at a ratio of 100:0.1 attracted more virgin males compared to the sex pheromone blend. These findings improve our understanding of the olfactory coding mechanisms in this important pest and provide promising potential for enhancing insect capture of pheromone traps.

A detailed comparative in silico and functional analysis of ccd1 gene in maize gives new insights of its expression and functions

BACKGROUND

Biofortified maize with enhanced carotenoid content was developed to combat vitamin A deficiency. However, it was observed that during storage, carotenoids present in maize grain get degraded and it has been reported that carotenoid cleavage dioxygenase1 (ccd1) is responsible for this degradation.

METHODS AND RESULTS

In our current study, comprehensive in-silico analysis deciphered a complete overview of the ccd1 gene in maize including the gene structures, phylogeny, chromosomal locations, promoter analysis, conserved motifs and interacting protein partners. In addition to these, a comparative in-silico analysis of the ccd1 gene in maize, rice and Arabidopsis was performed. An intronic region of ccd1, unique to the maize genome, was matched significantly with a lot of long non-coding RNA and was identified. Also, growth stage-specific ccd1 expression analysis was performed in two maize inbred lines, V335PV and HKI161PV. The results indicate that both inbred lines displayed higher ccd1 expression during reproductive stages compared to vegetative stages, with the highest expression level observed at the milking stage in both inbreds.

CONCLUSION

This detailed in-silico characterisation and expression analysis of the ccd1 gene contributes to our understanding of its activity and expression pattern in maize in stage and tissue-specific manner. This study will further provide an effective strategy for manipulating the ccd1 gene to enhance the carotenoid content of maize grain, thereby aiding in the combat against vitamin A deficiency.

Missense variants in MC4R gene are associated with obesity in cats

Obesity stands out as the most common multifactorial nutritional problem affecting domestic cats. According to studies, the prevalence of overweight or obese cats varies between 11.5% and 63%. Various factors such as breed, age, gender, reproductive status, owner-pet relationship, diet type, and environmental factors have been identified as potential risk factors for the development of obesity in cats. Among the genes involved in regulating energy balance, one of the prominent genes is melanocortin-4 receptor gene (MC4R). A specific missense variant in the feline MC4R gene (c.92 C > T) has been associated with overweight in diabetic domestic shorthaired cats. In this study, it was aimed to determine the polymorphisms in MC4R gene in random bred cats and cats belonging to a registered breed in Turkey and to investigate their relationship with obesity. Blood samples from 30 obese and 20 non-obese cats were collected into sterile vacuum EDTA tubes. Exon 1 of the MC4R was amplified and sequenced. As a result of DNA sequence analysis, we identified a total of six SNPs in the feline MC4R gene, four of which were found for the first time in this study. As a result of comparing allele frequencies in obese and non-obese cats, a significant relationship was found between SNP rs783632116 and obesity. The results of regression analyses evaluating the effects of SNP genotypes, sex and infertility status on feline Body Mass Index (fBMI) indicated that non-synonymous SNPs rs783632116, ss11356259660 and ss11356259661 were significantly associated with fBMI.

Analysis of the CRK expressions in bottle gourd (Lagenaria siceraria) under Fusarium oxysporum f. sp. lagenariae stress by using genome-wide identification strategy

BACKGROUND

The cysteine-rich receptor-like kinases (CRKs) family in plants have been reported to perform multiple functions against various stresses. However, the CRK family in bottle gourd (Lagenaria siceraria) has not been well-explored. Herein, a comprehensive genome-wide identification and characterization of the CRK gene family has been carried out in bottle gourd under Genome-wide characterization of CRK genes in bottle gourds under Fusarium oxysporum f. sp. lagenariae infection.

RESULTS

A stringent set of bioinformatic analyses identified 18 LsCRKs in the bottle gourd genome. Chromosomal mapping of the identified LsCRKs revealed that the LsCRKs were distributed in 4 chromosomes in the bottle gourd genome. The phylogenetic analysis of LsCRKs divided them into two subgroups on the tree. The synteny and collinearity analysis of the LsCRKs among themselves and other plant CRKs provided insights into their conservancy and expansion. Gene ontology analysis of the identified LsCRKs suggested their possible roles in regulating different physiological processes and stress responses in bottle gourd. To assess the involvement of the LsCRKs under F. oxysporum f. sp. lagenariae infection, bottle gourd seedlings were transplanted into the pots with F. oxysporum-infected soil. The expression analysis revealed that multiple LsCRKs exhibited induced expression, suggesting their involvement in bottle gourd-F. oxysporum interactions. Additionally, the protein-protein interaction analysis suggested some important interacting partners of LsCRKs crucial to different physiological processes in bottle gourd.

CONCLUSIONS

The present work explored and analyzed the LsCRKs in bottle gourd. Functional predictions and interaction network analysis suggested the roles of LsCRKs in modulating multiple physiological processes in bottle gourd. The expression dynamics of LsCKRs under fungal pathogen infection suggest their involvement in stress response in bottle gourds. Overall, the results of the study provide basic information about the CRK family in bottle gourds and their involvement in fungal pathogen response.

Vascular Streak Dieback: A Novel Threat to Redbud and Other Woody Ornamental Production in the United States

Eastern redbud (Cercis canadensis L.) is a popular and high-value woody ornamental plant native to the Eastern and South Central United States. In recent years, redbud production in the Southeastern United States has been greatly affected by a novel threat: vascular streak dieback (VSD). Infected plants exhibit a common set of symptoms, including leaf scorch, tip dieback, and vascular streaking that creates a marbled pattern in stem cross-section. Based on both conventional diagnosis and molecular identification, it has been found that the fungus Ceratobasidium sp. D.P. Rogers (Csp) is consistently associated with VSD-symptomatic eastern redbuds. However, the causal agent(s) of VSD has not yet been conclusively confirmed. Although eastern redbud has been the most frequently identified host tree, more than 25 other native plant genera have been confirmed to have VSD associated with Csp. The near-obligate nature of this fungus has made it challenging to culture, extract DNA, and conduct further studies to confirm its pathogenicity. This article highlights the emerging challenges of VSD, focusing on the following: (i) the recent history of VSD; (ii) the increasing importance of VSD to woody ornamental nursery production in the United States; (iii) the currently available protocols for isolating, culturing, storing, and maintaining the putative causal agent; (iv) the rapid molecular detection of Csp; (v) phylogenetic findings on the origin and relatedness of Csp to previously recorded diseases, especially VSD in cacao (Theobroma cacao L.); and (vi) preliminary results and observations from fungicide trials and cultivar screening in Tennessee. The article also outlines research needed to comprehensively understand VSD and accelerate the development of effective management strategies.

The genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars

Japanese soybeans are traditionally bred to produce soy foods such as tofu, miso and boiled soybeans. Here, to investigate their distinctive genomic features, including genomic structural variations (SVs), we constructed 11 nanopore-based genome references for Japanese and other soybean lines. Our assembly-based comparative method, designated 'Asm2sv', identified gene-level SVs comprehensively, enabling pangenome analysis of 462 worldwide cultivars and varieties. Based on these, we identified selective sweeps between Japanese and US soybeans, one of which was the pod-shattering resistance gene PDH1. Genome-wide association studies further identified several quantitative trait loci that accounted for large-seed phenotypes of Japanese soybean lines, some of which were also close to regions of the selective sweeps, including PDH1. Notably, specific combinations of alleles, including SVs, were found to increase the seed size of some Japanese landraces. In addition to the differences in cultivation environments, distinct food processing usages might result in changes in Japanese soybean genomes.

Exploring the fibrinolytic potential of marine Actinoalloteichus caeruleus isolated from Bay of Bengal coast

BACKGROUND

One of the main causes of several cardiovascular diseases that have an elevated mortality rate globally is intravascular thrombosis. The current fibrinolytic enzymes, are quite expensive and have a lot of side effects, thus it is necessary to develop alternate, economical techniques for the low-cost manufacture of these vital enzymes. Microbial fibrinolytic enzymes have the capacity to break up these clots and are relatively cheaper with minimal side effects and quick growth rate. Marine actinomycetota are the most prolific prokaryotes, which are capable of synthesizing novel secondary metabolites and are of industrial importance in pharmaceutical and various other industries. Thus, the objective of the research is to isolate, screen and characterize fibrinolytic protease producing actinomycetota from marine samples.

RESULTS

In this study, 35 actinomycetota have been successfully isolated from marine water and sediment samples. Among them, 12 isolates were protease positive and on secondary screening 5 isolates showed fibrinolytic activity. Out of the 5 isolates, one potent isolate's clot lysis activity was found out to be 93.12 ± 0.18% and its fibrinolytic potential was determined on fibrin agar plates. Based on the morphological, physiological, biochemical, and molecular analysis, the potent strain (NK60) was identified as Actinoalloteichus caeruleus.

CONCLUSIONS

In this present study, a rare actinomycetota has been isolated from the Bay of Bengal coast. This is the first study reporting the potent fibrinolytic activity of A. caeruleus, isolated from marine water. This clot-busting enzyme has significant pharmacological value in the management of coronary artery diseases. In the near future, A. caeruleus can serve as an explicit source for commercial production of fibrinolytic enzymes.

Integrative analysis of seed morphology, geographic origin, and genetic structure in Medicago with implications for breeding and conservation

BACKGROUND

Seed morphology and color are critical agronomic traits in Medicago spp., reflecting adaptations to diverse environments and influencing seedling establishment and vigor. Understanding the interplay between seed traits, geographic origin, and genetic diversity is crucial for effective germplasm conservation and breeding. This study presents a comprehensive analysis of these factors in a diverse collection of Medicago accessions, leveraging machine learning to illuminate these complex relationships.

RESULTS

We analyzed seed size, shape, and color data from 318 Medicago accessions representing 29 species/subspecies from 31 countries. Machine learning models, including Neural Boost, Bootstrap Forest, and Support Vector Machines, effectively classified accessions based on seed traits and geographic origin, achieving up to 80% accuracy. Seed size was accurately predicted (R-squared > 0.80) using a combination of species, geographic origin, and shape descriptors. Hierarchical clustering of 189 M. sativa accessions based on 8,565 SNP markers revealed 20 distinct genetic clusters, indicating substantial population structure. A machine learning-based genome-wide association (GWA) analysis identified SNPs on chromosomes 1, 6, and 8 with high importance for predicting geographic origin. Notably, the most significant SNPs were located in or near genes involved in stress response and genome stability, suggesting their potential role in local adaptation. Finally, we successfully imputed missing M. sativa SNP genotypes using multiple machine learning approaches, achieving over 70% accuracy overall and over 80% for individual nucleotides (A, T, C, G), enhancing the utility of genomic datasets with missing data.

CONCLUSIONS

Our integrated analysis of phenotypic, genetic, and geographic data, coupled with a machine learning-based GWAS approach, provides valuable insights into the diverse patterns within Medicago spp. We demonstrate the power of machine learning for germplasm characterization, trait prediction, and imputation of missing genomic data. These findings have significant implications for seed trait improvement, germplasm management, and understanding adaptation in Medicago and other diverse crop species. The identified candidate genes associated with geographic origin provide a foundation for future investigations into the functional mechanisms of local adaptation. Furthermore, our imputation method offers a valuable data for maximizing the utility of genomic resources in Medicago and other species.

Genome-wide identification and characterization of FORMIN gene family in cotton (Gossypium hirsutum L.) and their expression profiles in response to multiple abiotic stress treatments

FORMIN proteins distinguished by FH2 domain, are conserved throughout evolution and widely distributed in eukaryotic organisms. These proteins interact with various signaling molecules and cytoskeletal proteins, playing crucial roles in both biotic and abiotic stress responses. However, the functions of FORMINs in cotton (Gossypium hirsutum L.) remain uncovered. In this study, 46 FORMIN genes in G. hirsutum (referred to as GhFH) were systematically identified. The gene structures, conserved domains, and motifs of these GhFH genes were thoroughly explored. Phylogenetic and structural analysis classified these 46 GhFH genes into five distinct groups. In silico subcellular localization, prediction suggested that GhFH genes are distributed across various cellular compartments, including the nucleus, extracellular space, cytoplasm, mitochondria, cytoskeleton, plasma membrane, endoplasmic reticulum, and chloroplasts. Evolutionary and functional diversification analyses, based on on-synonymous (Ka) and synonymous (Ks) ratios and gene duplication events, indicated that GhFH genes have evolved under purifying selection. The analysis of cis-acting elements suggested that GhFH genes may be involved in plant growth, hormone regulation, light response, and stress response. Results from transcriptional factors TFs and gene ontology analysis indicate that FORMIN proteins regulate cell wall structure and cytoskeleton dynamics by reacting to hormone signals associated with environmental stress. Additionally, 45 putative ghr-miRNAs were identified from 32 families targeting 33 GhFH genes. Expression analysis revealed that GhFH1, GhFH10, GhFH20, GhFH24, and GhFH30 exhibited the highest levels of expression under red, blue, and white light conditions. Further, GhFH9, GhFH20, and GhFH30 displayed higher expression levels under heat stress, while GhFH20 and GhFH30 showed increased expression under salt stress compared to controls. The result suggests that GhFH20 and GhFH30 genes could play significant roles in the development of G. hirsutum under heat and salt stresses. Overall these findings enhance our understanding of the biological functions of the cotton FORMIN family, offering prospects for developing stress-resistant cotton varieties through manipulation of GhFH gene expression.

Role of fibronectin type III domain in enhancing the substrate accessibility of modular GH9 endocellulase by reducing non-specific binding to lignin

Utilizing lignocellulosic biomass effectively can lessen reliance on fossil fuels and facilitate the production of second-generation biorefinery feedstocks. The nonspecific binding of lignin to cellulases is one of the main factors affecting their enzymatic performance and hampering their efficiency in degrading lignocellulose. Processive endocellulase from Acidothermus cellulolyticus 11B has a modular structure consisting of several carbohydrate-binding modules, a glycoside hydrolase family 9 catalytic domain, and a fibronectin type III (FN3) domain. This study investigated the role of the FN3 in the degradation of lignocellulose by constructing multiple mutants. The results showed that the FN3 could improve the thermal stability of the enzyme and resist the nonspecific binding of lignin to cellulase. This characteristic can significantly increase the lignocellulose's enzymatic efficiency and offer a novel approach to the artificial design of multi-modular cellulases.

Green revolution gene drives adaptation of Arabidopsis to the extremely high altitude

To elucidate the process of adaptation, particularly the traits subject to natural selection and the molecular mechanisms underlying their natural variation, is one of the primary objectives of evolutionary biology. The uplifted landscape offers an excellent framework for understanding how organisms adapt to dramatic climatic gradients. To investigate the genetic basis of plant adaptation to the extremely high altitude, we first compared the genomic and phenotypic variations of two closely related Arabidopsis thaliana accessions from high altitude (Xizang, also known as "Tibet") and low altitude (Yunnan), respectively. The Xizang population represents a relict group characterized by a small effective population size. Notably, the Xizang genome has more transposable elements (TEs) and more gene loss-of-function (LoF) mutations. Differentially expressed genes were enriched in biological processes of cellular response to oxygen-containing compound, regulation of defense response, and response to light intensity. Intriguingly, the phenotypic selection analysis revealed that silique density was under natural selection. Furthermore, we genetically mapped and validated that the LoF mutation of GA20ox1, the homologous gene of green revolution in rice, resulted in a higher silique density in Xizang Arabidopsis. Given that GA20ox1 is linked to Arabidopsis adaptation to the Alps Mountains, its parallel evolution plays an important role in the adaptation to Alpine habitats. Overall, our results highlight that identifying adaptive traits and elucidating the molecular mechanisms underlying natural variation of these traits is crucial for unraveling the mystery of adaptive evolution and has significant implications for crop breeding.