Search

Context: Wheat (Triticum aestivum L.) is an important crop that provides food to millions of people all over the world. Currently, wheat production is limited due to various biotic and abiotic stresses resulting from uneven patterns of climate change. Therefore, it is very important to develop climate-resilient wheat cultivars. Crop genetic diversity allows the scientific community to identify genetic variations that can be utilised in the development of improved cultivars. Aims: This study planned to characterise the wheat germplasm with the iPBS-retrotransposons marker system. Methods: A total of 30 iPBS-retrotransposons markers were screened and among these, the 12 most polymorphic markers were selected for further analysis. Key results: Molecular characterisation yielded a total of 170 bands, of which 143 were polymorphic. A substantial level of genetic diversity was observed (mean effective number of alleles: 1.37, Shannon's information index: 0.23, gene diversity: 0.35). Maximum genetic distance was observed in G9 and G60 genotypes. Analysis of molecular variance revealed that most genetic variation (95%) occurred within the populations. The model-based structure algorithm divided the studied germplasm into three populations based on their collection regions. Similarly, the neighbour-joining analysis also divided 70 tested wheat genotypes into three populations, whereas principal coordinate analysis divided the evaluated germplasm into four populations. Conclusions: This study confirms the iPBS-retrotransposons as an ideal marker for the genetic diversity assessment studies for any crop, especially for wheat. Implications: The results presented here will be helpful for the scientific community in the marker-assisted breeding of wheat. Wheat, a vital global food source, faces production limitations due to climate-induced stresses. Developing resilient cultivars is crucial. Genetic diversity aids in identifying variations for improved cultivars. This study utilised iPBS-retrotransposons to characterise wheat germplasm, yielding 170 bands. Genetic distance highlighted G9 and G60 as genetically distinct genotypes. Different methods identified three or four distinct groups of genotypes amongst the studied germplasm. This informs targeted breeding strategies for enhanced wheat varieties. This article belongs to the Collection Plant breeding- and genetics-based tools for food security under changing climate. [ABSTRACT FROM AUTHOR]

The use of medicinal plants for managing diabetes and related conditions has been an integral part of traditional healthcare systems throughout the world including Nagaland, India. Authentic identification of these medicinal plants is crucial for their safe and effective use. A study was aimed for authentic identification of some anti-diabetic potential ethnomedicinal plants from Nagaland, India using DNA sequence based molecular characterization by amplifying and sequencing of ITS, rbcL and matK barcode regions. DNA barcode loci from the nuclear and chloroplast genomes from 15 different ethnomedicinal anti-diabetic plants of Nagaland, India, were studied for molecular characterisation. Based on the ITS, rbcL and matK region sequences, three main discrimination methods, i.e., BLAST, Phylogenetic tree and genetic distance, were adopted to identify the species. Utilising DNA markers for identification is both highly advantageous and efficient due to its reliability and rapidity. Successful amplification across species and high blast hits (100 % identity) highlighted their potential for molecular characterisation. Phylogenetic trees constructed using various models showed distinct clades and subclades, with matK revealing hypervariability and rbcL demonstrating consistent matches. Genetic distances revealed varying levels of similarity, with certain species establishing close relationships based on pairwise comparisons. GC% variations were detected, potentially indicating nucleotide composition differences and functional constraints among species genomes. The findings of this study highlight that the ITS, rbcL , and matK regions serve as effective markers for verifying the authenticity of anti-diabetic medicinal plants indigenous to Nagaland, India. [Display omitted] • DNA markers based species identification of 15 antidiabetic plants from Nagaland. • ITS, matK and rbcL based identification complemented with phonological identification. • Consistency in rbcL and matK regions showing reliability as DNA barcode markers. • Sequence length variations attributed to genomic differences among plants. [ABSTRACT FROM AUTHOR]

The application of microsatellite simple sequence repeat (SSR) markers has proven to be highly effective in genetically characterising the origins of various fruit species. Bosnia and Herzegovina boast abundant cornelian cherry (Cornus mas L.) germplasm within its natural habitats. This study focuses on three geographically distant regions in Bosnia and Herzegovina–Drvar, Mostar and Zenica–comprising a sample of 60 cornelian cherry genotypes. The genetic analysis of cornelian cherry utilised eight microsatellite primers to characterise the genetic makeup of the 60 genotypes. Notably, all observed loci in the three populations demonstrated 100% polymorphism. The total genetic differentiation is 0.042, which is also confirmed by the analysis of molecular variance (AMOVA), which indicates that 3% of the total genetic variation is between groups, 8% between individuals and 89% within individuals. The results of pairwise Fst analysis (pFst) indicate that the greatest differentiation is between the populations of Mostar and Zenica (0.037), between Drvar and Zenica (0.026) and between Drvar and Mostar (0.025). The results of the genetic distance according to Nei confirm these results. Also, the largest difference was observed between the populations of Mostar and Zenica (0.316), then between Drvar and Zenica (0.285), and the smallest between Drvar and Mostar (0.251). This research contributes valuable insights into the genetic diversity and characterisation of cornelian cherry populations in different regions of Bosnia and Herzegovina. [ABSTRACT FROM AUTHOR]

Wheat cultivation is important in Turkish agriculture, which ranks 10th among international wheat producers, and is an important wheat exporter, particularly to Europe. Fusarium-related threats, such as Fusarium Head Blight (FHB) and Fusarium Crown and Root Rots (FCR, FRR), and related mycotoxin seed contamination, jeopardize product quality. This study analysed 65 wheat seed samples for presence of Fusarium species, from cultivars of Triticum aestivum (bread wheat) and T. durum (durum wheat) collected from seven regions of Türkiye. PCR with specific primers, and phylogenetic analyses of TEF1-α segments, discriminated Fusarium species. Levels of the mycotoxin deoxynivalenol (DON) in flour samples were also evaluated. Out of 195 Fusarium isolates, the prominent species included F. graminearum (32% of isolates), F. proliferatum (16%), F. avenaceum (11%), F. clavum (11%), and F. verticillioides (7%). Less frequently isolated species were F. oxysporum (6%), F. acuminatum (3%), F. ramigenum (3%), F. culmorum (3%), F. poae (2%), F. sambucinum (2%), F. tricinctum (2%), Fusarium sp. FTSC12 (2%), F. andiyazi (1%), and F. equiseti, F. incarnatum, and F. fasciculatum (each 0.5%). Five of the 65 samples tested positive for DON, with two exceeding the European Commission threshold for mycotoxin contamination; one bread wheat from the Black Sea region, known for its annual rainfall, and a durum wheat sample from southeastern Anatolia, which had the highest detected DON level of 1730 μg kg-1. Among these samples F. graminearum was the predominant species. As F. andiyazi and F. ramigenum are not normally associated with wheat plants, a pathogenicity test was conducted with two isolates of each of these species, revealing no pathogenicity on the durum wheat cultivar ‘San Carlo’. These results provide a basis for managing fungal threats and mycotoxin contamination, safeguarding the quality of wheat grain as an essential agricultural product. [ABSTRACT FROM AUTHOR]

Context: With growing World population, the demand for higher-yield crops becomes more evident. The genetic diversity, which is crucial for breeding superior cultivars, can be shown by using molecular techniques such as start codon targeted (SCoT) markers. Aims: The motivation of this study was to unfold the genetic diversity of Turkish germplasm. Methods: Ninety-four pea samples (90 landraces, 3 pea breeding materials, and 1 registered variety), were assessed for their diversity by using SCoT markers. Key results: Eight SCoT markers produced a total of 84 scorable bands, of which 74 (88.1%) were polymorphic. There was an average of 9.25 polymorphic bands per primer. The range of diversity indices evaluated, such as polymorphism information content (0.13–0.38), effective numbers of alleles (1.22–1.69), Shannon's diversity index (0.21–0.54), and gene diversity (0.13–0.38), showed great genetic variation in the germplasm under this study. STRUCTURE algorithm suggested the presence of two populations. Polymorphism percentage was 87% and 74%, whereas fixation index was 0.21 and 0.01 for population A and population B respectively. According to analysis of molecular variance, most of the difference was found to lie within population (99%) rather than between populations (1%). In contrast, principal coordinates analysis suggested separation into three populations. Conclusions: The Nei's genetic distance of 94 Turkish pea samples revealed that Antalya_2 and Canakkale_2 are genetically the most diverse and can be utilised as parental lines for breeding purposes. Implications: The wide range of pea varieties found in the Turkish germplasm can serve as a valuable genetic resource for the overall pea breeding efforts. Ensuring universal food security is a crucial concern for all of humanity. Pea, as one of the most important legumes, faces many growing challenges in the light of changing climate, whereas growing superior cultivars is a key strategy to meet the ever-growing demands. Turkish pea germplasm encompasses a rich diversity that can be utilised in breeding programs, particularly among the more diverse samples, to generate cultivars adapted to new changing environments. This article belongs to the Collection Plant breeding- and genetics-based tools for food security under changing climate. [ABSTRACT FROM AUTHOR]

Summary: Cryptaphelenchus species are wood- or bark-inhabiting nematodes, generally mycetophagous and reported to have endophoretic associations with insects. In the present study, we describe two new and one known Cryptaphelenchus species detected in imported and domestic wood samples. Cryptaphelenchus americanum n. sp. and C. minutus were detected in the log samples of Pinus taeda imported from the USA, whereas C. orientalis n. sp. was isolated from the bark of dying Pinus sylvestris trees in Inner Mongolia, China. Both new species displayed characteristic features, including a relatively short body length, four lateral lines, a short post-vulval uterine sac in females, and a distinct cloacal apophysis in male tails. Newly recovered and known species were characterised molecularly, and phylogenetic trees were constructed to study their relationship with related Cryptaphelenchus species. Notably, the genetic divergence observed among Cryptaphelenchus species was found to be more significant compared to morphometrical differences, highlighting the importance of molecular data in taxonomy. The identification of new and known species expands our understanding of the genus and suggests that Cryptaphelenchus species may be under studied, underscoring the necessity for continued exploration. [ABSTRACT FROM AUTHOR]

As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. This Technical Note to the applicants puts together requirements and recommendations for the quality assessment of the methodology, analysis and reporting when DNA sequencing is used for the molecular characterisation of GM plants. In particular, it applies to the use of Sanger sequencing and next‐generation sequencing for the characterisation of the inserted genetic material and its flanking regions at each insertion site, the determination of the copy number of all detectable inserts and the analysis of the genetic stability of the inserts. This updated document replaces the EFSA 2018 Technical Note and reflects the current knowledge in scientific‐technical methods for generating and verifying, in a standardised manner, DNA sequencing data in the context of RA of GM plants. It does not take into consideration the verification and validation of the detection method which remains under the remit of the Joint Research Centre (JRC). [ABSTRACT FROM AUTHOR]

Olfactory neuroblastomas are uncommon malignancies that arise from olfactory receptor cells located high in the nasal cavity. Accurate diagnosis plays a crucial role in determining clinical results and guiding treatment decisions. Diagnosis can be a major challenge for pathologists, especially when dealing with tumours with poor differentiation. The discovery of several molecular and immunohistochemical markers would help to overcome classification difficulties. Due to the paucity of large-scale studies, standardisation of diagnosis, treatment and prediction of outcome remains a challenge. Surgical resection by endoscopic techniques with the addition of postoperative irradiation is the treatment of choice. In addition, it is advisable to consider elective neck irradiation to minimise the risk of nodal recurrence. Molecular characterisation will help not only to make more accurate diagnoses but also to identify specific molecular targets that can be used to develop personalised treatment options tailored to each patient. The present review aims to summarise the current state of knowledge on histopathological diagnosis, the molecular biology and management of this disease. [ABSTRACT FROM AUTHOR]

The clinical management of metastatic urothelial carcinoma (mUC) is undergoing a major paradigm shift; the integration of immune checkpoint inhibitors (ICIs) and antibody–drug conjugates (ADCs) into the mUC therapeutic strategy has succeeded in improving platinum-based chemotherapy outcomes. Given the expanding therapeutic armamentarium, it is crucial to identify efficacy-predictive biomarkers that can guide an individual patient's therapeutic strategy. We reviewed the literature data on mUC genomic alterations of clinical interest, discussing their prognostic and predictive role. In particular, we explored the role of the fibroblast growth factor receptor (FGFR) family, epidermal growth factor receptor 2 (HER2), mechanistic target of rapamycin (mTOR) axis, DNA repair genes, and microsatellite instability. Currently, based on the available clinical data, FGFR inhibitors and HER2-directed ADCs are effective therapeutic options for later lines of biomarker-driven mUC. However, emerging genomic data highlight the opportunity for earlier use and/or combination with other drugs of both FGFR inhibitors and HER2-directed ADCs and also reveal additional potential drug targets that could change mUC management. [ABSTRACT FROM AUTHOR]

Fifty-seven Gallid alphaherpesvirus 2 (GaHV-2) isolates, collected during a 30-year period (1990–2019) from commercial poultry flocks affected by Marek's disease (MD), were molecularly characterised. The GaHV-2 meq gene was amplified and sequenced to evaluate the virus virulence, based on the number of PPPPs within the proline-rich repeats (PRRs) of its transactivation domain. The present illustration of virus virulence evaluation on a large scale of field virus isolates by molecular analysis exemplifies the practical benefit and usefulness of the molecular marker in commercial GaVH-2 isolates. The alternative assay of GaVH-2 virulence pathotyping is the classical Gold Standard ADOL method, which is difficult and impossible to employ on a large scale using the Specific Pathogen Free (SPF) chicks of the ADOL strains kept in isolators for two months. The phylogenetic analysis performed in the present study showed that the meq gene amino acid sequences of the 57 Israeli strains divide into 16 phylogenetic branches. The virulence evaluation was performed in comparison with 36 GaHV-2 prototype strains, previously characterised by the in vivo Gold Standard ADOL assay. The results obtained revealed that the GaHV-2 strains circulating in Israel have evolved into a higher virulence potential during the years, as the four-proline stretches number in the meq gene decreased over the investigated period, typically of very virulent virus prototypes. The present study supports the meq gene molecular markers for the assessment of field GaVH-2 strains virulence. [ABSTRACT FROM AUTHOR]

Abstract As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. This Technical Note to the applicants puts together requirements and recommendations for the quality assessment of the methodology, analysis and reporting when DNA sequencing is used for the molecular characterisation of GM plants. In particular, it applies to the use of Sanger sequencing and next‐generation sequencing for the characterisation of the inserted genetic material and its flanking regions at each insertion site, the determination of the copy number of all detectable inserts and the analysis of the genetic stability of the inserts. This updated document replaces the EFSA 2018 Technical Note and reflects the current knowledge in scientific‐technical methods for generating and verifying, in a standardised manner, DNA sequencing data in the context of RA of GM plants. It does not take into consideration the verification and validation of the detection method which remains under the remit of the Joint Research Centre (JRC).

Streptococcus agalactiae (S. agalactiae) is a pathogen causing bovine mastitis that results in considerable economic losses in the livestock sector. To understand the distribution and drug resistance characteristics of S. agalactiae from dairy cow mastitis cases in China, multilocus sequence typing (MLST) was carried out and the serotypes and drug resistance characteristics of the bacteria in the region were analysed.

The whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is posing major havoc on vegetable production jeopardizing Indian agriculture. During, April 2023, whitefly, B. tabaci sample was collected from the cucumber fields of Muthagadahalli village in the Bengaluru North taluk, Bengaluru district of Karnataka. The total genomic DNA was extracted from a single adult whitefly using the Chelex 100 method. The identification of whitefly cryptic species was performed by amplifying the mitochondrial cytochrome oxidase subunit one (mtCOI) gene using gene-specific primers of B. tabaci. PCR results revealed expected amplificon size of 800 bp. Subsequently, the PCR product was subjected to Sanger sequencing. The nucleotide (nt) sequence of the whitefly sample collected from Muthagadahalli exhibited 98-100 per cent identity with sequences belonging to Asia I whitefly cryptic species known to infect different crops worldwide. The sequence demarcation graph and phylogenetic analysis provided substantial evidence for the present findings. [ABSTRACT FROM AUTHOR]

The clinical management of metastatic urothelial carcinoma (mUC) is undergoing a major paradigm shift; the integration of immune checkpoint inhibitors (ICIs) and antibody–drug conjugates (ADCs) into the mUC therapeutic strategy has succeeded in improving platinum-based chemotherapy outcomes. Given the expanding therapeutic armamentarium, it is crucial to identify efficacy-predictive biomarkers that can guide an individual patient’s therapeutic strategy. We reviewed the literature data on mUC genomic alterations of clinical interest, discussing their prognostic and predictive role. In particular, we explored the role of the fibroblast growth factor receptor (FGFR) family, epidermal growth factor receptor 2 (HER2), mechanistic target of rapamycin (mTOR) axis, DNA repair genes, and microsatellite instability. Currently, based on the available clinical data, FGFR inhibitors and HER2-directed ADCs are effective therapeutic options for later lines of biomarker-driven mUC. However, emerging genomic data highlight the opportunity for earlier use and/or combination with other drugs of both FGFR inhibitors and HER2-directed ADCs and also reveal additional potential drug targets that could change mUC management.

Simple Summary: Cryptosporidium spp. and Giardia duodenalis are widely distributed pathogens in vertebrates. Both protozoa are among the major causes of diarrhoea in humans. Wild boars are known hosts of both parasites and are able to harbour zoonotic species. The main goal of this study was to molecularly evaluate the presence of Cryptosporidium spp. and Giardia duodenalis in faecal samples taken from hunted wild boar in eastern Spain. This area is experiencing a rapid increase in the wild boar population, which is colonising all habitats, including urban and peri-urban areas, thereby increasing interactions with humans. Both parasites were found in our study, evidencing a high prevalence, mainly of Cryptosporidium scrofarum and Cryptosporidium suis, which have been previously reported to affect humans. These results point out the potential for wild boar-human transmission because of close contact interactions, such as space sharing or dressing for meat consumption. The protozoans Giardia duodenalis and Cryptosporidium spp. are common causes of gastrointestinal disease in humans and animals. While both are commonly documented in domestic animals, few studies have analysed their presence in wildlife. To assess the prevalence of both parasites in wild boar (Sus scrofa) in the Valencian Community (eastern Spain), 498 wild boar faecal samples were collected from 2018 to 2022. Cryptosporidium spp. was detected by performing a nested PCR targeting a 578 bp sequence of the small subunit ribosomal RNA gene (SSU rRNA), followed by sequencing and phylogenetic analysis. For G. duodenalis, a qPCR amplifying a fragment of 62 bp from the SSU rRNA was employed. Positive samples were genotyped for glutamate dehydrogenase and β-giardin genes. Different epidemiological factors were considered potential modulating variables in the transmission of both parasites. G. duodenalis prevalence was 1.20%, while Cryptosporidium spp. prevalence reached 21.7%. Coinfection was observed in 0.2%. Genotyping of G. duodenalis isolates only detected genotype E. Two species of Cryptosporidium spp. were identified: Cryptosporidium scrofarum and Cryptosporidium suis. The results of this study demonstrate that the exposure to Cryptosporidium spp. in wild boars is high, particularly among young individuals belonging to the Typical Mediterranean climate. Moreover, the probability of infection is dependent on both the season and the density of wild boars. On the other side, exposure to G. duodenalis seems scarce and is influenced, in turn, by the climate. Both Cryptosporidium species detected in the present study have been reported in humans. Due to wild boar increasing in number and their colonisation of urban and peri-urban areas, this could represent an inherent health risk for the human population. [ABSTRACT FROM AUTHOR]

The submerged surfaces of boats act as microbial seed banks which introduce non-indigenous microbial strains in the marine habitat. This study focuses on the morphological, biochemical and molecular characterisation of bacteria isolated from water and submerged painted boat hulls in Badagry lagoon, Lagos state, Nigeria using standard techniques. The mean bacterial density obtained were 1.9 x 109 CFU/mL and 2.03 x 104 CFU/g for water samples and hull samples respectively. Morphological, biochemical and molecular characterisation confirmed the bacteria to be Bacillus subtilis, B. flexus, B. cereus, Brevibacillus agri, Aeromonas punctata, Staphylococcus sciuri, B. licheniformis, Kurthia gibsonii and Leclercia adecarboxylata. Results of the study showed that some of the isolates (B. cereus, B. flexus, S. sciuri and L. adecarboxylata) are pathogenic while others (B. agri and A. punctate) are opportunistic pathogens. The proportion of pathogenic strains isolated in this study is greater than the non-pathogenic strains. [ABSTRACT FROM AUTHOR]

Environmental context: Organic matter (OM) biodegradation plays a key role as it is one of the main processes causing changes in the amount, composition and properties of OM in sediment. However, a complete understanding of its processes and mechanisms is still not reached. In this study, we aim to explore the chemical composition changes during biodegradation and identify underlying processes. Rationale: Although the scientific community has widely investigated organic matter biodegradation processes, only a limited number of studies have explored the molecular changes of this material, whereas its structure, composition and origin play a key role in these processes. Methodology: We decided to examine the effects of biodegradation on the chemical composition of sedimentary organic matter and to explore the underlying mechanisms. We conceived a laboratory-based degradation experiment utilising organic-rich sediments artificially composed of two contrasting organic matter end-members (i.e. soil and algae) under two oxygen conditions. The sediment samples before and after incubation were then analysed by laser desorption ionisation–Fourier-transform–ion cyclotron resonance–mass spectrometry for molecular characterisation and by thermally assisted hydrolysis and methylation gas chromatography–mass spectrometry in order to offer insights into the mechanisms driving the biodegradation processes. Results: Our results from molecular characterisation unveiled distinct pathways of biodegradation contingent upon the source material. Moreover, they hinted at a predilection for altering high molecular weight compounds like lignin & carboxylic-rich alicyclic molecules (CRAM) and condensed aromatic structures (CAS), manifesting as a conversion into lower molecular weight counterparts. Furthermore, the complementary findings from biomarker analyses underscored the influence of environmental factors – specifically oxygen conditions and microbial communities – on organic matter decomposition. Discussion: Although this study is a controlled laboratory experiment and more studies are needed, it demonstrates the intricate interplay among chemical, biological and environmental factors that profoundly shape the reactivity of organic matter. This study underscores the critical need for persistent inquiry, aimed at unravelling the factors and conditions governing the diverse pathways of biodegradation. Environmental context. Organic matter (OM) biodegradation plays a key role as it is one of the main processes causing changes in the amount, composition and properties of OM in sediment. However, a complete understanding of its processes and mechanisms is still not reached. In this study, we aim to explore the chemical composition changes during biodegradation and identify underlying processes. [ABSTRACT FROM AUTHOR]

• Morphological, Quantitative, bio chemical and molecular characterization of 32 annual and perennial Moringa oleifera genotypes. • D2 analysis grouped the high yielding genotype CBE MO 13 and CBE MO 19 in one cluster. • SSR primers MO 01 and SSR 9522 were found to be polymorphic. Moringa is an indigenous vegetable of India which is also known as the miracle tree due to its application in various fields owing to its nutritional, pharmacological, biotechnological potential. Despite its multidimensional uses, it remains neglected in terms of breeding programme. In order to bring the crop into large scale commercial cultivation, it is necessary to exploit the variability present in it and to develop varieties with improved quantitative and qualitative traits. Hence the present investigation was carried out with 32 accessions to evaluate the per se performance, variability and molecular characterization in order to select elite accessions for hybridization. Characterization based on 14 quantitative and 12 biochemical traits revealed that a considerable amount of variation exists among the accessions for all the traits studied. The distinctness was further confirmed through molecular characterization. Out of 30 SSR primers employed SSR MO 01 (0.566) and SSR 9522 (0.556) were found to be polymorphic with high PIC value. The ranking based on the evaluation of the mean performance and D2 method of variability studied for 32 genotypes elucidated that the genotypes, CBE MO 13, CBE MO 15, CBE MO 19, CBE MO 28, CBE MO 29 and CBE MO 31 were found to be promising. Hence these genotypes can be engrossed to get desirable combinations with all the key traits for further breeding programme. [ABSTRACT FROM AUTHOR]

Dissolved organic matter (DOM) plays a fundamental role in nutrient cycling dynamics in riverine systems. Recent research has confirmed that the concentration of riverine DOM is not the only factor regulating its functional significance; the need to define the chemical composition of DOM is a priority. Past studies of riverine DOM rested on bulk quantification, however technological advancements have meant there has been a shift towards analytical methods which allow the characterisation of DOM either at compound class or more recently molecular level. However, it is important to consider that all analytical methods only consider a defined analytical window. Thus, herein, we explore the use of a hierarchy of methods which can be used in combination for the investigation of a wide range of DOM chemistries. By using these methods to investigate the DOM composition of a range of streams draining catchments of contrasting environmental character, a wide range of compounds were identified across a range of polarities and molecular weight, thereby extending the analytical window. Through the elucidation of the DOM character in stream samples, information can be collected about likely the sources of DOM. The identification of individual key compounds within the DOM pool is a key step in the design of robust and informative bioassay experiments, used to understand in-stream ecosystem responses. This is critical if we are to assess the role of DOM as a bioavailable nutrient resource and/or ecotoxicological factor in freshwater. [ABSTRACT FROM AUTHOR]

Coronavirus disease 2019 (COVID-19) seriously threatens human health and has been disseminated worldwide. Although there are several treatments for COVID-19, its control is currently suboptimal. Therefore, the development of novel strategies to treat COVID-19 is necessary. Ion channels are located on the membranes of all excitable cells and many intracellular organelles and are key components involved in various biological processes. They are a target of interest when searching for drug targets. This study aimed to reveal the relevant molecular features of ion channel genes in COVID-19 based on bioinformatic analyses. The RNA-sequencing data of patients with COVID-19 and healthy subjects (GSE152418 and GSE171110 datasets) were obtained from the Gene Expression Omnibus (GEO) database. Ion channel genes were selected from the Hugo Gene Nomenclature Committee (HGNC) database. The RStudio software was used to process the data based on the corresponding R language package to identify ion channel-associated differentially expressed genes (DEGs). Based on the DEGs, Gene Ontology (GO) functional and pathway enrichment analyses were performed using the Enrichr web tool. The STRING database was used to generate a protein–protein interaction (PPI) network, and the Cytoscape software was used to screen for hub genes in the PPI network based on the cytoHubba plug-in. Transcription factors (TF)–DEG, DEG–microRNA (miRNA) and DEG–disease association networks were constructed using the NetworkAnalyst web tool. Finally, the screened hub genes as drug targets were subjected to enrichment analysis based on the DSigDB using the Enrichr web tool to identify potential therapeutic agents for COVID-19. A total of 29 ion channel-associated DEGs were identified. GO functional analysis showed that the DEGs were integral components of the plasma membrane and were mainly involved in inorganic cation transmembrane transport and ion channel activity functions. Pathway analysis showed that the DEGs were mainly involved in nicotine addiction, calcium regulation in the cardiac cell and neuronal system pathways. The top 10 hub genes screened based on the PPI network included KCNA2, KCNJ4, CACNA1A, CACNA1E, NALCN, KCNA5, CACNA2D1, TRPC1, TRPM3 and KCNN3. The TF–DEG and DEG–miRNA networks revealed significant TFs (FOXC1, GATA2, HINFP, USF2, JUN and NFKB1) and miRNAs (hsa-mir-146a-5p, hsa-mir-27a-3p, hsa-mir-335-5p, hsa-let-7b-5p and hsa-mir-129–2-3p). Gene-disease association network analysis revealed that the DEGs were closely associated with intellectual disability and cerebellar ataxia. Drug-target enrichment analysis showed that the relevant drugs targeting the hub genes CACNA2D1, CACNA1A, CACNA1E, KCNA2 and KCNA5 were gabapentin, gabapentin enacarbil, pregabalin, guanidine hydrochloride and 4-aminopyridine. The results of this study provide a valuable basis for exploring the mechanisms of ion channel genes in COVID-19 and clues for developing therapeutic strategies for COVID-19. [ABSTRACT FROM AUTHOR]

Infection with Blastocystis sp. has been reported in free-living and captive non-human primates (NHPs); however, surveys on Blastocystis sp. from north-western South America are scarce. This study aimed to identify Blastocystis sp. in free-ranging NHPs living in Colombia. A total of 212 faecal samples were collected from Ateles hybridus, Cebus versicolor, Alouatta seniculus, Aotus griseimembra, Sapajus apella, and Saimiri cassiquiarensis. Smears and flotation were used for morphological identification. For samples microscopically classified as positive for Blastocystis sp., we used conventional PCR to amplify and sequence two regions of the SSU rRNA gene and used Maximum Likelihood methods and Median Joining Network analyses for phylogenetic analyses. Via microscopy, 64 samples were Blastocystis sp. positive. Through molecular analyses, 18 sequences of Blastocystis sp. subtype 8 (ST8) were obtained. Strain and allele assignment together with a comparative phylogenetic approach confirmed that the sequences were ST8. Alleles 21, 156, and 157 were detected. Median Joining network analyses showed one highly frequent haplotype shared by specimens from Colombia and Peru and close relationships between haplotypes circulating in NHPs from Colombia, Ecuador, Brazil, and Mexico. This survey could support the elaboration of a more accurate epidemiological picture of the Blastocystis sp. infecting NHPs. [ABSTRACT FROM AUTHOR]

Information regarding genetic alterations of driver cancer genes in circulating tumour cells (CTCs) and their surrounding immune microenvironment nowadays can be employed as a real-time monitoring platform for translational applications such as patient response to therapeutic targets, including immunotherapy. This study aimed to investigate the expression profiling of these genes along with immunotherapeutic target molecules in CTCs and peripheral blood mononuclear cells (PBMCs) in patients with colorectal carcinoma (CRC). Expression of p53, APC, KRAS, c-Myc, and immunotherapeutic target molecules PD-L1, CTLA-4, and CD47 in CTCs and PBMCs were analysed by qPCR. Their expression in high versus low CTC-positive patients with CRC was compared and clinicopathological correlations between these patient groups were analysed. CTCs were detected in 61% (38 of 62) of patients with CRC. The presence of higher numbers of CTCs was significantly correlated with advanced cancer stages (p = 0.045) and the subtypes of adenocarcinoma (conventional vs. mucinous, p = 0.019), while being weakly correlated with tumour size (p = 0.051). Patients with lower numbers of CTCs had higher expression of KRAS. Higher KRAS expression in CTCs was negatively correlated with tumour perforation (p = 0.029), lymph node status (p = 0.037), distant metastasis (p = 0.046) and overall staging (p = 0.004). CTLA-4 was highly expressed in both CTCs and PBMCs. In addition, CTLA-4 expression was positively correlated with KRAS (r = 0.6878, p = 0.002) in the enriched CTC fraction. Dysregulation of KRAS in CTCs might evade the immune system by altering the expression of CTLA-4, providing new insights into the selection of therapeutic targets at the onset of the disease. Monitoring CTCs counts, as well as gene expression profiling of PBMCs, can be helpful in predicting tumour progression, patient outcome and treatment. [ABSTRACT FROM AUTHOR]

The submerged surfaces of boats act as microbial seed banks which introduce non-indigenous microbial strains in the marine habitat. This study focuses on the morphological, biochemical and molecular characterisation of bacteria isolated from water and submerged painted boat hulls in Badagry lagoon, Lagos state, Nigeria using standard techniques. The mean bacterial density obtained were 1.9 x 109 CFU/mL and 2.03 x 104 CFU/g for water samples and hull samples respectively. Morphological, biochemical and molecular characterisation confirmed the bacteria to be Bacillus subtilis, B. flexus, B. cereus, Brevibacillus agri, Aeromonas punctata, Staphylococcus sciuri, B. licheniformis, Kurthia gibsonii and Leclercia adecarboxylata. Results of the study showed that some of the isolates (B. cereus, B. flexus, S. sciuri and L. adecarboxylata) are pathogenic while others (B. agri and A. punctate) are opportunistic pathogens. The proportion of pathogenic strains isolated in this study is greater than the non-pathogenic strains.

Summary: Two populations of bacterial-feeding nematodes belonging to the genus Panagrolaimus were recovered from infected slugs collected from gardens, agricultural areas and nurseries of the Baghpat district (India). Initial morphological characterisation of these populations show that they resemble Panagrolaimus labiatus from China and Bulgaria, P. burdwanensis from India, and P. cf. labiatus from Iran. To clarify taxonomical affiliations, we morphologically compared these two new populations to those recovered from China, Bulgaria, India and Iran. In addition, we sequenced several taxonomically relevant genes and used them to reconstruct phylogenetic relationships. Our results show that the two Indian populations do not significantly differ morphologically from the specimens used to describe the species P. labiatus , and also do not differ among them. We only observed small variations in the size of males and females. In addition, morphologically, the nematodes used to describe P. burdwanensis are very similar to the nematodes used to describe P. labiatus and to the two populations described in this study. Therefore, we propose P. burdwanensis as a junior synonym of P. labiatus and that the two populations recovered from India belong to the P. labiatus species. Phylogenetic analyses using the nucleotide sequences of the internal transcribed spacer (ITS), 18S and 28S rRNA gene sequences support our morphological conclusions. Our study therefore provides a detailed morphological description and molecular marker 18S and 28S gene sequences that can support future taxonomical studies of this species and highlights the importance of using both molecular and morphological data for the proper description of soil microfauna. [ABSTRACT FROM AUTHOR]

Attention-deficit/hyperactivity disorder (ADHD) is a common childhood-onset neurodevelopmental disorder characterised by persistent inattention, hyperactivity and impulsivity. Moreover, ADHD is commonly associated with other comorbid diseases (depression, anxiety, bipolar disorder, etc.). The ADHD symptomatology interferes with subject function and development. The treatment of ADHD requires a multidisciplinary approach based on a combination of non-pharmacological and pharmacological treatments with the aim of ameliorating the symptomatology; among first-line pharmacological treatments are stimulants [such as methylphenidate (MPH) and lisdexamfetamine dimesylate (LDX)]. In this review we explored recent ADHD- and stimulants-related literature, with the aim of compiling available descriptions of molecular pathways altered in ADHD, and molecular mechanisms of current first-line stimulants MPH and LDX. While conducting the narrative review, we applied structured search strategies covering PubMed/MEDLINE database and performed handsearching of reference lists on the results of those searches. The aetiology and pathophysiology of ADHD are incompletely understood; both genetic and environmental factors have been associated with the disorder and its grade of burden, and also the relationship between the molecular mechanisms of pharmacological treatments and their clinical implications. The lack of comprehensive understanding of the underlying molecular pathology makes both the diagnosis and treatment difficult. Few published studies evaluating molecular data on the mechanism of action (MoA) of MPH and LDX on ADHD are available and most of them are based on animal models. Further studies are necessary to improve the knowledge of ADHD pathophysiology and how the MoAs of MPH and LDX differentially modulate ADHD pathophysiology and control ADHD symptomatology. [ABSTRACT FROM AUTHOR]

• New hosts for Iodamoeba were confirmed; goat, dromedary, fallow deer, and donkey. • These animals may not constitute a reservoir for Iodamoeba colonization of humans. • Nuclear Iodamoeba SSU rRNA genes may code for different SSU rDNA sequences. Iodamoeba is a single-celled intestinal parasite, which is common in humans in certain parts of the world, and also in pigs. For the first time, we provide DNA-based evidence of goat, dromedary, fallow deer, and donkey as hosts of Iodamoeba and show that Iodamoeba -specific nucleotide sequences from these four hosts do not appear to overlap with those of humans, unlike those from pigs. We moreover show that similar strains of Iodamoeba can be found in Madagascar, Western Sahara, and Ecuador and that intra-sample diversity is typically extensive across even small fragments of DNA in both human and non-human hosts. [ABSTRACT FROM AUTHOR]

Hypoxia-inducible factor (HIF)-1α is a transcription factor stabilized by hypoxia by inducing or suppressing the homeostatic regulatory gene expression, enabling tissues and cells to survive despite fluctuations in environmental circumstances. As the name implies, hypoxia-inducible factor-1 is secreted not only as a cellular response to hypoxia but also in heat stress and oxidative stress. The goal of this work was to determine the molecular characterisation of the HIF-1α gene coding region as well as the differences in HIF-1αprotein primary structure between Vechur cattle and other cattle breeds in the online databases. Total RNA was isolated from blood samples of 6 Vechur cattle using the trizol reagent method, and full-length c sequences of the HIF-1α gene were sequenced. The base pair length of composite HIF-1αcDNA of Vechur cattle and encoding ORFis 3956 bp and 2469 bp respectively. The 5′UTR was recognized to be 279 bp in length. The start codon was identified at nucleotide 280–282, the stop codon UGA at 2746–2748 bp and a 1208 bp 3′UTR which included a poly-A tail of 27 adenine residues. In a comparative analysis of the cDNA, point transitions causing guanine to adenine (G>A) changes at 1211th and 2699th positions were noticed as a heterozygous condition in the whole 3956 bp sequence. These two SNVs in the coding regions were responsible for two amino acid changes in the deduced 823 amino acid sequence. Since the predicted amino acid arginine had been replaced with lysine at 311th and 807th positions, it showed 99.76 percent sequence identity with Bos taurus. The phylogenetic tree revealed that the HIF-1α protein of Vechur cattle had a lesser evolutionary distance from the same gene of related species emphasising the highly conserved nature of this particular protein. This structural variation observed in the present study should be evaluated on a larger population to assess its functional relevance for thermo-tolerance.

Babesiosis is a tick-borne disease caused by an intra-erythrocytic protozoan of the genus Babesia. The genus contains a large number of species capable of infecting a variety of mammalian hosts, including humans. Misdiagnosis of the infection is a major setback in disease management, monitoring, and control. Therefore, timely and precise identification of infecting Babesia species is critical. This study aimed at detecting and characterizing the Babesia species infecting dogs in the Federal Capital Territory (FCT) Abuja. Blood samples were collected from apparently healthy dogs (n=480), thin smears were prepared, Giemsa-stained, and examined under a microscope. DNA was extracted from positive blood samples (n=15), and PCR amplification of the 18S rRNA gene was performed using generic primers. PCR products were purified, electrophoresed on 1.5% agarose gels and thereafter, sequenced bidirectionally. The prevalence of Babesia species in thin smear was 3.1%. The prevalence in the six Area Councils was 5.0%, 3.75%, 2.5%, 2.5%, 2.5% and 2.5% for Gwagwalada, Municipal, Bwari, Kuje, Kwali and Abaji respectively. The prevalence in relation to age was 3.87% in dogs >1year old and 1.76% in dogs ≤ 1 year old. Prevalence by breed, was 4.38% in exotic dogs, 3.23% in local and 2.35% in crossbred. The prevalence in relation to sex was 3.96% in males and 2.37% in females. The BLAST search was carried out in the NCBI database, and a phylogenetic tree was constructed using nucleotide sequences in GenBank. Electrophoresed PCR products revealed a band size of about 612bp. Blast in NCBI demonstrated 100% similarity with Babesia canis vogeli nucleotide sequences. This study reaffirmed the molecular identification of B. c. vogeli in apparently healthy dogs in Nigeria and it may be of clinical importance to veterinary clinicians in the management and control of the disease. [ABSTRACT FROM AUTHOR]

Molecular characterization of Cryptosporidium has led to increased recognition of the diversity of species infecting animals. A Cryptosporidium Copro-Enzyme Linked Immuno Assay (Copro-ELISA) antigen detection manufactured by Savyon® Diagnostics Ltd., Ashdod, Israel, was used to screen faecal samples from cattle. Copro-ELISA Cryptosporidium antigen positive faecal samples were subjected to Nested PCR for the amplification of 830bp fragments of small subunit (SSU) rRNA gene and followed by nucleotide sequencing by targeting the 18S gene in cattle. Of the 384 bovine faeces screened, 31 (8.07%) were ELISA positive out of the 384 screened samples and 19.4% (6/31) were Cryptosporidium positive using PCR technique. Nucleotide sequencing of the bovine PCR products showed the presence of C. bovis 2 (6.5%), C. ryanae 2 (6.5%), C. andersoni 1 (3.2%) and C. ubiquitum 1(3.2%). C. ubiquitum has also been found in this study in Wurno LGA of Sokoto state, it is a new specie in the genus previously identified as Cryptosporidium Cervine genotype which was reported in wild and domestic ruminants, rodents, carnivores and primates including humans. In calves, there were no significant associations (p>0.05) in prevalence of Cryptosporidium between breeds; between sources of drinking water; between physical nature of faeces (OR=3.61:95% CI on OR: 0.36

The protozoans Giardia duodenalis and Cryptosporidium spp. are common causes of gastrointestinal disease in humans and animals. While both are commonly documented in domestic animals, few studies have analysed their presence in wildlife. To assess the prevalence of both parasites in wild boar (Sus scrofa) in the Valencian Community (eastern Spain), 498 wild boar faecal samples were collected from 2018 to 2022. Cryptosporidium spp. was detected by performing a nested PCR targeting a 578 bp sequence of the small subunit ribosomal RNA gene (SSU rRNA), followed by sequencing and phylogenetic analysis. For G. duodenalis, a qPCR amplifying a fragment of 62 bp from the SSU rRNA was employed. Positive samples were genotyped for glutamate dehydrogenase and β-giardin genes. Different epidemiological factors were considered potential modulating variables in the transmission of both parasites. G. duodenalis prevalence was 1.20%, while Cryptosporidium spp. prevalence reached 21.7%. Coinfection was observed in 0.2%. Genotyping of G. duodenalis isolates only detected genotype E. Two species of Cryptosporidium spp. were identified: Cryptosporidium scrofarum and Cryptosporidium suis. The results of this study demonstrate that the exposure to Cryptosporidium spp. in wild boars is high, particularly among young individuals belonging to the Typical Mediterranean climate. Moreover, the probability of infection is dependent on both the season and the density of wild boars. On the other side, exposure to G. duodenalis seems scarce and is influenced, in turn, by the climate. Both Cryptosporidium species detected in the present study have been reported in humans. Due to wild boar increasing in number and their colonisation of urban and peri-urban areas, this could represent an inherent health risk for the human population.

Background There is a lack of whole-genome sequencing (WGS) data on multidrug-resistant (MDR) bacteria from the Uttarakhand region of India. The aim of this study was to generate WGS data of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates recovered from patients in Uttarakhand's tertiary care centre. Methods A cross-sectional study included 29 MDR K. pneumoniae test isolates obtained from various clinical samples submitted to the bacteriology laboratory for culture and sensitivity testing from July 2018 to August 2019. After preliminary identification and antibiotic susceptibility testing, these isolates were subjected to WGS. Results A total of 27 of 29 isolates were CRKP. ST14 was the most common sequence type (n=8 [29.6%]). Carbapenem resistance was mainly encoded by OXA-48-like genes (21/27 [77.8%]). All isolates had a varied arsenal of resistance genes to different antibiotic classes. KL2 (9/27 [33.3%]) and KL51 (8/27 [29.6%]) were dominant K loci types. O1 and O2 together accounted for 88.9% (n=27) of CRKP isolates. Genes encoding yersiniabactin (ybt) and aerobactin (iuc) were identified in 88.9% (24/27) and 29.6% (8/27) of isolates. The predominant plasmid replicons present were ColKP3 (55.5%), IncFII(K) (51.8%) and IncFIB(pQil) (44.4%). Conclusions This study emphasises the need for continued genomic surveillance of MDR bacteria that could be instrumental in developing treatment guidelines based on integrating phenotypic and molecular methods. [ABSTRACT FROM AUTHOR]

Orf is a disease of small ruminant animals, including goats and sheep, that is caused by a parapoxvirus. Although the mortality rate is low, economic losses may occur due to the clinical signs. Bovine herpesvirus 1 (BoHV-1) infection is known to cause respiratory and reproductive disorders mainly in cattle; however, it has been found to circulate among goats and sheep as well. In contrast to orf virus (ORFV), BoHV-1 does not induce clinical disease in goats. In this study, we aimed to detect the presence of ORFV by molecular methods and to uncover eventual simultaneous herpesvirus infections masked by orf disease signs. To this end, 82 goats, housed near to a cattle herd, were tested. By polymerase chain reaction (PCR), three goats (3.7%) were found to harbour both viruses, while an additional goat was positive for ORFV only. The PCR products were sequenced and phylogenetic analyses were performed. This study revealed that ORFV and BoHV-1 may be present simultaneously in an animal causing a concurrent infection. These data should be taken into consideration when looking for secondary pathogens in diseased goats, and the prevention methods should be developed accordingly. [ABSTRACT FROM AUTHOR]

Abstract Background The present study was aimed at establishing the prevalence, epidemiology and molecular characterization of major haemoprotozoons (Babesia and Theileria) and rickettsia (Anaplasma) of cattle in Jammu region (North India) using microscopy and Polymerase Chain Reaction (PCR). Hematology, microscopy and PCR based prevalence studies were undertaken with 278 whole blood samples from cattle. Molecular prevalence studies were followed by genetic characterization of the isolates of Babesia, Anaplasma and Theileria spp. based on 18S rRNA, 16S rRNA and Tams1 gene, respectively. The data related to metrology and epidemiological variables like temperature, rainfall, season, age and type of livestock rearing was analyzed and correlated with occurrence of disease by statistical methods. Results The prevalence based on microscopy was 12.9% (36/278) whereas PCR recorded 30.22% (84/278) animals positive for haemoparasitic infections. All the samples found positive by microscopy were also recorded positive by PCR. Thus the study revealed prevalence of Babesia bigemina, Anaplasma marginale and Theileria annulata to be 9.7, 16.5 and 0.7% respectively. The metrological and epidemiological variables made inroads for the propagation of vector ticks and occurrence of infection. Haematological alterations predominantly related to decrease in haemoglobin, red blood cell count and packed cell volume were evident in diseased animals and collaterally affected the productivity. Further the genetic characterization of Babesia bigemina. (MN566925.1, MN567603, MN566924.1), Anaplasma marginale. (MH733242.1, MN567602.1) and Theileria annulata (MT113479) provided a representative data of the isolates circulating in the region and their proximity with available sequences across the world. Conclusions Despite holding much significance to the animal sector, comprehensive disease mapping has yet not been undertaken in several parts of India. The present study provides a blue print of disease mapping, epidemiological correlations and genomic diversity of Babesia bigemina, Anaplasma marginale and Theileria annulata circulating in the region.

Infection with Blastocystis sp. has been reported in free-living and captive non-human primates (NHPs); however, surveys on Blastocystis sp. from north-western South America are scarce. This study aimed to identify Blastocystis sp. in free-ranging NHPs living in Colombia. A total of 212 faecal samples were collected from Ateles hybridus, Cebus versicolor, Alouatta seniculus, Aotus griseimembra, Sapajus apella, and Saimiri cassiquiarensis. Smears and flotation were used for morphological identification. For samples microscopically classified as positive for Blastocystis sp., we used conventional PCR to amplify and sequence two regions of the SSU rRNA gene and used Maximum Likelihood methods and Median Joining Network analyses for phylogenetic analyses. Via microscopy, 64 samples were Blastocystis sp. positive. Through molecular analyses, 18 sequences of Blastocystis sp. subtype 8 (ST8) were obtained. Strain and allele assignment together with a comparative phylogenetic approach confirmed that the sequences were ST8. Alleles 21, 156, and 157 were detected. Median Joining network analyses showed one highly frequent haplotype shared by specimens from Colombia and Peru and close relationships between haplotypes circulating in NHPs from Colombia, Ecuador, Brazil, and Mexico. This survey could support the elaboration of a more accurate epidemiological picture of the Blastocystis sp. infecting NHPs.

Information regarding genetic alterations of driver cancer genes in circulating tumour cells (CTCs) and their surrounding immune microenvironment nowadays can be employed as a real-time monitoring platform for translational applications such as patient response to therapeutic targets, including immunotherapy. This study aimed to investigate the expression profiling of these genes along with immunotherapeutic target molecules in CTCs and peripheral blood mononuclear cells (PBMCs) in patients with colorectal carcinoma (CRC). Expression of p53, APC, KRAS, c-Myc, and immunotherapeutic target molecules PD-L1, CTLA-4, and CD47 in CTCs and PBMCs were analysed by qPCR. Their expression in high versus low CTC-positive patients with CRC was compared and clinicopathological correlations between these patient groups were analysed. CTCs were detected in 61% (38 of 62) of patients with CRC. The presence of higher numbers of CTCs was significantly correlated with advanced cancer stages (p = 0.045) and the subtypes of adenocarcinoma (conventional vs. mucinous, p = 0.019), while being weakly correlated with tumour size (p = 0.051). Patients with lower numbers of CTCs had higher expression of KRAS. Higher KRAS expression in CTCs was negatively correlated with tumour perforation (p = 0.029), lymph node status (p = 0.037), distant metastasis (p = 0.046) and overall staging (p = 0.004). CTLA-4 was highly expressed in both CTCs and PBMCs. In addition, CTLA-4 expression was positively correlated with KRAS (r = 0.6878, p = 0.002) in the enriched CTC fraction. Dysregulation of KRAS in CTCs might evade the immune system by altering the expression of CTLA-4, providing new insights into the selection of therapeutic targets at the onset of the disease. Monitoring CTCs counts, as well as gene expression profiling of PBMCs, can be helpful in predicting tumour progression, patient outcome and treatment.

Summary: A new species of cyst-forming nematode, Heterodera amaranthusiae n. sp., is described and illustrated from the weed, Amaranthus retroflexus , in a potato field in Yunnan Province, China. It is characterised by having canary to russet-brown and asymmetric lemon-shaped cyst, distinct neck, bifenestrate vulval cone, relatively short vulval slit of 29 (28-32) μ m, bullae absent and underbridge absent or weak if present. Second-stage juveniles are characterised by a well-developed stylet of 23 (22-25) μ m with robust shaft and basal knobs concave anteriorly, tail conoid, 51 (48-58) μ m long and hyaline region comprising 48 (41-53)% of its length. Morphologically and morphometrically it most resembles H. vallicola in the Humuli group. The ITS, 28S and COI gene sequences of H. amaranthusiae n. sp. clearly differentiate it from other Heterodera species. For diagnostic purposes, restriction enzyme analysis of the ITS region and three restriction enzymes, Alu I, Bsu RI (Hae III) and Cfo I (Hha I), were selected, clearly distinguishing H. amaranthusiae n. sp. from representative species in the Humuli group. Phylogenetic relationships with other species of the genus, inferred from two ribosomal regions and the cytochrome oxidase c subunit 1 region, based on Bayesian analysis, consistently showed that H. amaranthusiae n. sp. clustered with high support with other Humuli group species but with separate species status. [ABSTRACT FROM AUTHOR]

Background: Vancomycin resistant enterococci (VRE) has rapidly become one of the leading cause of nosocomial infections and major growing problems in health care facilities globally. Objectives: To determine prevalence, perform molecular characterization and to see the clinical outcome of VRE at a tertiary care centre. Materials and methods: A total of 122 enterococci isolates collected from various clinical specimens except stool obtained in Clinical Microbiology Laboratory of Rama Medical College Hospital and Research Centre, Kanpur were processed for species differentiation. VRE were detected by MIC determination of vancomycin using agar dilution method. Molecular characterisation of VRE was done for detection of VanA and VanB genes by conventional PCR. Clinical outcome of VRE infected cases were analysed by patient medical records. Results: Prevalence of VRE was found to be 6.5% (8/122). (75%) 6/8 were E. faecium and (25%) 2/8 were E. faecalis. By AST report, among VRE, resistance to teicoplanin was 100%, that to penicillin was 100%, norfloxacin 100%, levofloxacin 100%, high level gentamycin (HLG) 100%, high level streptomycin (HLS) 87.5%, erythromycin 87.5%, ciprofloxacin 87.5%, nitrofurantoin 83.3% and that to linezolid was 12.5%. Gene detection by PCR showed 3 VanA and 1 VanB genes out of 8 VRE and among 5 VRE, VanA or VanB genes were not detected. Mortality was seen in one case of VRE, who had mixed infection with Klebsiella pneumoniae and was resistant to linezolid. Conclusion: Prevalence of VRE and high level aminoglycoside resistance among them seems high. Prudent use of vancomycin, strict enforcement of infection control policies in hospital and surveillance detection of VRE in hospital should be done regularly.

Abstract Background To determine the phenotype, molecular characterisation and risk factors of postoperative meningitis induced by Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (EPE) in China. Methods We performed a multi-centre comparative cohort study of postoperative meningitis patients infected with Enterobacteriaceae in 4 neurosurgical centres in China from January 2014 to December 2019. Phenotype and molecular characteristics of the isolates were reviewed and tested, and independent risk factors of the EPE meningitis were evaluated by binary logistic regression. Results In total, 220 Enterobacteriaceae include 78 EPE were available in this study. 85.6% (67/78) ESBL-related genes were tested, and bla SHV (14.9%) and bla SHV + bla TEM + bla CTX-M-9 (20.9%) were found to be the most frequent mono and combined ESBL-related genes harboured by Enterobacteriaceae. On binary logistic analysis, craniotomy (OR. 2.583, 95% C.I. 1.274–5.235, P = 0.008) and malignancy (OR. 2.406, 95% C.I. 1.299–4.456, P = 0.005) were the associated independent risk factors to meningitis induced by EPE. Conclusions To the best of our knowledge, this is the largest series focusing on risk factors of EPE meningitis which has been conducted in China. Craniotomy and malignancy were independent risk factors for EPE meningitis. The risk factors identified may be further utilized in clinical practice and research to avoid and reduce the mortality in future.

ABSTRACT The melon (Cucumis melo L.) is one of the most important horticultural crops in the northeast of Brazil. The characterisation of germplasm is an efficient process for managing plant genetic resources, as it contributes to better conservation and improved use in breeding programs. In the present study, the genetic divergence between sub-accessions of the melon taken from traditional agriculture in the semi-arid region of Brazil was evaluated using ISSR and RAPD markers, verifying the level of agreement with the botanical classification. Twenty-six sub-accessions preserved in the Active Germplasm Bank of Cucurbitaceae for the northeast of Brazil, located at Embrapa Semiárido in Petrolina, Pernambuco, were analysed. The binary matrix of the molecular data was used to obtain the genetic dissimilarities using the complement of the Jaccard index. The genetic dissimilarities were represented in dendrograms generated using the UPGMA method. Twenty-eight ISSR primers and 26 RAPD primers were polymorphic. A total of 686 fragments were obtained, of which 451 were polymorphic. The mean polymorphism of the RAPD markers was greater than that of the ISSR markers. The number of markers was considered sufficient to accurately determine the genetic diversity. The ISSR dendrogram allowed the formation of three groups, the RAPD dendrogram, four groups, and the joint dendrogram, three groups. The study demonstrated the genetic variability between the sub-accessions, and the strong association between the characterisation made by the molecular markers and the taxonomic classification of the genotypes under study.

Endophytic fungi are prolific generators of bioactive metabolites with natural antioxidant properties that have a range of potential uses. In the present work, the antioxidant activity and phylogenetic diversity of endophytic fungi obtained from semi-arid terrestrial plants and the fungi obtained from the mangrove soil samples are investigated. The fungal isolates were identified by employing molecular characterisation and phylogenetic analysis by internal transcribed spacer (ITS) sequences. Fungi belonging to six taxonomic orders of Ascomycota associated with nine genera were identified, these being Diaporthales, Eurotiales, Hypocreales, Onygenales, Pleosporales and Xylariales. The antioxidant activity of the methanolic extracts of the fungal isolates was determined using modified 2,2’-diphenyl-1-picrylhydrazyl (DPPH) and 2,2’-azino-bis (3-ethylbenzothiazoline-6-sulphonicacid) (ABTS) methods. Amongst the fungal isolates, Aspergillus sp. AREF023 and Neocosmospora sp. AREF014, obtained from different parts of Datura metel, displayed the highest level of radical inhibition (80.76% and 70.62% respectively). GC/MS analysis of the active isolates confirmed the presence of known antioxidant phenolic compounds, including 2-tert-Butyl-5-hydroxymethyl-5-methyl-[1,3]dioxolan-4-one and 2,5-ditert-butylphenol, in the their crude extracts. Our findings suggest that fungal isolates from D. metel can be a sustainable resource for natural antioxidants. [ABSTRACT FROM AUTHOR]

Cancer is a disease that occurs in tissues and organs as a result of uncontrolled cell divisions. There are numerous types of cancer related with different frequencies and mortality rate. Ovarian cancer is the seventh common type of cancer worldwide and is the fifth cause of cancer-related death. Although there are standard treatment methods for cancer types, people give different responses to these treatment methods. In spite of all the treatment strategy developed, ovarian cancer still has a high mortality rate. For this reason, it is very important to better understand the drug resistance mechanisms that prevent the effecttiveness of today's treatment methods, to develop new treatment methods and the determination of molecular characterization. In recent years, research has focused on methods containing pathway analysis within the scope of developing targeted therapy strategies for ovarian cancer. In this context, the activity status of onco-proteins in pathways such as WNT, Hedgehog and NOTCH signaling pathways were evaluated. In addition, the innovative treatment efficiency of Nanog protein and photodynamic therapy options on ovarian cancer has been detailed in recent years. It will be possible to increase the quality of the healing process of patients suffering from this disease by enlightening the molecular characterizations of the treatment methods that are available and still being developed in the treatment of ovarian cancer. [ABSTRACT FROM AUTHOR]

Green shield bug (GSB) Palomena prasina (L.) causes significant yield and quality losses in hazelnut production of Turkey. Alive and dead adults of GSB were collected from the main hazelnut cultivation areas of Turkey during 2018 and 2019. The entomopathogenic fungi (EPF) were isolated from GSB individuals and identified by DNA sequencing of the internal transcribed spacer of the rRNA. Phylogenetic analysis based on the maximum likelihood method of these sequences with reference sequences retrieved from GenBank revealed that 20 native isolates were Beauveria bassiana (6), B. pseudobassiana (1), Cordyceps confragosa (5), Akanthomyces muscarius (4), Purpureocillium lilacinum (2), Isaria fumosorosea (1), and Bionectria sp. (1). Furthermore, the isolates were tested for their efficacy against GSB adults at 1 × 108 spores mL−1 concentration under laboratory conditions. Registered bio-insecticides were applied at the same concentration to compare the efficacy of the isolates. Beauveria spp. isolates were most effective among the tested isolates with LT50 and LT90 values ranging between 3.65–6.14 and 5.26–8.25 days, respectively. These isolates caused 100% mortality in GSB adults within 6–10 days. The isolates of A. muscarius (TR-OR-1) and P. lilacinum (TR-SM-7) were highly effective and caused 100% mortality 10 and 11 days after the treatment, respectively. These results indicated that some EPF isolates obtained in this study are more promising as an alternative control agent against GSB. [ABSTRACT FROM AUTHOR]

Background: Pseudomonas aeruginosa (P. aeruginosa) is prevalent in hospital-acquired surgical wound infections. It exhibits both innate and acquired resistance to a broad range of antimicrobials and remains a principal problem in clinical practice. Methods: In total, 284 sterile surgical wound swabs (142 each) were collected from two government hospitals: Central Hospital Benin (CHB) and University of Benin Teaching Hospital (UBTH) in Benin City, Nigeria. Pseudomonas spp. isolated from both hospitals were screened with eight different antibiotics by way of disk diffusion method. Polymerase chain reaction (PCR) amplification of 34 multiple drug-resistant isolates was carried out using genus-specific primer set on extracted genomic DNA for the identification of Pseudomonas spp. and substituent 16S rRNA sequencing to determine the prevailing strains in the two locations. Results: Sixty-two Pseudomonas spp. were isolated from the two locations (27 isolates from CHB and 35 isolates from the UBTH). Surgical wound infections screened with regularly used antibiotics revealed that 17 (62.9%) isolates from CHB and 20 (57.1%) isolates from UBTH were multiple drug resistant Pseudomonas spp. PCR identification using Pseudomonas spp. specific primer showed that 16 (94.1%) isolates from CHB and 18 (90%) isolates from UBTH were confirmed. The 16S DNA sequencing revealed that P. aeruginosa strain H25883 was dominant in both locations. Conclusion: High antibiotic resistance among P. aeruginosa isolates was established in our study. PCR technique revealed a more reliable method of bacterial identification. H25883 strain of P. aeruginosa is the prevalent strain in both locations and it should be given attention in nosocomial surgical wound infections. [ABSTRACT FROM AUTHOR]

White root rot (WRR) disease which is caused by Rigidoporus microporus is a major agricultural disease. The disease affects tropical fruits, forest trees, ornamental trees as well as rubber (Hevea brasiliensis) trees. Although WRR causes significant economic losses to planters, there is no effective method to control this disease. The understanding on the population genetics of R. microporus isolates could mitigate WRR disease in plant management. Therefore, the objective of this work was to elucidate molecular phylogeny of R. microporus isolated from rubber trees. Twenty seven R. microporus isolates were characterised using internal transcribed spacer (ITS), Beta-tubulin (β-tubulin) and translation elongation factor-a (tef1-a) sequences data. Phylogenetic tree analyses of R. microporus isolates were divided into two major groups; the Asian and African groups. However, there was no distinct geographical structuring in the Asian group, suggesting gene flow happened among the populations. Somatic Incompatibility (SI) test and Inter Simple Sequence Repeat (ISSR) marker revealed that the R. microporus in the rubber plantations partially clustered based on geographical regions. The genetic diversity of R. microporus by ISSR revealed four major groups. The findings of the present study provide a baseline data for breeders and plant pathologists to enable them strategise effective and sustainable WRR disease management. [ABSTRACT FROM AUTHOR]

Background: The present study was aimed at establishing the prevalence, epidemiology and molecular characterization of major haemoprotozoons (Babesia and Theileria) and rickettsia (Anaplasma) of cattle in Jammu region (North India) using microscopy and Polymerase Chain Reaction (PCR). Hematology, microscopy and PCR based prevalence studies were undertaken with 278 whole blood samples from cattle. Molecular prevalence studies were followed by genetic characterization of the isolates of Babesia, Anaplasma and Theileria spp. based on 18S rRNA, 16S rRNA and Tams1 gene, respectively. The data related to metrology and epidemiological variables like temperature, rainfall, season, age and type of livestock rearing was analyzed and correlated with occurrence of disease by statistical methods. Results: The prevalence based on microscopy was 12.9% (36/278) whereas PCR recorded 30.22% (84/278) animals positive for haemoparasitic infections. All the samples found positive by microscopy were also recorded positive by PCR. Thus the study revealed prevalence of Babesia bigemina, Anaplasma marginale and Theileria annulata to be 9.7, 16.5 and 0.7% respectively. The metrological and epidemiological variables made inroads for the propagation of vector ticks and occurrence of infection. Haematological alterations predominantly related to decrease in haemoglobin, red blood cell count and packed cell volume were evident in diseased animals and collaterally affected the productivity. Further the genetic characterization of Babesia bigemina. (MN566925.1, MN567603, MN566924.1), Anaplasma marginale. (MH733242.1, MN567602.1) and Theileria annulata (MT113479) provided a representative data of the isolates circulating in the region and their proximity with available sequences across the world. Conclusions: Despite holding much significance to the animal sector, comprehensive disease mapping has yet not been undertaken in several parts of India. The present study provides a blue print of disease mapping, epidemiological correlations and genomic diversity of Babesia bigemina, Anaplasma marginale and Theileria annulata circulating in the region. [ABSTRACT FROM AUTHOR]