A Framework for Timely and More Informative Epidemic Diseases Surveillance: The Case of Tanzania

This research article published by the Journal of Health Informatics in Developing Countries, 2018Background: A number of health facilities in the United Republic of Tanzania use different Hospital Management Information Systems (HoMISs) for capturing and managing clinical and administrative information for report generation. Despite the potentials of the data in the systems for use in epidemic diseases surveillance, timely extraction of the data for integrated data mining and analysis to produce more informative reports is still a challenge. This paper identifies the candidate data attributes for epidemic diseases surveillance to be extracted and analyzed from the Government of Tanzania Hospital Management Information System (GoT-HoMIS). It also examines the current reporting setup for epidemic diseases surveillance in Tanzania from the health facilities to the district, regional, and national levels. Methods: The study was conducted at the Ministry of Health, Community Development, Gender, Elderly, and Children (MoHCDGEC), Tumbi Designated Regional Referral Hospital (TDRRH), Muhimbili University of Health and Allied Sciences (MUHAS), and Mzumbe Health Centre, all in the United Republic of Tanzania. A total of 10 key informants (medical doctors, epidemiologists, and focal persons for various health information systems in Tanzania) were interviewed to obtain primary data. Data entry process in the GoT-HoMIS was also observed. Documents were reviewed to broaden understanding on several aspects. Results: All the respondents (100%) suggested patients’ gender, age, and residence as suitable attributes for epidemic diseases surveillance. Other suggested attributes were occupation (85.71%), diagnosis (57.14%), catchment area population (57.14%), vital status (57.14%), date of onset (57.14%), tribe (42.86%), marital status (42.86%), and religion (14.29%). Timeliness, insufficient immediate particulars on an epidemic-prone case(s), aggregated data limiting extensive analytics, missing community data and ways to analyze rumors, and poor data quality were also identified as challenges in the current reporting setup. Conclusion: A framework is proposed to guide researchers in integrating data from health facilities with those from social media and other sources for enhanced epidemic disease surveillance. Data entrants in the systems should also be informed on the essence and applications of data they feed, as quality data are the roots of quality reports

A roadmap for research in octoploid strawberry

The cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant–pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.Peer reviewe

Genomic Responses to Abnormal Gene Dosage: The X Chromosome Improved on a Common Strategy

This new primer, which discusses a study by Zhang et al., provides an overview of the process by which chromosomes achieve dose compensation and the mechanisms underlying this phenomenon in Drosophila S2 cells

Eco-engineered rock pools: a concrete solution to biodiversity loss and urban sprawl in the marine environment

journal_title: Environmental Research Letters article_type: lett article_title: Eco-engineered rock pools: a concrete solution to biodiversity loss and urban sprawl in the marine environment copyright_information: © 2016 IOP Publishing Ltd license_information: cc-by Original content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. date_received: 2016-05-12 date_accepted: 2016-08-10 date_epub: 2016-09-1

Recent advances in understanding the roles of whole genome duplications in evolution

Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Background: Brassica carinata (Ethiopian mustard) is an ancient crop from the Ethiopian highlands with remarkable heat and drought tolerance that has potential as a sustainable oil source for biofuel production. The resilience of this species might be due to hybrid vigor, as B. carinata is a species derived from a hybridization between Brassica nigra (black mustard) and Brassica oleracea (kale, broccoli, etc.). Thus, the B. carinata genome is allotetraploid with two parental genomes, or subgenomes, merged in one nucleus. We present a high-quality, chromosome-scale reference assembly of the B. carinata genome, which is the last of six genomes comprising the classic Triangle of U model used to study hybridization and polyploid evolution. Question: Here, we compare B. carinata to the other Triangle of U genomes for insight into the remarkable heat and drought tolerance of this crop. We investigate the evolutionary trajectory of the B. carinata genome as it returns to the diploid state to elucidate the mechanisms that act on duplicated genes, such as functional divergence of gene families and the biased fractionation of one subgenome. Findings: The B. carinata genome is the largest among the Triangle of U with notable expansions in repetitive DNA sequences and gene families related to transcriptional regulation and stress tolerance. We characterized patterns of subgenome bias, finding that the subgenome derived from B. nigra is likely dominant over the subgenome from B. oleracea. Furthermore, we comprehensively characterize subgenomic bias in homoeologous exchanges, or meiotic crossover between subgenomes, in the Triangle of U allotetraploids. Next steps: The presented B. carinata genome is a crucial resource for its expanded use as a biofuel feedstock and insight into polyploid evolution. Unraveling the genomic basis of the stress resilience of B. carinata provides an opportunity to introgress these traits to other cruciferous vegetables, which are used worldwide as vegetable and oil sources.Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.We gratefully acknowledge the support of the Nevada Agricultural Experiment Station (Grant No. NEV00384) and VPRI research funding (University of Nevada, Reno).The Pires lab is funded by the National Science Foundation (NSF IOS 1339156) and the Department of Energy Defense Threat Reduction Agency (HDTRA 1-16-1-0048). The Edger lab is funded by the National Science Foundation (NSF IOS 2029959). The Mason lab is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC 2070 - 390732324). The Alvarez-Ponce lab is funded by the National Science Foundation (NSF MCB 1818288)

Current status of the multinational Arabidopsis community

The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plant Arabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the “fourth decadal roadmap,” which will advise and coordinate the global activities of the Arabidopsis research community

The odds of duplicate gene persistence after polyploidization

Background: Gene duplication is an important biological phenomenon associated with genomic redundancy,degeneration, specialization, innovation, and speciation. After duplication, both copies continue functioning when natural selection favors duplicated protein function or expression, or when mutations make them functionally distinct before one copy is silenced. Results: Here we quantify the degree to which genetic parameters related to gene expression, molecular evolution, and gene structure in a diploid frog - Silurana tropicalis - influence the odds of functional persistence of orthologous duplicate genes in a closely related tetraploid species - Xenopus laevis. Using public databases and 454 pyrosequencing, we obtained genetic and expression data from S. tropicalis orthologs of 3,387 X. laevis paralogs and 4,746 X. laevis singletons - the most comprehensive dataset for African clawed frogs yet analyzed. Using logistic regression, we demonstrate that the most important predictors of the odds of duplicate gene persistence in the tetraploid species are the total gene expression level and evenness of expression across tissues and development in the diploid species. Slow protein evolution and information density (fewer exons, shorter introns) in the diploid are also positively correlated with duplicate gene persistence in the tetraploid. Conclusions: Our findings suggest that a combination of factors contribute to duplicate gene persistence following whole genome duplication, but that the total expression level and evenness of expression across tissues and through development before duplication are most important. We speculate that these parameters are useful predictors of duplicate gene longevity after whole genome duplication in other taxa

The pangenome of an agronomically important crop plant Brassica oleracea

There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis