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African populations are diverse in their ethnicity, language, culture, and genetics. Although plagued by high disease burdens, until recently the continent has largely been excluded from biomedical studies. Along with limitations in research and clinical infrastructure, human capacity, and funding, this omission has resulted in an underrepresentation of African data and disadvantaged African scientists. This review interrogates the relative abundance of biomedical data from Africa, primarily in genomics and other omics. The visibility of African science through publications is also discussed. A challenge encountered in this review is the relative lack of annotation of data on their geographical or population origin, with African countries represented as a single group. In addition to the abovementioned limitations,the global representation of African data may also be attributed to the hesitation to deposit data in public repositories. Whatever the reason, the disparity should be addressed, as African data have enormous value for scientists in Africa and globally.

Precision medicine has brought new hopes for patients around the world with the applications of novel technologies for understanding genetics of complex diseases and their translation into clinical services. Such applications however require a foundation of skills, knowledge and infrastructure to translate genetics for health care. The crucial element is no doubt the availability of genomics data for the target populations, which is seriously lacking for most parts of Africa. We discuss here why it is vital to prioritize genomics data for the South West Indian Ocean region where a mosaic of ethnicities co-exist. The islands of the SWIO, which comprise Madagascar, La Reunion, Mauritius, Seychelles and Comoros, have been the scene for major explorations and trade since the 17th century being on the route to Asia. This part of the world has lived through active passage of slaves from East Africa to Arabia and further. Today’s demography of the islands is a diverse mix of ancestries including European, African and Asian. The extent of admixtures has yet to be resolved. Except for a few studies in Madagascar, there is very little published data on human genetics for these countries. Isolation and small population sizes have likely resulted in reduced genetic variation and possible founder effects. There is a significant prevalence of diabetes, particularly in individuals of Indian descent, while breast and prostate cancers are on the rise. The island of La Reunion is a French overseas territory with a high standard of health care and close ties to Mauritius. Its demography is comparable to that of Mauritius but with a predominantly mixed population and a smaller proportion of people of Indian descent. On the other hand, Madagascar’s African descendants inhabit mostly the lower coastal zones of the West and South regions, while the upper highlands are occupied by peoples of mixed African-Indonesian ancestries. Historical records confirm the Austronesian contribution to the Madagascar genomes. With the rapid progress in genomic medicine, there is a growing demand for sequencing services in the clinical settings to explore the incidence of variants in candidate disease genes and other markers. Genome sequence data has become a priority in order to understand the population sub-structures and to identify specific pathogenic variants among the different groups of inhabitants on the islands. Genomic data is increasingly being used to advise families at risk and propose diagnostic screening measures to enhance the success of therapies. This paper discusses the complexity of the islands’ populations and argues for the needs for genotyping and understanding the genetic factors associated with disease risks. The benefits to patients and improvement in health services through a concerted regional effort are depicted. Some private patients are having recourse to external facilities for molecular profiling with no return of data for research. Evidence of disease variants through sequencing represents a valuable source of medical data that can guide policy decisions at the national level. There are presently no such records for future implementation of strategies for genomic medicine.

Background The wealth of biological information available nowadays in public databases has triggered an unprecedented rise in multi-database search and data retrieval for obtaining detailed information about key functional and structural entities. This concerns investigations ranging from gene or genome analysis to protein structural analysis. However, the retrieval of interconnected data from a number of different databases is very often done repeatedly in an unsystematic way. Results Here, we present TAxonomy, Gene, Ontology, Protein, Structure INtegrated (TAGOPSIN), a command line program written in Java for rapid and systematic retrieval of select data from seven of the most popular public biological databases relevant to comparative genomics and protein structure studies. The program allows a user to retrieve organism-centred data and assemble them in a single data warehouse which constitutes a useful resource for several biological applications. TAGOPSIN was tested with a number of organisms encompassing eukaryotes, prokaryotes and viruses. For example, it successfully integrated data for about 17,000 UniProt entries of Homo sapiens and 21 UniProt entries of human coronavirus. Conclusion TAGOPSIN demonstrates efficient data integration whereby manipulation of interconnected data is more convenient than doing multi-database queries. The program facilitates for instance interspecific comparative analyses of protein-coding genes in a molecular evolutionary study, or identification of taxa-specific protein domains and three-dimensional structures. TAGOPSIN is available as a JAR file at https://github.com/ebundhoo/TAGOPSIN and is released under the GNU General Public License.

The Leptostemonum clade (Solanum subgenus Leptostemonum Bitter) species Solanum melongena L. (the aubergine) is an economically important crop which requires the acquisition of adaptive traits, potentially from its wild relatives of the same clade, to reduce its susceptibility to biotic and abiotic stress. The application of matK, rbcL, psbA-trnH and ITS2 to Leptostemonum clade phylogeny and DNA barcoding is not documented. In this study, PCR amplification and direct sequencing of these markers from S. melongena, S. violaceum Ortega and S. torvum Sw., with commonly used primers, were tested. The four DNA regions were amplified from these species. matK, rbcL and psbA-trnH were successfully sequenced. Unlike rbcL, matK and psbA-trnH could singly produce species-specific groups in phylogenetic analyses, which showed species relationships consistent with those from previously published phylogenies determined using other chloroplast and nuclear DNA regions. The phylogeny from matK+psbA-trnH exhibited high bootstrap support for the S. melongena group as well as intraspecific resolution within S. violaceum. In the context of testing the use of DNA barcoding to discriminate between S. violaceum and S. anguivi Lam., interspecific and intraspecific p-distances for matK, rbcL and psbA-trnH in these two species were compared. No barcode gap or diagnostic character was found, thus eliminating these three markers as potential DNA barcodes to discriminate between S. violaceum and S. anguivi.

Childhood cancers present unique challenges for variant interpretation in a clinical context due to their rarity, low mutation burden, diversity of molecular alterations, and heterogeneity among patients. Consequently, genes and variants associated with childhood tumors are under-represented in public cancer databases and knowledgebases. A focused effort is needed for the structured curation of genetic variant-level data to document diagnostic, prognostic, and therapeutic biomarkers for childhood cancers. The Pediatric Cancer Curation Advancement Subcommittee (PCCAS), a collaboration between the Clinical Interpretations of Variants in Cancer knowledgebase (CIViC; civicdb.org), the ClinGen Somatic Pediatric Cancer Taskforce, Disease Ontology (DO; disease-ontology.org) and CIViCmine (bionlp.bcgsc.ca/civicmine/), is addressing this challenge through enhanced curation, tagging, and automation. PCCAS created a pediatric specific curation standard operating procedure (SOP) to harmonize pediatric evidence entered in CIViC. Our SOP provides general guidance and considerations to define and classify childhood cancers and to represent childhood cancer evidence on a spectrum of age-related incidence and presentation. For instance, pediatric evidence in CIViC is now tagged using Human Phenotype Ontology (HPO) age of onset terms, allowing pediatric evidence to be easily searched, tracked, and sorted. We also initiated the addition of new age of onset terms to enhance the granularity of these tags. WHO ICD-O nomenclature has been chosen for pediatric disease classification in CIViC. ICD-O provides updated terminology including specific genetic subtypes, which are important in pediatric cancers where their underlying molecular profiles often define the disease. To aid curator selection of disease, we verified pediatric relevant ICD-O terms inclusion in DO and restructured DO disease hierarchies to ensure proper mapping. CIViC highlights our pediatric cancer initiative in multiple areas including a homepage feature linking directly to a dedicated pediatric advanced search that returns all evidence tagged with pediatric or young adult age of onset. Most importantly, our childhood specific SOP and initiatives are included in all ClinGen Somatic Cancer and CIViC training sessions for consistent implementation. CIViCmine supports CIViC by using natural language processing to identify important cancer biomarkers in the literature. To better identify pediatric biomarkers, we are adapting and refining CIViCmine to use MeSH terms and other approaches to enhance accuracy in the identification of childhood evidence in both the literature and CIViC. In conclusion, implementation of these procedures, features, and automation are pushing to make childhood cancer variant evidence more accessible and interpretable. Citation Format: Jason Saliba, Jake Lever, Kilannin Krysiak, Arpad Danos, Alex Wagner, Heather E. Williams, Laveniya Satgunaseelan, David Meredith, Cameron J. Grisdale, Chimene Kesserwan, Jianling Ji, Shruti Rao, Catherine Cottrell, Alanna Church, Mark Evans, Yasmina Jaufeerally-Fakim, Lynn M. Schriml, Angshumoy Roy, Gordana Raca, Malachi Griffith, Obi L. Griffith. Enhancing pediatric cancer variant curation and representation through standardized classification and automation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1193.

A number of examples of putative eukaryote-to-prokaryote horizontal gene transfer (HGT) have been proposed in the past using phylogenetic analysis in support of these claims but none have attempted to map these gene transfers to the presence of genomic islands (GIs) in the host. Two of these cases have been examined in detail, including an ATP sulfurylase (ATPS) gene and a class I fructose bisphosphate aldolase (FBA I) gene that were putatively transferred to cyanobacteria of the genus Prochlorococcus from either green or red algae, respectively. Unlike previous investigations of HGT, parametric methods were initially used to detect genomic islands, then more traditional phylogenomic and phylogenetic methods were used to confirm or deny the HGT status of these genes. The combination of these three methods of analysis- detection of GIs, the determination of genomic neighborhoods, as well as traditional phylogeny, lends strong support to the claim that trans-domain HGT has occurred in only one of these cases and further suggests a new insight into the method of transmission of FBA I, namely that cyanophage-mediated transfer may have been responsible for the HGT event in question. The described methods were then applied to a range of prochlorococcal genomes in order to characterize a candidate for eukaryote-to-prokaryote HGT that had not been previously studied by others. Application of the same methodology used to confirm or deny HGT for ATPS and FBA I identified a ⊗12 fatty acid desaturase (FAD) gene that was likely transferred to Prochlorococcus from either green or red algae.

Clinical significance of somatic gene variants needs to be comprehensively characterized for their diagnostic, prognostic and/or therapeutic actionability in patient management. However, challenges remain due to discrepancies in interpretation and reporting of these somatic variants among different testing labs. Therefore, standardized curation, clinical interpretation and reporting of somatic variants in hematologic cancers is critical. To address this issue, the Hematologic Cancer Taskforce (HCT), composed of 52 multi-disciplinary experts including oncologists, molecular pathologists, lab directors, genomic scientists and biocurators, was formed in January 2020 within the ClinGen Somatic Cancer Clinical Domain Working Group (CDWG) with a goal to undertake systematic curation and evidence-based clinical interpretation of genes/somatic variants associated with hematologic malignancies. In collaboration with the Clinical Interpretation of Variants in Cancer (CIViC) (civicdb.org) knowledgebase, HCT members curate, edit, and verify Evidence Items for each variant extracted from peer-reviewed publications. Monthly discussions based on these Evidence Items lead to the preparation of variant Assertions, which summarize the state of the field consensus variant interpretation and include tiering based on the AMP/ASCO/CAP guidelines (PMID: 27993330). FMS-like tyrosine kinase 3 (FLT3) encodes a class III receptor tyrosine kinase expressed in hematopoietic cells. FLT3 mutations, including both internal tandem duplication (ITD) and mutations in the tyrosine kinase domain (TKD), are the most common mutations in acute myeloid leukemia (AML), occurring in approximately 30% of all AML cases. Implementing FLT3 tyrosine kinase inhibitors (TKIs) in different treatment regimens for FLT3 mutated AML patients has led to significantly improved overall survival. Type I FLT3 inhibitors, including midostaurin, gilteritinib, sunitinib, lestaurtinib, and crenolanib, bind to the ATP-binding site when the receptor is in active conformation. Type II FLT3 inhibitors, including sorafenib, ponatinib, and quizartinib, interact with a hydrophobic region directly adjacent to the ATP-binding domain that is only accessible when the receptor is inactive, which prevents receptor activation. Generally in AML cells, type I FLT3 inhibitors prevent activity for both ITD and TKD mutations, while Type II inhibitors target ITD but lack efficiency against TKD mutations. The development of TKD mutations in AML cells with ITD have proved to be a mechanism of acquired, or secondary resistance to Type II FLT3 inhibitors. The HCT is piloting curation assessments of FLT3 alterations, including ITD, TKD and non-TKD variants, in AML. So far, the HCT has curated 75 evidence items for FLT3 somatic variants. FLT3-ITD, as well as D835 and I836 were asserted as tier 1 level A variants based on the prediction of response to gilteritinib in relapsed/refractory AML (PMIDs: 27993330, 31665578, 28645776, 28516360, 27908881). Recent curation activities are focused on FLT3 D839G and N676K, as clinical trials using large AML patient cohorts are lacking in their ability to validate drug response/resistance associations of these two TKD variants due to their low frequency. Functional studies showed both variants result in increased proliferation and protection from apoptosis, supporting the oncogenic potential of these two variants (PMIDs: 26891877, 2468088). FLT3 D839G combined with ITD confers resistance to pexidartinib and ponatinib, both Type II FLT3 inhibitors (PMIDs: 25847190, 23430109). FLT3 N676K predicts response to the Type I FLT3 inhibitor, gilteritinib, when N676K is present alone or in combination with ITD. Interestingly, FLT3 N676K in the absence of ITD predicts response to sorafenib, a Type II FLT3 inhibitor (PMIDs: 32040554, 32984009). However, these results are mostly derived from in vitro studies. Two separate Tier II, Level D Assertions have been submitted for FLT3-ITD&D839G for its response to pexidartinib and ponatinib, and more evidence is being collected to form an Assertion for FLT3 N676K. The complexity of the prediction of response/resistance associated with FLT3 D839G and N676K supports the importance of evidence-based curation and collection for these variants in the context of the overall mutation profile, disease context and specific FLT3 TKIs to clearly define their clinical impact. Disclosures Pullarkat: Stemline Therapeutics: Honoraria.

With the expansion of biological data sources available online, integration is a major challenge facing researchers wishing to explore this information. Users often need to integrate data derived from multiple, diverse and heterogeneous sources for investigation. This paper presents the features of Infect-DB, a data warehouse that can localize and integrate genomes of pathogenic species, retrieved from NCBI, based on information from the American Biological Safety Association (ABSA). The list of bacteria and their corresponding host specificity were programmatically accessed from ABSA and integrated into Infect-DB. The list of organisms obtained from ABSA was used to target the automated download of corresponding genomes from the NCBI FTP site. Infect-DB provides a set of analysis tools, including a comparison of genomes using local-BLAST, dN/dS analysis, multiple sequence alignment, phylogenetic analysis and visualization tools. To date, Infect-DB has integrated 854 bacterial genomes from 207 genera considered as important pathogens causing infectious diseases.

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03286-9.

Identification of differentially expressed genes is a direct approach to understand the molecular basis of physiological processes. In this study, the GeneFishing™ PCR technique was used to identify genes which were differentially expressed in two Solanum lycopersicum lines, the resistant Lycopersicon cerasiforme and a susceptible cultivar known as Quatre carrees, after inoculation with a phylotype I strain of Ralstonia solanacearum. With twenty annealing control primers (ACPs), nineteen differentially expressed genes (DEGs) were identified, 17 of which were from the L. cerasiforme line and 2 from the Quatre carrees cultivar. Six DEGs (DEG1, DEG5, DEG8, DEG12, DEG15 and DEG18) were chosen for further studies based on the blast results. Primers were designed for the six DEGs and quantitative real-time PCR was carried out to confirm the differential expression. Expression of the six DEGs was also tested in Solanum commersonii, the Solanum tuberosum cultivar, Spunta and the S. lycopersicum lines MST 32/1, CRA 66 and Hawaii 7996. Level of expression was closely related to the phenotype of the plants, in terms of susceptibility and resistance to the pathogen. The resistant lines L. cerasiforme, S. commersonii, CRA 66 and Hawaii 7996 always had higher levels of gene expression than the moderately resistant MST 32/1 cultivar and the susceptible Quatre carrees and Spunta cultivars.

Shiga-toxigenic Escherichia coli (STEC) are important human pathogens associated with diarrhea and in some cases haemorrhagic colitis. Contaminated food derived from cattle and wildlife species are often associated with disease outbreaks. In this study, we report the prevalence, serogroup diversity and virulence profiles of STEC strains derived from cattle, rusa deer and pig. Of the 422 samples analyzed, STEC were detected in 40% (80/200) of cattle, 27.0% (33/122) of deer and 13.0% (13/100) of pigs. STEC isolates belonged to 38 O-serogroups whereby 5.2% (24/462) of the isolates belonged to clinically important EHEC-7 serogroups: O26 (n = 2), O103 (n = 1), O145 (n = 3) and O157 (n = 18). Fourteen serogroups (O26, O51, O84, O91, O100, O104, O110, O117, O145, O146, O156, O157, O177 and ONT) displayed multiple virulence profiles. We also identified two serovars (O117 and O119) in deer which are not well-documented in epidemiological surveys. 73.7% (28/38) of recovered O-serogroups are known to be associated with serious human illnesses including haemolytic uremic syndrome (HUS) and bloody diarrhea. STEC isolates harboring single genotypes stx1, stx2, eae and hlyA accounted for 3.0% (14/462), 9.1% (42/462), 47.6% (220/462) and 1.7% (8/462) of all STEC isolates screened, respectively. Virulence combinations stx1 and stx2 were harboured by 1.3% of isolates while strains with genetic profiles eae/hlyA were the second most prevalent amongst STEC isolates. The full known virulent genotypes (stx2/eae, stx1/stx2/eae, stx1/stx2/hlyA and stx2/eae/hlyA) were present in 22 of the 462 STEC strains. A total of 10 different virulence patterns were recovered amongst animal species. Phylogeny of the gnd gene showed that amongst STEC strains, serovar O100 outlined the main cluster. Fourteen (n = 14) different sequence types (STs) were identified from a panel of twenty (n = 20) STEC isolates. One of the isolate (PG007B) possessed a unique ST (adk 10, fumC 693, gyrB 4, icd 1, mdh 8, purA 8, recA 2) that could not be assigned using MLST databases. None of the ST's recovered in deer were observed in domestic species. Our findings shows that food associated animals found on the tropical island of Mauritius carry a diversity of STEC strains with many serovars known to be associated with human disease. This report indicates that increased awareness, surveillance and hygienic attention at critical stages of the human food chain are warranted.

A major area of research is biomarker discovery using gene expression data. Such data is huge and often needs to be classified into classes or clustered, using different machine learning techniques, for further analysis. An important preprocessing step is feature selection (FS) and different such methods have been devised. However, applying different FS techniques to the same dataset do not always produce the same results. In this work, the robustness of FS methods will be looked into. Robustness is defined here as the stability of a given gene pool with respect to the data and the FS method used. Our approach is to investigate the resulting feature subset obtained when running diverse FS methods on different gene expression datasets. As a first step, 10 FS methods were executed using 2 different datasets. Based on the results obtained, 2 of these methods were further investigated using 10 different datasets. The effects of selecting an increasing number of features on the percentage similarity inter-methods were also studied. Our results show that the studied methods exhibit a high amount of variability in the resulting feature subset. The selected feature subsets differed both inter-methods and intra-methods for different datasets. The reason behind this is not clear and possible objective assessment on the ideal (best) subset should be further investigated.

Although Anthurium is an attractive and commercially popular ornamental plant, its genetic enhancement has lagged behind that of other ornamental crops. There are several agronomically important traits in need of improvement. These include novel flower colors and morphologies, increased shelf and vase lives, and resistance to bacterial blight (Xanthomonas axonopodis pv. dieffenbachiae), burrowing nematodes and abiotic stresses. The production of transgenic Anthuriums is critical because the conventional breeding of a cultivar with beneficial traits typically requires 8–10 years. This review evaluates the problems, challenges and progress associated with developing molecular markers for Anthurium and in genetically transforming this ornamental. Recent improvements have hastened the tissue culture and regeneration of transgenic plants primarily using Agrobacterium-based methods. Promoter analyses have focused on constitutive and tissue-enhanced gene expression with the green fluorescent protein being a more reliable reporter than β-glucuronidase. The development of molecular markers assists with phylogenetic analyses and PCR-based markers such as RAPD, SSR, SPAR, ISSR and AFLP can be used to differentiate cultivars and for genetic fingerprinting. The marker-assisted breeding of Anthurium will become more feasible once available data are used for association to specific traits. Work on the identification of quantitative trait loci for disease resistance and other traits such as flower colour is required and should incorporate new approaches, such as next-generation sequencing technologies. By highlighting the aforementioned bottlenecks and successes in this review, it is expected that the pace of Anthurium genetic improvement will increase with the multifaceted incorporation of focused priorities and new technology advancements.

Microarray technologies produce very large amounts of data that need to be classified for interpretation. Large data coupled with small sample sizes make it challenging for researchers to get useful information and therefore a lot of effort goes into the design and testing of feature selection tools; literature abounds with description of numerous methods. In this paper we select five representative review papers in the field of feature selection for microarray data in order to understand their underlying classification of methods. Finally, on this base, we propose an extended taxonomy for categorizing feature selection techniques and use it to classify the main methods presented in the selected reviews.

Shiga‐toxigenic Escherichia coli (STEC), also known as enterohemorrhagic E. coli (EHEC) pose a significant threat to public health worldwide. Livestock animals are well known reservoirs of STEC. In this study, cattle were investigated in situ on the tropical island of Mauritius. This island is of economic importance as it has a consolidated tourism industry and possesses several attributes which are increasingly being experienced by other tropical oceanic islands. Throughout our research, STEC were recovered in 20.3% (146/718) of E. coli isolates screened from faecal, milk, and meat samples. Prevalence‐wise, non‐EHEC‐7 dominates EHEC‐7 (seven serogroups classified as most virulent) and accounts for 77.4% and 22.6% of data set, respectively. Different virulent profiles were observed, with eaeA and EHEC‐hlyA genes being more frequent. These virulent E. coli strains represents potential threats to both local and international travelers. Mauritius today may thus serve as an “overview” of the potential threat encountered by many other oceanic islands. PRACTICAL APPLICATIONS: As in any risk assessment procedures, there is a need for identification and characterization of potential threats. With the flourishing tourism industry and increasing population in the Indian Ocean region, a greater demand for safe food justifies the need for a more effective surveillance system approach. Given the gap in the Indian Ocean surveillance system and the presence of Shiga‐toxigenic Escherichia coli in cattle with potential for zoonotic transmission to humans resulting from this study, we believe that providing information to policy makers and public health decision makers will enable the setting up of an Indian Ocean Zoonoses Control Programme supervised by the WHO to help promote prevention, public health education, research, surveillance, and control of zoonoses in this part of the globe, most commonly associated with diarrheal disease among both local and international travelers of the Indian Ocean region.

In the context of recent international initiatives to bolster genomics research for Africa, and more specifically to develop bioinformatics expertise and networks across the continent, a workshop on computational metagenomics was organized during the end of 2014 at the University of Mauritius. The workshop offered background on various aspects of computational biology, including databases and algorithms, sequence analysis fundamentals, metagenomics concepts and tools, practical exercises, journal club activities and research seminars. We have discovered a strong interest in metagenomics research across Africa, to advance practical applications both for human health and the environment. We have also realized the great potential to develop genomics and bioinformatics through collaborative efforts across the continent, and the need for further reinforcing the untapped human potential and exploring the natural resources for stronger engagement of local scientific communities, with a view to contributing towards the improvement of human health and well-being for the citizens of Africa.

SUMMARY Suppression subtractive hybridization was used to isolate the genes which are specifically up-regulated in the biotrophic phase of the incompatible interaction between a potato genotype, 1512 c(16), containing the resistance gene R2, and a Phytophthora infestans isolate containing the avirulence gene Avr2. Eight cDNAs were up-regulated in the biotrophic phase of the incompatible interaction. Seven of these were also up-regulated in the compatible interaction, but not until late in the necrotrophic phase. Amongst the sequences to be isolated were genes encoding the cysteine protease cathepsin B, StCathB, and an oxysterol binding protein, StOBP1; equivalent genes are involved in programmed cell death (PCD) processes in animals, but have yet to be implicated in such processes in plants. Whereas StOBP1 was up-regulated early in potato plants containing either R gene-mediated or moderate to high levels of field resistance, the highest levels of up-regulation of StCathB were observed early in R gene-mediated resistance but gradually increased from the early to late stages of field resistance, revealing these genes to be components of independent defence pathways and providing a means of distinguishing between these forms of resistance. StOBP1 was up-regulated by oligogalacturonides (plant cell wall breakdown products generated by pectinase activities), indicating that it is also a component of a general, non-specific defence pathway and is unlikely to play a role in PCD. In contrast, the expression of StCathB was unaffected by oligogalacturonide treatment, further associating its up-regulation specifically with the gene-for-gene interaction.

H3Africa is developing capacity for health-related genomics research in Africa

Shiga-toxigenic Escherichia coli (STEC) are important human pathogens (1). They are characterized by their ability to pro­duce Shiga toxins ( stx1 and stx2 ). Seven STEC have been shown to withstand food processing procedures that are expected to ensure food safety. Clinical symptoms associated with STEC infection can vary from abdominal cramps and acute bloody diarrhea to more severe aftereffects including hemorrhagic coli­tis, hemolytic uremic syndrome and thrombocytopenic purpura, which can lead to kidney failure and death. Dairy cattle, which excrete STEC in their feces, are a major source of STEC infection (2). Humans become infected with STEC through direct contact with infected animals or by inges­tion of contaminated water, raw and unpasteurized milk, meat products, and/or plant-derived products (4–6). The objectives of this study were to estimate both cow-level and farm-level point prevalence estimates of STEC fecal shedding in Mauritian dairy cattle and to characterize putative STEC isolates based on their virulence factors. A cross-sectional study was conducted to investigate the preva­lence of STEC in the dairy cattle population of Mauritius. Fecal samples were collected from 150 individual dairy cattle from 38 dairy farms located throughout the nine district regions of the island. Collected samples were enriched in modified Tryptic Soy broth followed by isolation on CHROMagar TM STEC (3). Suspected isolates were streaked onto EMB agar, further puri­fied on nutrient agar and subsequently cryopreserved in glyc­erol until further investigation. Putative isolates were charac­terized using molecular techniques (7, 8) for the presence of chromosomal sequences encoding Shiga toxin genes ( stx1 and stx2 ), the intimin protein ( eaeA ) and the plasmid-encoded hemo­lysin ( hlyA ). Out of the 38 farm samples, 29 farms (76%) were found to be positive for presumptive STEC isolates. From the 150 fecal samples collected, 111 (74%) were found to harbor presump­tive STEC isolates (Table I). Polymerase-chain-reaction- (PCR-) based characterization has confirmed the presence of STEC in a number of fecal samples. Results obtained so far indicate that STEC are common members of the gut microbiome of dairy cattle in Mauritius. Presumptive STEC isolates are currently being screened with PCR targeting stx1 , stx2 , eaeA and hlyA genes. This epidemiological study on STEC is the first of its kind in Mauritius and in the Indian Ocean region. It aims at providing new information concerning the presence of STEC in Mauritian dairy cattle. It involves the use of the latest chromogenic agar (CHROMagar TM STEC) available on the market. This culture medium has been designed for the detection of a wide range of STEC from different sources. The study highlights the importance of implementing proper sanitary measures at the dairy farm level to prevent cross contamination of milk and the surrounding environment.

Endophytes are fungi associated with plants without causing symptoms, and they are quite diverse and have enormous potential for production of important secondary metabolites for the pharmaceutical industry. In this study, we report for the first time fungi (both endophytes and saprobes) from Antidesma madagascariense, a medicinal plant in Mauritius, in view of identifying potential candidates for screening of fungi for pharmaceutical importance. In addition the phylogenetic placement of fungi recovered from leaves samples was investigated based on rDNA sequence analysis. Most commonly isolated fungi were related to Aspergillus, Guignardia, Fusarium, Penicillium, Pestalotiopsis, and Trichoderma. Phylogenetic analyses revealed that fungi recovered belong to 5 different fungal lineages (Hypocreaceae, Trichocomaceae, Nectriaceae, Xylariaceae, and Botryosphaeriaceae). DNA data from the ITS regions were reliable in classification of all recovered isolates up to genus level, but identification to an exact species name was not possible at this stage. Despite criticisms pertaining to the use of ITS sequence data in molecular systematics, our approach here provides an opportunity to justify the reliability of ITS sequence data for possible identification and discovering of evolutionary scenarios among isolates that do not sporulate under cultural conditions.

Nucleotide sequences of catalase were obtained following amplification using specific primers and were blasted against Musa acuminata catalase 2 mRNA from NCBI (157418810). Clustering of the amino acid sequences from NCBI was done using Clustal X. The latter revealed that FHIA18 catalase is more related to Ravenala madagascariensis (Musa relative) catalase while the Williams catalase is more related to a clade containing a Musa acuminata (Musa ancestor) catalase from NCBI. The tertiary structures and the catalase consensus functional sites, based on the Pseudomonas syringae catalase structural template, were obtained for FHIA18, Williams, Ravenala madagascariensis and Musa acuminata catalases. They were found to differ slightly. Using known features of catalase active sites, four pre-requisite criteria were defined to find such sites: (1) Position of tyrosine axial to heme determined by X-ray diffraction, (2) 7 conserved amino acids in the active site found by sequence alignment, (3) favourable docking energy, and (4) presence of an unobstructed long tunnel that leads the ligand to the active site. Two differing potential docking sites were found for both FHIA18 and Williams that fit a maximum number of criteria. In terms of 1D sequence, the region of the docking site for Williams is within the catalase domains as seen upon NCBI blast. The counterpart of FHIA18 for the same region is not. This sequence difference between FHIA18 and Williams affects the best docking site in FHIA18 and Williams in silico.

The phylogenetic relationships between species of Coffea and Psilanthus remain poorly understood, owing to low levels of sequence variation recovered in previous studies, coupled with relatively limited species sampling. In this study, the relationships between Coffea and Psilanthus species are assessed based on substantially increased molecular sequence data and greatly improved species sampling.Phylogenetic relationships are assessed using parsimony, with sequence data from four plastid regions [trnL-F intron, trnL-F intergenic spacer (IGS), rpl16 intron and accD-psa1 IGS], and the internal transcribed spacer (ITS) region of nuclear rDNA (ITS 1/5.8S/ITS 2). Supported lineages in Coffea are discussed within the context of geographical correspondence, biogeography, morphology and systematics.Several major lineages with geographical coherence, as identified in previous studies based on smaller data sets, are supported. Other lineages with either geographical or ecological correspondence are recognized for the first time. Coffea subgenus Baracoffea is shown to be monophyletic, but Coffea subgenus Coffea is paraphyletic. Sequence data do not substantiate the monophyly of either Coffea or Psilanthus. Low levels of sequence divergence do not allow detailed resolution of relationships within Coffea, most notably for species of Coffea subgenus Coffea occurring in Madagascar. The origin of C. arabica by recent hybridization between C. canephora and C. eugenioides is supported. Phylogenetic separation resulting from the presence of the Dahomey Gap is inferred based on sequence data from Coffea.