Determinants of HIV/AIDS treatment and care service quality in Woliso Town, Oromia, Ethiopia: in the case of HIV prevention and control project.

In Ethiopia, even though there is an effort to increase ART services, different challenges remain in the provision of HIV/AIDS treatment and care services, and little has been done to evaluate patient satisfaction levels. The purpose of this study is to assess the determinants of HIV/AIDS treatment and care service quality. A facility-based cross-sectional study was conducted during from October 2023 to November 2023 in Woliso Town. The total sample size was generated using a systematic random sampling method from the source population. The results of the study showed that client satisfaction with HIV/AIDS treatment and care service quality was 272 (81.4%) with 95% CI: 76.9-85.3%. Government employees were 67% less likely to be satisfied with HIV/AIDS treatment and care service quality (AOR = 0.33 95% CI: 0.11, 0.99) when compared to unemployed clients. The odds of client satisfaction were 6.72 times higher among study participants who do not have health insurance membership cards (AOR = 6.72 95% CI: 3.42, 13.91) compared to those who have health insurance membership cards. The odds of client satisfaction were 2.77 times higher among study participants who reported the availability of community referral for any social support (AOR = 2.77 95% CI: 1.12, 6.84) when compared to those who did not report. Those study participants for whom privacy was kept during the examination were 8.67 times higher to be satisfied (AOR = 8.67 95% CI: 2.53, 29.68) compared to those for whom privacy was not kept during the examination. In conclusion, the client satisfaction on HIV/AIDS treatment and care service quality was relatively high in the study area. Occupational status, health insurance membership cards, availability of community referral for any social support and keeping privacy during examination have significant associations with HIV/AIDS treatment and care service quality in terms of client satisfaction.

Factors Affecting Virological Failure in Children Receiving First-Line Antiretroviral Therapy in Ethiopian Healthcare Facilities: A Retrospective Analysis.

Background: The causes of virological failure are poorly recognized and investigated. This study aimed to identify determinant factors of viral failure in children taking first-line ART at a randomly selected federal hospital in Addis Ababa, Ethiopia. Methods: A facility-based unmatched case-control study was carried out from May 10, 2022, to July 20, 2022, G.C. among HIV-infected children on first-line antiretroviral therapy. There were 209 HIV-positive youngsters in the study's overall sample size, comprising 53 cases and 156 controls. Data was gathered by chart review using an organized checklist in English. The data were entered using Epi-data 4.2 and exported into SPSS version 24 for analysis. The relationship between each explanatory variable and the result variable was described using both bivariate and multivariate analysis. An adjusted odds ratio with 95% confidence intervals was conducted, and a p-value <0.05 was considered statistically significant. Results: Being male (AOR= 4.504; 95% CI: 1.498, 13.539), duration on ART exceeding 47 months (AOR=40.6; 95% CI:9.571,172.222), fair and poor drug adherence (AOR=16.348; 95% CI:4.690,56.990), missed clinical appointments (AOR = 3.177; 95% CI: 1.100-9.174), and baseline WHO clinical stage 4 disease (AOR = 6.852; 95% CI: 1.540-30.49) were associated with an increased risk of virological failure. Conversely, a history of drug change and a CD4 count ranging from 250 to 500 cells/mm3 were significantly protective factors (AOR = 0.071; 95% CI: 0.024-0.214 and AOR=0.118; 95% CI: 0.030, 0.464, respectively). Conclusion: Being male, duration on ART >47 months, fair and poor adherence, missed clinical appointments, and baseline WHO Stage 4 are factors that increase the odds of virological failure. History of ART Drug change and a CD4 count between 250 and 500 cells/mm3 are factors that decrease the odds of virological failure.

Central cell-derived peptides regulate early embryo patterning in flowering plants.

Plant embryogenesis initiates with the establishment of an apical-basal axis; however, the molecular mechanisms accompanying this early event remain unclear. Here, we show that a small cysteine-rich peptide family is required for formation of the zygotic basal cell lineage and proembryo patterning in Arabidopsis. EMBRYO SURROUNDING FACTOR 1 (ESF1) peptides accumulate before fertilization in central cell gametes and thereafter in embryo-surrounding endosperm cells. Biochemical and structural analyses revealed cleavage of ESF1 propeptides to form biologically active mature peptides. Further, these peptides act in a non-cell-autonomous manner and synergistically with the receptor-like kinase SHORT SUSPENSOR to promote suspensor elongation through the YODA mitogen-activated protein kinase pathway. Our findings demonstrate that the second female gamete and its sexually derived endosperm regulate early embryonic patterning in flowering plants.

Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes.

Plant genomes contain several hundred defensin-like (DEFL) genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. Little is known about the expression patterns or functions of many DEFLs because most were discovered recently and hence are not well represented on standard microarrays. We designed a custom Affymetrix chip consisting of probe sets for 317 and 684 DEFLs from Arabidopsis thaliana and Medicago truncatula, respectively for cataloging DEFL expression in a variety of plant organs at different developmental stages and during symbiotic and pathogenic associations. The microarray analysis provided evidence for the transcription of 71% and 90% of the DEFLs identified in Arabidopsis and Medicago, respectively, including many of the recently annotated DEFL genes that previously lacked expression information. Both model plants contain a subset of DEFLs specifically expressed in seeds or fruits. A few DEFLs, including some plant defensins, were significantly up-regulated in Arabidopsis leaves inoculated with Alternaria brassicicola or Pseudomonas syringae pathogens. Among these, some were dependent on jasmonic acid signaling or were associated with specific types of immune responses. There were notable differences in DEFL gene expression patterns between Arabidopsis and Medicago, as the majority of Arabidopsis DEFLs were expressed in inflorescences, while only a few exhibited root-enhanced expression. By contrast, Medicago DEFLs were most prominently expressed in nitrogen-fixing root nodules. Thus, our data document salient differences in DEFL temporal and spatial expression between Arabidopsis and Medicago, suggesting distinct signaling routes and distinct roles for these proteins in the two plant species.

Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes.

BACKGROUND: The GeneChip(R) Medicago Genome Array, developed for Medicago truncatula, is a suitable platform for transcript profiling in tetraploid alfalfa [Medicago sativa (L.) subsp. sativa]. However, previous research involving cross-species hybridization (CSH) has shown that sequence variation between two species can bias transcript profiling by decreasing sensitivity (number of expressed genes detected) and the accuracy of measuring fold-differences in gene expression. RESULTS: Transcript profiling using the Medicago GeneChip(R) was conducted with elongating stem (ES) and post-elongation stem (PES) internodes from alfalfa genotypes 252 and 1283 that differ in stem cell wall concentrations of cellulose and lignin. A protocol was developed that masked probes targeting inter-species variable (ISV) regions of alfalfa transcripts. A probe signal intensity threshold was selected that optimized both sensitivity and accuracy. After masking for both ISV regions and previously identified single-feature polymorphisms (SFPs), the number of differentially expressed genes between the two genotypes in both ES and PES internodes was approximately 2-fold greater than the number detected prior to masking. Regulatory genes, including transcription factor and receptor kinase genes that may play a role in development of secondary xylem, were significantly over-represented among genes up-regulated in 252 PES internodes compared to 1283 PES internodes. Several cell wall-related genes were also up-regulated in genotype 252 PES internodes. Real-time quantitative RT-PCR of differentially expressed regulatory and cell wall-related genes demonstrated increased sensitivity and accuracy after masking for both ISV regions and SFPs. Over 1,000 genes that were differentially expressed in ES and PES internodes of genotypes 252 and 1283 were mapped onto putative orthologous loci on M. truncatula chromosomes. Clustering simulation analysis of the differentially expressed genes suggested co-expression of some neighbouring genes on Medicago chromosomes. CONCLUSIONS: The problems associated with transcript profiling in alfalfa stems using the Medicago GeneChip as a CSH platform were mitigated by masking probes targeting ISV regions and SFPs. Using this masking protocol resulted in the identification of numerous candidate genes that may contribute to differences in cell wall concentration and composition of stems of two alfalfa genotypes.

Rapid and specific method for evaluating Streptomyces competitive dynamics in complex soil communities.

Quantifying target microbial populations in complex communities remains a barrier to studying species interactions in soil environments. Quantitative PCR (qPCR) assays were developed for quantifying pathogenic Streptomyces scabiei and antibiotic-producing Streptomyces lavendulae strains in complex soil communities. This assay will be useful for evaluating the competitive dynamics of streptomycetes in soil.

Phosphorus stress in common bean: root transcript and metabolic responses.

Phosphorus (P) is an essential element for plant growth. Crop production of common bean (Phaseolus vulgaris), the most important legume for human consumption, is often limited by low P in the soil. Functional genomics were used to investigate global gene expression and metabolic responses of bean plants grown under P-deficient and P-sufficient conditions. P-deficient plants showed enhanced root to shoot ratio accompanied by reduced leaf area and net photosynthesis rates. Transcript profiling was performed through hybridization of nylon filter arrays spotted with cDNAs of 2,212 unigenes from a P deficiency root cDNA library. A total of 126 genes, representing different functional categories, showed significant differential expression in response to P: 62% of these were induced in P-deficient roots. A set of 372 bean transcription factor (TF) genes, coding for proteins with Inter-Pro domains characteristic or diagnostic for TF, were identified from The Institute of Genomic Research/Dana Farber Cancer Institute Common Bean Gene Index. Using real-time reverse transcription-polymerase chain reaction analysis, 17 TF genes were differentially expressed in P-deficient roots; four TF genes, including MYB TFs, were induced. Nonbiased metabolite profiling was used to assess the degree to which changes in gene expression in P-deficient roots affect overall metabolism. Stress-related metabolites such as polyols accumulated in P-deficient roots as well as sugars, which are known to be essential for P stress gene induction. Candidate genes have been identified that may contribute to root adaptation to P deficiency and be useful for improvement of common bean.

Insights into symbiotic nitrogen fixation in Medicago truncatula.

In silico analysis of the Medicago truncatula gene index release 8.0 at The Institute for Genomic Research identified approximately 530 tentative consensus sequences (TC) clustered from 2,700 expressed sequence tags (EST) derived solely from Sinorhizobium meliloti-inoculated root and nodule tissues. A great majority (76%) of these TC were derived exclusively from nitrogen-fixing and senescent nodules. A cDNA filter array was constructed using approximately 58% of the in silico-identified TC as well as cDNAs representing selected carbon and nitrogen metabolic pathways. The purpose of the array was to analyze transcript abundance in M. truncatula roots and nodules following inoculation by a wild-type S. meliloti strain, a mutant strain that forms ineffective nodules, an uninoculated root control, and roots following nitrate or ammonium treatments. In all, 81 cDNAs were upregulated in both effective and ineffective nodules, and 78% of these cDNAs represent in silico-identified TC. One group of in silico-identified TC encodes genes with similarity to putative plant disease resistance (R) genes of the nucleotide binding site-leucine-rich repeat type. Expression of R genes was enhanced in effective nodules, and transcripts also were detected in ineffective nodules at 14 days postinoculation (dpi). Homologous R gene sequences also have been identified in the Medicago genome. However, their functional importance in nodules remains to be established. Genes for enzymes involved in organic acid synthesis along with genes involved in nitrogen metabolism were shown to be coexpressed in nitrate-fed roots and effective nodules of M. truncatula.

Identification of candidate phosphorus stress induced genes in Phaseolus vulgaris through clustering analysis across several plant species.

Common bean (Phaseolus vulgaris L.) is the world's most important grain legume for direct human consumption. However, the soils in which common bean predominate are frequently limited by the availability of phosphorus (P). Improving bean yield and quality requires an understanding of the genes controlling P acquisition and use, ultimately utilising these genes for crop improvement. Here we report an in silico approach for the identification of genes involved in adaptation of P. vulgaris and other legumes to P-deficiency. Some 22 groups of genes from four legume species and Arabidopsis thaliana, encoding diverse functions, were identified as statistically over-represented in EST contigs from P-stressed tissues. By combining bioinformatics analysis with available micro / macroarray technologies and clustering results across five species, we identified 52 P. vulgaris candidate genes belonging to 19 categories as induced by P-stress response. Transport-related, stress (defence and regulation) signal transduction genes are abundantly represented. Manipulating these genes through traditional breeding methodologies and / or biotechnology approaches may allow us to improve crop P-nutrition.

The Affymetrix Medicago GeneChip® array is applicable for transcript analysis of alfalfa (Medicago sativa).

The recently released Affymetrix GeneChip® Medicago Genome Array contains approximately 52 700 probe sets representing genes in both the model legume Medicago truncatula Gaertn. and the closely related crop species Medicago sativa L. (alfalfa). We evaluated the utility of the Medicago GeneChip® for monitoring genome-wide expression of M. truncatula and alfalfa seedlings grown to the first trifoliate leaf stage. We found that approximately 40-54% of the Medicago probes were detected in leaf or root samples of alfalfa or M. truncatula. Approximately 45-59% of the detected Medicago probes were called 'present' in all replicate GeneChips of Medicago species, indicating a considerable overlap in the number and type of Medicago probes detected between root and leaf organs. Nevertheless, gene expression differences between roots and leaf organs accounted for approximately 17% of the total variation, regardless of the Medicago species from which the samples were harvested. The result shows that the Medicago GeneChip® is applicable for transcript analysis for both alfalfa and M. truncatula.

A comparison of constitutive promoters for expression of transgenes in alfalfa (Medicago sativa).

The activity of constitutive promoters was compared in transgenic alfalfa plants using two marker genes. Three promoters, the 35S promoter from cauliflower mosaic virus (CaMV), the cassava vein mosaic virus (CsVMV) promoter, and the sugarcane bacilliform badnavirus (ScBV) promoter were each fused to the beta-glucuronidase (gusA) gene. The highest GUS enzyme activity was obtained using the CsVMV promoter and all alfalfa cells assayed by in situ staining had high levels of enzyme activity. The 35S promoter was expressed in leaves, roots, and stems at moderate levels, but the promoter was not active in stem pith cells, root cortical cells, or in the symbiotic zones of nodules. The ScBV promoter was active primarily in vascular tissues throughout the plant. In leaves, GUS activity driven by the CsVMV promoter was approximately 24-fold greater than the activity from the 35S promoter and 38-fold greater than the activity from the ScBV promoter. Five promoters, the double 35S promoter, figwort mosaic virus (FMV) promoter, CsVMV promoter, ScBV promoter, and alfalfa small subunit Rubisco (RbcS) promoter were used to control expression of a cDNA from Trichoderma atroviride encoding an endochitinase (ech42). Highest chitinase activity in leaves, roots, and root nodules was obtained in plants containing the CsVMV:ech42 transgene. Plants expressing the endochitinase were challenged with Phoma medicaginis var. medicaginis, the causal agent of spring black stem and leaf spot of alfalfa. Although endochitinase activity in leaves of transgenic plants was 50- to 2650-fold greater than activity in control plants, none of the transgenic plants showed a consistent increase in disease resistance compared to controls. The high constitutive levels of both GUS and endochitinase activity obtained demonstrate that the CsVMV promoter is useful for high-level transgene expression in alfalfa.