Search Results (1,245)

Background. Alagille syndrome (ALGS) is a rare autosomal dominant genetic disease caused by pathogenic variants in two genes: Jagged Canonical Notch Ligand 1 (JAG1) and Notch Receptor 2 (NOTCH2). It is characterized by phenotypic variability and incomplete penetrance with multiorgan clinical signs. Methods. Using Next Generation Sequencing (NGS), we analyzed a panel of liver-disease-related genes in a population of 230 patients with cholestasis and hepatopathies. For the rare variants, bioinformatics predictions and pathogenicity classification were performed. Results. We identified eleven rare NOTCH2 variants in 10 patients, two variants being present in the same patient. Ten variants had never been described before in the literature. It was possible to classify only two null variants as pathogenic, whereas the most of variants were missense (8 out of 11) and were classified as uncertain significance variants (USVs). Among patients with ALGS suspicion, two carried null variants, two carried variants predicted to be pathogenic by bioinformatics, one carried a synonymous variant and variants in glycosylation-related genes, and two carried variants predicted as benign in the PEST domain. Conclusions. Our results increased the knowledge about NOTCH2 variants and the related phenotype, allowing us to improve the genetic diagnosis of ALGS. Full article

Studies performed in North America, Africa, and South America have led to the isolation of four new species of Kastovskya, a filamentous cyanobacterial genus that before this manuscript had only one species, Kastovskya adunca from Chile. Kastovskya nitens and K. viridissima were isolated from soils on San Nicolas Island, K. sahariensis was isolated from hypolithic habitats from the Sahara Desert in Algeria, and K. circularithylacoides was isolated from hypolithic habitats in Chile. The molecular analyses are corroborated by morphological data, morphometric analysis, and ecological and biogeographical considerations for robust polyphasic descriptions of all taxa. The peculiar transatlantic distribution of this genus bears similarity to other taxa in recently published studies and is in agreement with a hypothesis suggesting that cyanobacteria in Africa may disperse to the Americas on dust particles during windstorms. This work is unusual in that species in a single rare cyanobacterial genus with a disjunct distribution are described simultaneously from three continents. The 16S rRNA gene analyses performed for this study also revealed that another recent genus, Arizonema, is clearly a later synonym of Symplocastrum. This issue is resolved here with the collapsing of the type species Arizonema commune into Symplocastrum flechtnerae. Full article

Species of the Rhodnius genus have a complex taxonomy because the events of phenotypic plasticity and cryptic speciation make it difficult to correctly classify these vectors. During the taxonomic history of the genus, five synonymization events occurred. Additionally, some authors suggest that R. milesi possibly represent only phenotypic polymorphisms of R. neglectus. Thus, we analyzed the specific status of R. milesi in relation to R. neglectus using phylogenetic studies with the mitochondrial gene cytochrome B and the study of reproductive barriers. The phylogenetic reconstruction grouped R. milesi together with R. neglectus from different localities, demonstrating that these taxa represent the same species based on the phylogenetic species concept. Experimental crosses demonstrate the absence of pre- and postzygotic barriers under laboratory conditions. Additionally, when the hatch rates of crosses are compared to intraspecific crosses, it can be noted that they are high and very similar. Finally, the mortality rate of the hybrids does not indicate hybrid inviability, the absence of chromosome pairing errors does not indicate hybrid sterility, and the proportion between male and female hybrids demonstrates that Haldane’s rule was not acting. Therefore, we perform the formal synonymization of R. milesi with R. neglectus. Full article

The taxonomic status of butterfly rays within the genus Gymnura remains a subject of ongoing debate among researchers. Some authors recognize up to five valid species for the Americas, while others considered several to be synonyms, which has posed a persistent challenge. We aimed to shed light on this complexity by employing molecular operational taxonomic units (MOTUs) based on the mitochondrial gene cytochrome oxidase I (COI). Genetic sequences were obtained from fresh muscle tissue collected in the marine ecoregions corresponding to the type locality from all the nominal butterfly ray species distributed along the Eastern Tropical Pacific (ETP). Our results unveiled compelling findings; all the species delimitation models used consistently identified seven MOTUs for the American continent and an extra G. altavela MOTU restricted to Africa. In addition, our results and models exceeded the worldwide accepted interspecific threshold of 2.0%. Remarkably, our results support the taxonomic reinstatement of Gymnura afuerae (Hildebrand, 1946) as a valid species, with a range expanding into the ETP in the Southern Hemisphere. Similarly, our data support the recent suggestion of resurrecting Gymnura valenciennii (Duméril, 1865) as a valid species in the western Atlantic. These findings urge a reassessment of the conservation status and a comprehensive taxonomic revision of American butterfly rays. Full article

Considering that the presence of a leafy head is a key morphological characteristic that determines the yield and quality of Chinese cabbage, identifying the major genes regulating the formation of a leafy head is crucial for variety improvement. A heading-related gene, BrKS, was previously predicted from a non-heading mutant, nhm1, derived from a heading variety, which encodes a key enzyme involved in gibberellin biosynthesis. Here, another mutant, nhm2, was identified from the same EMS-mutagenized population, and the phenotype of nhm2 was consistent with that of nhm1. We crossed mutants nhm1 and nhm2, and their F₁ plants exhibited the mutant phenotype, which indicated that their mutant genes were allelic. A single non-synonymous mutation in the fourth exon of BrKS in mutant nhm1 and another single non-synonymous mutation in the tenth exon of BrKS in mutant nhm2. The same gene mutation in mutants nhm1 and nhm2 produced a similar non-heading phenotype, which confirmed the role of BrKS in the leafy head formation of Chinese cabbage. RNA-Seq analysis indicated that a transcription factor gene, BrERF1A, which is associated with leaf development, significantly down-regulated expression in mutant nhm1, and after the mutant was treated with GA₃, the expression level of BrERF1A was recovered, which indicated that BrKS might be involved in leafy head formation through regulating the expression level of BrERF1A. Our findings provide important clues for revealing the molecular mechanism of leafy head formation in Chinese cabbage. Full article

Lexical substitution aims to generate a list of equivalent substitutions (i.e., synonyms) to a sentence’s target word or phrase while preserving the sentence’s meaning to improve writing, enhance language understanding, improve natural language processing models, and handle ambiguity. This task has recently attracted much attention in many languages. Despite the richness of Arabic vocabulary, limited research has been performed on the lexical substitution task due to the lack of annotated data. To bridge this gap, we present the first Arabic lexical substitution benchmark dataset AraLexSubD for benchmarking lexical substitution pipelines. AraLexSubD is manually built by eight native Arabic speakers and linguists (six linguist annotators, a doctor, and an economist) who annotate the 630 sentences. AraLexSubD covers three domains: general, finance, and medical. It encompasses 2476 substitution candidates ranked according to their semantic relatedness. We also present the first Arabic lexical substitution pipeline, AraLexSub, which uses the AraBERT pre-trained language model. The pipeline consists of several modules: substitute generation, substitute filtering, and candidate ranking. The filtering step shows its effectiveness by achieving an increase of 1.6 in the F1 score on the entire AraLexSubD dataset. Additionally, an error analysis of the experiment is reported. To our knowledge, this is the first study on Arabic lexical substitution. Full article

Drought poses a significant challenge to plant growth and productivity, particularly in arid regions like northern Kazakhstan. Dehydration-responsive element-binding (DREB) transcription factors play an important role in plant response to drought and other abiotic stresses. In Arabidopsis thaliana, the DREB subfamily consists of six groups, designated DREB1 to DREB6. Among these, DREB2 is primarily associated with drought and salinity tolerance. In the chickpea genome, two DREB genes, CaDREB2c and CaDREB2h, have been identified, exhibiting high sequence similarity to Arabidopsis DREB2 genes. We investigated the nucleotide sequences of CaDREB2c and CaDREB2h genes in several chickpea cultivars commonly grown in northern Kazakhstan. Interestingly, the CaDREB2h gene sequence was identical across all varieties and corresponded to the sequence deposited in the GenBank. However, the CaDREB2c gene sequence exhibited variations among the studied varieties, categorized into three groups: the first group (I), comprising 20 cultivars, contained a CaDREB2c gene sequence identical to the GenBank (Indian cultivar CDC Frontier). The second group (II), consisting of 4 cultivars, had a single synonymous substitution (T to C) compared to the deposited CaDREB2c gene sequence. The third group, encompassing 5 cultivars, displayed one synonymous substitution (C to T) and two non-synonymous substitutions (G to T and G to A). Furthermore, we assessed the gene expression patterns of CaDREB2c and CaDREB2h in different chickpea varieties under drought conditions. Chickpea cultivars 8 (III), 37 (I), 6 (III), and 43 (I) exhibited the highest drought resistance. Our analysis revealed a strong positive correlation between drought resistance and CaDREB2h gene expression under drought stress. Our findings suggest that the chickpea’s adaptive responses to water deprivation are associated with changes in CaDREB2 gene expression. To further elucidate the mechanisms underlying drought tolerance, we propose future research directions that will delve into the molecular interactions and downstream targets of CaDREB2 genes. Full article

Biallelic variants in USH2A are associated with retinitis pigmentosa (RP) and Type 2 Usher Syndrome (USH2), leading to impaired vision and, additionally, hearing loss in the latter. Although the introduction of next-generation sequencing into clinical diagnostics has led to a significant uplift in molecular diagnostic rates, many patients remain molecularly unsolved. It is thought that non-coding variants or variants of uncertain significance contribute significantly to this diagnostic gap. This study aims to demonstrate the clinical utility of the reverse transcription–polymerase chain reaction (RT-PCR)–Oxford Nanopore Technology (ONT) sequencing of USH2A mRNA transcripts from nasal epithelial cells to determine the splice-altering effect of candidate variants. Five affected individuals with USH2 or non-syndromic RP who had undergone whole genome sequencing were recruited for further investigation. All individuals had uncertain genotypes in USH2A, including deep intronic rare variants, c.8682-654C>G, c.9055+389G>A, and c.9959-2971C>T; a synonymous variant of uncertain significance, c.2139C>T; p.(Gly713=); and a predicted loss of function duplication spanning an intron/exon boundary, c.3812-3_3837dup p.(Met1280Ter). In silico assessment using SpliceAI provided splice-altering predictions for all candidate variants which were investigated using ONT sequencing. All predictions were found to be accurate; however, in the case of c.3812-3_3837dup, the outcome was a complex cryptic splicing pattern with predominant in-frame exon 18 skipping and a low level of exon 18 inclusion leading to the predicted stop gain. This study detected and functionally characterised simple and complex mis-splicing patterns in USH2A arising from previously unknown deep intronic variants and previously reported variants of uncertain significance, confirming the pathogenicity of the variants. Full article

Apostasia fujianica belongs to the genus Apostasia and is part of the basal lineage in the phylogenetic tree of the Orchidaceae. Currently, there are only ten reported complete mitochondrial genomes in orchids, which greatly hinders the understanding of mitochondrial evolution in Orchidaceae. Therefore, we assembled and annotated the mitochondrial genome of A. fujianica, which has a length of 573,612 bp and a GC content of 44.5%. We annotated a total of 44 genes, including 30 protein-coding genes, 12 tRNA genes, and two rRNA genes. We also performed relative synonymous codon usage (RSCU) analysis, repeat sequence analysis, intergenomic transfer (IGT) analysis, and Ka/Ks analysis for A. fujianica and conducted RNA editing site analysis on the mitochondrial genomes of eight orchid species. We found that most protein-coding genes are under purifying selection, but nad6 is under positive selection, with a Ka/Ks value of 1.35. During the IGT event in A. fujianica’s mitogenome, the trnN-GUU, trnD-GUC, trnW-CCA, trnP-UGG, and psaJ genes were identified as having transferred from the plastid to the mitochondrion. Compared to other monocots, the family Orchidaceae appears to have lost the rpl10, rpl14, sdh3, and sdh4 genes. Additionally, to further elucidate the evolutionary relationships among monocots, we constructed a phylogenetic tree based on the complete mitogenomes of monocots. Our study results provide valuable data on the mitogenome of A. fujianica and lay the groundwork for future research on genetic variation, evolutionary relationships, and breeding of Orchidaceae. Full article

Crude oil and petroleum products contain various types of sulfur compounds: aliphatic and aromatic mercaptans, hydrogen sulfide, sulfides, disulfides, thiophene derivatives, etc. Some of these may dissolve in water only slightly, but their toxicity and corrosiveness indicate that even these small amounts should be eliminated from water. This work examines, for the first time, the removal of thiophenol (synonyms: benzenethiol, phenyl mercaptan) from water using sepiolite. This clay mineral (evaluated by SEM analysis) is an attractive natural sorbent characterized by its microporosity, which results from its crystalline structure and large specific surface area. Because the structure of thiophenol changes depending on the pH of the aqueous solution (due to the loss of a proton), the research was conducted at pH 4, 7 and 9. The detection of thiophenol in aqueous solution was investigated using UV spectroscopy. It was found that the adsorption of thiophenol is possible, but it occurs only in an acidic environment (pH 4). No sorption is observed at pH 7 or 9. The adsorption of thiophenol at pH 4 does not change significantly after changing the ionic strength of the aqueous solution (distilled water, 0.01 NaCl and 0.1 NaCl). The adsorption capacity of sepioliteis approximately 0.23–0.34 mg/g. Studies using infrared spectroscopy and fitting of Freundlich and Langmuir isotherm models to the results of adsorption experiments indicate that adsorption on unmodified sepiolite follows a physisorption mechanism. Additionally, to understand the behavior of thiophenol in the presence of sepiolite across different pH ranges, DFT/PCM/B3LYP/Aug-CC-pVDZ calculations were used to analyze the charge distribution on particular atoms in its structure. Full article

Most species of Papilionidae are large and beautiful ornamental butterflies. They are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. Complete mitochondrial genomes (mitogenomes) have been widely used in phylogenetic studies of butterflies, but mitogenome knowledge within the family Papilionidae is limited, and its phylogeny is far from resolved. In this study, we first report the mitogenome of Byasa confusa from the subfamily Papilioninae of Papilionidae. The mitogenome of B. confusa is 15,135 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an AT-rich control region (CR), closely mirroring the genomic structure observed in related butterfly species. Comparative analysis of 77 Papilionidae mitogenomes shows gene composition and order to be identical to that of an ancestral insect, and the AT bias, Ka/Ks, and relative synonymous codon usage (RSCU) are all consistent with that of other reported butterfly mitogenomes. We conducted phylogenetic analyses using maximum-likelihood (ML) and Bayesian-inference (BI) methods, with 77 Papilionidae species as ingroups and two species of Nymphalidae and Lycaenidae as outgroups. The phylogenetic analysis indicated that B. confusa were clustered within Byasa. The phylogenetic trees show the monophyly of the subfamily Papilioninae and the tribes Leptocircini, Papilionini, and Troidini. The data supported the following relationships in tribe level on Papilioninae: (((Troidini + Papilionini) + Teinopalpini) + Leptocircini). The divergence time analysis suggests that Papilionidae originated in the late Creataceous. Overall, utilizing the largest number of Papilionidae mitogenomes sequenced to date, with the current first exploration in a phylogenetic analysis on Papilionidae (including four subfamilies), this study comprehensively reveals the mitogenome characteristics and mitogenome-based phylogeny, providing information for further studies on the mitogenome, phylogeny, evolution, and taxonomic revision of the Papilionidae family. Full article

The detection of cryptic species in complexes that have undergone recent speciation is often difficult, since many standard nuclear markers have not yet accumulated differences between closely related taxa, and differences in mitochondrial markers can be leveled out due to mitochondrial introgressions. In these cases, the use of derived chromosomal characters such as non-ancestral chromosomal numbers and/or unusual karyotype features may be a solution to the species delimitation problem. However, non-ancestral but similar karyotypes may arise secondarily as a result of homoplastic evolution, and their interpretation as homologies may lead to incorrect taxonomic conclusions. In our study, we show that the combined use of mitochondrial DNA barcodes and karyotypes helps to solve this problem and identifies cryptic species in situations where each of these markers does not work individually. Using this approach, we show that the fauna of Armenia and adjacent Iran includes the following cryptic taxa of the Polyommatus ripartii species complex (haploid chromosome number, n in parentheses): P. ripartii paralcestis (n = 90), P. ripartii kalashiani, subsp. nov (n close to 90), P. emmeli, sp. nov. (n = 77–79), P. keleybaricus, sp. nov. (n = 86), P. demavendi belovi (n = 73–75), P. demavendi antonius, subsp. nov. (n = 71–73), P. admetus anatoliensis (n = 79) and P. eriwanensis (n = 29–34). Polyommatus admetus yeranyani is synonymized with P. admetus anatoliensis. Full article

In this paper, we present an innovative approach inspired by the Path-scan model to detect paths with k adjacent edges (k-path) exhibiting unusual behavior (synonymous with anomaly) within network communications. This work is motivated by the challenge of identifying malicious activities carried out in vulnerable k-path in a small to medium-sized computer network. Each observed edge (time series of the number of events or the number of packets exchanged between two computers in the network) is modeled using the three-state observed Markov model, as opposed to the Path-scan model which uses a two-state model (active state and inactive state), to establish baselines of behavior in order to detect anomalies. This model captures the typical behavior of network communications, as well as patterns of suspicious activity, such as those associated with brute force attacks. We take a perspective by analyzing each vulnerable k-path, enabling the accurate detection of anomalies on the k-path. Using this approach, our method aims to enhance the detection of suspicious activities in computer networks, thus providing a more robust and accurate solution to ensure the security of computer systems. Full article

Valvata (Cincinna) piscinalis (Müller, 1774) is a widespread and variable Palaearctic freshwater snail species. Some authors have separated more depressed forms with a wider umbilicus as a distinct species, Valvata (Cincinna) ambigua Westerlund, 1873. The latter species was described from Scandinavia and has also been reported from Siberia and Kazakhstan and more recently from Central Europe. We conducted an integrative study of the delimitation and relationships of V. ambigua and V. piscinalis using both morphometric and molecular genetic analyses. Analyses of the morphometric data did not reveal differentiation into distinct clusters. Rather, the shell characteristics used to distinguish V. ambigua and V. piscinalis showed continuous variation. There is little variability in mitochondrial DNA sequences in the V. piscinalis complex. A median-joining network based on cytochrome oxidase sequences showed that the morphological character states supposedly characteristic of V. ambigua and V. piscinalis did not correlate with the genetic relationships of the individuals studied. We therefore consider V. ambigua to be synonymous with V. piscinalis. Full article

Online Mendelian Inheritance in Animals (OMIA is a freely available information resource, which includes information for Equus inherited traits/diseases (collectively called phenes). The database focuses on Mendelian traits and their likely causal variants (mutations). Some of these Mendelian traits are favored by humans, e.g., coat color, while others are diseases. Additions to OMIA are based on publications of peer-reviewed research. Maintaining up-to-date information in OMIA is a challenge, owing to the multiplicity of species, the increase in the number of relevant publications, and as reference genomes and methods of citation continue to evolve. This challenge has been successfully aided by contributions from scientists from around the world. In some cases, those scientists are faculty members who charge their students with curation as an educational activity. Recently, OMIA has introduced computerized lists of standardized names and synonyms (called ontologies) for breeds of Equus and other animals and for phene categories. These ontologies facilitate increased connectivity between OMIA and other online resources. OMIA is and will continue to be a major reference resource for Mendelian phenes in the genus Equus. Full article