HIV and Tuberculosis Trends in the United States and Select Sub-Saharan Africa Countries

Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) are two catastrophic diseases affecting millions of people worldwide every year; and are considered to be pandemic by the World Health Organization. This study aims to compare the recent trends in TB and HIV in the United States and Sub-Saharan African Countries. Data (incidence, prevalence and death rates of HIV and TB) for the United States, Cameroon, Nigeria, and South Africa were collected from The Joint United Nations Programme for HIV/AIDS (UNAIDS), US Census Bureau and World Health Organization (WHO) databases and analyzed using Statistical Analysis Software (SAS v 9.1). Analysis of Variance (ANOVA) was performed to compare the variables of interest between the countries and across time. Results showed that percent rates of TB cases, TB deaths, HIV cases and HIV deaths were significantly different (P < 0.001) among these countries from 1993 to 2006. South Africa had the highest rates of HIV and TB; while US had the lowest rates of both diseases. Tuberculosis and HIV rates for Cameroon and Nigeria were significantly higher when compared to the United States, but were significantly lower when compared to South Africa (P < 0.001). There were significant differences (P < 0.001) in the prevalence of TB and HIV between the United States and the Sub-Saharan African countries, as well as differences within the Sub-Saharan African countries from 1993 to 2006. More analysis needs to be carried out in order to determine the prevalence and incidence of HIV and TB among multiple variables like gender, race, sexual orientation and age to get a comprehensive picture of the trends of HIV and TB

Developmental Regulation of Genes Encoding Universal Stress Proteins in Schistosoma mansoni

The draft nuclear genome sequence of the snail-transmitted, dimorphic, parasitic, platyhelminth Schistosoma mansoni revealed eight genes encoding proteins that contain the Universal Stress Protein (USP) domain. Schistosoma mansoni is a causative agent of human schistosomiasis, a severe and debilitating Neglected Tropical Disease (NTD) of poverty, which is endemic in at least 76 countries. The availability of the genome sequences of Schistosoma species presents opportunities for bioinformatics and genomics analyses of associated gene families that could be targets for understanding schistosomiasis ecology, intervention, prevention and control. Proteins with the USP domain are known to provide bacteria, archaea, fungi, protists and plants with the ability to respond to diverse environmental stresses. In this research investigation, the functional annotations of the USP genes and predicted nucleotide and protein sequences were initially verified. Subsequently, sequence clusters and distinctive features of the sequences were determined. A total of twelve ligand binding sites were predicted based on alignment to the ATP-binding universal stress protein from Methanocaldococcus jannaschii. In addition, six USP sequences showed the presence of ATP-binding motif residues indicating that they may be regulated by ATP. Public domain gene expression data and RT-PCR assays confirmed that all the S. mansoni USP genes were transcribed in at least one of the developmental life cycle stages of the helminth. Six of these genes were up-regulated in the miracidium, a free-swimming stage that is critical for transmission to the snail intermediate host. It is possible that during the intra-snail stages, S. mansoni gene transcripts for universal stress proteins are low abundant and are induced to perform specialized functions triggered by environmental stressors such as oxidative stress due to hydrogen peroxide that is present in the snail hemocytes. This report serves to catalyze the formation of a network of researchers to understand the function and regulation of the universal stress proteins encoded in genomes of schistosomes and their snail intermediate hosts

A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library

The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9× coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species

Plasmodium falciparum kelch13 polymorphisms identified after treatment failure with artemisinin-based combination therapy in Niger

Abstract Background Artemisinin-based combination therapy (ACT) is the most effective treatment for malaria, and has significantly reduced morbimortality. Polymorphisms associated with the Plasmodium falciparum Kelch gene (Pfkelch13) have been associated with delayed parasite clearance even with ACT treatment. Methods The Pfkelch13 gene was sequenced from P. falciparum infected patients (n = 159) with uncomplicated malaria in Niger. An adequate clinical and parasitological response (ACPR) was reported in 155 patients. Four (n = 4) patients had treatment failure (TF) that were not reinfections—two of which had late parasitological failures (LPF) and two had late clinical failures (LCF). Results Thirteen single nucleotide polymorphisms (SNPs) were identified of which seven were non-synonymous (C469R, T508S, R515T, A578S, I465V, I437V, F506L,), and three were synonymous (P443P, P715P, L514L). Three SNP (C469R, F506L, P715P) were present before ACT treatment, while seven mutations (C469R, T508S, R515T, L514L, P443P, I437V, I465V) were selected by artemether/lumefantrine (AL)—five of which were non-synonymous (C469R, T508S, R515T, I437V, I465V). Artesunate/amodiaquine (ASAQ) has selected any mutation. One sample presented three cumulatively non-synonymous SNPs—C469R, T508S, R515T. Conclusions This study demonstrates intra-host selection of Pfkelch13 gene by AL. The study highlights the importance of LCF and LPF parasites in the selection of resistance to ACT. Further studies using gene editing are required to confirm the potential implication of resistance to ACT with the most common R515T and T508S mutations. It would also be important to elucidate the role of cumulative mutations

Supplemental Material for Hoffberg et al., 2018

Figure S1: Comparison of the size distribution of library inserts in the Meraculous and HiRise assemblies.<div><br></div><div>Figure S2: The frequency of kmers at each kmer length. </div><div><br></div><div>Figure S3: The distribution of scaffold lengths in the HiRise assembly. </div><div><br></div><div>Figure S4: The cumulative percent of the assembly for a given scaffold size in the Meraculous and HiRise assemblies. </div><div><br></div><div>Table S1: A detailed list of the number of copies and percent of the assembly of transposons and repeatable elements. </div><div><br></div><p>File S1: Submission script for MAKER.</p><p><br></p> <p>File S2: MAKER executable file (maker_exe.ctl).</p><p><br></p> <p>File S3: Specifications for downstream filtering of BLAST and Exonerate alignments (maker_bopts.ctl).</p><p><br></p> <p>File S4: Primary configuration of MAKER specific options (maker_opts.ctl).</p><p><br></p> <p>File S5: Commands for training SNAP.</p> <p><br></p><p>File S6: Submission script for BLAST comparing <i>Gambusia affinis</i> with related fish.</p> <p><br></p><p>File S7: Submission script for BUSCO.</p> <p><br></p><p>File S8: Submission script for predicting ncRNAs.</p> <p><br></p><p>File S9: Illumina reads mapped to the reference in BAM format.</p><p><br></p><p>File S10: Sequence of tRNAs.</p> <p><br></p><p>File S11: Structure of tRNAs.</p> <div><br></div><div>File S12: rRNA, snRNA, snoRNA, and miRNA sequences.</div><div><br></div