DNA Sequence Of Gene Research Articles

Genetic resistance factors and antimicrobial resistance phenotypes in methicillin- resistant Staphylococcus aureus isolates of animals and humans

Objective: To investigate the prevalence, genetic resistance factors, and antimicrobial resistance phenotypes of methicillin-resistant Staphylococcus (S.) aureus (MRSA) from clinically healthy animals (horses, dogs, and cats) and their human handlers, providing a baseline for broader genes sequencing based on One Health studies to the emergence of resistance as well as guides regarding specific therapies, hospital antibiotic usage/stewardship, and target-specific infection control measures. Methods: This cross-sectional study involved both human and animals. S. aureus isolates derived were characterised for their antimicrobial phenotypes through antimicrobial susceptibility testing with PCR detection of mecA, mecC, and DNA sequencing of mepR, mepA, mepB, and sapep genes for correlation with their antimicrobial resistance phenotypes. Results: Seventy S. aureus isolates from 149 human handlers, 240 horses, and 206 companion animals, including dogs and cats were studied. The prevalence of resistance was highest for penicillins (100.0%) and amoxicillin (94.3%), followed by erythromycin (87.7%), trimethoprim (78.6%), azithromycin (77.1%), imipenem (61.4%), and tetracycline (40.0%). Lower resistance prevalences were observed for ciprofloxacin (27.1%), chloramphenicol (20.0%), trimethoprim-sulfamethoxazole (12.9%), and gentamicin (2.9%). Twenty-six isolates had their DNA sequenced for mepR, mepA, mepB, and sapep genes for correlation with their antimicrobial phenotypes. Transcriptional profiling revealed that both animal and human MRSA isolates exhibited a gene cluster mepRAB (multidrug export protein gene), encoding a MarR-likc transcriptional regulator (mepR), a M20/ M25/M40 metallo-hydrolase protein gene (sapep) encoding resistance to biocides and carbapenems, and a hypothetical protein gene of unknown function (mepB). Conclusions: This study demonstrated extensive multidrug resistance in MRSA, revealing similarities in the resistance patterns and multiple antibiotic resistance indices among the isolates. These findings suggest the potential presence of non-mec resistance mechanisms in MRSA, in addition to the mec gene mechanism.

Alpha-1-Antitrypsin Deficiency Targeted Testing and Augmentation Therapy: A Canadian Thoracic Society Meta-analysis and Clinical Practice Guideline.

Alpha-1-Antitrypsin (A1AT) deficiency is a common hereditary disorder associated with increased risk of developing chronic obstructive pulmonary disease (COPD). Many individuals with severe A1AT deficiency go undiagnosed, or are diagnosed late, and fail to benefit from disease-specific counseling and modifying care. Since the 2012 Canadian Thoracic Society (CTS) A1AT deficiency clinical practice guideline, new approaches to optimal diagnosis using modern genetic testing and studies of A1AT augmentation therapy have been published. We performed a systematic review and meta-analysis, which along with expert clinical input, informed recommendations. We conditionally recommend testing for A1AT deficiency in all individuals with COPD at the time of diagnosis, individuals with adult-onset asthma with persistent airway obstruction, and individuals with unexplained bronchiectasis. We suggest genetic testing with DNA sequencing of SERPINA1 gene as the initial test for individuals with high clinical suspicion for A1AT deficiency, and initial measurement of serum A1AT levels in individuals with moderate clinical suspicion of A1AT deficiency, followed by genetic testing with DNA sequencing of SERPINA1 gene if A1AT level is <23 μmol/L (<1.2 g/L). Following identification of an abnormal gene for A1AT in individuals, whether heterozygote or homozygote, we suggest first-degree relatives be provided genetic counseling and offered testing for A1AT deficiency. The panel conditionally recommends A1AT augmentation therapy to non-smoking or ex-smoking patients with COPD (FEV1 < 80% predicted; associated with emphysema), with documented deficiency genotypes and severely reduced A1AT level (< 11 μmol/L or < 0.57 g/L) in addition to receiving optimal pharmacological and nonpharmacological therapies for COPD.

Systematics of minute strabomantid frogs allocated to the genus Noblella (Amphibia: Anura) with description of a new genus, seven new species, and insights into historical biogeography

Abstract Noblella is a genus of 17 recognized nominal species of ground-dwelling, direct-developing frogs. It consists of two clades that do not form a monophyletic group: a northern clade from northern Peru, Ecuador, Colombia, and Brazil and a southern clade from southern Peru and Bolivia. Herein, we present a systematic review of Noblella with emphasis on the northern clade, including a new phylogeny based on DNA sequences of mitochondrial and nuclear genes. We also describe the osteology of five species from the northern clade using X-ray computed tomography. Based on our results, we resurrect the genus Phyllonastes for species of the northern clade (i.e. eight described species plus six new species described herein) and restrict the genus Noblella to the southern clade. We describe a new genus of Holoadeninae, sister to Phyllonastes: Urkuphryne gen. nov., from northern Ecuador. The new genus is distinguished by unique morphological characteristics that are diagnostic of different genera in Strabomantidae. We describe seven new species diagnosable based on morphology. Phyllonastes has five morphological synapomorphies, including the absence of vomerine teeth. Phyllonastes originated in the Pacific basin, Chocó region, ~21 Mya.

Alpha-1-Antitrypsin Deficiency Targeted Testing and Augmentation Therapy: A Canadian Thoracic Society Meta-analysis and Clinical Practice Guideline

ABSTRACT Alpha-1-Antitrypsin (A1AT) deficiency is a common hereditary disorder associated with increased risk of developing chronic obstructive pulmonary disease (COPD). Many individuals with severe A1AT deficiency go undiagnosed, or are diagnosed late, and fail to benefit from disease-specific counseling and modifying care. Since the 2012 Canadian Thoracic Society (CTS) A1AT deficiency clinical practice guideline, new approaches to optimal diagnosis using modern genetic testing and studies of A1AT augmentation therapy have been published. We performed a systematic review and meta-analysis, which along with expert clinical input, informed recommendations. We conditionally recommend testing for A1AT deficiency in all individuals with COPD at the time of diagnosis, individuals with adult-onset asthma with persistent airway obstruction, and individuals with unexplained bronchiectasis. We suggest genetic testing with DNA sequencing of SERPINA1 gene as the initial test for individuals with high clinical suspicion for A1AT deficiency, and initial measurement of serum A1AT levels in individuals with moderate clinical suspicion of A1AT deficiency, followed by genetic testing with DNA sequencing of SERPINA1 gene if A1AT level is <23 μmol/L (<1.2 g/L). Following identification of an abnormal gene for A1AT in individuals, whether heterozygote or homozygote, we suggest first-degree relatives be provided genetic counseling and offered testing for A1AT deficiency. The panel conditionally recommends A1AT augmentation therapy to non-smoking or ex-smoking patients with COPD (FEV1 < 80% predicted; associated with emphysema), with documented deficiency genotypes and severely reduced A1AT level (< 11 μmol/L or < 0.57 g/L) in addition to receiving optimal pharmacological and nonpharmacological therapies for COPD.

Phylogeny and Taxonomy of the Naematelia aurantialba Complex in Southwestern China.

Naematelia aurantialba and its allies are important edible and medicinal mushrooms in China. They are usually called Jiner () and have been cultivated on a commercial scale. However, due to the lack of DNA sequences from the holotype of Naematelia aurantialba, the taxonomic issues of the species complex are unresolved. In this study, the authors successfully generated DNA sequences from the holotype of N. aurantialba by a genome skimming approach and additional allied species by Sanger sequencing. Based on morphological characteristics, molecular phylogenetic data, and geographic distribution patterns, four species, including three new ones, in the complex in southwestern China were uncovered. Naematelia aurantialba occurs at high altitudes (over 3000 m above sea level), with subalpine dead plants as its substrates, and has larger basidiospores, while the commonly cultivated species, described as N. sinensis in this work, is distributed in subtropical areas at altitudes between 1800 m and 2600 m on the dead wood of subtropical plants and has smaller basidiospores. The third species, namely N. nodulosa, has habitats similar to those of N. sinensis but differs from the latter in its basidiomata with an uneven nodulose surface, a loose context with small internal cavities, and numerous conidia. The fourth species, N. pedicellata, is easily distinguished from the others by its basidia, with long basal stalks and broadly ellipsoid basidiospores measuring 10.5-12.5 × 8.0-10.0 μm. All these species are parasitic on Stereum species. This study provides a solid basis for future guidance for the selection of new strains and cultivation practices of these valuable fungi.

Basic Molecular Biology, Metabolic and Immunological Mechanisms of Fecal Microbiota Transplantation

Aim: demonstration of basic molecular biological, metabolic and immunological effects of fecal microbiota transplantation (FMT), on the example of a rare case of acute graft-versus-host disease (GVHD) with intestinal damage in a patient after allogeneic hematopoietic stem cell transplantation (allo-HSCT).Materials and methods. To monitor the basic effects of FMT, we performed targeted DNA sequencing of 16S rRNA gene (V3–V4) using MiSeq platform as well as multiplex real-time PCR, MS/gas chromatography technique, immunophenotyping of blood lymphocytes, histological and immunohistochemical techniques.Clinical case. A 40-year-old female patient diagnosed with myelodysplastic syndrome, with a history of two unsuccessful allo-HSCTs due to graft failure, underwent the third haploidentical HSCT (haplo-HSCT) from her father as ‘salvage’ therapy. Due to early viral/bacterial colitis post-transplant associated with a multidrug-resistant strain of K. pneumoniae and herpes virus type 6, FMT was performed on days 46 and 47 after allo-HSCT. Complete resolution of the enteropathy symptoms was noted following FMT. However, immunosuppressive therapy was canceled on D+106 after haplo-HSCT due to the detection of minimal residual disease causing development of the ‘overlap’-type GVHD with damage skin lesions grade 4, and intestinal mucous membranes grade 3. This complication required resumption and subsequent intensification of immunosuppressive therapy with complete resolution of GVHD symptoms. Following FMT treatment, the patient showed complete resolution of clinical colitis symptoms. According to results of 16S rRNA sequencing, the species-specific diversity of fecal microbiota increased significantly, along with decreased relative contents of opportunistic bacteria (Klebsiella, Enterococcus, Streptococcus genera). A significant growth was revealed for commensal Bacteroidota, and re-emergence of Faecalibacterium, Blautia, Roseburia. Acute gastrointestinal GVHD promoted by tacrolimus withdrawal was associated with repeated depletion of intestinal microbiota. Upon resolution of GVHD and resumed immunosuppression, increased microbiota diversity (Shannon index) was again recorded, and the parameters of patient’s fecal microbiota reached the donor values. The microbiota shifts at all clinical stages (before and after FMT, at the peak of acute intestinal GVHD and intensive immunosuppressive therapy) showed some relations with metabolism of bile and fatty acids in blood plasma and immune parameters.Conclusions. FMT may be a component of complex therapy aimed at early reconstitution of immune system and organic acid metabolism in patients after allo-HSCT. The composition of fecal microbiota, metabolic profile and spectrum of lymphocyte subpopulations may be markers for monitoring complex rehabilitation after allo-HSCT.

Human Schistosomiasis due to Schistosoma bovis in Nigeria.

Schistosomiasis is a global public health challenge, especially in sub-Saharan Africa, where Nigeria has the highest burden of disease. Schistosoma hybrids have been discovered in various countries, including Nigeria, where livestock and human beings share common water resources. This study, carried out in three communities, two of which are endemic for urinary schistosomiasis, aimed to identify the urinary schistosomiasis causative agent by using a species-specific molecular technique and their evolutionary relationship. Polymerase chain reaction using primers specific for a partial DNA sequence of the mitochondrial cox1 gene of Schistosoma haematobium was carried out on pooled urine sediments preserved in 70% ethanol. DNA from the high-intensity pooled samples from Onye-Uku camp amplified, and a BLAST search identified the pooled samples as Schistosoma bovis, whereas S. haematobium DNA did not amplify. The phylogenetic relationship of the sequence showed that it clustered with an S. bovis hybrid obtained from a human host in Côte d'Ivoire and had close ancestry with isolates from cattle in Cameroon. This finding revealed the prevalence of S. bovis among some inhabitants in a zone in Nigeria where schistosomiasis is endemic.

TFinder: A Python Web Tool for Predicting Transcription Factor Binding Sites.

Transcription is a key cell process that consists of synthesizing several copies of RNA from a gene DNA sequence. This process is highly regulated and closely linked to the ability of transcription factors to bind specifically to DNA. TFinder is an easy-to-use Python web portal allowing the identification of Individual Motifs (IM) such as Transcription Factor Binding Sites (TFBS). Using the NCBI API, TFinder extracts either promoter or gene terminal regulatory regions, through a simple query of NCBI gene name or ID. It enables simultaneous analysis across five different species for an unlimited number of genes. TFinder searches for Individual Motifs in different formats, including IUPAC codes and JASPAR entries. Moreover, TFinder also allows de novo generations of a Position Weight Matrix (PWM) and the use of already established PWM. Finally, the data are provided in a tabular and a graph format showing the relevance and the P-value of the Individual Motifs found as well as their location relative to the Transcription Start Site (TSS) or the terminal region of the gene. The results are then sent by email to users facilitating the subsequent data analysis and sharing. TFinder is written in Python and freely available on GitHub under the MIT license: https://github.com/Jumitti/TFinder. It can be accessed as a web application implemented in Streamlit at https://tfinder-ipmc.streamlit.app. Resources are available on Streamlit "Resources" tab. TFINDER strength is that it relies on an all-in-one intuitive tool allowing users inexperienced with bioinformatics tools to retrieve gene regulatory regions sequences in multiple species and to search for individual motifs in a huge number of genes.

Gene and Its Promoter Cloning, and Functional Validation of JmSOC1 Revealed Its Role in Promoting Early Flowering and the Interaction with the JmSVP Protein.

Juglans mandshurica, a notable woody oil tree species, possesses both fruit and timber value. However, the complete heterodichogamous flowering mechanism in this species remains elusive. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) is a crucial regulator of flower bud development in Arabidopsis thaliana. In this study, we cloned the coding DNA sequence (CDS) of the JmSOC1 gene, revealing a 705 base pair (bp) sequence that encodes a protein of 234 amino acids. The JmSOC1 protein contains a highly conserved MADS-box domain, indicating its role as a transcription factor, and is predominantly localized in the nucleus. The JmSOC1 gene expressed the highest in flower buds. The peak expression level of JmSOC1 during the physiological differentiation phase occurred earlier in male flower buds of protandry (MPD) on April 10th compared to female flower buds of protandry (FPD) on April 14th; similarly, the peak expression in female flower buds of protogyny (FPG) on April 2nd preceded that in male flower buds of protogyny (MPG) on April 14th. This may be the primary reason for the earlier differentiation of the male flowers in protandry individuals and the female flowers in protogyny individuals. Overexpression of JmSOC1 in wild-type A. thaliana resulted in earlier flowering, accompanied by an upregulation of key flowering-related genes such as LEAFY (LFY), APETALA1 (AP1), and FLOWERING LOCUS T (FT). To further explore the function of JmSOC1, a 782 bp promoter sequence of JmSOC1 gene was cloned, which has been verified to have promoter activity by GUS staining. Furthermore, the interaction between the JmSOC1 gene promoter and its upstream regulatory protein JmSVP was verified using a yeast one-hybrid. These results offer valuable insights into the molecular mechanisms underpinning the promotion of early flowering in J. mandshurica and hold promise for laying a theoretical foundation for the flowering regulation network of this species.

Muscle Weakness - new genetic defect transmitted to Polish Holstein-Friesian cattle.

The aim of the study was to find out whether carriers of new genetic defect Muscle Weakness (MW) occur in the population of Polish Holstein-Friesian bulls. Fifty bulls were included in the analysis. Bulls were selected as having in the pedigree known carrier of MW. All bulls were diagnosed by DNA sequencing of CACNA1S gene containing single nucleotide substitution (rs3423414874) responsible for 97% of MW cases. Among 50 bulls, 19 MW carriers were found. Our results show that causal mutation for MW is already transmitted to Polish Holstein-Friesian cattle which is sufficient ground to take practical action in order to avoid further spreading of mutation causing MW.

Prevalence of Human Polyomaviruses in Oral and Oropharyngeal Squamous Cell Carcinoma From Patients Treated at a Cancer Center in Sao Paulo, Brazil.

Head and neck squamous cell carcinoma (SCC) predisposing factors include smoking and alcohol consumption. However, other agents have been investigated, including viruses. We aimed to investigate the presence of DNA of four different types of human polyomavirus (HPyV) in the oral cavity and oropharyngeal SCC samples from an oncology center in Brazil and evaluate the association between HPyV detection and clinical and sociodemographic characteristics. Sixty fresh frozen samples from three different anatomical sites (tongue, floor of the mouth, and oropharynx, 20 samples for each region) were retrospectively selected. Data from medical records such as age, sex, alcohol consumption, smoking, tumor staging and death in less than 5 years of diagnosis were collected. DNA was extracted for the identification of MCPyV, BKPyV, JCPyV, and TSPyV using PCR followed by Sanger sequencing of positive samples. The identity of the generated DNA sequences was confirmed by alignment reference sequences. The investigation of the presence of HPyV DNA showed positivity of 5% for MCPyV (n = 3), 0% for both BKPyV or TSPyV, and 60% for JCPyV (n = 36). No association was found between the positivity of any HPyV in samples with any clinical or sociodemographic characteristics of the patients, nor with a certain anatomical site, except for the association between death in less than 5 years after diagnosis and positivity for JCPyV (p = 0.009). Positivity for HPyV in oral cavity and oropharyngeal SCC was low for MCPyV, high for JCPyV and null for BKPyV and TSPyV. Further studies should be carried out to better understand the high prevalence of JCPyV found in oral cavity and oropharyngeal SCC.

Co-infection of HSV-1 amplicons containing the XPC gene and a human artificial chromosome vector into primary XPC deficient fibroblast cells

Gene therapy for xeroderma pigmentosum (XP), a rare, recessive DNA repair disease, has been considered since defects in XP genes result in severe and debilitating symptoms. Mutations in the XPC DNA repair gene result in a more that 1000-fold increased sensitivity to sunlight-induced skin cancer. The XPC gene is large (33 Kb) and the entire genomic locus is a difficult candidate for many gene therapy vectors to incorporate into their system by conventional cloning. Artificial chromosome vectors were developed to accommodate large genes and their regulatory sequences to allow full gene expression in cells. The HSV-1 human artificial chromosome (HAC) vectors we previously generated incorporated genes up to 100 Kb in a single vector. Subsequently, we modified the system to allow larger (>100 Kb) DNA gene sequences to be introduced by simultaneously infecting cells with two separate HSV-1 vector particles, one containing DNA required for HAC formation and the other with the desired gene. Following transduction, recombination of DNA formed a gene expressing HAC in vitro. The dual transduction system was successful for introduction and expression of the HPRT gene in human 3D engineered tissues and stem cells. In this study, we report the XPC gene delivery and transient gene expression via the dual transduction system in human cultured fibrosarcoma (HT1080) and primary XPC deficient patient cells.

Genetic screening of α-thalassemia fusion gene using routine flow-through hybridization.

The fusion gene is a rare form of α-thalassemia. Patients carrying the fusion gene could be misdiagnosed as normal or -α4.2deletion by the conventional thalassemia detection methods. The aim of this study was to present the detection of fusion genes using routine flow-through hybridization, as well as to analyze hematological and molecular characteristics. Samples were collected at our hospital from January 2019 to January 2024. Common thalassemia mutations in the Chinese population were conducted by flow-through hybridization. Samples showing faint coloration at the -α4.2 mutation site on hybridization membrane were considered suspicious. Samples detected as suspicious for -α4.2deletion were rechecked by conventional Gap-PCR. Those samples suspected of having -α4.2deletions were finally confirmed with specific primers for Gap-PCR and Sanger sequencing. Of the 32,083 samples, 25 samples (0.08%) were detected as suspected of having -α4.2 deletion by flow-through hybridization. However, upon reevaluation wtih conventional Gap-PCR reagents capable of detecting -α4.2 deletion, all were found to be negative for the deletion. Specific primers for Gap-PCR were designed, and fusion gene fragments were amplified. DNA sequencing of the HBA gene showed a 7-base mutation corresponding to the α-thalassemia fusion gene. Among the 25 samples, 22 were heterozygous carriers. Three samples were combined: one with Hb QS, one with β-thalassemia, and one with Hb G-Honolulu.Most hematological indices and capillary electrophoresis results were in the normal reference range. The fusion gene was present in 0.08% of the population in the Guangzhou region of Guangdong province, southern China. Conventional genetic methods tend to misdiagnose the fusion gene but can be effectively screened with flow-through hybridization.

Characterizing the urobiome in geriatric males with chronic indwelling urinary catheters: an exploratory longitudinal study.

The impact of chronic indwelling urinary catheters (IUCs) on the composition and stability of the urinary microbiota remains unknown. The primary aim of this study was to describe the urinary microbiomes of geriatric males with chronic IUCs. A secondary aim was to explore clinical catheter-associated urinary tract infection (CAUTI) courses of the participants. Geriatric male patients with chronic IUCs were followed longitudinally. Catheterized urine, catheter tips, and both urethral and periurethral swabs were collected from participants at monthly intervals. Microbes were isolated and identified from each specimen using an enhanced culture method called expanded quantitative urine culture (EQUC) and targeted 16S rRNA gene DNA sequencing. Microbial outcomes were examined both in the absence of urinary symptoms and in the context of clinical diagnosis of CAUTI. Ten male participants (mean age 86 years) were enrolled. Urinary microbiomes differed for each participant. However, within each individual, microbiomes were similar over time and across niches (bladder, catheter, urethra, and periurethra). Within-niche microbiomes differed across individuals, and this was observed over time. The most abundant bacteria isolated from all niches were known uropathogens. Six of 10 individuals met diagnostic criteria for CAUTI at least once during the 12-month observation period, but no evidence of this or antibiotic treatment/response was discernable in our monthly samples. The microbiomes of each participant were unique and remained similar over time and across niches. Longitudinal EQUC or 16S rRNA gene sequencing data could be useful to clinicians when diagnosing or treating possible CAUTI.IMPORTANCECatheter-associated urinary tract infections (CAUTIs) are serious but preventable nosocomial infections. The most common risk factor for developing CAUTI is prolonged use of indwelling urinary catheters (IUCs). This study provides the first longitudinal description of the urinary microbiomes of geriatric males with chronic IUCs, in the absence of urinary signs and symptoms, as a first step toward enhancing our knowledge of the impact of chronic IUCs on the composition and stability of the urinary microbiota. This is an understudied area, particularly for males.

Transcription Factor Binding Site Prediction Using CnNet Approach.

Controlling the gene expression is the most important development in a living organism, which makes it easier to find different kinds of diseases and their causes. It's very difficult to know what factors control the gene expression. Transcription Factor (TF) is a protein that plays an important role in gene expression. Discovering the transcription factor has immense biological significance, however, it is challenging to develop novel techniques and evaluation for regulatory developments in biological structures. In this research, we mainly focus on 'sequence specificities' that can be ascertained from experimental data with 'deep learning' techniques, which offer a scalable, flexible and unified computational approach for predicting transcription factor binding. Specifically, Multiple Expression motifs for Motif Elicitation (MEME) technique with Convolution Neural Network (CNN) named as CnNet, has been used for discovering the 'sequence specificities' of DNA gene sequences dataset. This process involves two steps: a) discovering the motifs that are capable of identifying useful TF binding site by using MEME technique, and b) computing a score indicating the likelihood of a given sequence being a useful binding site by using CNN technique. The proposed CnNet approach predicts the TF binding score with much better accuracy compared to existing approaches. The source code and datasets used in this work are available at https://github.com/masoodbai/CnNet-Approach-for-TFBS.git.

Xoconochcothelphusa, a new genus for Ehecatusa chiapensis (Rodríguez & Smalley, 1972), with notes on Spirothelphusa Pretzmann, 1965 (Crustacea: Decapoda: Pseudothelphusidae).

The species of the genus Ehecatusa Ng & Low, 2010, E. chiapensis (Rodríguez & Smalley, 1972) and E. mixtepensis (Rodríguez & Smalley, in Smalley, 1970), were referred to as incertae sedis in the classification system of the tribe Pseudothelphusini Ortmann, 1897, proposed by Villalobos-Hiriart (2005) and Villalobos & Alvarez(2010) and as members of the subfamily Pseudothelphusinae in the recent phylogenetic proposal by Álvarez et al. (2020), supported with morphology and molecular information. The recent discovery of a new specimen of E. chiapensis, from Chiapas, Mexico, comes to expose again the unresolved taxonomic situation of this species in the genus Ehecatusa. New morphologic evidence from the male first gonopod and a phylogenetic analysis based on partial DNA sequences of mitochondrial and nuclear genes (COI, 16S and H3), support the placement of the two species in different genera. Consequently, Xoconochcothelphusa n. gen. is erected to receive X. chiapensis n. comb. The phylogenetic relationships of X. chiapensis n. gen., n. comb. and E. mixtepensis with other genera of the subfamily Pseudothelphusinae Ortmann, 1893 (Ehecatusa, Smalleyus Alvarez, 1989, and Spirothelphusa Pretzmann, 1965) distributed in Mexico, are examined and a key to the identification of the genera of this subfamily is provided.

Pharmacokinetic, Pharmacodynamic and Pharmacogenetic Studies Related to Vincristine-Induced Peripheral Neuropathy in Chinese Pediatric ALL Patients.

Vincristine (VCR) can cause vincristine-induced peripheral neuropathy (VIPN) during the treatment of acute lymphoblastic leukemia (ALL) and the mechanisms are complicated. The aim of this study was to investigate the influencing factors on the population pharmacokinetics (PopPK) and pharmacodynamics (PD) related to VIPN, including clearance routes, drug-drug interactions (DDI), and genetic characteristics. Pediatric patients being treated for ALL were recruited to PK study where VCR and its metabolite (M1) were measured using a novel assay. The incidence of VIPN was also recorded. DNA sequencing of relevant PK and PD genes was performed. PopPK and PK/PD models were developed, pharmacogenetic and DDI analyses were conducted. In total, 79 children were recruited. The results showed that allometric scaling, ABCB1-rs1128503 genotype, and posaconazole (POS) significantly improved the PopPK model fit. VIPN was significantly correlated with the exposure of VCR. Co-administration with POS shifted the effect curve for VIPN to the left, indicating increased VIPN risk at the same exposure levels. No significant effects on VIPN were observed for CYP3A5 (rs776746), CYP3A4 (rs2242480), CEP72 (rs924607), or various ABCB1 variants (rs1128503, rs2032582, rs1045642, rs4728709, rs4148737, and rs10276036), nor with the co-administration of fluconazole or dasatinib. In summary, co-administration of POS increased VCR exposure by 0.4-fold and raised the risk of VIPN, with an occurrence probability generally exceeding 0.7. Therapeutic drug monitoring of VCR in clinical practice may be necessary to enable appropriate dose adjustments and individualized treatment.

Barcoding of Italian mosquitoes (BITMO): generation and validation of DNA barcoding reference libraries for native and alien species of Culicidae

BackgroundMosquitoes (Culicidae), as disease vectors, represent a risk for human health worldwide. Repeated introductions of alien mosquito species and the spread of invasive species have been recorded in different countries. Traditionally, identification of mosquitoes relies on morphological observation. However, morphology-based identification is associated with a number of potential disadvantages, such as the high level of specialisation of the operator and its limited applicability to damaged samples. In these cases, species identification is achieved through molecular methods based on DNA amplification. Molecular-based taxonomy has also enabled the development of techniques for the study of environmental DNA (eDNA). Previous studies indicated the 16S mitochondrial ribosomal RNA (rRNA) gene as a promising target for this application; however, 16S rRNA sequences are available for only a limited number of mosquito species. In addition, although primers for the 16S rRNA gene were designed years ago, they are based on limited numbers of mosquito sequences. Thus, the aims of this study were to: (i) design pan-mosquito 16S rRNA gene primers; (ii) using these primers, generate a 16S rRNA gene mosquito reference library (with a focus on mosquitoes present in Italy); and (iii) compare the discriminatory power of the 16S rRNA gene with two widely used molecular markers, cytochrome c oxidase subunit 1 mitochondrial gene (COI) and internal transcribed spacer 2 (ITS2).MethodsA total of six mosquito genera (28 mosquito species) were included in this study: Aedes (n = 16 species), Anopheles (5 species), Coquillettidia (1 species), Culex (3 species), Culiseta (2 species) and Uranotaenia (1 species). DNA was extracted from the whole mosquito body, and more than one specimen for each species was included in the analysis. Sanger sequencing was used to generate DNA sequences that were then analysed through the Barcode of Life Data Systems (BOLD). Phylogenetic analyses were also performed.ResultsNovel 16S rDNA gene, COI and ITS2 sequences were generated. The 16S rRNA gene was shown to possess sufficient informativeness for the identification of mosquito species, with a discriminatory power equivalent to that of COI.ConclusionsThis study contributes to the generation of DNA barcode libraries, focussed on Italian mosquitoes, with a significant increase in the number of 16S rRNA gene sequences. We hope that these novel sequences will provide a resource for studies on the biodiversity, monitoring and metabarcoding of mosquitoes, including eDNA-based approaches.Graphical abstract

Pico-ampere resolution current measurement circuit using Gm-C filter sigma-delta modulator for low-power nanopore DNA sequencing

New generation DNA sequencers use an array of electrochemical cells equipped with nanopores, which produce pico-ampere current levels. Due to the large number of channels, low current levels and bandwidths in the order of a few kHz, in the design of these readout circuits, 2D arrays of in-channel, low noise and low power analog to digital converters are preferred. Previously many different sigma-delta modulators have been presented to convert the nanopore current signal into a digital code. Conventionally, the opamps required in these converters will eventually increase the power dissipation of each channel. In this paper a novel Gm-C filter based second order sigma-delta converter is proposed. In the given design, rather than relying on multiple opamps to achieve the necessary gain and noise performance, only a 4 transistor Gm block is used. Evaluations show that while the input referred noise remains close to previous methods, the power dissipation is considerably reduced. A prototype is also implemented to show the effectiveness of the approach. In a 180-nm design, an ENOB of 12.16 bits, RMS input referred noise of 0.2 pA at 10 kHz bandwidth and power dissipation of 8.27 μW is obtained per channel.

Molecular diagnostics of familial hypercholesterolemia in Russia: yesterday, today and tomorrow

Familial hypercholesterolemia is a severe hereditary disease leading to the development of atherosclerosis and its complications in the form of angina pectoris, myocardial infarction, cerebral stroke, or even leading to sudden death. Since the description of the disease, the concept of it has undergone significant evolution. First, it became clear that the prevalence of this disease was significantly higher than originally thought (1:300 for heterozygous familial hypercholesterolemia and not as 1:500 as estimated earlier). Secondly, it has been established that it is not based on the pathology of the low-density lipoprotein receptor gene alone, but includes at least four monogenic forms (defects of the APOB, PCSK9, ARH genes) and may also have a multigenic nature. Thirdly, with the development of DNA analysis methods from the initially available Southern hybridization to next generation DNA sequencing, the exceptional molecular heterogeneity of familial hypercholesterolemia became obvious and, accordingly, the need to establish national spectra of mutations leading to the development of familial hypercholesterolemia was established. Researchers have moved from characterizing individual mutations to creating national registries and databases. Finally, research into the genetics of familial hypercholesterolemia has led to the emergence of new classes of cholesterol-lowering drugs. In Russia, molecular diagnostics of familial hypercholesterolemia has also undergone significant changes since the beginning of the study of familial hypercholesterolemia in 1987 and to the present, consideration of these changes formed the basis of this review.