Search Results (11)

Serratia species are opportunistic human pathogens found in diverse environmental habitats. Here, we report the first isolation of Serratia nevei from food samples in Nigeria. During a two-month epidemiological surveillance at a local food market in Dutsin-Ma, Katsina State, Nigeria, a total of 180 food samples were collected, and isolation and species identification were performed using chromogenic agar and MicroScan autoSCAN-4, respectively. Antimicrobial susceptibility and minimum inhibitory concentrations (MICs) were determined using the MicroScan autoSCAN-4 system. Strain F129B, recovered from a fresh, unprocessed beef sample, was initially identified as Klebsiella pneumoniae by chromogenic agar and MicroScan autoSCAN-4, and subsequently as Serratia marcescens by MALDI-TOF MS. Only Whole Genome Sequencing (WGS) and bioinformatics analyses confirmed its identity as S. nevei. The strain was then selected for further characterization by Whole Genome Sequencing (WGS) and bioinformatics analyses to confirm its identity. The strain was phenotypically resistant to amoxicillin/clavulanic acid and colistin, with elevated MICs for aztreonam (4 mg/L) and cefuroxime (16 mg/L). In silico analyses of its genome confirmed the isolate as S. nevei, harboring genes conferring resistance to β-lactams (blaSTR-2), aminoglycosides (aac (6′)-Ic), fosfomycin (fosA), streptomycin (satA), and tetracycline (tet (41)). Its virulence repertoire comprises genes associated with adhesion (yidE, yidR, yidQ), colicin tolerance (creA and creD), and heavy metal resistance (czcD, chrBACF operon). These findings underscore the need for genomic characterization for accurate species identification within the Serratia genus. Our findings revealed the emergence of S. nevei in the food supply chain and highlighted its potential for zoonotic transmission. Robust surveillance of the local food supply chain is urgently needed in north-western Nigeria. Full article

Accurate segmentation of navigable waters and obstacles is critical for unmanned surface vessel navigation yet remains challenging in real aquatic environments characterized by complex water textures and blurred boundaries. Current models often struggle to simultaneously capture long-range contextual dependencies and fine spatial details, frequently leading to fragmented segmentation results. In order to resolve these issues, we present a novel segmentation model based on the CoAtNet architecture. Our framework employs an enhanced convolutional attention encoder, where a Fused Mobile Inverted Bottleneck Convolution (Fused-MBConv) module refines boundary features while a Convolutional Block Attention Module (CBAM) enhances feature awareness. The model incorporates a Bi-level Former (BiFormer) to enable collaborative modeling of global and local features, complemented by a Multi-scale Attention Aggregation (MSAA) module that effectively captures contextual information across different scales. The decoder, based on U-Net, restores spatial resolution gradually through skip connections and upsampling. In our experiments, the model achieves 95.15% mIoU on a self-collected dataset and 98.48% on the public MaSTr1325 dataset, outperforming DeepLabV3+, SeaFormer, and WaSRNet. These results show the model’s ability to effectively interpret complex aquatic environments for autonomous navigation. Full article

Propiconazole (PRO), a triazole fungicide, controls fungal diseases by disrupting ergosterol production in fungal cells. It is used in crops such as cereals and fruits. However, there are concerns regarding its potential to disrupt the endocrine system and cause reproductive toxicity. This study examined the effects of PRO on mouse testes, germ cells, and GC-1 spermatogonia. After eight weeks, PRO reduced testicular diameter and downregulated key germ cell genes (Sall4, Piwil, Nanos2, and Dazl). A histological examination revealed smaller seminiferous tubules and fewer SALL4+ cells. PRO also impaired steroidogenesis by downregulating genes (StAR, Cyp11a1, 3β-HSD1) and reducing sperm motility, with a decline in Velocity Straight Line (VSL), Linearity (LIN), Straightness (STR), and motile sperm. PRO caused dose-dependent cytotoxicity in GC-1 spermatogonia, decreased proliferation, and increased apoptosis, marked by cleaved caspase-3 and BAX. PRO also induced autophagy, as presented by elevated levels of autophagy-related genes (LC3 and ATG12) and proteins (ATG5 and LC3A/B). 3-Methyladenine (3-MA), an autophagy inhibitor, downregulates levels of autophagy- and apoptosis-related proteins when 3-MA and PRO are simultaneously treated in vitro. This suggests that both apoptosis and autophagy contribute to PRO-induced testicular cytotoxicity. This study is the first to detail that PRO affects sperm motility in mice and induces autophagy-mediated apoptosis in GC-1 spg. Full article

A newly discovered deposit on the bed of the Steinhatchee River produced a moderately diverse assemblage of 15 vertebrate taxa herein designated the Steinhatchee River 2A (STR 2A) local fauna. Mammalian taxa isotopically shown from other sites to be either grazers or grazing-dominated mixed-feeders numerically dominate the fauna, especially a species of Equus. About 75% of the 552 identifiable fossils from STR 2A, representing a minimum of nine individuals, are referred to the informally named Equus (Equus) sp. A. The site produced the first known examples of associated upper and lower cheekteeth and lower incisors for this species, and also one of just two records outside of central and southern peninsular Florida. Like most Pleistocene sites in Florida, xenarthrans are diverse, with two cingulates, Dasypus and Holmesina, and two pilosans, Paramylodon and Megalonyx. An astragalus and several metatarsals of Holmesina are within the size range of H. septentrionalis, but also have some characteristics found in the older species H. floridanus. These finds corroborate that an evolutionary transition between these two species occurred in Florida during the Irvingtonian. The age of STR 2A is most likely middle Irvingtonian, ca. 0.5–0.7 Ma, an interval poorly known in Florida and the rest of the southeastern USA. Full article

(1) Background: Glioblastoma (GBM) is the most common malignant brain tumor in adults. Due to a lack of level 1 evidence, there is no clear consensus on the optimal extent of resection to improve overall survival. This umbrella review aggregates existing meta-analyses (MAs) to assess overall survival in patients undergoing subtotal resection (STR) versus gross total resection (GTR). (2) Methods: A systematic search of PubMed, Scopus, and Web of Science identified 441 studies, with four MAs meeting inclusion criteria. Data were analyzed using the metaumbrella R package, focusing on overall survival. Quality was assessed using AMSTAR2, with scores ranging from 0 to 11. The Ioannidis criteria were applied to evaluate the credibility of the evidence. (3) Results: The quality assessment rated all four studies highly, with a mean AMSTAR2 score of 10.25. The pooled analysis revealed a significant survival advantage for GTR over STR. However, the Ioannidis classification graded the evidence as Class III, indicating weak credibility. (4) Conclusions: GTR offers a slight survival benefit over STR in GBM patients, but the credibility of the evidence is weak, highlighting the need for further research. Full article

Short Tandem Repeat (STR) testing via capillary electrophoresis is undoubtedly the most popular forensic genetic testing method. However, its low multiplexing capabilities and limited performance with challenging samples are among the factors pushing scientists towards new technologies. Next-generation sequencing (NGS) methods overcome some of these limitations while also enabling the testing of Single-Nucleotide Polymorphisms (SNPs). Nonetheless, these methods are still under optimization, and their adoption into practice is limited. Among the available kits, Thermo Fisher Scientific (Waltham, MA, USA) produces three Precision ID Panels: GlobalFiler NGS STR, Identity, and Ancestry. A clear review of these kits, providing information useful for the promotion of their use, is, however, lacking. To close the gap, a literature review was performed to investigate the popularity, applications, and performance of these kits. Following the PRISMA guidelines, 89 publications produced since 2015 were identified. China was the most active country in the field, and the Identity Panel was the most researched. All kits appeared robust and useful for low-quality and low-quantity samples, while performance with mixtures varied. The need for more population data was highlighted, as well as further research surrounding variables affecting the quality of the sequencing results. Full article

Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. Cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. Malaccensis segregating populations, segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on chromosome 3 of ‘DH-Pahang’ reference assembly v4. Within this region, there was a cluster of pattern recognition receptors, namely leucine-rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell-wall-associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins, positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant progenies but not in the susceptible F₂ progenies at the onset of infection. This suggests that one or several of these genes may control resistance at this locus. To confirm the segregation of single-gene resistance, we generated an inter-cross between the resistant parent ‘Ma850’ and a susceptible line ‘Ma848’, to show that the STR4 resistance co-segregated with marker ‘28820’ at this locus. Finally, an informative SNP marker 29730 allowed the locus-specific resistance to be assessed in a collection of diploid and polyploid banana plants. Of the 60 lines screened, 22 lines were predicted to carry resistance at this locus, including lines known to be TR4-resistant, such as ‘Pahang’, ‘SH-3362’, ‘SH-3217’, ‘Ma-ITC0250’, and ‘DH-Pahang/CIRAD 930’. Additional screening in the International Institute for Tropical Agriculture’s collection suggests that the dominant allele is common among the elite ‘Matooke’ NARITA hybrids, as well as in other triploid or tetraploid hybrids derived from East African highland bananas. Fine mapping and candidate gene identification will allow characterization of molecular mechanisms underlying the TR4 resistance. The markers developed in this study can now aid the marker-assisted selection of TR4 resistance in breeding programs around the world. Full article

Forensic DNA profiles are established by multiplex PCR amplification of a set of highly variable short tandem repeat (STR) loci followed by capillary electrophoresis (CE) as a means to assign alleles to PCR products of differential length. Recently, CE analysis of STR amplicons has been supplemented by high-throughput next generation sequencing (NGS) techniques that are able to detect isoalleles bearing sequence polymorphisms and allow for an improved analysis of degraded DNA. Several such assays have been commercialised and validated for forensic applications. However, these systems are cost-effective only when applied to high numbers of samples. We report here an alternative, cost-efficient shallow-sequence output NGS assay called maSTR assay that, in conjunction with a dedicated bioinformatics pipeline called SNiPSTR, can be implemented with standard NGS instrumentation. In a back-to-back comparison with a CE-based, commercial forensic STR kit, we find that for samples with low DNA content, with mixed DNA from different individuals, or containing PCR inhibitors, the maSTR assay performs equally well, and with degraded DNA is superior to CE-based analysis. Thus, the maSTR assay is a simple, robust and cost-efficient NGS-based STR typing method applicable for human identification in forensic and biomedical contexts. Full article

Sorbus L. is a genus of controversy on its taxonomic concept due to great variations in morphological characteristics. Sorbus sensu stricto species, being monophyletic, are characterized as pinnate leaves. However, phylogenetic relationships of these species are somewhat fluid based on morphological characteristics and genetic markers. In this study, the chloroplast (cp) genomes of eight Sorbus s. str. species were characterized and compared with those of twelve released species in this genus. Our results indicated that the plastomes of the twenty Sorbus species had a conserved quadripartite structure, and 129 annotated genes had the same order and showed a good collinearity. Additionally, numerous SSRs were observed in the cp genome of each Sorbus species; most of the sequence variations appeared in non-coding regions, and four intergenic regions were identified as mutation spots. By contrast, protein-coding genes showed low variations under purifying selection. The phylogenetic and molecular-dating analysis showed that Sorbus was resolved into two major clades, in which S. americana forms one clade originating at 51.78 Ma, and the rest of Sorbus formed another clade, splitting at 36.77 Ma into two sister groups with high support values. These results provide a basis for further studying the phylogenetic relationship and biogeography of Sorbus species. Full article

Mixed human deoxyribonucleic acid (DNA) samples present one of the most challenging pieces of evidence that a forensic analyst can encounter. When multiple contributors, stochastic amplification, and allele drop-out further complicate the mixture profile, interpretation by hand becomes unreliable and statistical analysis problematic. Probabilistic genotyping software has provided a tool to address complex mixture interpretation and provide likelihood ratios for defined sets of propositions. The MaSTR™ software is a fully continuous probabilistic system that considers a wide range of STR profile data to provide likelihood ratios on DNA mixtures. Mixtures with two to five contributors and a range of component ratios and allele peak heights were created to test the validity of MaSTR™ with data similar to real casework. Over 280 different mixed DNA profiles were used to perform more than 2600 analyses using different sets of propositions and numbers of contributors. The results of the analyses demonstrated that MaSTR™ provided accurate and precise statistical data on DNA mixtures with up to five contributors, including minor contributors with stochastic amplification effects. Tests for both Type I and Type II errors were performed. The findings in this study support that MaSTR™ is a robust tool that meets the current standards for probabilistic genotyping. Full article

Forensic investigation for the identification of offenders, recognition of human remains, and verification of family relationships requires the analysis of particular types of highly informative DNA markers, which have high discriminatory power and are efficient for typing degraded samples. These markers, called STRs (Short Tandem Repeats), can be amplified by multiplex-PCR (Polymerase Chain Reaction) allowing attainment of a unique profile through which it is possible to distinguish one individual from another with a high statistical significance. The rapid and progressive evolution of analytical techniques and the advent of Next-Generation Sequencing (NGS) have completely revolutionized the DNA sequencing approach. This technology, widely used today in the diagnostic field, has the advantage of being able to process several samples in parallel, producing a huge volume of data in a short time. At this time, although default parameters of interpretation software are available, there is no general agreement on the interpretation rules of forensic data produced via NGS technology. Here we report a pilot study aimed for a comparison between NGS (Precision ID GlobalFiler™ NGS STR Panel v2, Thermo Fisher Scientific, Waltham, MA, USA) and traditional methods in their ability to identify major and minor contributors in DNA mixtures from saliva and urine samples. A quantity of six mixed samples were prepared for both saliva and urine samples from donors. A total of 12 mixtures were obtained in the ratios of 1:2; 1:4; 1:6; 1:8; 1:10; and 1:20 between minor and major contributors. Although the number of analyzed mixtures is limited, our results confirm that NGS technology offers a huge range of additional information on samples, but cannot ensure a higher sensitivity in respect to traditional methods. Finally, the Precision ID GlobalFiler™ NGS STR Panel v2 is a powerful method for kinship analyses and typing reference samples, but its use in biological evidence should be carefully considered on the basis of the characteristics of the evidence. Full article