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101. Additional file 11: Fig. S2. of Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus

Author

Wamonje, Francis, Michuki, George, Braidwood, Luke, Njuguna, Joyce, J. Musembi Mutuku, Djikeng, Appolinaire, Jagger Harvey, and Carr, John

Subjects
body regions, nervous system, fungi
Abstract

RT-PCR confirmation of Rhopalosiphum padi virus in maize samples collected from Kitui County. (PDF 84 kb)

Published
2017
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102. Additional file 10: Fig.S1. of Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus

Author

Wamonje, Francis, Michuki, George, Braidwood, Luke, Njuguna, Joyce, J. Musembi Mutuku, Djikeng, Appolinaire, Jagger Harvey, and Carr, John

Subjects
nervous system, viruses, fungi, food and beverages, biochemical phenomena, metabolism, and nutrition
Abstract

Confirmation of the presence of Aphid lethal paralysis virus (ALPV) and a Big Sioux River-like virus. (PDF 1.5 MB)

Published
2017
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103. Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats

Author

Tarekegn, Getinet Mekuriaw, primary, Tesfaye, Kassahun, additional, Mwai, Okeyo Ally, additional, Djikeng, Appolinaire, additional, Dessie, Tadelle, additional, Birungi, Josephine, additional, Osama, Sarah, additional, Zergaw, Netsanet, additional, Alemu, Alubel, additional, Achieng, Gloria, additional, Tutah, Jack, additional, Mutai, Collins, additional, Njuguna, Joyce, additional, and Mwacharo, Joram M., additional

Published
2018
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104. Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus

Author

Wamonje, Francis O., primary, Michuki, George N., additional, Braidwood, Luke A., additional, Njuguna, Joyce N., additional, Musembi Mutuku, J., additional, Djikeng, Appolinaire, additional, Harvey, Jagger J. W., additional, and Carr, John P., additional

Published
2017
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106. Microbial Community Structure and Diversity in an Integrated System of Anaerobic-Aerobic Reactors and a Constructed Wetland for the Treatment of Tannery Wastewater in Modjo, Ethiopia

Author

Mark Wamalwa, Moses N. Njahira, Djikeng Appolinaire, Seyoum Leta, Fassil Assefa, Francesca Stomeo, and Adey Feleke Desta

Subjects
Operational taxonomic unit, Bacteroidia, Multidisciplinary, biology, Ecology, Applied Microbiology, lcsh:R, lcsh:Medicine, Bacteroidetes, Biology and Life Sciences, biology.organism_classification, Microbiology, Microbial Ecology, Clostridia, Gammaproteobacteria, Botany, Constructed wetland, lcsh:Q, Anaerobic bacteria, lcsh:Science, Betaproteobacteria, Research Article, Biotechnology
Abstract

A culture-independent approach was used to elucidate the microbial diversity and structure in the anaerobic-aerobic reactors integrated with a constructed wetland for the treatment of tannery wastewater in Modjo town, Ethiopia. The system has been running with removal efficiencies ranging from 94%-96% for COD, 91%-100% for SO4(2-) and S(2-), 92%-94% for BOD, 56%-82% for total Nitrogen and 2%-90% for NH3-N. 16S rRNA gene clone libraries were constructed and microbial community assemblies were determined by analysis of a total of 801 unique clone sequences from all the sites. Operational Taxonomic Unit (OTU)--based analysis of the sequences revealed highly diverse communities in each of the reactors and the constructed wetland. A total of 32 phylotypes were identified with the dominant members affiliated to Clostridia (33%), Betaproteobacteria (10%), Bacteroidia (10%), Deltaproteobacteria (9%) and Gammaproteobacteria (6%). Sequences affiliated to the class Clostridia were the most abundant across all sites. The 801 sequences were assigned to 255 OTUs, of which 3 OTUs were shared among the clone libraries from all sites. The shared OTUs comprised 80 sequences belonging to Clostridiales Family XIII Incertae Sedis, Bacteroidetes and unclassified bacterial group. Significantly different communities were harbored by the anaerobic, aerobic and rhizosphere sites of the constructed wetland. Numerous representative genera of the dominant bacterial classes obtained from the different sample sites of the integrated system have been implicated in the removal of various carbon- containing pollutants of natural and synthetic origins. To our knowledge, this is the first report of microbial community structure in tannery wastewater treatment plant from Ethiopia.

Published
2014

108. Genetic markers associated with resistance to beta-lactam and quinolone antimicrobials in non-typhoidal Salmonella isolates from humans and animals in central Ethiopia

Author

Eguale, Tadesse, primary, Birungi, Josephine, additional, Asrat, Daniel, additional, Njahira, Moses N., additional, Njuguna, Joyce, additional, Gebreyes, Wondwossen A., additional, Gunn, John S., additional, Djikeng, Appolinaire, additional, and Engidawork, Ephrem, additional

Published
2017
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109. Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia

Author

Onyango, Maria G, Aitken, Nicola C, Jack, Cameron, Chuah, Aaron, Oguya, James, Djikeng, Appolinaire, Kemp, Steve, Bellis, Glenn A, Nicholas, Adrian, Walker, Peter J, Duchemin, Jean-Bernard, Onyango, Maria G, Aitken, Nicola C, Jack, Cameron, Chuah, Aaron, Oguya, James, Djikeng, Appolinaire, Kemp, Steve, Bellis, Glenn A, Nicholas, Adrian, Walker, Peter J, and Duchemin, Jean-Bernard

Abstract

BACKGROUND The advent of genotyping by Next Generation Sequencing has enabled rapid discovery of thousands of single nucleotide polymorphism (SNP) markers and high throughput genotyping of large populations at an affordable cost. Genotyping by sequencing (GBS), a reduced representation library sequencing method, allows highly multiplexed sequencing of genomic subsets. This method has limitations for small organisms with low amounts of genomic DNA, such as the bluetongue virus (BTV) vectors, Culicoides midges. RESULTS This study employed the GBS method to isolate SNP markers de novo from whole genome amplified Culicoides brevitarsis genomic DNA. The individuals were collected from regions representing two different Australian patterns of BTV strain distribution: the Northern Territory (NT) and the east coast. We isolated 8145 SNPs using GBS. Phylogenetic analysis conducted using the filtered 3263 SNPs revealed the presence of a distinct C. brevitarsis sub-population in the NT and this was confirmed by analysis of mitochondrial DNA. Two loci showed a very strong signal for selection and were unique to the NT population. Bayesian analysis with STRUCTURE indicated a possible two-population cluster. CONCLUSIONS The results suggest that genotyping vectors with high density markers in combination with biological and environmental data is useful. However, more extensive sampling over a wider spatial and temporal range is needed. The presence of sub-structure in populations and loci under natural selection indicates the need for further investigation of the role of vectors in shaping the two Australian systems of BTV transmission. The described workflow is transferable to genotyping of small, non-model organisms, including arthropod vectors of pathogens of economic and medical importance.

Published
2016

110. Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia

Author

Onyango, Maria G., primary, Aitken, Nicola C., additional, Jack, Cameron, additional, Chuah, Aaron, additional, Oguya, James, additional, Djikeng, Appolinaire, additional, Kemp, Steve, additional, Bellis, Glenn A., additional, Nicholas, Adrian, additional, Walker, Peter J., additional, and Duchemin, Jean-Bernard, additional

Published
2016
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111. A countrywide molecular survey leads to a seminal identification of the invasive cattle tick Rhipicephalus (Boophilus) microplusin Cameroon, a decade after it was reported in Cote d’Ivoire

Author

Silatsa, Barberine A., Kuiate, Jules-Roger, Njiokou, Flobert, Simo, Gustave, Feussom, Jean-Marc K., Tunrayo, Alabi, Amzati, Gaston S., Bett, Bernard, Bishop, Richard, Githaka, Naftaly, Opiyo, Stephen O., Djikeng, Appolinaire, and Pelle, Roger

Abstract

The cattle tick Rhipicephalus microplusis the most important arthropod vector of livestock diseases globally. Since its introduction in West Africa a decade ago, it has been reported in Ivory Coast, Benin, Togo, Mali, Burkina Faso and Nigeria with potentially far-reaching adverse impacts on the livestock sector in the region. Cameroon is located on a major route for transboundary cattle trade between Central and West Africa and it is therefore at risk from R. microplusinvasion. This study investigated the occurrence of R. microplusin Cameroon, the genetic polymorphism of the tick and population structure of isolates from different regions of the country to provide data that underpin the design of future vector control programs.

Published
2019
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112. Comparative genomic analysis and phylogenetic position of Theileria equi

Author

Kappmeyer, Lowell S., Thiagarajan, Mathangi, Herndon, David R., Ramsay, Joshua D., Caler, Elisabet, Djikeng, Appolinaire, Gillespie, Joseph J., Lau, Audrey O. T., Roalson, Eric H., Silva, Joana C., Silva, Marta G., Suarez, Carlos E., Ueti, Massaro W., Nene, Vishvanath M., Mealey, Robert H., Knowles, Donald P., and Brayton, Kelly A.

Subjects
animal diseases, parasitic diseases
Abstract

Background Transmission of arthropod-borne apicomplexan parasites that cause disease and result in death or persistent infection represents a major challenge to global human and animal health. First described in 1901 as Piroplasma equi, this re-emergent apicomplexan parasite was renamed Babesia equi and subsequently Theileria equi, reflecting an uncertain taxonomy. Understanding mechanisms by which apicomplexan parasites evade immune or chemotherapeutic elimination is required for development of effective vaccines or chemotherapeutics. The continued risk of transmission of T. equi from clinically silent, persistently infected equids impedes the goal of returning the U. S. to non-endemic status. Therefore comparative genomic analysis of T. equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T. equi relative to sequenced apicomplexan parasites. Results The known immunodominant proteins, EMA1, 2 and 3 were discovered to belong to a ten member gene family with a mean amino acid identity, in pairwise comparisons, of 39%. Importantly, the amino acid diversity of EMAs is distributed throughout the length of the proteins. Eight of the EMA genes were simultaneously transcribed. As the agents that cause bovine theileriosis infect and transform host cell PBMCs, we confirmed that T. equi infects equine PBMCs, however, there is no evidence of host cell transformation. Indeed, a number of genes identified as potential manipulators of the host cell phenotype are absent from the T. equi genome. Comparative genomic analysis of T. equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp. Conclusions The EMA family does not fit the paradigm for classical antigenic variation, and we propose a novel model describing the role of the EMA family in persistence. T. equi has lost the putative genes for host cell transformation, or the genes were acquired by T. parva and T. annulata after divergence from T. equi. Our analysis identified 50 genes that will be useful for definitive phylogenetic classification of T. equi and closely related organisms. Published version

Published
2012

114. HIV-PDI: A Protein-Drug Interaction Resource for Structural Analyses of HIV Drug Resistance: 1. Concepts and Associated Database

Author

Ouwe-Missi-Oukem-Boyer Odile, Kelbert Patricia, Djikeng Appolinaire, Maigret Bernard, Keminse Lionel, Fokam Joseph, Devignes Marie-Dominique, Sma L-Tabbone Malika, Ghemtio Leo, Knowledge representation, reasonning (ORPAILLEUR), INRIA Lorraine, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS), The J. Craig Venter Institute (JCVI), The J. Craig Venter Institute, Centre international de référence Chantal Biya pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), Fondation Chantal Biya (FCB), and Harmonic Phama

Subjects
Drug, 0303 health sciences, 030306 microbiology, Viral protein, business.industry, media_common.quotation_subject, virus diseases, Drug interaction, Bioinformatics, medicine.disease_cause, medicine.disease, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, 03 medical and health sciences, Antibiotic resistance, Resource (project management), Acquired immunodeficiency syndrome (AIDS), medicine, Identification (biology), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, HIV drug resistance, 030304 developmental biology, media_common
Abstract

International audience; Overcoming the problem of resistance to antiretroviral drugs (ARVs) in HIV-infected patients is a major issue in AIDS research today. Advances in genome sequencing have facilitated the identification of a growing number of individual genotypes. Hence, it is now possible to understand HIV drug resistance at the molecular level by considering the three-dimensional (3D) structural interactions between ARVs and the mutated viral proteins of patients. Therefore, identification of the critical interactions lost further to one or several HIV mutations, and consequently the modifications of other molecular factors, could be indicators to propose appropriate ARVs escaping the resistance. This paper introduces the HIV-PDI (Protein-Drug Interactions) resource designed to be a decision making tool to propose alternative ARVs against a particular mutated viral protein, and thus to provide a personalized antiretroviral treatment. The HIV-PDI was conceived to serve as an integrated resource for studying HIV drug resistance at the structural level of the protein-drug interaction, with a special emphasis on the active site of the HIV drug target. As a first step, we focus on the well documented protease and related drugs. The HIV-PDI includes clinical information on patients, resistance to given ARVs treatments, HIV proteins structures and mutations, HIV protein/ARV drugs and their 3D interactions. The HIV-PDI may be queried using multiple combinations of fields including protein, drug and treatment conditions and coupled to visualization/analysis tools of 3D Protein-Drug interactions. The HIV-PDI resource can be used in order to help understand the appearance of resistance and to promote further novel drug and treatment developments based on analyses of 3D pattern of protein-drug interactions. A web-based version of HIV-PDI is available at http://hiv-pdi.loria.fr.

Published
2011
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115. HIV-PDI: A Protein Drug Interaction Resource for Structural Analyses of HIV Drug Resistance: 2. Examples of Use and Proof-of-Concept

Author

Souchet Michel, Kelbert Patricia, Ritchie W David, Ghemtio Leo, Keminse Lionel, Djikeng Appolinaire, Ouwe-Missioukem Boyer Odile, Maigret Bernard, Knowledge representation, reasonning (ORPAILLEUR), INRIA Lorraine, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS), Harmonic Phama, The J. Craig Venter Institute (JCVI), The J. Craig Venter Institute, Centre international de référence Chantal Biya pour la recherche sur la prévention et la prise en charge du VIH/SIDA (CIRCB), and Fondation Chantal Biya (FCB)

Subjects
0303 health sciences, Biological data, Decision support system, Data collection, 030306 microbiology, business.industry, Drug resistance, Drug interaction, Bioinformatics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, 03 medical and health sciences, Medicine, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Medical prescription, business, Set (psychology), HIV drug resistance, 030304 developmental biology
Abstract

International audience; The HIV-PDI resource was designed and implemented to address the problems of drug resistance with a central focus on the 3D structure of the target-drug interaction. Clinical and biological data, structural and physico-chemical information and 3D interaction data concerning the targets (HIV protease) and the drugs (ARVs) were meticulously integrated and combined with tools dedicated to study HIV mutations and their consequences on the efficacy of drugs. Here, the capabilities of the HIV-PDI resource are demonstrated for several different scenarios ranging from retrieving information associated with patients to analyzing structural data relating cognate proteins and ligands. HIV-PDI allows such diverse data to be correlated, especially data linking antiretroviral drug (ARV) resistance to a given treatment with changes in three-dimensional interactions between a drug molecule and the mutated protease. Our work is based on the assumption that ARV resistance results from a loss of affinity between the mutated HIV protease and a drug molecule due to subtle changes in the nature of the protein-ligand interaction. Therefore, a set of patients whose resistance to first line treatment was corrected by a second line treatment was selected from the HIV-PDI database for detailed study, and several queries regarding these patients are processed via its graphical user interface. Considering the protease mutations found in the selected set of patients, our retrospective analysis was able to establish in most cases that the first line treatment was not suitable, and it predicted a second line treatment which agreed perfectly with the clincian's prescription. The present study demonstrates the capabilities of HIV-PDI. We anticipate that this decision support tool will help clinicians and researchers find suitable HIV treatments for individual patients. The HIVPDI database is thereby useful as a system of data collection allowing interpretation on the basis of all available information, thus helping in possible decision-makings.

Published
2011
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116. Assessment of population genetic structure in the arbovirus vector midge, Culicoides brevitarsis (Diptera: Ceratopogonidae), using multi-locus DNA microsatellites

Author

Onyango, Maria G., Beebe, Nigel W., Gopurenko, David, Bellis, Glenn, Nicholas, Adrian, Ogugo, Moses, Djikeng, Appolinaire, Kemp, Steve, Walker, Peter J., Duchemin, Jean-Bernard, Onyango, Maria G., Beebe, Nigel W., Gopurenko, David, Bellis, Glenn, Nicholas, Adrian, Ogugo, Moses, Djikeng, Appolinaire, Kemp, Steve, Walker, Peter J., and Duchemin, Jean-Bernard

Abstract

Bluetongue virus (BTV) is a major pathogen of ruminants that is transmitted by biting midges (Culicoides spp.). Australian BTV serotypes have origins in Asia and are distributed across the continent into two distinct episystems, one in the north and another in the east. Culicoides brevitarsis is the major vector of BTV in Australia and is distributed across the entire geographic range of the virus. Here, we describe the isolation and use of DNA microsatellites and gauge their ability to determine population genetic connectivity of C. brevitarsis within Australia and with countries to the north. Eleven DNA microsatellite markers were isolated using a novel genomic enrichment method and identified as useful for genetic analyses of sampled populations in Australia, northern Papua New Guinea (PNG) and Timor-Leste. Significant (P < 0.05) population genetic subdivision was observed between all paired regions, though the highest levels of genetic sub-division involved pair-wise tests with PNG (PNG vs. Australia (FST = 0.120) and PNG vs. Timor-Leste (FST = 0.095)). Analysis of multi-locus allelic distributions using STRUCTURE identified a most probable two-cluster population model, which separated PNG specimens from a cluster containing specimens from Timor-Leste and Australia. The source of incursions of this species in Australia is more likely to be Timor-Leste than PNG. Future incursions of BTV positive C. brevitarsis into Australia may be genetically identified to their source populations using these microsatellite loci. The vector’s panmictic genetic structure within Australia cannot explain the differential geographic distribution of BTV serotypes.

Published
2015

118. Correction: Analyses of Twelve New Whole Genome Sequences of Cassava Brown Streak Viruses and Ugandan Cassava Brown Streak Viruses from East Africa: Diversity, Supercomputing and Evidence for Further Speciation

Author

Ndunguru, Joseph, primary, Sseruwagi, Peter, additional, Tairo, Fred, additional, Stomeo, Francesca, additional, Maina, Solomon, additional, Djikeng, Appolinaire, additional, Kehoe, Monica, additional, and Boykin, Laura M., additional

Published
2015
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119. Assessment of population genetic structure in the arbovirus vector midge, Culicoides brevitarsis (Diptera: Ceratopogonidae), using multi-locus DNA microsatellites

Author

Onyango, Maria G, primary, Beebe, Nigel W, additional, Gopurenko, David, additional, Bellis, Glenn, additional, Nicholas, Adrian, additional, Ogugo, Moses, additional, Djikeng, Appolinaire, additional, Kemp, Steve, additional, Walker, Peter J, additional, and Duchemin, Jean-Bernard, additional

Published
2015
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120. TpUB05, a Homologue of the Immunodominant Plasmodium falciparum Protein UB05, Is a Marker of Protective Immune Responses in Cattle Experimentally Vaccinated against East Coast Fever

Author

Dinga, Jerome Nyhalah, primary, Wamalwa, Mark, additional, Njimoh, Dieudonné Lemuh, additional, Njahira, Moses N., additional, Djikeng, Appolinaire, additional, Skilton, Rob, additional, Titanji, Vincent Pryde Kehdingha, additional, and Pellé, Roger, additional

Published
2015
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124. Identification of Schistosoma mansoni microRNAs

Author

Simões, Mariana C, Simões, Mariana C, Lee, Jonathan, Djikeng, Appolinaire, Cerqueira, Gustavo C, Zerlotini, Adhemar, da Silva-Pereira, Rosiane A, Dalby, Andrew R, LoVerde, Philip, El-Sayed, Najib M, Oliveira, Guilherme, Simões, Mariana C, Simões, Mariana C, Lee, Jonathan, Djikeng, Appolinaire, Cerqueira, Gustavo C, Zerlotini, Adhemar, da Silva-Pereira, Rosiane A, Dalby, Andrew R, LoVerde, Philip, El-Sayed, Najib M, and Oliveira, Guilherme

Abstract

MicroRNAs (miRNAs) constitute a class of single-stranded RNAs which play a crucial role in regulating development and controlling gene expression by targeting mRNAs and triggering either translation repression or messenger RNA (mRNA) degradation. miRNAs are widespread in eukaryotes and to date over 14,000 miRNAs have been identified by computational and experimental approaches. Several miRNAs are highly conserved across species. In Schistosoma, the full set of miRNAs and their expression patterns during development remain poorly understood. Here we report on the development and implementation of a homology-based detection strategy to search for miRNA genes in Schistosoma mansoni. In addition, we report results on the experimental detection of miRNAs by means of cDNA cloning and sequencing of size-fractionated RNA samples. Homology search using the high-throughput pipeline was performed with all known miRNAs in miRBase. A total of 6,211 mature miRNAs were used as reference sequences and 110 unique S. mansoni sequences were returned by BLASTn analysis. The existing mature miRNAs that produced these hits are reported, as well as the locations of the homologous sequences in the S. mansoni genome. All BLAST hits aligned with at least 95% of the miRNA sequence, resulting in alignment lengths of 19-24 nt. Following several filtering steps, 15 potential miRNA candidates were identified using this approach. By sequencing small RNA cDNA libraries from adult worm pairs, we identified 211 novel miRNA candidates in the S. mansoni genome. Northern blot analysis was used to detect the expression of the 30 most frequent sequenced miRNAs and to compare the expression level of these miRNAs between the lung stage schistosomula and adult worm stages. Expression of 11 novel miRNAs was confirmed by northern blot analysis and some presented a stage-regulated expression pattern. Three miRNAs previously identified from S. japonicum were also present in S. mansoni. Evidence for the presence

Published
2011

129. Characterization of the novelTrypanosoma bruceiinosine 5′-monophosphate dehydrogenase

Author

BESSHO, TOMOAKI, primary, MORII, SHOKO, additional, KUSUMOTO, TOSHIHIDE, additional, SHINOHARA, TAKAHIRO, additional, NODA, MASANORI, additional, UCHIYAMA, SUSUMU, additional, SHUTO, SATOSHI, additional, NISHIMURA, SHIGENORI, additional, DJIKENG, APPOLINAIRE, additional, DUSZENKO, MICHAEL, additional, MARTIN, SAMUEL K., additional, INUI, TAKASHI, additional, and KUBATA, KILUNGA B., additional

Published
2013
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130. Identification of Schistosoma mansoni microRNAs

Author

Simões, Mariana C, primary, Lee, Jonathan, additional, Djikeng, Appolinaire, additional, Cerqueira, Gustavo C, additional, Zerlotini, Adhemar, additional, da Silva-Pereira, Rosiane A, additional, Dalby, Andrew R, additional, LoVerde, Philip, additional, El-Sayed, Najib M, additional, and Oliveira, Guilherme, additional

Published
2011
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133. Viral genome sequencing by random priming methods

Author

Djikeng, Appolinaire, primary, Halpin, Rebecca, additional, Kuzmickas, Ryan, additional, DePasse, Jay, additional, Feldblyum, Jeremy, additional, Sengamalay, Naomi, additional, Afonso, Claudio, additional, Zhang, Xinsheng, additional, Anderson, Norman G, additional, Ghedin, Elodie, additional, and Spiro, David J, additional

Published
2008
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134. An evaluation of human immunodeficiency virus oral screening test awareness and preferences in the West region of Cameroon.

Author

Nkenfou, Celine N., Kembou, Japhette T., Djikeng, Appolinaire, Domkam, Irenee, and Tchuinkam, Timoleon

Abstract

Summary HIV serological diagnosis has evolved during the last decade to give rise to rapid testing using biological materials, such as blood or oral mucosal transudate (OMT). However, blood collection is not always welcomed, justifying the evaluation of OMT-based devices. In a cross sectional study carried out in May 2011 aimed at evaluating the level of awareness about OMT based HIV tests, questionnaires were administered to participants who consented to take part in the study. Eighty-five percent ( n = 1520) of participants reported a lack of awareness of HIV oral screening before the study, and surprisingly, no association was found between the awareness of participants and their educational level ( p = 0.768). There was also no association ( p = 0.743) found between having had previous screening tests and awareness of oral testing. The percentage of participants who accepted the oral test before being informed about it was 31.3% ( n = 1520). After sensitization, 76.3% ( n = 1520) preferred oral screening for future tests ( p = 0). These results reveal that if the OMT based test is affordable, its implementation as a screening tool in the general population could greatly increase participation in screening campaigns and is welcomed by those who want to self-test in a non-invasive way. This will create a better estimation of the national HIV prevalence. Its use could then have a significant public health impact on HIV prevention and clinical management. [ABSTRACT FROM AUTHOR]

Published
2015
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137. Comparative Genomics of Trypanosomatid Parasitic Protozoa

Author

El-Sayed, Najib M., primary, Myler, Peter J., additional, Blandin, Gaëlle, additional, Berriman, Matthew, additional, Crabtree, Jonathan, additional, Aggarwal, Gautam, additional, Caler, Elisabet, additional, Renauld, Hubert, additional, Worthey, Elizabeth A., additional, Hertz-Fowler, Christiane, additional, Ghedin, Elodie, additional, Peacock, Christopher, additional, Bartholomeu, Daniella C., additional, Haas, Brian J., additional, Tran, Anh-Nhi, additional, Wortman, Jennifer R., additional, Alsmark, U. Cecilia M., additional, Angiuoli, Samuel, additional, Anupama, Atashi, additional, Badger, Jonathan, additional, Bringaud, Frederic, additional, Cadag, Eithon, additional, Carlton, Jane M., additional, Cerqueira, Gustavo C., additional, Creasy, Todd, additional, Delcher, Arthur L., additional, Djikeng, Appolinaire, additional, Embley, T. Martin, additional, Hauser, Christopher, additional, Ivens, Alasdair C., additional, Kummerfeld, Sarah K., additional, Pereira-Leal, Jose B., additional, Nilsson, Daniel, additional, Peterson, Jeremy, additional, Salzberg, Steven L., additional, Shallom, Joshua, additional, Silva, Joana C., additional, Sundaram, Jaideep, additional, Westenberger, Scott, additional, White, Owen, additional, Melville, Sara E., additional, Donelson, John E., additional, Andersson, Björn, additional, Stuart, Kenneth D., additional, and Hall, Neil, additional

Published
2005
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138. The Genome of the African Trypanosome Trypanosoma brucei

Author

Berriman, Matthew, primary, Ghedin, Elodie, additional, Hertz-Fowler, Christiane, additional, Blandin, Gaëlle, additional, Renauld, Hubert, additional, Bartholomeu, Daniella C., additional, Lennard, Nicola J., additional, Caler, Elisabet, additional, Hamlin, Nancy E., additional, Haas, Brian, additional, Böhme, Ulrike, additional, Hannick, Linda, additional, Aslett, Martin A., additional, Shallom, Joshua, additional, Marcello, Lucio, additional, Hou, Lihua, additional, Wickstead, Bill, additional, Alsmark, U. Cecilia M., additional, Arrowsmith, Claire, additional, Atkin, Rebecca J., additional, Barron, Andrew J., additional, Bringaud, Frederic, additional, Brooks, Karen, additional, Carrington, Mark, additional, Cherevach, Inna, additional, Chillingworth, Tracey-Jane, additional, Churcher, Carol, additional, Clark, Louise N., additional, Corton, Craig H., additional, Cronin, Ann, additional, Davies, Rob M., additional, Doggett, Jonathon, additional, Djikeng, Appolinaire, additional, Feldblyum, Tamara, additional, Field, Mark C., additional, Fraser, Audrey, additional, Goodhead, Ian, additional, Hance, Zahra, additional, Harper, David, additional, Harris, Barbara R., additional, Hauser, Heidi, additional, Hostetler, Jessica, additional, Ivens, Al, additional, Jagels, Kay, additional, Johnson, David, additional, Johnson, Justin, additional, Jones, Kristine, additional, Kerhornou, Arnaud X., additional, Koo, Hean, additional, Larke, Natasha, additional, Landfear, Scott, additional, Larkin, Christopher, additional, Leech, Vanessa, additional, Line, Alexandra, additional, Lord, Angela, additional, MacLeod, Annette, additional, Mooney, Paul J., additional, Moule, Sharon, additional, Martin, David M. A., additional, Morgan, Gareth W., additional, Mungall, Karen, additional, Norbertczak, Halina, additional, Ormond, Doug, additional, Pai, Grace, additional, Peacock, Chris S., additional, Peterson, Jeremy, additional, Quail, Michael A., additional, Rabbinowitsch, Ester, additional, Rajandream, Marie-Adele, additional, Reitter, Chris, additional, Salzberg, Steven L., additional, Sanders, Mandy, additional, Schobel, Seth, additional, Sharp, Sarah, additional, Simmonds, Mark, additional, Simpson, Anjana J., additional, Tallon, Luke, additional, Turner, C. Michael R., additional, Tait, Andrew, additional, Tivey, Adrian R., additional, Van Aken, Susan, additional, Walker, Danielle, additional, Wanless, David, additional, Wang, Shiliang, additional, White, Brian, additional, White, Owen, additional, Whitehead, Sally, additional, Woodward, John, additional, Wortman, Jennifer, additional, Adams, Mark D., additional, Embley, T. Martin, additional, Gull, Keith, additional, Ullu, Elisabetta, additional, Barry, J. David, additional, Fairlamb, Alan H., additional, Opperdoes, Fred, additional, Barrell, Barclay G., additional, Donelson, John E., additional, Hall, Neil, additional, Fraser, Claire M., additional, Melville, Sara E., additional, and El-Sayed, Najib M., additional

Published
2005
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141. Implications of Human Microbiome Research for the Developing World.

Author

Djikeng, Appolinaire, Nelson, Barbara Jones, and Nelson, Karen E.

Abstract

The human microbiome refers to all of the species that inhabit the human body, residing both on and in it. Over the past several years, there has been a significantly increased interest directed to the understanding of the microorganisms that reside on and in the human body. These studies of the human microbiome promise to reveal all these species and increase our understanding of the normal inhabitants, those that trigger disease and those that vary in response to disease conditions. It is anticipated that these directed research efforts, coupled with new technological advances, will ultimately allow one to gain a greater understanding of the relationships of these species with their human hosts. The various chapters in this book present a range of aspects of human microbiome research, explain the scientific and technological rationale, and highlight the significant potential that the results from these studies hold. In this chapter, we begin to address the potential and long-term implications of the knowledge gained from human microbiome research (which currently is centered in the developed world) for the developing world, which has often lagged behind in the benefits of these new technologies and their implications to new research areas. [ABSTRACT FROM AUTHOR]

Published
2011
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144. Analysis of Gene Function in Trypanosoma brucei Using RNA Interference.

Author

Walker, John M., Gott, Jonatha M., Djikeng, Appolinaire, Shen, Shuiyuan, Tschudi, Christian, and Ullu, Elisabetta

Abstract

Trypanosoma brucei, a flagellate protozoa of the family Trypanosomatidae, has become one of the model systems for unicellular pathogens to study fundamentally important biological phenomena. Currently, the method of choice to examine gene function in these organisms is RNA interference (RNAi). mRNA degradation is triggered by double-stranded RNA (dsRNA) produced in vivo from transgenes transcribed from opposing tetracycline (tet)-inducible T7 RNA polymerase promoters, or hairpin RNA transcribed from the tet-inducible procyclic acidic repetitive protein promoter. In this chapter, we describe some of the methods we employ for ablation of gene expression by RNAi in T. brucei with particular emphasis on transfection and cloning of procyclic cells, induction of dsRNA expression, isolation of RNA and analysis of dsRNA, and target mRNA. [ABSTRACT FROM AUTHOR]

Published
2004
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145. Characterization of a candidate Trypanosoma brucei U1 small nuclear RNA gene

Author

Djikeng, Appolinaire, primary, Ferreira, Ludmila, additional, D'Angelo, Maximiliano, additional, Dolezal, Pavel, additional, Lamb, Tracey, additional, Murta, Silvane, additional, Triggs, Veronica, additional, Ulbert, Sebastian, additional, Villarino, Alejandro, additional, Renzi, Sarah, additional, Ullu, Elisabetta, additional, and Tschudi, Christian, additional

Published
2001
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147. A new twist in trypanosome RNA metabolism: cis-splicing of pre-mRNA

Author

MAIR, GUNNAR, primary, SHI, HUAFANG, additional, LI, HONGJIE, additional, DJIKENG, APPOLINAIRE, additional, AVILES, HERNAN O., additional, BISHOP, JOSEPH R., additional, FALCONE, FRANCO H., additional, GAVRILESCU, CRISTINA, additional, MONTGOMERY, JACQUI L., additional, SANTORI, M. ISABEL, additional, STERN, LEAH S., additional, WANG, ZEFENG, additional, ULLU, ELISABETTA, additional, and TSCHUDI, CHRISTIAN, additional

Published
2000
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148. Tackling human resources in Africa

Author

Oukem-Boyer, Odile, Djikeng, Appolinaire, Cappelli, Giulia, and Fouda, Pierre

Subjects
Biomedical engineers -- Human resource management, Laboratory technicians -- Human resource management, Research institutes -- Human resource management, Company personnel management
Published
2009

150. A Look into Genetic Diversity of Enset ( Ensete ventricosum (Welw.) Cheesman) Using Transferable Microsatellite Sequences of Banana in Ethiopia.

Author

Getachew, Selamawit, Mekbib, Firew, Admassu, Belayneh, Kelemu, Segenet, Kidane, Sisay, Negisho, Kefyalew, Djikeng, Appolinaire, and Nzuki, Inosters

Subjects
CROP diversification, CROP genetics, MICROSATELLITE repeats in plants, NUCLEOTIDE sequence, BANANAS
Abstract

Microsatellite sequences are one of the best options for the study of genetic diversity in plant species. However, because of the high cost of their development, it is important to test whether existing sequences from related species can be exploited. Enset (Ensete ventricosum(Welw.) Cheesman) has remained largely unimproved partly due to lack of its genetic information, thus there is a need to study the genetic diversity of current accessions and build on it to develop new cultivars/varieties with desired agronomic traits. Transferability of 71 SSR loci from banana (Musa accuminata) to enset was investigated using 220 Enset accessions. Among the 71 SSRs tested, 12 (16.9%) were successfully transferable to enset. Eleven (16.9%) of these were used to examine the diversity of the 220 enset accessions that had been collected from eight different zones in Ethiopia. [ABSTRACT FROM PUBLISHER]

Published
2014
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