Close Relation Research Articles

A new geminialphasatellite associated with wheat dwarf virus identified in winter barley in France.

Using a high-throughput sequencing (HTS) approach, we report the discovery of a new alphasatellite identified in a winter barley plant collected in France in 2022 that was also infected by wheat dwarf virus (WDV). The presence of the satellite and of WDV was confirmed by several independent PCR assays, and the complete genome sequence was determined. The circular satellite genome is 1424 nt long and shows typical hallmarks of members of the subfamily Geminialphasatellitinae, including a replication-associated hairpin with a CAGTATTAC sequence and a Rep-encoding open reading frame (ORF). It also possesses a second ORF, embedded in a different frame within the Rep ORF, which is also observed in clecrusatellites and a few other members of the family Alphasatellitidae. Pairwise sequence comparisons and phylogenetic analysis showed that this satellite represents a novel species. Its closest relatives are in the genus Colecusatellite, but it likely represents a new genus given its divergence from other genera of the subfamily Geminialphasatellitinae. Given that WDV was the only virus observed in coinfection with the satellite, the name "wheat dwarf virus-associated alphasatellite" is proposed for this novel agent.

Unraveling sauropod diversity in the Portezuelo Formation of Patagonia through a comprehensive analysis of new and existing material

The Portezuelo Formation preserves an outstanding record of the upper Turonian – lower Coniacian. Despite the discovery of a significant quantity of sauropod fossil material from the formation, only two species have been formally described to date: Malarguesaurus florenciae and Futalognkosaurus dukei. Here we present new sauropod material mostly composed of non-articulated caudal vertebrae (MCF-PVPH 916 and 917) that belong to two titanosauriforms on the basis of the following features: anterior caudal vertebrae with procoelous-opisthoplatyan articulations, transverse processes that reach the posterior articular face of the centrum and neural spines with a transverse width of around 50% of their anteroposterior length; anterior and middle caudal vertebrae with the neural arch restricted to the anterior half of the centrum; middle caudal centra with circular cross-section. Phylogenetic analysis recovers the new material in close relation to Malarguesaurus within a monophyletic clade at the base of Somphospondyli. This clade shares large pedicel height with a vertical anterior border on the middle caudal vertebrae, a vertical orientation of the neural spines on the distalmost middle caudal vertebrae and proximalmost posterior caudal vertebrae, and subequal relative lengths of the proximal ulnar condylar processes. The specimens presented here are distinct not only from Futalognkosaurus, but also from other indeterminate titanosaurian remains from the same formation. However, there are no significant differences between the specimen MCF-PVPH 917 and Malarguesaurus, but there are differences between the posterior caudal vertebrae of MCF-PVPH 916 and Malarguesaurus, so they could be considered different species. Whilst we err on the side of caution in not naming new taxa here, the two specimens significantly expand what we know about sauropods in the Turonian–Coniacian ecosystems of Patagonia, which will continue to do so as more material is discovered.

Alike but genetically divergent: The resurrection of Urotrygon asterias (Jordan & Gilbert, 1883) from its closest relatives, the Munda and the Blotched stingray.

The genus Urotrygon comprises small- to medium-sized endemic round rays on the American continent and has undergone several synonymization processes. Here, we used an integrative taxonomic approach, including meristic, morphometric, and mtDNA analyses, to resolve the particularly intricate relationship among Urotrygon munda Gill, 1863, Urotrygon chilensis (Günther, 1872), and Urotrygon asterias (Jordan & Gilbert, 1883). The latter species is currently a synonym of U. munda but is also considered the U. chilensis "northern morphotype." These taxonomic entities have historically been confounded, mainly due to their phenotypical resemblance along their geographic distribution in the eastern Pacific. We assessed 78 specimens (43 "northern" and 30 "southern morphotypes" of U. chilensis, as well as 5 U. munda) using 19 external variables for taxonomic and morphometric analysis. Distinct meristic patterns, including pectoral and pelvic ceratotrichia, vertebrae number, and thorn distribution along the dorsal midline, were observed in the series-type specimens of the three taxonomic entities. Our multivariate morphometric analyses consistently differentiated the three groups as distinct taxonomic entities, with an overall classification accuracy of 66.7%. The meristic results also provided reliable information distinguishing the three entities. Based on the nicotinamide adenine dinucleotide (NADH2) and cytochrome oxidase subunit I (COI) genes, our phylogenetic analysis were consistent with the morphometric and meristic data, supporting these three entities as distinct species having their own evolutionary lineages. Our comprehensive approach confidently demonstrated that the northern U. chilensis morphotype matched and corresponded to the description of the Starry round ray, U. asterias, confirming its taxonomic resurrection as a valid species distinct from U. chilensis and U. munda. The geographic distribution of U. asterias spans from the tropical west coast of Mexico (including the Gulf of California) to Costa Rica, revealing that microevolutionary processes have well-defined population clades within this range. Furthermore, U. chilensis is unequivocally established as the sole Urotrygon species occurring south of the Guayaquil marine ecoregion. In addition, the public COI and NADH2 sequences available for Urotrygon hosted in the ad hoc online databases were found to be misidentified, emphasizing the need for rigorous taxonomic scrutiny in this group. Finally, our research underscores the significance of an integrative approach that combines morphometric, meristic, and molecular techniques with historical data to disentangle the complexities of closely related taxa.

A genome-wide association study suggests new susceptibility loci for primary antiphospholipid syndrome.

Primary antiphospholipid syndrome (PAPS) is a rare autoimmune disease characterized by the presence of antiphospholipid antibodies and the occurrence of thrombotic events and pregnancy complications. Our study aimed to identify novel genetic susceptibility loci associated with PAPS. We performed a genome-wide association study comprising 5,485 individuals (482 affected individuals) of European ancestry. Significant and suggestive independent variants from a meta-analysis of approximately 7 million variants were evaluated for functional and biological process enrichment. The genetic risk variability for PAPS in different populations was also assessed. Hierarchical clustering, Mahalanobis distance, and Dirichlet Process Mixtures with uncertainty clustering methods were used to assess genetic similarities between PAPS and other immune-mediated diseases. We revealed genetic associations with PAPS in a regulatory locus within the HLA class II region near HLA-DRA and in STAT1-STAT4 with a genome-wide level of significance. 34 additional suggestive genetic susceptibility loci for PAPS were also identified. The disease risk allele near HLA-DRA is associated with overexpression of HLA-DRB6, HLA-DRB9, HLA-DQA2 and HLA-DQB2 in immune cells, vascular tissue, and nervous tissue. This association is independent of the association between PAPS and HLA-DRB1*1302. Functional analyses highlighted immune-related pathways in PAPS-associated loci. The comparison with other immune-mediated diseases revealed a close genetic relatedness to neuromyelitis optica, systemic sclerosis, and Sjögren's syndrome, suggesting colocalized causal variations close to STAT1-STAT4, TNPO3, and BLK. This study represents a comprehensive large-scale genetic analysis for PAPS and provides new insights into the genetic basis and pathophysiology of this rare disease.

Saccharopolyspora mangrovi sp. nov., a novel mangrove soil actinobacterium with distinct metabolic potential revealed by comparative genomic analysis.

A novel mangrove soil-derived actinomycete, strain S2-29T, was found to be most closely related to Saccharopolyspora karakumensis 5K548T based on 16S rRNA sequence (99.24% similarity) and genomic phylogenetic analyses. However, significant divergence in digital DNA-DNA hybridization, average nucleotide identity, and unique biosynthetic gene cluster possession distinguished S2-29T as a distinct Saccharopolyspora species. Pan genome evaluation revealed exceptional genomic flexibility in genus Saccharopolyspora, with > 95% accessory genome content. Strain S2-29T harbored 718 unique genes, largely implicated in energetic metabolisms, indicating different metabolic capacities from its close relatives. Several uncharacterized biosynthetic gene clusters in strain S2-29T highlighted the strain's untapped capacity to produce novel functional compounds with potential biotechnological applications. Designation as novel species Saccharopolyspora mangrovi sp. nov. (type strain S2-29T = JCM 34,548T = CGMCC 4.7716T) was warranted, expanding the known Saccharopolyspora diversity and ecology. The discovery of this mangrove-adapted strain advances understanding of the genus while highlighting an untapped source of chemical diversity.

A description of two novel Psilocybe species from southern Africa and some notes on African traditional hallucinogenic mushroom use

ABSTRACT Two new Psilocybe species (Hymenogastraceae), P. ingeli and P. maluti, are described from southern Africa. Morphology and phylogeny were used to separate the two novel fungi from their closest relatives in the genus. Psilocybe ingeli was found fruiting on bovine manure–enriched grasslands in the Kwa-Zulu Natal Province of South Africa and differs from its closest relative P. keralensis and others in the internal transcribed spacer ITS1-5.8S-ITS2, partial 28S nuc rDNA, and translation elongation factor 1-alpha regions, distribution, and having larger basidiospores. Similarly, P. maluti was collected from the Free State Province of South Africa and observed in the Kingdom of Lesotho, growing on bovine manure. A secotioid pileus, geographic distribution, and differences in the same DNA regions distinguish P. maluti from its closest relative P. chuxiongensis. Furthermore, the spore dispersal and traditional, spiritualistic use of P. maluti are discussed here.

Assessing the Impacts of Land Use on Water Quality in the Acacias River Basin, Colombia

Surface water resources have played a fundamental role in the development of human societies. Considering that different agricultural and industrial activities are carried out in the Acacias River basin, the main objective of this research was to analyze the influence of land use on the water quality in this area by identifying the main sources that influence river water quality. The methodology consisted of establishing 12 sampling stations with different land uses at three times. The National Sanitation Foundation-Water Quality Index (NSF-WQI) was applied to the obtained water quality evaluation data. The main results showed that the stations associated with urban centers presented a higher concentration in the following variables: fecal coliforms, biochemical oxygen demand (BOD) and phosphates. The principal components analysis revealed a close relation between the parameters of fecal coliforms, phosphates and BOD, and the pollution processes by organic matter, which are probably related to domestic and industrial wastewater discharges, and to detergents in urbanized areas. The parameters with the greatest range of values were total dissolved solids and turbidity. These results coincide with what was observed in the correlation analysis. Finally, nitrates showed higher concentrations at stations 6 and 7, associated with agricultural and industrial influence areas (i.e., oil palm crops in the basin). This study about the Acacias River is, thus, extremely important for the region, and concludes that the river’s self-purifying capacity allows improved water quality in the areas where the predominant land use is not associated with human settlements.

COVID-19 Pandemic Effects on Epileptic Children and Interleukin 6 Levels in Recently Diagnosed Epileptic Patients: A Cross Sectional Study

Abstract Background Epilepsy is a disease with wide range of definitions. It is considered a multifactorial condition that may present at various ages and in many forms, which makes it challenging for physicians. In late 2019, SARS-CoV-2 (COVID-19) emerged as a novel coronavirus. Both epilepsy and COVID-19 can be linked in more than one way. Aim of the Study To Determine the effects of COVID-19 pandemic on the health-related quality of life and psychosocial aspects of children with epilepsy & to Determine whether COVID-19 infection is an inflicting cause for epilepsy in newly diagnosed cases. Patients and Methods We interviewed 50 patients with Epilepsy and their parents, for the blood tests we sampled 40 and 40 close relatives with no medical condition of similar age and sex. Results 50 subjects’ results were demonstrated, 28 males and 22 females, median age was 9 years old. Unfortunately, almost all were experiencing depression, data showed that 1 (2%) didn’t have depression, 15 (30%) had mild depression, 27 (54%) had moderate depression and 7 (14%) had been experiencing severe depression, Mostly, all in our study were experiencing anxiety, data showed that 1 (2%) didn’t experience anxiety, 7 (14%) experienced mild anxiety, 16 (32%) experienced moderate anxiety while 26 (52%) experienced severe anxiety. Fair physical, social and emotional health overall, data showed that the average physical health quality of life was 450 (SD 197.65), the average emotional health quality of life was 275 (SD 126.91), the average social health quality of life was 275 (SD 123.61) and the average school performance quality of life was 287.5 (SD 154.31). There were 9 cases newly diagnosed with epilepsy who were COVID IgM. Among subjects with COVID IgM positive, 3 (25%) had no neurological manifestations. Cases had higher levels of IL-6 compared to control children 187.5+/-68.89 and 77.33+/-27.94 respectively with statistically significant difference p < 0.001. However, no significant difference was found upon comparing COVID IgM levels of the 2 relevant groups. Conclusion COVID-19 pandemic has major impacts on health-related quality of life, causing depression, anxiety, decreased social and physical activities and poor school performance. COVID-19 can cause new onset seizures and epilepsy, or increase the frequency of seizures, IL-6 is a useful marker for severity of diseases as COVID-19, also for following up the progression of the disease, but not a marker for diagnosing it.

Prorocentrum canariense sp. nov., a case of pseudo-cryptic speciation in the cosmopolitan dinoflagellate P. compressum (Prorocentrales, Dinophyceae).

The planktonic dinoflagellate Prorocentrum compressum is widespread in warm and temperate seas. A strain identified as P. cf. compressum BEA 0681B isolated from the island of Gran Canaria, NE Atlantic Ocean, showed a divergence in rDNA/ITS phylogenies with respect to P. compressum. The Canarian strain was oval, with an average length-to-width ratio of 1.35, smooth thecal surface with less than 150 thecal pores, including oblique pores, sometimes with a bifurcated opening. In contrast, P. compressum was rounder, with a length-to-width ratio < 1.2, with reticulate-foveate ornamentation and 200-300 pores per valve. We propose Prorocentrum canariense sp. nov. These species clustered as the most early-branching lineage in the clade Prorocentrum sensu stricto. Although this clade mainly contains planktonic species, the closer relatives were the benthic species P. tsawwassenense and P. elegans. Interestingly, P. compressum and P. canariense sp. nov. are widely distributed in temperate and warm seas without an apparent morphological adaptation to planktonic life. The formation of two concentric hyaline mucilaginous walls could contribute to this success. We discuss the use of Prorocentrum bidens to solve the nomenclature issue of P. compressum that was described citing a diatom as basionym.

An empirical study on the state-of-the-art methods for requirement-to-code traceability link recovery

Requirements-to-code traceability link recovery (RC-TLR) can establish connections between requirements and target code artifacts, which is critical for the maintenance and evolution of large software systems. However, to the best of our knowledge, there is no existing experimental study focused on state-of-the-art (SOTA) methods for the RC-TLR problem, and there is also a lack of uniform benchmarks for evaluating new methods in the field. We developed a framework to identify SOTA methods using the Systematic Literature Review method and applied it to research in the RC-TLR field from 2018 to 2023. Through experiments replication on 13 datasets using 6 methods, we observed that for information retrieval-based methods, Close Relations between Target artifacts-based method (CRT), TraceAbility Recovery by Consensual biTerms (TAROT), and Fine-grained TLR (FTLR) performed well on COEST dataset, while Combining Part-Of-Speech with information-retrieval techniques (Conpos) and TAROT achieve promising results in large datasets. As concerns machine learning-based methods, Random Forest consistently exhibits strong performances on all datasets. We hope that this study can provide a comparative benchmark for performance evaluation in the RC-TLR field. The resource repository that we have established is expected to alleviate the workload of researchers in performance analysis , and promote progress of the field.

Serosurvey of canine leishmaniasis in five departments near an identified human clinical case in Marseille (France)

Leishmania infantum is a protozoan parasite of the family Trypanosomatidae, transmitted by the bite of phlebotomine sand flies (Diptera: Psychodidae). It is responsible for human and canine leishmaniasis in countries bordering the Mediterranean basin. Here we describe a clinical case of human cutaneous leishmaniasis in a 76-year-old female patient living in Marseille. Upon interrogation, the patient had no history of recent travel or contact with animals. The study involved clinical, serological, and molecular investigation of the occurrence of Leishmania infection in 718 dogs from five departments within a 130 km radius perimeter around Marseille. Five dogs showed signs of moderate leishmaniasis. Additionally, the serological survey of dogs revealed a global seroprevalence of 5.1%, with a significantly different prevalence in the Vaucluse department. Molecular analysis and phylogenetic studies highlighted the close relatedness of Leishmania strains between human and canine hosts with 99.6% of identity, indicating local transmission. The findings underscore the importance of serological surveillance in dogs and human. In a One Health approach, it is necessary to continue investigating Leishmania infection in all potential reservoirs, especially for zoonotic L. infantum in wildlife (red foxes, leporids, rodents, etc.) but also in dogs, cats, and equids.

Predictive and Experimental Motif Interaction Analysis Identifies Functions of the WNK-OSR1/SPAK Pathway.

The WNK-OSR1/SPAK protein kinase signaling pathway regulates ion homeostasis and cell volume, but its other functions are poorly understood. To uncover undefined signaling functions of the pathway we analyzed the binding specificity of the conserved C-terminal (CCT) domains of OSR1 and SPAK to find all possible interaction motifs in human proteins. These kinases bind the core consensus sequences R-F-x-V/I and R-x-F-x-V/I. Motifs were ranked based on sequence, conservation, cellular localization, and solvent accessibility. Out of nearly 3,700 motifs identified, 90% of previously published motifs were within the top 2% of those predicted. Selected candidates (TSC22D1, CAVIN1, ATG9A, NOS3, ARHGEF5) were tested. Upstream kinases WNKs 1-4 and their close relatives, the pseudokinases NRBP1/2, contain CCT-like domains as well. We identified additional distinct motif variants lacking the conserved arginine previously thought to be required, and found that the NRBP1 CCT-like domain binds TSC22D1 via the same motif as OSR1 and SPAK. Our results further highlight the rich and diverse functionality of CCT and CCT-like domains in connecting WNK signaling to cellular processes.

Optimizing bacteriophage treatment of resistant Pseudomonas.

Phage therapy is increasing in relevance as an alternative treatment to combat antibiotic resistant bacteria. Phage cocktails are the state-of-the-art method of administering phages in clinical settings, preferred over monophage treatment because of their ability to eliminate multiple bacterial strains and reduce resistance formation. In our study, we compare monophage applications and phage cocktails to our chosen method of phage sequential treatments. To do so, we isolated four novel bacteriophages capable of infecting Pseudomonas alcaligenes T3, a close relative of P. aeruginosa, and characterized them using sequencing and transmission electron microscopy. While investigating monophage treatments, we observed that different phage concentrations had a strong impact on the timing and amount of resistance formation. When using phage cocktails, we observed that P. alcaligenes were capable of forming resistance in the same timespan it took them to become resistant to single phages. We isolated mutants resistant to each single phage as well as mutants exposed to phage cocktails, resulting in bacteria resistant to all four phages at once. Sequencing these mutants showed that different treatments yielded unique single nucleotide polymorphism mutation patterns. In order to combat resistance formation, we added phages one by one in intervals of 24 h, thus managing to delay resistance development and keeping bacterial growth significantly lower compared to phage cocktails.IMPORTANCEWHO declared antimicrobial resistance a top threat to global health; while antibiotics have stood at the forefront in the fight against bacterial infection, the increasing number of multidrug-resistant bacteria highlights a need to branch out in order to address the threat of antimicrobial resistance. Bacteriophages, viruses solely infecting bacteria, could present a solution due to their abundance, versatility, and adaptability. For this study, we isolated new phages infecting a fast-mutating Pseudomonas alcaligenes strain capable of forming resistance within 30 h. By using a sequential treatment approach of adding one phage after another, we were able to curb bacterial growth significantly more compared to state-of-the-art phage cocktails.

Tepidibacillus marianensis sp. nov., a novel heterotrophic iron-reducing bacterium isolated from Mariana Trench sediment.

A novel chemoheterotrophic iron-reducing micro-organism, designated as strain LSZ-M11000T, was isolated from sediment of the Marianas Trench. Phylogenetic analysis based on the 16S rRNA gene revealed that strain LSZ-M11000T belonged to genus Tepidibacillus, with 97 % identity to that of Tepidibacillus fermentans STGHT, a mesophilic bacterium isolated from the Severo-Stavropolskoye underground gas storage facility in Russia. The polar lipid profile of strain LSZ-M11000T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, as well as other unidentified phospholipids and lipids. The major fatty acids were C16 : 0 (28.4 %), C18 : 0 (15.8 %), iso-C15 : 0 (12.9 %), and anteiso-C15 : 0 (12.0 %). Strain LSZ-M11000T had no menaquinone. Genome sequencing revealed that the genome size of strain LSZ-M11000T was 2.97 Mb and the DNA G+C content was 37.9 mol%. The average nucleotide identity values between strain LSZ-M11000T and its close phylogenetic relatives, Tepidibacillus fermentans STGHT and Tepidibacillus decaturensis Z9T, were 76.4 and 72.6 %, respectively. The corresponding DNA-DNA hybridization estimates were 20.9 and 23.4 %, respectively. Cells of strain LSZ-M11000T were rod-shaped (1.0-1.5×0.3-0.5 µm). Using pyruvate as an electron donor, it was capable of reducing KMnO4, MnO2, As(V), NaNO3, NaNO2, Na2SO4, Na2S2O3, and K2Cr2O7. Based on phenotypic, genotypic, and phylogenetic evidence, strain LSZ-M11000T is proposed to be a novel strain of the genus Tepidibacillus, for which the name Tepdibacillus marianensis is proposed. The type strain is LSZ-M11000T (=CCAM 1008T=JCM 39431T).

Leptospira infection in bats in Vietnam

Bats from three provinces in Vietnam (Lai Chau, Son La, and Dong Thap) were examined for the presence of pathogenic Leptospira or specific antibodies using polymerase chain reaction (PCR), enzyme-linked immunosorbent assay (ELISA), and microscopic agglutination test (MAT). Tissue specimens from 298 bats belonging to 11 species were analyzed using a real-time PCR assay specific for leptospires of pathogenic species. Leptospiral DNA was identified in 40 bats from following species: Rousettus amplexicaudatus (5/9; 55.5%), Rousettus leschenaultii (17/42; 40.4%), Myotis hasseltii (8/25; 32%), Taphozous longimanus (3/12; 25%), and Eonycteris spelaea (7/32; 21.9%). Based on secY phylogeny, sequences from M. hasseltii bore a strong resemblance to L. borgpetersenii. Sequences from other species revealed unique lineages: one of them resembled Leptospira sp., previously identified in Rousettus madagascariensis (Madagascar) and Rousettus aegyptiacus (South Africa); the second lineage showed close relation to L. kirshneri; and the third held an intermediary position between L. noguchii and L. interrogans. Through ELISA, anti-Leptospira antibodies were found in 83 of 306 bats, with the highest seroprevalence observed in R. leschenaultii (44/48; 91.6%), R. amplexicaudatus (6/8; 75%), and E. spelaea (19/25; 76%). 66 of these ELISA-positive samples were tested using MAT; 41 of them were confirmed in MAT as positive. The predominant serogroups in our study were Tarassovi and Mini.

Pseudomonas aeruginosa producing FIM-1-metallo-β-lactamase: emergence and cross-transmission in a long-term acute care rehabilitation hospital.

FIM-1 metallo-β-lactamase was previously detected in sporadic Pseudomonas aeruginosa clinical isolates. Here, we report on FIM-1-positive P. aeruginosa from two patients who had shared the same ward in a long-term acute care rehabilitation hospital. Whole-genome sequencing analysis revealed close relatedness of these isolates, which belonged to an ST235 sublineage (clade 8/14) different from those previously reported. Results highlighted the occurrence of clonal diversity among FIM-positive strains and the possibility of their cross-transmission in some healthcare settings.

Involvement of ArlI, ArlJ, and CirA in archaeal type IV pilin-mediated motility regulation.

Many prokaryotes use swimming motility to move toward favorable conditions and escape adverse surroundings. Regulatory mechanisms governing bacterial flagella-driven motility are well-established; however, little is yet known about the regulation underlying swimming motility propelled by the archaeal cell surface structure, the archaella. Previous research showed that the deletion of the adhesion pilins (PilA1-6), subunits of the type IV pili cell surface structure, renders the model archaeon Haloferax volcanii non-motile. In this study, we used ethyl methanesulfonate mutagenesis and a motility assay to identify motile suppressors of the ∆pilA[1-6] strain. Of the eight suppressors identified, six contain missense mutations in archaella biosynthesis genes, arlI and arlJ. In trans expression of arlI and arlJ mutant constructs in the respective multi-deletion strains ∆pilA[1-6]∆arlI and ∆pilA[1-6]∆arlJ confirmed their role in suppressing the ∆pilA[1-6] motility defect. Additionally, three suppressors harbor co-occurring disruptive missense and nonsense mutations in cirA, a gene encoding a proposed regulatory protein. A deletion of cirA resulted in hypermotility, while cirA expression in trans in wild-type cells led to decreased motility. Moreover, quantitative real-time PCR analysis revealed that in wild-type cells, higher expression levels of arlI, arlJ, and the archaellin gene arlA1 were observed in motile early-log phase rod-shaped cells compared to non-motile mid-log phase disk-shaped cells. Conversely, ∆cirA cells, which form rods during both early- and mid-log phases, exhibited similar expression levels of arl genes in both growth phases. Our findings contribute to a deeper understanding of the mechanisms governing archaeal motility, highlighting the involvement of ArlI, ArlJ, and CirA in pilin-mediated motility regulation.IMPORTANCEArchaea are close relatives of eukaryotes and play crucial ecological roles. Certain behaviors, such as swimming motility, are thought to be important for archaeal environmental adaptation. Archaella, the archaeal motility appendages, are evolutionarily distinct from bacterial flagella, and the regulatory mechanisms driving archaeal motility are largely unknown. Previous research has linked the loss of type IV pili subunits to archaeal motility suppression. This study reveals three Haloferax volcanii proteins involved in pilin-mediated motility regulation, offering a deeper understanding of motility regulation in this understudied domain while also paving the way for uncovering novel mechanisms that govern archaeal motility. Understanding archaeal cellular processes will help elucidate the ecological roles of archaea as well as the evolution of these processes across domains.

Investigation of the usage of carbon-based two dimensional materials in lithium sulfide (Li–S) batteries

After the synthesis of graphene (Gr), the other two-dimensional (2D) allotropes of carbon based materials have been predicted theoretically or synthesized by experimentally. Two of these nanomaterials are graphyne (Gy) and graphdiyne (Gdy) which are close relatives of Gr and can be synthesized in bulk. While carbon atoms in Gr bonds with sp2 bonds, Gy and Gdy comprise sp and sp2 hybridized carbon atoms with high degrees of π conjugation that features uniformly distributed pores. So, these intrinsic nanopores add distinction to Gy and Gdy with respect to the Gr especially for energy storage applications. Nowadays, the researchers are studying to improve the storage capacity of Lithium-ion batteries (LIBs). However, Lithium–Sulfur (Li–S) batteries can store approximately five times more energy in terms of energy density compared to LIBs. In this study, we have systematically investigated the lithium polysulfides (LixSy; 1≤x≤2,1≤ y ≤ 8) adsorbed on Gr, Gy and Gdy monolayers by means of density functional theory (DFT) calculations. Our results reveal that, the presence of sp bonds and the size of nanopores in the structure extremely affect the adsorption energy of small sized LixSy clusters. However, the adsorption energies obtained with increasing the size of LixSy clusters are almost similar in Gr, Gy and Gdy monolayers. The diffusion barrier energy values obtained for LixSy clusters indicate that the migration of clusters on Gr may be easy but it is hard on Gdy and especially on Gy due to the pore networks in the structures acting as traps to anchor the LixSy clusters. In addition, we have investigated the double adsorption of LixSy clusters on Gr, Gy and Gdy structures to search the shuttle effect. It can be reported that LixSy clusters do not bind each others and do not create long polysulfide chains, which is not requested.

Geographic origin, ancestry, and death circumstances at the Cornaux/Les Sauges Iron Age bridge, Switzerland

Cornaux/Les Sauges (Switzerland, Late Iron Age) revealed remnants of a wooden bridge, artifacts, and human and animal skeletal remains. The relationship between the collapsed structure and the skeletal material, whether it indicates a potential accident or cultural practices, remains elusive. We evaluate the most plausible scenario for Cornaux based on osteological, taphonomic, isotopic, and paleogenomic analysis of the recovered individuals. The latter amount to at least 20 individuals, mostly adult males. Perimortem lesions include only blunt force traumas. Radiocarbon data fall between the 3rd and 1st c. BCE, although in some cases predating available dendrochronological estimates from the bridge. Isotopic data highlight five to eight nonlocals. No close genetic relatedness links the analyzed skeletons. Paleogenomic results, the first for Iron Age Switzerland, point to a genetic affinity with other Central and Western European Iron Age groups. The type of skeletal lesions supports an accidental event as the more plausible explanation. Radiocarbon data and the demographic structure of the sample may suggest a sequence of different events possibly including executions and/or sacrifices. Isotopic and paleogenomic data, while not favoring one scenario over the other, do support earlier interpretations of the last centuries BCE in Europe as a dynamic period from a biocultural perspective.

Genomic characterization of infectious bursal disease virus in Argentina provides evidence of the recent transcontinental spread of Chinese genotype A2dB1b

ABSTRACT The infectious bursal disease virus (IBDV) is a significant pathogen affecting the poultry industry worldwide. Its epidemiological history has been marked by the emergence of strains with different antigenic, pathogenic, and genetic features, some of which have shown notable spread potential. The A2dB1b genotype, also known as novel variant, has become widespread and gained increased relevance in IBDV epidemiology. This genotype was described in China in the 2010s and rapidly spread in Asia and Africa. The present study describes the circulation of the A2dB1b genotype in Argentina. Applying a next-generation sequencing approach, we obtained the complete coding sequence of 18 Argentine viruses. The high level of genomic homogeneity observed amongst these viruses, their monophyletic clustering in both partial and complete segments A and B derived phylogenies, and their close relatedness to some Chinese strains suggest that a unique transcontinental spread event from China to Argentina occurred recently. The apparent success of the A2dB1b genotype spreading throughout Asia, Africa, and South America may partially be due to specific amino acid characteristics. Novel residues in the hypervariable region of VP2 may help A2dB1b IBDVs evade the protection elicited by the applied commercial vaccines. Our findings underscore the importance of continuous characterization of field samples and evaluation of the control measures currently applied to fight against this specific IBDV genotype.