Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency

Citation: Serba, D. D., Uppalapati, S. R., Krom, N., Mukherjee, S., Tang, Y. H., Mysore, K. S., & Saha, M. C. (2016). Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency. Bmc Genomics, 17, 14. doi:10.1186/s12864-016-3377-8Background: Switchgrass, a warm-season perennial grass studied as a potential dedicated biofuel feedstock, is classified into two main taxa - lowland and upland ecotypes - that differ in morphology and habitat of adaptation. But there is limited information on their inherent molecular variations. Results: Transcriptome analysis by RNA-sequencing (RNA-Seq) was conducted for lowland and upland ecotypes to document their gene expression variations. Mapping of transcriptome to the reference genome (Panicum virgatum v1. 1) revealed that the lowland and upland ecotypes differ substantially in sets of genes transcribed as well as levels of expression. Differential gene expression analysis exhibited that transcripts related to photosynthesis efficiency and development and photosystem reaction center subunits were upregulated in lowlands compared to upland genotype. On the other hand, catalase isozymes, helix-loop-helix, late embryogenesis abundant group I, photosulfokinases, and S-adenosyl methionine synthase gene transcripts were upregulated in the upland compared to the lowlands. At >= 100x coverage and >= 5% minor allele frequency, a total of 25,894 and 16,979 single nucleotide polymorphism (SNP) markers were discovered for VS16 (upland ecotype) and K5 (lowland ecotype) against the reference genome. The allele combination of the SNPs revealed that the transition mutations are more prevalent than the transversion mutations. Conclusions: The gene ontology (GO) analysis of the transcriptome indicated lowland ecotype had significantly higher representation for cellular components associated with photosynthesis machinery controlling carbon fixation. In addition, using the transcriptome data, SNP markers were detected, which were distributed throughout the genome. The differentially expressed genes and SNP markers detected in this study would be useful resources for traits mapping and gene transfer across ecotypes in switchgrass breeding for increased biomass yield for biofuel conversion

Client preferences and acceptability for medical abortion and MVA as early pregnancy termination method in Northwest Ethiopia

<p>Abstract</p> <p>Background</p> <p>Increasing access to safe abortion services is the most effective way of preventing the burden of unsafe abortion, which is achieved by increasing safe choices for pregnancy termination. Medical abortion for termination of early abortion is said to safe, effective, and acceptable to women in several countries. In Ethiopia, however, medical methods have, until recently, never been used. For this reason it is important to assess women's preferences and the acceptability of medical abortion and manual vacuum aspiration (MVA) in the early first trimester pregnancy termination and factors affecting acceptability of medical and MVA abortion services.</p> <p>Methods</p> <p>A prospective study was conducted in two hospitals and two clinics from March 2009 to November 2009. The study population consisted of 414 subjects over the age of 18 with intrauterine pregnancies of up to 63 days' estimated gestation. Of these 251 subjects received mifepristone and misoprostol and 159 subjects received MVA. Questionnaires regarding expectations and experiences were administered before the abortion and at the 2-week follow-up visit.</p> <p>Results</p> <p>The study groups were similar with respect to age, marital status, educational status, religion and ethnicity. Their mean age was about 23, majority in both group completed secondary education and about half were married. Place of residence and duration of pregnancy were associated with method choice. Subjects undergoing medical abortions reported significantly greater satisfaction than those undergoing surgical abortions (91.2% vs 82.4%; <it>P </it>< .001). Of those women who had medical abortion, (83.3%) would choose the method again if needed, and (77.4%) of those who had MVA would also choose the method again. Ninety four percent of women who had medical abortion and 86.8% of those who had MVA would recommend the method to their friends.</p> <p>Conclusions</p> <p>Women receiving medical abortion were more satisfied with their method and more likely to choose the same method again than were subjects undergoing surgical abortion. We conclude that medical abortion can be used widely as an alternative method for early pregnancy termination.</p

Mortality and Disability-adjusted Life-years (DALYs) for common neglected tropical Diseases in Ethiopia, 1990 to 2015: evidence from the Global Burden of Disease Study 2015

Introduction: Neglected tropical diseases (NTDs) are important public health problems in Ethiopia. In 2013, the Federal Ministry of Health (FMOH) has launched a national NTD master plan to eliminate major NTDs of public health importance by 2020. Benchmarking the current status of NTDs in the country is important to monitor and evaluate the progress in the implementation of interventions and their impacts. Therefore, this study aims to assess the trends of mortality and Disability-adjusted Life-Years (DALY) for the priority NTDs over the last 25 years. Methods: We used the Global Burden of Disease (GBD) 2015 estimates for this study. The GBD 2015 data source for cause of death and DALY estimation included verbal autopsy (VA), Demographic and Health Surveys (DHS), malaria indicator surveys (MICS) and other disease specific surveys, Ministry of Health reports submitted to United Nations (UN) agencies and published scientific articles. Cause of Death Ensemble modeling (CODEm) and/or natural history models were used to estimate malaria and NTDs mortality rates. DALY were estimated as the sum of Years of Life Lost (YLL) due to premature mortality and Years Lived with Disability (YLD). Results: All NTDs caused an estimated of 6,293 deaths (95% uncertainty interval (UI): 3699 – 10,080) in 1990 and 3,593 deaths (95% UI: 2051 – 6178) in 2015, a 70% reduction over the 25 years. Age-standardised mortality rates due to schistosomiasis, STH and leshmaniasis have declined by 91.3%, 73.5% and 21.6% respectively between 1990 to 2015. The number of DALYs due to all NTDs has declined from 814.4 thousand (95% UI: 548 thousand–1.2 million) in 1990 to 579.5 thousand (95%UI: 309.4 thousand – 1.3 million) in 2015. Age-standardised DALY rates due to all NTDs declined by 30.4%, from 17.6 per 1000(95%UI: 12.5-26.5) in 1990 to 12.2 per 1000(95%UI: 6.5 – 27.4) in 2015. Age-standardised DALY rate for trachoma declined from 92.7 per 100,000(95% UI: 63.2 – 128.4) in 1990 to 41.2 per 100,000(95%UI: 27.4 – 59.2) in 2015, a 55.6% reduction between 1990 and 2015. Age-standardised DALY rates for onchocerciasis, schistosomiasis and lymphiatic filariasis decreased by 66.2%, 29.4% and 12.5% respectively between 1990 and 2015. DALY rate for ascariasis fell by 56.8% over the past 25 years. Conclusions: Ethiopia has made a remarkable progress in reducing the DALY rates for most of the NTDs over the last 25 years. The rapid scale of interventions and broader system strengthening may have a lasting impact on achieving the 2020 goal of elimination of most of NTDs. Ethiopia should strengthen the coverage of integrated interventions of NTD through proper coordination with other health programs and sectors and community participation to eliminate NTDs by 2020

Studies on Synthesis and Characterization of Fe3O4@SiO2@Ru Hybrid Magnetic Composites for Reusable Photocatalytic Application

Degradation of dye pollutants by the photocatalytic process has been regarded as the most efficient green method for removal organic dyes from contaminated water. The current research work describes the synthesis of Fe3O4@SiO2@Ru hybrid magnetic composites (HMCs) and their photocatalytic degradation of two azo dye pollutants, methyl orange (MO) and methyl red (MR), under irradiation of visible light. The synthesis of Fe3O4@SiO2@Ru HMCs involves three stages, including synthesis of Fe3O4 magnetic microspheres (MMSs), followed by silica (SiO2) coating to get Fe3O4@SiO2 MMSs, and then incorporation of presynthesized Ru nanoparticles (~3 nm) onto the surface of Fe3O4@SiO2 HMCs. The synthesized HMCs were characterized by XRD, FTIR, TEM, EDS, XPS, BET analysis, UV-DRS, PL spectroscopy, and VSM to study the physical and chemical properties. Furthermore, the narrow band gap energy of the HMC photocatalyst is a significant parameter that provides high photocatalytic properties due to the high light adsorption. The photocatalytic activity of synthesized Fe3O4@SiO2@Ru HMCs was assessed by researching their ability to degrade the aqueous solution of MO and MR dyes under visible radiation, and the influence of various functional parameters on photocatalytic degradation has also been studied. The results indicate that the photocatalytic degradation of MO and MR dyes is more than 90%, and acid media favors better degradation. The probable mechanism of photodegradation of azo dyes by Fe3O4@SiO2@Ru HMC catalysts has been proposed. Furthermore, due to the strong ferromagnetic Fe3O4 core, HMCs were easily separated from the solution after the photocatalytic degradation process for reuse. Also, the photocatalytic activity after six cycles of use is greater than 90%, suggesting the stability of the synthesized Fe3O4@SiO2@Ru HMCs.</jats:p

Age at menarche and the menstrual pattern of secondary school adolescents in northwest Ethiopia

<p>Abstract</p> <p>Background</p> <p>Population studies on normal and dysfunctional characteristics of menstrual cycles are scarce in Ethiopia. In addition variability in menarcheal age and menstrual characteristics are common. Knowledge on this variability is necessary for patient education and to guide clinical evaluation.</p> <p>Methods</p> <p>A cross sectional study was conducted in two small towns called Dabat and Kola Diba, northwest Ethiopia between April and May 2007. Systematic sampling method was used to select 622 school girls from two secondary schools. A pretested questionnaire prepared in Amharic was used to gather data. Selected girls cooperated in answering the questionnaire in their classrooms under the supervision of the research team. Only 612 of the adolescent females were included in the final analysis, of which 305 were from Koladiba High School and 307 from Dabat.</p> <p>Results</p> <p>The age of the study subjects ranges between 14 and 19 with a mean (standard deviation) of 16.9 ± 1 years. About 92.2% had attained menarche by the time the survey was conducted. The probit analysis of the <it>status quo </it>data yielded a median (CI) age at menarche of 14.8 (13.9-15.3) years. The average age at menarche by recall method was 15.8 ± 1 years. The mean age at menarche was 0.3 years younger for urban females compared with rural ones (p < 0.001). A cycle length between 21 and 35 days was observed in 70.3% of the girls. The mean duration of flow was 4 ± 1.3 days with a range of 2-7 days. The menstrual cycles were irregular in 42.8% of the subjects. The overall prevalence of dysmenorrhoea was 72% among these subjects. Premenstrual symptoms were present in 435 of the females (75.4%). The leading sources of menarcheal information to the adolescents were mothers (39.7%), followed by their friends (26.6%) and teachers (21.8%).</p> <p>Conclusion</p> <p>In this study age of menarche was found to be delayed which is even higher than the findings indicated similar studies conducted in Ethiopia and other African countries. A significant number of students complain of abnormal menstrual cycle, dysmenorrhoea and premenstrual symptoms which call for appropriate counselling and management.</p

Multispacer Sequence Typing Relapsing Fever Borreliae in Africa

In Africa, relapsing fevers are caused by four cultured species: Borrelia crocidurae, Borrelia duttonii, Borrelia hispanica and Borrelia recurrentis. These borreliae are transmitted by the bite of Ornithodoros soft ticks except for B. recurrentis which is transmitted by louse Pediculus humanus. They cause potentially undifferentiated fever infection and co-infection with malaria could also occur. The exact prevalence of each Borrelia is unknown and overlaps between B. duttonii and B. crocidurae have been reported. The lack of tools for genotyping these borreliae limits knowledge concerning their epidemiology. We developed multispacer sequence typing (MST) and applied it to blood specimens infected by B. recurrentis (30 specimens), B. duttonii (18 specimens) and B. crocidurae (13 specimens), delineating these 60 strains and the 3 type strains into 13 species-specific spacer types. B. crocidurae strains were classified into 8 spacer types, B. duttonii into 3 spacer types and B. recurrentis into 2 spacer types. These findings provide the proof-of-concept that that MST is a reliable tool for identification and genotyping relapsing fever borreliae in Africa

Assessing uncertainties in climate change adaptation and land management

The entire cascade of scenario generation, global and regional climate modeling, as well as concrete measures towards climate adaptation are subject to uncertainties. An exact prediction of how the climate will change in the coming years, and how it will affect land use, is not possible. There is thus a perceived need to identify ways via which uncertainties can be addressed. Based on the need to address the research gap in this area, this paper reports the findings of a study on uncertainty in a climate change adaptation context, and how it is perceived. It consists of a multi-stakeholder survey among climate change professionals, including academic staff at universities, representatives from international agencies, members of NGOs, policymakers, and representatives of industry from 50 countries, including a balanced representation of industrialized and developing nations. The results obtained suggest that uncertainties are often a hindrance to engagement in climate change adaptation efforts, and to land management. Furthermore, there is a range of tools to reduce climate change adaptation uncertainties, whose deployment may help to address them. The paper concludes by providing a list of lessons learned and suggestions as to how uncertainty can be better communicated, and by doing so, how a reduction in the levels of climate change vulnerability may be achieved, and how land management may be fostered

Assessing the impacts of climate change in cities and their adaptive capacity: Towards transformative approaches to climate change adaptation and poverty reduction in urban areas in a set of developing countries

Many cities across the world are facing many problems climate change poses to their populations, communities and infrastructure. These vary from increased exposures to floods, to discomfort due to urban heat, depending on their geographical locations and settings. However, even though some cities have a greater ability to cope with climate change challenges, many struggle to do so, particularly in cities in developing countries. In addition, there is a shortage of international studies which examine the links between climate change adaptation and cities, and which at the same time draw some successful examples of good practice, which may assist future efforts. This paper is an attempt to address this information need. The aim of this paper is to analyse the extent to which cities in a sample of developing countries are attempting to pursue climate change adaptation and the problems which hinder this process. Its goal is to showcase examples of initiatives and good practice in transformative adaptation, which may be replicable elsewhere. To this purpose, the paper describes some trends related to climate change in a set of cities in developing countries across different continents, including one of the smallest capital cities (Georgetown, Guyana) and Shanghai, one the world's most populous cities. In particular, it analyses their degree of vulnerability, how they manage to cope with climate change impacts, and the policies being implemented to aid adaptation. It also suggests the use of transformative approaches which may be adopted, in order to assist them in their efforts towards investments in low-carbon and climate-resilient infrastructure, thereby maximizing investments in urban areas and trying to address their related poverty issues. This paper addresses a gap in the international literature on the problems many cities in developing countries face, in trying to adapt to a changing climate

Iron deficiency anemia is not a rare problem among women of reproductive ages in Ethiopia: a community based cross sectional study

<p>Abstract</p> <p>Background</p> <p>In Ethiopia, the existence of iron deficiency anemia is controversial despite the fact that Ethiopia is one of the least developed in Africa with a high burden of nutrient deficiencies.</p> <p>Methods</p> <p>The first large nutrition study of a representative sample of women in Ethiopia was conducted from June to July 2005 and a systematically selected sub-sample of 970 of these subjects, 15 to 49 years old, were used in this analysis of nutritional anemia. Hemoglobin was measured from capillary blood using a portable HemoCue photometer. For serum ferritin, venous blood from antecubital veins was measured by an automated Elecsys 1020 using commercial kits. Diets were assessed via simplified food frequency questionnaire. The association of anemia to demographic and health variables was tested by chi-square and a stepwise backward logistic regression model was applied to test the significant associations observed in chi square tests.</p> <p>Results</p> <p>Mean hemoglobin ± SD was 11.5 ± 2.1 g/dL with a 29.4% prevalence of anemia. Mean serum ferritin was 58 ± 41.1 ug/L with a 32.1% prevalence of iron deficiency. The overall prevalence rate of iron deficiency anemia was 18.0%. Prevalence of anemia, iron deficiency, and iron deficiency anemia was highest among those 31-49 years old (p < 0.05). Intake of vegetables less than once a day and meat less than once a week was common and was associated with increased anemia (p = 0.001). Although the prevalence of anemia was slightly higher among women with parasitic infestation the difference was not significant (p = 0.9). Nonetheless, anemia was significantly higher in women with history of illness and the association was retained even when the variable was adjusted for its confounding effect in the logistic regression models (AOR = 0.3; 95%CI = 0.17 to 0.5) signifying that the most probable causes of anemia is nutrition related and to some extent chronic illnesses.</p> <p>Conclusion</p> <p>Moderate nutritional anemia in the form of iron deficiency anemia is a problem in Ethiopia and therefore, the need for improved supplementation to vulnerable groups is warranted to achieve the United Nation's Millennium Development Goals. Chronic illnesses are another important cause of anemia.</p