Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences

@#Objective: To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles (An.) subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2 (ITS2) and cytochrome C oxidase I (COI) sequences deposited at the GenBank. Methods: Seventy-five ITS2, 210 COI and 26 concatenated sequences available in the NCBI database were used. Phylogenetic analysis was performed using Bayesian likelihood trees, whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis. Genetic diversity indices and genetic differentiation were also calculated. Results: Two genetically divergent molecular forms of An. subpictus species complex corresponding to sibling species A and B are established. Species A evolved around 37-82 million years ago in Sri Lanka, India, and the Netherlands, and species B evolved around 22-79 million years ago in Sri Lanka, India, and Myanmar. Vietnam, Thailand, and Cambodia have two molecular forms: one is phylogenetically similar to species B. Other forms differ from species A and B and evolved recently in the above mentioned countries, Indonesia and the Philippines. Genetic subdivision among Sri Lanka, India, and the Netherlands is almost absent. A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances. Genetic diversity indices reveal the presence of a long-established stable mosquito population, at mutation-drift equilibrium, regardless of population fluctuations. Conclusions: An. subpictus species complex consists of more than two genetically divergent molecular forms. Species A is highly divergent from the rest. Sri Lanka and India contain only species A and B.

Investigation,traceability analysis,and discussion of food poisoning caused by Salmonella typhimurium ST19 / 中国人兽共患病学报

To perform a comprehensive analysis of the pathogenic causes of a food poisoning case in a district of Wuhan Cit-y,we investigated the molecular epidemiological relationships among pathogenic bacteria,to aid in traceability analysis of food-borne disease outbreaks,as well as clinical diagnosis and treatment.The pathogenic bacteria in this food poisoning case were i-solated and identified according to GB789.4-2016.The isolated strains were subjected to genotyping with pulsed field gel elec-trophoresis(PFGE).Drug resistance gene analysis,multi-locus sequence typing(MLST),and genome-wide single-nucleotide polymorphism analysis(wgSNP)were conducted via whole genome sequencing(WGS).The evolutionary tree for cluster analy-sis was constructed in fasttree software.Drug susceptibility testing was conducted with the broth microdilution method.A total of 12 strains of Salmonella were detected in seven anal swab samples and two fecal samples from the case,as well as three anal swab samples from unaffected individuals.The serotype of the strains was Salmonella typhimurium.The strain exhibited severe multiple drug resistance,including resistance to amikacin,ampi-cillin,cefazolin,gentamicin,piperacillin,and tetracycline,but susceptibility to other antibiotics.The coincidence rate between drug resistance genes and drug resistance phenotypes was high.PFGE revealed that nine strains from this food poisoning case were highly homologous.WGS revealed that the MLST type was ST19,and varying numbers of SNPs(1-6)were present a-mong strains.The phylogenetic tree revealed nine isolated strains forming a distinct cluster,differing from other Salmonella strains in the database and belonging to a novel clonal branch.The single nucleotide site in the strains was highly homologous to that of GCF in Jiangxi_020221795.1.The food poisoning case was caused by Salmonella typhimurium ST19,and all nine iso-lated strains originated from the same source.The chef is closely connected to this food poisoning case.This strain of Salmo-nella typhimurium belongs to a new clonal branch and exhibits multiple drug resistance.

Heavy metal and genetic diversity studies in three populations of Snail (Achatina achatina Linnaeus, 1758) from Southwest, Nigeria / Estudos de heavy metal e diversidade genética em três populações de Snail (Achatina achatina Linnaeus, 1758) do sudoeste da Nigéria

Environmental pollutants may often alter the genetic components of natural populations. In this study, heavy metals and genetic diversity in land snail (Achatina achatina) from three populations of south-western Nigeria were investigated, using the Atomic Absorption Spectrometry and DNA Sequencing technology respectively. Metal analysis revealed that the snails accumulated lead (Pb) and nickel (Ni) in high concentrations in two of the three states, while cadmium (Cd) was the least detected. Editing and alignment of the sequences of all snail accessions generated a range of 384bp to 419 bp. Analysis of Molecular Variance (AMOVA) in all 18 accessions was low at only 16%. The query coverage (QC) ranged between 96% and 100%, with 14 (77.8%) of the 18 accessions showing 100% identity. Pairwise comparison of the accessions studied also showed a high genetic similarity. The unweighted pair group method with arithmetic mean (UPGMA) generated two main clusters. Cluster I was unique and contain one sample (AaOy06) while the other cluster are very closely related and can be further sub-divided into sub-clusters. The similarity index of between the clusters is 0.5357. The close similarity among the accessions may be due to the geographical proximity of the three states. The uniqueness of accession AaOy06 in comparison to other accessions might be due to the negative influence of heavy metal, particularly lead. The determination of evolutionary relationships among snail populations may be useful towards the breeding efforts of the species in Nigeria.

Os poluentes ambientais podem frequentemente alterar os componentes genéticos das populações naturais. Neste estudo, metais pesados e diversidade genética em caramujos terrestres (Achatina achatina) de três populações do sudoeste da Nigéria foram investigados, usando a tecnologia de espectrometria de absorção atômica e sequenciamento de DNA, respectivamente. A análise dos metais revelou que os caramujos acumularam chumbo (Pb) e níquel (Ni) em altas concentrações em dois dos três estados, enquanto o cádmio (Cd) foi o menos detectado. A edição e o alinhamento das sequências de todos os acessos de caramujos geraram uma faixa de 384pb a 419pb. A análise de variância molecular (AMOVA) em todos os 18 acessos foi baixa em apenas 16%. A cobertura da consulta (QC) variou entre 96% e 100%, com 14 (77,8%) dos 18 acessos apresentando 100% de identidade. A comparação pareada dos acessos estudados também mostrou alta similaridade genética. O método de grupo de pares não ponderados com média aritmética (UPGMA) gerou dois clusters principais. O cluster I era único e contém uma amostra (AaOy06), enquanto o outro cluster está intimamente relacionado e pode ser subdividido em subclusters. O índice de similaridade entre os clusters é 0,5357. A grande semelhança entre os acessos pode ser devido à proximidade geográfica dos três estados. A singularidade do acesso AaOy06 em comparação com outros acessos pode ser devido à influência negativa de metais pesados, particularmente chumbo. A determinação das relações evolutivas entre as populações de caramujos pode ser útil para os esforços de reprodução da espécie na Nigéria.

Nutrient Management Strategies for Groundnut-blackgram Cropping Sequences

Aims: To refine nutrient management practices for the groundnut-blackgram cropping sequence, focusing on enhancing both yield and quality.Study Design: The experiment was conducted in a split-plot design with three replications.Place and Duration of Study: Regional Research Station in Vridhachalam during the Kharif and rabi season of 2016-17.Methodology: The experimental encompassed various nutrient levels applied to groundnut in the main plots: M1-Control, M2-100% RDF, M3-125% RDF, and M4-150% RDF. Additionally, different nutrient levels were applied to the blackgram subplot: S1-Control, S2-50% RDF, S3-75% RDF, and S4-100% RDF.Results: Analysis of the results indicated that use of 125% RDF in groundnut significantly provide higher pod yield (2657 kg/ha). However, the control group recorded a significantly lower pod yield. Subsequent blackgram seed yield was notably influenced by inorganic fertilizers applied to the preceding groundnut crop. In blackgram, the application of 75% RDF resulted in a higher number of pods per plant (34.6), No. of branches/plant (7.8) and seed yield (823 kg/ha). This performance was comparable to the application of 100% RDFConclusion: These findings underscore the importance of optimizing nutrient management practices, particularly the combination of 125% RDF for groundnut, to enhance pod yield, while the application of 75% RDF demonstrated positive effects on subsequent blackgram seed yield.

Kaufman Oculocerebrofacial syndrome in a newborn: a case report and literature review / 中国新生儿科杂志

Objective:To study the clinical features, treatment, and prognostic features of Kaufman Oculocerebrofacial syndrome.Methods:The clinical characteristics of a newborn with Kaufman Oculocerebrofacial syndrome admitted to the neonatal unit of Guiyang Maternal and Child Health Care Hospital was reported. Using "Kaufman Oculocerebrofacial syndrome", "Blepharophimosis-ptosis-intellectual disability syndrome" and "UBE3B gene" as keywords, databases including CNKI, VIP database, Wanfang database, Chinese medical journals full-text database, PubMed, Web of Science database and Embase database were searched from the date of establishment to June 2022. The clinical characteristics, treatment and prognosis of Kaufman Oculocerebrofacial syndrome from published literature were summarized.Results:The proband was a boy presenting with small lid fissure, wide eye spacing and feeding difficulties. Whole exome sequencing revealed compound heterozygous mutation in the UBE3B gene, c.1445_1448dupTCAC inherited from his father and c.1703dupA inherited from his mother, both variants had not been reported in the domestic and foreign literature thus far. A total of 34 newborn cases were summarized from 11 case reports, including this report. The main clinical manifestations were developmental delay (35/35), peculiar facial features (35/35), narrow eye slits (35/35), feeding difficulties (33/35), ear abnormalities (33/35), hypotonia (32/35), mouth abnormalities (31/35), breathing difficulties (26/35), small jaws (25/35) and low birth weight (16/35).There is no effective treatment available, and a total of 4 cases followed up to over 16 years old have been reported, all of which have severe mental retardation, language deficiency, along with other serious neurological diseases.Conclusions:when children exhibit symptoms such as narrow eye fissures, feeding difficulties, hypotonia, developmental delays, and peculiar facial features in the neonatal period, whole exome sequence can be used to aid diagnosis and evaluate for Kaufman Oculocerebrofacial syndrome. Families with children of Kaufman Oculocerebrofacial syndrome may undergo prenatal diagnosis based on genetic findings.

The airway management and treatment of newborns with micrognathia and laryngomalacia / 临床耳鼻咽喉头颈外科杂志

Objective:To explore the perioperative airway management and treatment of newborns with micrognathia and laryngomalacia. Methods:From January to December 2022, a total of 6 newborns with micrognathia and laryngomalacia were included. Preoperative laryngoscopy revealed concomitant laryngomalacia. These micrognathia were diagnosed as Pierre Robin sequences. All patients had grade Ⅱ or higher symptoms of laryngeal obstruction and required oxygen therapy or non-invasive ventilatory support. All patients underwent simultaneous laryngomalacia surgery and mandibular distraction osteogenesis. The shortened aryepiglottic folds were ablated using a low-temperature plasma radiofrequency during the operation. Tracheal intubation was maintained for 3-5 days postoperatively. Polysomnography（PSG） and airway CT examination were performed before and 3 months after the surgery. Results:Among the 6 patients, 4 required oxygen therapy preoperatively and 2 required non-invasiveventilatory support. The mean age of patients was 40 days at surgery. The inferior alveolar nerve bundle was not damaged during the operation, and there were no signs of mandibular branch injury such as facial asymmetry after the surgery. Laryngomalacia presented as mixed type: type Ⅱ+ type Ⅲ. The maximum mandibular distraction distance was 20 mm, the minimum was 12 mm, and the mean was 16 mm. The posterior airway space increased from a preoperative average of 3.5 mm to a postoperative average of 9.5 mm. The AHI decreased from a mean of 5.65 to 0.85, and the lowest oxygen saturation increased from a mean of 78% to 95%. All patients were successfully extubated after the surgery, and symptoms of laryngeal obstruction such as hypoxia and feeding difficulties disappeared. Conclusion:Newborns with micrognathia and laryngomalacia have multi-planar airway obstruction. Simultaneous laryngomalacia surgery and mandibular distraction osteogenesis are safe and feasible, and can effectively alleviate symptoms of laryngeal obstruction such as hypoxia and feeding difficulties, while significantly improving the appearance of micrognathia.

Gene mutation profiling and clinical significances in patients with renal cell carcinoma

Abstract Objectives The pathological mechanisms of patients with Renal Cell Carcinoma (RCC) remain defined. This study aimed to evaluate relationships between the landscape of gene mutations and their clinical significance in RCC patients. Methods Tissue and peripheral blood samples of 42 patients with RCC were collected and performed for the Next Generation Sequencing (NGS) with Geneseeq PrimeTM 425-gene panel probes. Their landscapes of gene mutation were analyzed. We also carried out an evaluation of Tumor-Node-Metastasis (TNM) staging, RENAL nephelometry score, surgery, and targeted drug treatment of patients. Then we compared the correlations of landscape in gene mutations and the prognosis. Results The most common gene alternations, including BAP1, PBRM1, SETD2, CSF1R, NPM1, EGFR, POLE, RB1, and VHL genes, were identified in tissue and blood samples of 75% of patients. EGFR, POLE, and RB1 gene mutations frequently occurred in relapsed and metastatic patients. BAP1, CCND2, KRAS, PTPN11, ERBB2/3, JAK2, and POLE were presented in the patients with > 9 RENAL nephelometry score. Univariable analysis indicated that SETD2, BAP1, and PBRM1 genes were key factors for Disease-Free Survival (DFS). Multivariable analysis confirmed that mutated SETD1, NPM1, and CSF1R were critical factors for the Progression Free Survival (PFS) of RCC patients with target therapy. Conclusions Wild-type PBRM1 and mutated BAP1 in patients with RCC were strongly associated with the outcomes of the patient. The PFS of the patients with SETD2, NPM1, and CSF1R mutations were significantly shorter than those patients without variants.

Identification of Cordyceps cicadae and Tolypocladium dujiaolongae based on ITS sequences and chemical pattern recognition method / 中国中药杂志

Based on ITS sequences, the molecular identification of Cordyceps cicadae and Tolypocladium dujiaolongae was carried out, and high-performance liquid chromatography(HPLC) fingerprint combined with chemical pattern recognition method was established to differentiate C. cicadae from its adulterant T. dujiaolongae. The genomic DNA from 10 batches of C. cicadae and five batches of T. dujiaolongae was extracted, and ITS sequences were amplified by PCR and sequenced. The stable differential sites of these two species were compared and the phylogenetic tree was constructed via MEGA 7.0. HPLC was used to establish the fingerprints of C. cicadae and T. dujiaolongae, and similarity evaluation, cluster analysis(CA), principal component analysis(PCA), and partial least squares discriminant analysis(PLS-DA) were applied to investigate the chemical pattern recognition. The result showed that the sources of these two species were different, and there were 115 stable differential sites in ITS sequences of C. cicadae and T. dujiao-longae. The phylogenetic tree could distinguish them effectively. HPLC fingerprints of 18 batches of C. cicadae and 5 batches of T. dujiaolongae were established. The results of CA, PCA, and PLS-DA were consistent, which could distinguish them well, indicating that there were great differences in chemical components between C. cicadae and T. dujiaolongae. The results of PLS-DA showed that six components such as uridine, guanosine, adenosine, and N~6-(2-hydroxyethyl) adenosine were the main differential markers of the two species. ITS sequences and HPLC fingerprint combined with the chemical pattern recognition method can serve as the identification and differentiation methods for C. cicadae and T. dujiaolongae.

Efficacy of chemotherapy combined with sorafenib for FLT3-ITD-positive acute myeloid leukemia / 中国基层医药

Objective:To investigate the effect of chemotherapy combined with sorafenib on the prognosis of FLT3 internal tandem duplication (FLT3-ITD)-positive acute myeloid leukemia and to find a more effective treatment.Methods:The clinical data of 60 patients who were newly diagnosed with acute myeloid leukemia and who received treatment in The Second Affiliated Hospital of Qiqihar Medical University from January 2015 to January 2017 were retrospectively analyzed. The patients were divided into three groups according to whether they were positive for FLT3-ITD and the treatment method they used. The observation group (FLT3-ITD-positive, n = 19) were treated with sorafenib based on routine chemotherapy. The control group 1 (FLT3-ITD-positive, n = 21) was treated only with routine chemotherapy. The control group 2 (FLT3-ITD-negative, n = 20) was treated only with routine chemotherapy. After the first and fourth courses of treatment, clinical efficacy was compared among the three groups. Results:After the first course of treatment, the complete remission rate in control group 2 was 50.0% (10/20), which was significantly higher than 15.8% (3/19) in the observation group and 4.8% (1/21) in the control group 1 ( H = 13.39, P < 0.05). After the fourth course of treatment, the complete remission rate in the observation group, control group 2, and control group 1 was 63.2% (12/19), 60.0% (12/20), and 4.8% (1/21), respectively, and the differences were statistically significant ( H = 19.21, P < 0.05). Four-year follow-up results showed that the median survival time in the observation group, control group 1, and control group 2 was 36.63, 24.15, and 45.00 months respectively. The event-free survival in the observation group, control group 1, and control group 2 was 18.00, 9.82, and 24.90 months, respectively. The median survival time and the event-free survival in the control group 2 were significantly longer than those in the observation group and control group 1 ( χ2 = 19.93, 23.04, both P < 0.001). Conclusion:Chemotherapy combined with sorafenib for treating newly-diagnosed FLT3-ITD-positive acute myeloid leukemia can provide comprehensive benefits and have advantages for survival over chemotherapy without sorafenib and chemotherapy alone.

Short Tandem Repeats in plants: genomic distribution and function prediction

BACKGROUND: Short Tandem repeats (STRs) existed as popular elements in both eukaryotic and prokaryotic genomes. RESULTS: In this study, we analyzed the characteristics, distributions, and motif features of STRs within whole-genomes of 140 plant species. The results showed that STR density was negatively correlated with the genome size. Hexanucleotide repeat was the most abundant type of STRs. The distribution of algae shows a preference different from that of other plants. By analyzing GC contents of STRs and genome, it was concluded that STR motif was influenced by GC contents. Analysis of the long STRs in genome (length 1000 bp) found that dicots have the more long STRs. For STR types, di- and tri-nucleotide accounted for the highest proportion. Analyzing and designing long STRs in CDS (length 500 bp) was to verify the role of long STRs in Gossypium hirsutum TM-1 and Solanum tuberosum. By comparing the long STRs found in Fragaria x ananassa with other species, some evolutionary characteristics of the long STRs were obtained. CONCLUSIONS: We got the characteristics, distribution, and motif features of STRs in the whole genome of 140 plants and obtained some evolutionary characteristics of long STRs. The study provides useful insights into STR preference, characteristics, and distribution in plants.

Immunomodulatory effect of adriamycin in mouse 4T1 model of breast cancer / 生物工程学报

To explore the immunomodulatory effect of adriamycin on 4T1 breast cancer. We used a tandem mass tag-based quantitative proteomic method to detect differential proteins in breast cancer tissues, and multiple bioinformatics databases to analyze the differentially expressed proteins in the proteome. Also, we used enzyme-linked immunosorbent assay to detect the effects of adriamycin on helper T cells 1 and 2 in breast cancer tissues, and flow cytometry to detect CD4+ T cells, CD8+ T cells and regulatory T cells. We discovered the immunomodulatory targets of adriamycin in differential proteins. In total 170 differential proteins were significantly up-regulated, whereas 58 were markedly down-regulated. In addition, 73 proteins were involved in immune regulation. Kyoto encyclopedia of genes and genomes enriched important protein pathways related to cytokines and factor receptors, interleukin 17 pathway and cancer transcriptional regulatory pathways. These pathways and important differential proteins related to immunomodulatory functions were ultimately regulated by adriamycin on CD4+ T cells, CD8+ T cells and regulatory T cells, thereby affecting the prognosis of breast cancer. Moreover, adriamycin significantly increased interleukin 2, CD4+ T and CD8+ T (P<0.01) and markedly reduced regulatory T cells (P<0.05). The function of adriamycin against triple-negative breast cancer was closely related to the immunoregulation process of the differential proteins Ighm, Igkc, S100A8, S100A9 and Tmsb4x. Adriamycin could regulate the content of helper T cells 1 cytokines, CD4+ T and CD8+ T lymphocytes in breast cancer and reduce the number of regulatory T cells to produce immunomodulatory effects.

Effect of interactions of chromatin regulatory elements with different promoters on the regulation of gene expression / 生物工程学报

The effect of altering the promoter region of ubiquitous chromatin-opening element (UCOE) and matrix attachment region (MAR) on stable and efficient expression of genes was investigated. Four different promoters were tested, namely, oct4 containing an enhancer region, sox2 having a CpG island, nanog having no regulatory elements, and CMV containing a CpG island and an enhancer region. Eight reporter plasmids were constructed: pOCT4-UCOE, pOCT4-MAR, pSOX2-UCOE, pSOX2-MAR, pNANOG-UCOE, pNANOG-MAR, pCMV-UCOE, and pCMV-MAR. Stable and efficient expression was observed when UCOE combined with the oct4 promoter, whereas the sox2 was the best promoter suited for MAR. Comparison of the stable clones of oct4-UCOE and sox2-MAR showed that UCOE-regulated expression is more stable and efficient than MAR-regulated expression. When CpG island-containing promoter is linked with UCOE, stable and efficient expression could be observed. These data suggest that an enhancer region in the promoter leads to high, yet unstable expression when combined with UCOE, whereas CpG islands stabilize expression. In conclusion, UCOE and MAR interact with regulatory elements on the promoter by altering the chromatin open state and chromatin loop to regulate gene expression.

A Novel Frequency Based Feature Extraction Technique for Classification of Corona Virus Genome and Discovery of COVID-19 Repeat Pattern

Abstract Genome sequence regulates the life of all living organisms on earth. Genetic diseases cause genomic disorders and therefore early prediction of severe genetic diseases is quite possible by Genome sequence analysis. Genomic disorders refer to the mutation that is rearrangement of bases in the Genome of an organism. Genome sequence analysis and mutation identification can help to classify the diseased genome which can be accomplished using Machine Learning techniques. Feature Extraction plays a crucial role in classification as it is used to convert the Genome sequences into a set of quantitative values. In this article, we propose a novel feature extraction technique called Frequency based Feature Extraction Technique which extracts 120 features from genome sequences for classification. In the current scenario, COVID-19 is the pandemic disease and Corona virus is the source of this disease. So, in this research work, we tested the proposed feature extraction technique with 1000 samples of Genome sequences of Corona virus affected patients across the world. The extracted features were classified using both Machine Learning and Deep Learning techniques. From the results, it is evident that the proposed feature extraction technique performs well with Convolutional Neural Network classifier giving an accuracy of 97.96%. The proposed technique also helps to find the most repeat patterns in the genome sequences. It is discovered that the pattern "TTGTT" is the most repeat pattern in COVID-19 genome.

First Genetically Differentiation between Upupa epops major and Upupa epops epops (Family: Upupidae)

Abstract Hoopoe has been traditionally treated as a single species within the order Coraciiformes. Presently, however, various authors have suggested separating the hoopoe into two or more species and even its order, Bucerotiformes. So, this work aimed to use the RAPD PCR and DNA sequences of the COI gene barcodes to confirm and to assess whether the Egyptian hoopoe is a different species named Upupa epops major from the European hoopoe called Upupa epops epops, and to determine the relationships among them. Five primers were used in this technique. Two hoopoes were taken in this work as studying birds, migratory and resident one. The results showed the highest genetic distance between them using different random primers while genetic identity was in general low, overall primers. DNA fingerprinting detected greater genetic distance between Upupa epops major and Upupa epops epops and low genetic identity, this may indicate that both hoopoes fall into two separate species. Furthermore, using mitochondrial cytochrome oxidase subunit I (COI) sequences in this study suggests the separation of Upupa epops major into a new species.

Advance in Genetic Mechanism of Primary Progressive Aphasia (review) / 中国康复理论与实践

Primary progressive aphasia (PPA) is a common neurodegenerative speech disease. Earlier studies on PPA merely observed preliminary pathogenic factors at the brain level. Based on genetic technology, almost 20% to 30% patients with autosomal dominant inheritance reveals that this deficit is closely relevant to gene mutation. C9 gene mutation is the primary factor related to amyotrophic lateral sclerosis and frontotemporal dementia, which is attributed to the main causes of PPA. Repeating expansion of C9 gene may influence the expression of C9 gene, block the combination of RNA and protein, and destroy RNA function.

Paciente masculino con cariotipo 46 XX negativo para el gen SRY y sin ambigüedad genital: reporte de un caso / Male patient 46, XX SRY -negative and unambiguous genitalia: A case report

En la mayoría de los casos, la diferenciación sexual masculina ocurre con la participación del gen SRY. Sin embargo, se pueden presentar otros genotipos excepcionales, como en el caso que se presenta en este reporte. Se trata de un paciente adulto de sexo masculino atendido en el Servicio de Paternidades del Instituto de Genética de la Universidad Nacional de Colombia. Se le hicieron los análisis del gen de la amelogenina y de repeticiones cortas en tándem (Short Tandem Repeat, STR) específicas para el gen SRY con estuches comerciales de identificación humana, así como los de cariotipo convencional e hibridación in situ fluorescente del SRY, y el estudio de microdeleciones del cromosoma Y mediante reacción en cadena de la polimerasa (PCR). Se le hizo la evaluación clínica y se le brindó asesoramiento genético. El paciente no presentaba ambigüedad genital, su cariotipo era 46 XX, y el perfil molecular era negativo para el gen SRY y positivo para el ZFY. Se le diagnosticó un trastorno de diferenciación sexual 46 XX testicular no sindrómico, una rara condición genética. Solo el 20 % de los pacientes con este diagnóstico son negativos para SRY y exhiben perfiles moleculares diversos. La información disponible parece indicar que el ZFY está relacionado con la diferenciación sexual masculina, aún en ausencia del gen SRY.

In most cases, male sexual differentiation occurs with SRY gene mediation. However, exceptional genotypes have been identified, as shown in this paper. This was a male adult patient seen at the Servicio de Paternidades, Instituto de Genética, Universidad Nacional de Colombia. The following procedures were carried out: Amelogenin gene and short tandem repeat analyses using human identification commercial kits, conventional karyotype, SRY fluorescent in situ hybridization, PCR analysis for Y chromosome microdeletions, clinical evaluation, and genetic counseling. We present an adult male with unambiguous genitalia, karyotype 46,XX, and an SRY negative and ZFY positive molecular profile. The diagnosis of nonsyndromic 46,XX testicular disorder of sex development (DSD) -a rare genetic condition- was established. Only 20 % of similarly diagnosed patients are SRY negative and exhibit diverse molecular profiles. Until now, available evidence seems to indicate that, even in the absence of SRY, the ZFY factor is involved in male sexual differentiation.

Utilizing bioinformatics to detect genetic similarities between African honey bee subspecies

Various honey bees, especially subspecies Apis mellifera, occur in Africa and are distribute across the continent. The genetic relationships and identical genetic characteristics between honey bee subspecies in Africa (African bee subspecies) have not been widely investigated using sequence analysis. On the other hand, bioinformatics are developed rapidly and have diverse applications. It is anticipated that bioinformatics can show the genetic relationships and similarities among subspecies. These points have high importance, especially subspecies with identical genetic characteristics can be infected with the same group of pathogens, which have implications on honey bee health. In this study, the mitochondrial DNA sequences of four African subspecies and Africanized bees were subjected to the analyses of base composition, phylogeny, shared gene clusters, enzymatic digestion, and open reading frames. High identical base composition was detected in the studied subspecies, and high identical results from all tests were found between A. m. scutellata and A. m. capensis followed by A. m. intermissa and A. m. monticola. The least genetic relationships were found between A. m. lamarckii and the other subspecies. This study presents insights into the genetic aspects of African bee subspecies and highlights similarity and dissimilarity aspects. Also, Africanized honey bees derived from A. m. scutellata showed high genetic similarities to other African bees, especially A. m.capensis. Additionally, specific primers to identify these subspecies were designed and tested.

Differential expression of lncRNA in the serum of ankylosing spondylitis patients / 中华骨科杂志

Objective@#To investigate the differential expression of lncRNA in the serum of ankylosing spondylitis (AS) patients, with the goal of findingnew potential biomarkers for the diagnosis and targeted treatment of AS.@*Methods@#A total of 19 AS patients and 19 age-matched healthy controls treated at Nanjing Drum Tower Hospitalfrom January 2017 to September 2017 were recruited. Average age were 38.74±7.42 (range, 25-51) and 37.00±6.86 (range, 26-50). High-throughput lncRNA sequencing technology was used to detect differently expressed lncRNAs in the serum of 3 AS patients and 3 healthy controls. Target lncRNAs for further validation were selected according to the P values and fold-changes. In the rest of the serum samples (16 AS patients and 16 healthy controls), Trizol-based technique was used to extract total RNA, and after reverse transcription to obtain cDNA, RT-qPCR was preformed to confirm the sequencing results.@*Results@#Using high-throughput lncRNA sequencing, a total of 41 up-regulated and 2 down-regulated lncRNAs were detected in the serum of AS patients. After sorted by the P values, 4 lncRNAswith a fold-change larger than 2 were chosen as the target genes for RT-qPCR (ENST00000365494.1, P=2.6×10-277, fold-change: 2.05; ENST00000364938.1, P=2.49×10-77, fold-change: 2.19; ENST 00000363046.1, P=2.67×10-29, fold-change: 2.51; ENST00000384756.1, P=6.17×10-21, fold-change: 2.28). RT-qPCR results showed the relative expression of lncRNA ENST00000365494.1 was 1.80±0.22 (P=0.304), lncRNA ENST00000364938.1was 0.78±0.07 (P=0.417), lncRNA ENST00000363046.1was 1.28±0.24 (P=0.793), lncRNA ENST00000384756.1 was 1.52±0.25 (P=0.611)and tendency of up-regulation was found in 3 of them, which was consistent with the sequencing results. However, the difference did not achieve statistical significance.@*Conclusion@#Sequencing result could not be confirmed by RT-qPCR with a larger sample size, which implied the differential expression of lncRNA might not exist in the peripheral blood of AS patients, and further studies regarding lncRNA in AS could focus more on its differential expression and function in the focal tissue.

Missed detections of influenza A(H1)pdm09 by real-time RT–PCR assay due to haemagglutinin sequence mutation, December 2017 to March 2018, northern Viet Nam

Introduction@#There are two methods of reverse transcription polymerase chain reaction (RT–PCR) that have been the common methods to detect influenza infections: conventional and real-time RT–PCR. From December 2017 to March 2018, several missed diagnoses of influenza A(H1)pdm09 using real-time RT–PCR were reported in northern Viet Nam. This study investigated how these missed detections occurred to determine their effect on the surveillance of influenza.@*Methods@#The haemagglutinin (HA) segments of A(H1N1)pdm09 from both real-time RT-PCR positive and negative samples were isolated and sequenced. The primer and probe sets in the HA gene were checked for mismatches, and phylogenetic analyses were performed to determine the molecular epidemiology of these viruses.@*Results@#There were 86 positive influenza A samples; 32 were A(H1)pdm09 positive by conventional RT–PCR but were negative by real-time RT–PCR. Sequencing was conducted on 23 influenza (H1N1)pdm09 isolates that were recovered from positive samples. Eight of these were negative for A(H1)pdm09 by real-time RT–PCR. There were two different mismatches in the probe target sites of the HA gene sequences of all isolates (n = 23) with additional mismatches only at position 7 (template binding site) identified for all eight negative real-time RT–PCR isolates. The prime target sites had no mismatches. Phylogenetic analysis of the HA gene showed that both the positive and negative real-time RT–PCR isolates were grouped in clade 6B.1; however, the real-time RT–PCR negative viruses were located in a subgroup that referred to substitution I295V.@*Conclusion@#Constant monitoring of genetic changes in the circulating influenza A(H1N1)pdm09 viruses is important for maintaining the sensitivity of molecular detection assays.

Low topotype diversity of recent foot-and-mouth disease virus serotypes O and A from districts located along the Uganda and Tanzania border

Foot-and-mouth disease (FMD) is one of the most important livestock diseases in East Africa with outbreaks reported annually that cause severe economic losses. It is possible to control disease using vaccination, but antigenic matching of the vaccine to circulating strains is critical. To determine the relationship between foot-and-mouth disease viruses circulating in districts along the Uganda and Tanzanian border between 2016 and 2017 and currently used vaccines, phylogenetic analysis of the full VP1 virus sequences was carried out on samples collected from both sides of the border. A total of 43 clinical samples were collected from animals exhibiting signs of FMD and VP1 sequences generated from 11 of them. Eight out of the 11 sequences obtained belonged to serotype O and three belonged to serotype A. The serotype O sequences obtained showed limited nucleotide divergence (average of 4.9%) and belonged to topotype East Africa-2, whereas the most common O-type vaccine strain used in the region (O/KEN/77/78) belonged to East Africa-1. The serotype A viruses belonged to topotype Africa-G1 (average nucleotide divergence 7.4%), as did vaccine strain K5/1980. However, vaccine strain K35/1980 belonged to Africa G VII with an average sequence divergence of 20.5% from the study sequences. The genetic distances between current vaccine strains and circulating field strains underscores the crucial need for regular vaccine matching and the importance of collaborative efforts for better control of FMD along this border area.