A systematic review and meta-analysis of trypanosome prevalence in tsetse flies

Background: The optimisation of trypanosomosis control programs warrants a good knowledge of the main vector of animal and human trypanosomes in sub-Saharan Africa, the tsetse fly. An important aspect of the tsetse fly population is its trypanosome infection prevalence, as it determines the intensity of the transmission of the parasite by the vector. We therefore conducted a systematic review of published studies documenting trypanosome infection prevalence from field surveys or from laboratory experiments under controlled conditions. Publications were screened in the Web of Science, PubMed and Google Scholar databases. Using the four-stage (identification, screening, eligibility and inclusion) process in the PRISMA statement the initial screened total of 605 studies were reduced to 72 studies. The microscopic examination of dissected flies (dissection method) remains the most used method to detect trypanosomes and thus constituted the main focus of this analysis. Meta-regression was performed to identify factors responsible for high trypanosome prevalence in the vectors and a random effects meta-analysis was used to report the sensitivity of molecular and serological tests using the dissection method as gold standard. Results: The overall pooled prevalence was 10.3% (95% confidence interval [CI] = 8.1%, 12.4%) and 31.0% (95% CI = 20. 0%, 42.0%) for the field survey and laboratory experiment data respectively. The country and the year of publication were found to be significantly factors associated with the prevalence of trypanosome infection in tsetse flies. The alternative diagnostic tools applied to dissection positive samples were characterised by low sensitivity, and no information on the specificity was available at all. Conclusion: Both temporal and spatial variation in trypanosome infection prevalence of field collected tsetse flies exists, but further investigation on real risk factors is needed how this variation can be explained. Improving the sensitivity and determining the specificity of these alternative diagnostic tools should be a priority and will allow to estimate the prevalence of trypanosome infection in tsetse flies in high-throughput

Applications of Automated Identification Technology in EHR/EMR

Although both the electronic health record (EHR) and the electronic medical record (EMR) store an individuals computerized health information and the terminologies are often used interchangeably, there are some differences between them. Three primary approaches in Automated Identification Technology (AIT) are barcoding, radio frequency identification (RFID), and biometrics. In this paper, technology intelligence, progress, limitations, and challenges of EHR/EMR are introduced. The applications and challenges of barcoding, RFID, and biometrics in EHR/EMR are presented respectively

Impact of sample preservation and manipulation on insect gut microbiome profiling : a test case with fruit flies (Diptera, Tephritidae)

High-throughput sequencing (HTS) techniques are of great value for the investigation of microbial communities, and have been extensively used to study the gut microbiome. While most studies focus on the human gut, many others have investigated insects. However, because of the rapid spread of HTS techniques, a lot of variation exists in the protocols for sample preparation. In the present study, we investigated the impact of two widely adopted sample-processing procedures preceding library preparation, i.e., preservation of insect tissue in 70% ethanol (EtOH) and sample dissection. We used the fruit fly Ceratitis capitata (Diptera: Tephritidae) as a model organism and set up two experiments, one comparing the effects of sample manipulation and preservation across life stages and the other across fruit samples from different sources. The results of this study showed no major effects of dissection on the outcome of HTS. However, EtOH preservation did have effects on the recovered gut microbiome, the main effect being a significant reduction of the dominant genus, Providencia, in EtOH-preserved samples. Less abundant bacterial groups were also affected resulting in altered microbial profiles obtained from samples preserved in 70% EtOH. These results have important implications for the planning of future studies and when comparing studies that used different sample preparation protocols

DNA Barcoding of Recently Diverged Species: Relative Performance of Matching Methods

Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a ‘barcode gap’ and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P<0.00001). Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001). The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2%) as well as empirical data (93.1%), indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification

Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiosperms

BACKGROUND: The chloroplast genes matK and rbcL have been proposed as a “core” DNA barcode for identifying plant species. Published estimates of successful species identification using these loci (70-80%) may be inflated because they may have involved comparisons among distantly related species within target genera. To assess the ability of the proposed two-locus barcode to discriminate closely related species, we carried out a hierarchically structured set of comparisons within Viburnum, a clade of woody angiosperms containing ca. 170 species (some 70 of which are currently used in horticulture). For 112 Viburnum species, we evaluated rbcL + matK, as well as the chloroplast regions rpl32-trnL, trnH-psbA, trnK, and the nuclear ribosomal internal transcribed spacer region (nrITS). RESULTS: At most, rbcL + matK could discriminate 53% of all Viburnum species, with only 18% of the comparisons having genetic distances >1%. When comparisons were progressively restricted to species within major Viburnum subclades, there was a significant decrease in both the discriminatory power and the genetic distances. trnH-psbA and nrITS show much higher levels of variation and potential discriminatory power, and their use in plant barcoding should be reconsidered. As barcoding has often been used to discriminate species within local areas, we also compared Viburnum species within two regions, Japan and Mexico and Central America. Greater success in discriminating among the Japanese species reflects the deeper evolutionary history of Viburnum in that area, as compared to the recent radiation of a single clade into the mountains of Latin America. CONCLUSIONS: We found very low levels of discrimination among closely related species of Viburnum, and low levels of variation in the proposed barcoding loci may limit success within other clades of long-lived woody plants. Inclusion of the supplementary barcodes trnH-psbA and nrITS increased discrimination rates but were often more effective alone rather than in combination with rbcL + matK. We surmise that the efficacy of barcoding in plants has often been overestimated because of the lack of comparisons among closely related species. Phylogenetic information must be incorporated to properly evaluate relatedness in assessing the utility of barcoding loci

Isolation and Identification of Fungi from Clinical Samples of Diabetic Patients and Studying the Anti-Fungal Activity of Some Natural Oils on Isolated Fungi

               تم عزل الفطريات من مائة عينة سريرية جمعت للفترة من من فبراير إلى يوليو 2019 من مستشفى الملك عبد الله (KAH) بيشة، المملكة العربية السعودية. والتي تعود الى  عشرين مريضاً مصابين بالسكر بنوعيه ومن مختلف الأعمار (30 - 70 سنة) عشرة ذكور وعشر إناث. وشملت العينات الدم والشعر والأظافر ومسحات الفم والجلد. تم تلقيح العينات على أجار Sabourauds Dextrose المحتوي على الكلورامفينيكول. وتم عزل وتشخيص ثلاثة عشر نوعا من الفطريات. الأنواع المعزولة هي: Aspergillus flavus، A. niger، A. terrus، A. nidulans، A. fumigatus، Candida albicans، C. krusei، C. parapsilosis، C. Tropicalis، Curvularia lunata، Fusarium solani، Penicillium marneffei and Saccharomyces cerevisiae . تم التعرف على هده الفطريات شكليًا ومجهريًا باستخدام الطرق والمفاتيح التصنيفية المعتمدة  ، بينما استخدام نظام API لتشخيص عزلات الخمائر. سجلت C. albicans أعلى عدد معزول حيث تم عزل 31 مستعمرة من 18 مريضاً ، اعطت كثافة نسبية 22.5٪. (R.D .: هو عدد أنواع فطرية معينة مقسومًا على العدد الإجمالي للفطريات). سجلت الأنواع الفطرية المعزولة الأخرى كثافة نسبية أقل من 16٪. تم تعرف الفطر الأكثر شيوعًا Candida albicans باستخدام 5.8S ومناطق ITS المرافقة. تم تقييم الفعالية المضادة للفطريات لبعض الزيوت العطرية الطبيعية (القرفة والزعتر وجوز الهند واللوز والقرنفل) ضد الفطريات المعزولة باستخدام طريقة الانتشار القرصي. كان التركيز المستخدم 5 ميكرولتر / طبق. تم تحديد قيم MIC أيضًا باستخدام تراكيز مختلفة من الزيت قيد الدراسة (1 ، 2.5 ، 5 ، 10 ، 20 و 40 ميكرولتر / قرص). الطريقة: تم إجراء عزل الفطريات في الفترة من فبراير إلى يوليو 2019. تم جمع مائة عينة سريرية من مستشفى الملك عبد الله بيشة بالمملكة العربية السعودية. تم جمع عينات من عشرين مريضا من مختلف الأعمار (30 - 70 سنة) عشرة ذكور وعشرة إناث. تم جمع العينات من مرضى السكري. وشملت العينات الدم والشعر والأظافر ومسحات الفم والجلد. تم تلقيح العينات على أجار Sabourauds Dextrose agar الذي يحتوي على الكلورامفينيكول. النتائج: تم عزل وتحديد ثلاثة عشر نوعا فطريا. الأنواع المعزولة هي: Aspergillus flavus و A. niger و A. terrus و A. nidulans و A. fumigatus و Candida albicans و C. krusei و C. parapsilosis و C. Tropicalis و Curvularia lunata و Fusarium solani و Penicillium marneffei و Saccharomyces cerevisiae . وقد تم تحديد القوالب من الناحية الشكلية والمجهرية باستخدام الطرق المتاحة وكتب التعريف ، في حين تم تحديد الخمائر باستخدام نظام API. سجلت C. albicans أعلى عدد معزولة حيث تم عزل 31 مستعمرة من 18 مريضا ، وهو ما يمثل كثافة نسبية 22.5 ٪. (R. D .: هو عدد أنواع فطرية معينة مقسومة على العدد الإجمالي للفطريات). الأنواع الفطرية المعزولة الأخرى المعاد تدويرها الكثافة النسبية أقل من 16 ٪. تم تحديد الجزيئات الفطرية المبيضة المبيضة الأكثر شيوعًا باستخدام الجزيئات 5.8S ومناطق ITS المجاورة لها. تم تقييم النشاط المضاد للفطريات لبعض الزيوت العطرية الطبيعية (القرفة والزعتر وجوز الهند واللوز والقرنفل) ضد الفطريات المعزولة باستخدام طريقة انتشار القرص. كان التركيز المستخدم 5 ميكرولتر / لوحة. تم تحديد قيم MIC أيضًا باستخدام تركيزات مختلفة من الزيت (1 ، 2.5 ، 5 ، 10 ، 20 و 40 ميكرولتر / قرص). الخلاصة: يمكن استخدام الزيوت المتطايرة للسيطرة على الفطريات المسببة للأمراض. كان زيت القرفة هو أفضل زيوت متطايرة مثبطة ، تليها زيوت القرنفل والزعتر ، على التوالي. سجلت الزيوت الأساسية الأخرى المختبرة نشاطًا مضادًا للفطريات ضعيفًا.  Isolation of fungi was performed from February to July, 2019. One hundred clinical specimens were collected from King Abdullah Hospital (KAH) Bisha, Saudi Arabia. Samples were collected from twenty patients of different ages (30 - 70 years old) ten males and ten females. The samples were collected from patients with the two types of diabetics. Specimens included blood, hair, nail, oral swabs and skin.  Specimens were inoculated on Sabourauds Dextrose agar containing chloramphenicol. Thirteen fungal species were isolated and identified. The isolated species were: Aspergillus flavus, A. niger, A. terrus, A. nidulans, A. fumigatus, Candida albicans, C. krusei, C. parapsilosis, C. Tropicalis, Curvularia lunata, Fusarium solani, Penicillium marneffei and Saccharomyces cerevisiae. Identification of molds was carried out morphologically and microscopically using available methods and books of identification, while identification of yeasts was carried out using API system. C. albicans recorded the highest isolated number where 31 colonies were isolated from 18 patients, representing relative density of 22.5%. (R. D.: is the number of a certain fungal species divided by the total number of fungi). Other isolated fungal species recorded relative density less than 16 %. The most common isolated fungus Candida albicans was molecularly identified using the 5.8S and flanking ITS regions. The antifungal activity of some natural essential oils (cinnamon, thyme, coconut, almond and clove) was assayed against isolated fungi using disk diffusion method. The used concentration was 5 µl / plate. The MIC values were also determined using different oil concentrations (1, 2.5, 5, 10, 20 and 40 µl / disc)

Does Triatoma brasiliensis occupy the same environmental niche space as Triatoma melanica?

Submitted by Nuzia Santos ([email protected]) on 2016-02-19T16:12:55Z No. of bitstreams: 1 Does Triatoma brasiliensis occupy the same.pdf: 568419 bytes, checksum: 8ebd865012b7ba92c6be897286f9868e (MD5)Approved for entry into archive by Nuzia Santos ([email protected]) on 2016-02-19T16:19:20Z (GMT) No. of bitstreams: 1 Does Triatoma brasiliensis occupy the same.pdf: 568419 bytes, checksum: 8ebd865012b7ba92c6be897286f9868e (MD5)Made available in DSpace on 2016-02-19T16:19:20Z (GMT). No. of bitstreams: 1 Does Triatoma brasiliensis occupy the same.pdf: 568419 bytes, checksum: 8ebd865012b7ba92c6be897286f9868e (MD5) Previous issue date: 2015Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Triatomíneos e Epidemiologia da Doença de Chagas. Belo Horizonte, Minas Gerais, Brazil.Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Triatomíneos e Epidemiologia da Doença de Chagas. Belo Horizonte, Minas Gerais, Brazil.Secretaria de Saúde do Estado do Ceará. Fortaleza, CE, Brasil.Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Triatomíneos e Epidemiologia da Doença de Chagas. Belo Horizonte, Minas Gerais, Brazil.IMBIV-CONICET. Córdoba, Argentina.Background: Triatomines (Hemiptera, Reduviidae) are vectors of Trypanosoma cruzi, the causative agent of Chagas disease, one of the most important vector-borne diseases in Latin America. This study compares the environmental niche spaces of Triatoma brasiliensis and Triatoma melanica using ecological niche modelling and reports findings on DNA barcoding and wing geometric morphometrics as tools for the identification of these species. Methods: We compared the geographic distribution of the species using generalized linear models fitted to elevation and current data on land surface temperature, vegetation cover and rainfall recorded by earth observation satellites for northeastern Brazil. Additionally, we evaluated nucleotide sequence data from the barcode region of the mitochondrial cytochrome c oxidase subunit I (CO1) and wing geometric morphometrics as taxonomic identification tools for T. brasiliensis and T. melanica. Results: The ecological niche models show that the environmental spaces currently occupied by T. brasiliensis and T. melanica are similar although not equivalent, and associated with the caatinga ecosystem. The CO1 sequence analyses based on pair wise genetic distance matrix calculated using Kimura 2-Parameter (K2P) evolutionary model, clearly separate the two species, supporting the barcoding gap. Wing size and shape analyses based on seven landmarks of 72 field specimens confirmed consistent differences between T. brasiliensis and T. melanica. Conclusion: Our results suggest that the separation of the two species should be attributed to a factor that does not include the current environmental conditions. However, as the caatinga is a biome that has existed in the area for at least the last 18,000 years, past conditions might have had an influence in the speciation process. The DNA Barcoding approach may be extended to these members of the subfamily Triatominae

The community ecology perspective of omics data

The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract