Molecular Evolution and Functional Diversification of Replication Protein A1 in Plants

Replication protein A (RPA) is a heterotrimeric, single-stranded DNA binding complex required for eukaryotic DNA replication, repair, and recombination. RPA is composed of three subunits, RPA1, RPA2, and RPA3. In contrast to single RPA subunit genes generally found in animals and yeast, plants encode multiple paralogs of RPA subunits, suggesting subfunctionalization. Genetic analysis demonstrates that five Arabidopsis thaliana RPA1 paralogs (RPA1A to RPA1E) have unique and overlapping functions in DNA replication, repair, and meiosis. We hypothesize here that RPA1 subfunctionalities will be reflected in major structural and sequence differences among the paralogs. To address this, we analyzed amino acid and nucleotide sequences of RPA1 paralogs from 25 complete genomes representing a wide spectrum of plants and unicellular green algae. We find here that the plant RPA1 gene family is divided into three general groups termed RPA1A, RPA1B, and RPA1C, which likely arose from two progenitor groups in unicellular green algae. In the family Brassicaceae the RPA1B and RPA1C groups have further expanded to include two unique sub-functional paralogs RPA1D and RPA1E, respectively. In addition, RPA1 groups have unique domains, motifs, cis-elements, gene expression profiles, and pattern of conservation that are consistent with proposed functions in monocot and dicot species, including a novel C-terminal zinc-finger domain found only in plant RPA1C-like sequences. These results allow for improved prediction of RPA1 subunit functions in newly sequenced plant genomes, and potentially provide a unique molecular tool to improve classification of Brassicaceae species

Genetic analysis of the Replication Protein A large subunit family in Arabidopsis reveals unique and overlapping roles in DNA repair, meiosis and DNA replication

Replication Protein A (RPA) is a heterotrimeric protein complex that binds single-stranded DNA. In plants, multiple genes encode the three RPA subunits (RPA1, RPA2 and RPA3), including five RPA1-like genes in Arabidopsis. Phylogenetic analysis suggests two distinct groups composed of RPA1A, RPA1C, RPA1E (ACE group) and RPA1B, RPA1D (BD group). ACE-group members are transcriptionally induced by ionizing radiation, while BD-group members show higher basal transcription and are not induced by ionizing radiation. Analysis of rpa1 T-DNA insertion mutants demonstrates that although each mutant line is likely null, all mutant lines are viable and display normal vegetative growth. The rpa1c and rpa1e single mutants however display hypersensitivity to ionizing radiation, and combination of rpa1c and rpa1e results in additive hypersensitivity to a variety of DNA damaging agents. Combination of the partially sterile rpa1a with rpa1c results in complete sterility, incomplete synapsis and meiotic chromosome fragmentation, suggesting an early role for RPA1C in promoting homologous recombination. Combination of either rpa1c and/or rpa1e with atr revealed additive hypersensitivity phenotypes consistent with each functioning in unique repair pathways. In contrast, rpa1b rpa1d double mutant plants display slow growth and developmental defects under non-damaging conditions. We show these defects in the rpa1b rpa1d mutant are likely the result of defective DNA replication leading to reduction in cell division

Stillbirths and hospital early neonatal deaths at Queen Elizabeth Central Hospital, Blantyre-Malawi

<p>Abstract</p> <p>Background</p> <p>Much of the data on still births and early neonatal deaths from resource-limited settings are obtained via maternal recall from national or community level surveys. While this approach results in useful information to be obtained, often such data suffer from significant recall bias and misclassification. In order to determine the prevalence of stillbirths (SB), early hospital neonatal death (EHND) and associated factors in Blantyre, Malawi, a prospective study of pregnant and post-natal women was conducted at the Queen Elizabeth Central Hospital (QECH), Malawi.</p> <p>Methods</p> <p>A prospective observational study was conducted between February 1, 2004 and October 30, 2005. Consecutive women attending the hospital for delivery were recruited. Data were collected on the health status of the fetus on admission to labor ward and immediately after delivery, whether alive or dead. Gestational age (GA) and birth weight (BW) and sex of the newborn were also noted. Similar data were also collected on the live births that died in the delivery room or nursery. Data were analyzed using SPSS (Statistical Package for the Social Sciences) statistical package.</p> <p>Results</p> <p>A total of 10,700 deliveries were conducted during the 12 months study period and of these deliveries, 845 (7.9%) were SB and EHND. Stillbirths comprised 3.4% of all deliveries; 20.2% of the ante-partum deaths occurred before the mother was admitted to the labor ward while a slightly higher proportion (22.7%) of fetal loss occurred during the process of labor and delivery. Fifty-sex percent of the perinatal deaths (PD) were EHND. The mean gestational age for the perinatal deaths was 34.7 weeks and mean birth weight was 2,155 g (standard deviation = 938 g). The majority, 468 (57.8%) of the perinatal deaths were males and 350 (43.2%) were females. Many of the perinatal deaths (57.9%) were deliveries between gestational ages of 20 and 37 weeks. Most (62.7%) of the mothers with a perinatal death had experienced a previous similar incident.</p> <p>Conclusion</p> <p>About 3.4% of all pregnant mothers past 20 weeks of gestation ended up in delivering a stillbirth; another 4.4% of the live births died before discharge from hospital, thus, 7.9% of pregnancy loss after 20 weeks (or 500 g estimated weight) of gestation. This is a higher loss when compared to international and regional data. We recommend attention be given to these unfavorable outcomes and preventive measures or intervention for preventable causes be considered seriously. These measures could include the provision of emergency obstetric care, improving access to deliveries by health professionals and resourcing of health facilities such that neonatal viability is promoted.</p

Exploratory Survey of Forest Plants in Traditional Treatment of Guinea Worm Infections (GWI)(Dracunculus medinensis Linn): Experiences from Nigeria and Ethiopia.

Traditional medicines using forest plants as the major source of raw materials has been the system of Medicare especially in treating guinea worm (Dracunculus medinensis LINN) infections in endemic areas of Africa such as Nigeria and Ethiopia. This system is age long and predates the advents of modern Medicare. With the problems of drug resistances and inability of poor people's access to modern Medicare, traditional medicines could still be the only source of succor. hence the relevance of this study which investigated the forest plants used in the traditional treatment of guinea worm infections (GWI) in some endemic areas of Nigeria and a cross check with the situation in Ethiopia. A total of 92 plant species were recorded representing 68 families. They were, trees (43species), shrubs (18species), herbs (24species) and climbers (7species).Majority of the species were sourced from the wild forests and fallow lands. Different parts of the plants such as roots, leaves, barks, fruits and sometimes whole are prepared and administered in various ways such as oral applications, rubbing, ingestion and therapeutic washing. Twenty nine of these species were found to be available and have similar uses in traditional Medicare in some parts of Ethiopia where water borne diseases are endemic. These findings has posed some challenges to African scientists especially in the area of knowledge and products developments .The conclusion was reached that with current rates of deforestation in Nigeria and Ethiopia, these plants could become ‘lost crops' before their potentials are realized. African Research Review Vol. 1 (3) 2007: pp. 108-12

In vitro antimicrobial activity of fermented spices and Capsicum Frutescens against multi drug resistance clinical isolate and standard reference bacteria

Introduction: Food preservation is required to maintain for a long period of time. Traditional organic food preservative, “Datta” is spice mainly made up of Chili Peppers which frequently used in southern and western part of Ethiopia. Datta can be consumed almost with every kind of foods and it is believed as appetizer and antimicrobial agent against food borne pathogen. This study aimed to assess in vitro antimicrobial activity of fermented condiment and Capsicum frutescens against multi drug resistance clinical isolate and standard reference bacteria.Method: Datta samples collected from different level hotels and Capsicum frutescens (Chili peppers) were extractedin different solvents.Agar well diffusion assay was used to determine antimicrobial activity and minimum inhibitory concentration (MIC) and minimum bactericidal concentration was determined by tube dilution method. One way analysis of variant was used in comparison of the finding.Results: Extracted fermented condiment (Datta) sample and Chili Pepper showed antimicrobial activities against multidrug resistant clinical isolate and standard reference bacteria in well diffusion assay. Datta extract showed MIC ranged from 25 mg/L to 66.7 mg/L and MBC ranged from 25 mg/L to 100 mg/L. The Datta and Chili pepper extracts showed high antimicrobial activities against standard Staphylococcus aureus. The water based extract of Datta sample were exhibited significantly low antimicrobial activities (P=0.000) as compared to the other extraction solvents.Conclusion: Water was weak extractor of active compounds having antimicrobial activities. Reference S. aureuswasmore susceptible organism while ATCC Salmonella enteritidis and clinical isolated multi-drug resistant E. coli less susceptible. The traditional use of fermented condiment for food preservation by the local people is supported by this study.Key words: Antimicrobial activity; Chili Pepper extract; Fermented condiment; Minimum bactericidal concentration; Minimum inhibition contractionActivite antimicrobienne en vitro d'epices fermentees et de fruits de capsicume pour la resistance aux medicaments isolate clinique et bacteries de reference standardIntroduction: La conservation des aliments est nécessaire pour maintenir pendant une longue période de temps. Conservateur de nourriture organiqu et raditionnel, "Datta" est l'épicé compose principalement de Chili Peppers qui fréquemment utilize dans le sud et l'ouest de l'Ethiopie. Datta peu têtre consommé presque avec toutes sortes d'aliments et on le croit comme un apéritif et un agent antimicrobien contre l'agent pathogène alimentaire. Cette etude visait à évaluer l'activité antimicrobienne in vitro du condiment fermenté et Capsicum frutescens contre l'isolement clinique de résistance aux médicaments multiples et les bactéries de référence standard.Méthode: Les échantillons de Datta prélevés dans des hôtels de différents niveaux et Capsicum frutescens (Chili Peppers) ont été extraits dans différents solvants. Un dosage de diffusion de puits a été utilisé pour determiner l'activité antimicrobienne et la concentration inhibitrice minimale (MIC) et la concentration bactericide minimale a été determine par la méthode de dilution du tube. Une analyse à sens unique de la variante a été utilisée en comparaison de la découverte.Résultats: L'échantillon extrait de condiments fermentés (Datta) et Chili Pepper ont montré des activités antimicrobiennes contre l'isolement Clinique résistant aux médicaments multiples et les bactéries de référence standard dans le dosage par diffusion de puits. L'extrait de Datta a montréque le MIC variait de 25 mg / L à 66,7 mg / L et le MBC variait de 25 mg / L à 100 mg / L. Les extraits de poisson de Datta et de Chili ont montré des activités antimicrobiennes élevées contre Staphylococcus aureus standard. L'extrait à base d'eau de l'échantillon de Datta a montré des activités antimicrobiennes significativement faibles (P = 0,000) par rapport aux autres solvants d'extraction.Conclusion: L'eauétaitun extracteur faible de composes actifs ayant des activités antimicrobiennes. Référence S. aureus était un organisme plus susceptible tandisque ATCC Salmonella enteritidis et E.coli. E. coli résistant aux médicaments multiples isolés était moins susceptible. L'utilisation traditionnelle du condiment fermenté pour la conservation des aliments par les populations locales est soutenue par cette étude.Mots clés: Activitéantimicrobienne; Extrait de poivre de piment; Condiment fermenté; Concentration bactéricide minimum; Contraction minimaled'inhibitio

Bio-based liquid fuels as a source of renewable energy: A review

Limited availability of fossil fuels and their associated environmental impact during combustion remains the primary basis for exploring alternative energy sources such as bio-based liquid fuels. Several feedstocks have been used to produce biofuels for different applications with their own pros and cons. For instance, production of bio-fuels using human food chain raw materials such as corn, soy, peanut, and sugarcane are receiving increased criticism due to the competing demands of the same sources for human consumption as food. However, the non-food biomass in the form of agricultural wastes, municipal wastes, waste vegetable oil, and microbial sources are abundantly available that can be utilized as feedstock for production of biofuels. Because of this reason, most biofuels have been produced using the feedstocks that do not affect the food chain. Thus, in this work, the feedstocks of different generation biofuels and their potential yield and associated greenhouse gas emissions, production technologies are critically surveyed. Moreover, the application of biofuels for different purposes are analyzed and compared with their corresponding conventional fuels. The survey also points out the recent issues and challenges of biofuels with their resolution. The future research directions are suggested to sustain biofuel production

Development and evaluation of a molecular diagnostic method to rapidly detect Histoplasma capsulatum var. farciminosum, the causative agent of epizootic lymphangitis, in equine clinical samples.

Histoplasma capsulatum var. farciminosum (HCF), the causative agent of epizootic lymphangitis (EZL), is endemic in parts of Africa. Diagnosis based on clinical signs and microscopy lacks specificity, and is a barrier to further understanding this neglected disease. Here, a nested PCR method targeting the ITS region of the rRNA operon was validated for application to equine clinical samples. Twenty-nine horses with signs of EZL, from different climatic regions of Ethiopia, were clinically examined. Blood samples and aspirates of pus from cutaneous nodules were taken, along with blood from a further 20 horses with no cutaneous EZL lesions. HCF was confirmed in DNA extracts of pus and blood samples from 25 and 17 horses, respectively, of the 29 suspected EZL cases. Positive PCR results were also obtained from heat-inactivated pus (24 horses) and blood (23 horses) spotted onto Whatman FTA cards. Two positives were obtained among blood samples from 20 horses that did not exhibit clinical signs of EZL. These are the first reports of the direct detection of HCF in equine blood, and at high frequency amongst horses exhibiting cutaneous lesions. The nested PCR outperformed conventional microscopic diagnosis, as characteristic yeast cells could only be observed in 14 pus samples. HCF DNA was confirmed by sequencing the cloned PCR products, and while alignment of the ITS amplicons showed very little sequence variation, there was preliminary SNP-based evidence for the existence of two subgroups of HCF. This molecular diagnostic method now permits investigation of the epidemiology of EZL

Development of sustainable land management policies and practices in five selected countries from 1960 to 2010.

ABSTRACT Since the 1930s there has been worldwide concern about the effects of land degradation. After the problems experienced in the Dust Bowl in the USA, much attention was paid to soil and water conservation in both developed and developing countries. Initially Governments have stimulated the establishment of physical control measures, such as terraces and check dams, and reforestation. This was achieved through top-down regulations, and Forestry Departments were often in charge of the implementation. Subsequently the measures were implemented through more specialised agencies, and later with incentives, such as food aid. In some cases farmers were mobilised to work together on the establishment of the measures. Because of the low success rate of this top-down approach with line interventions, it was realised that a more participatory approach had to be followed. And the emphasis then shifted to area interventions such as cover crops, mulching and composting. In some countries voluntary ways of collaboration between farmers were developed. More recently Conservation Agriculture has been promoted, focusing on less soil disturbance, continuous land cover and crop rotations. This paper analyses whether and to what extent countries have followed such general trends in their soil and water conservation policies, since the 1990s often referred to as sustainable land management, or whether countries have also followed their own specific strategies. A historical (1960-2010) and comparative analysis of the development of these sustainable land management policies and practices is made in five selected countries (Indonesia, Ethiopia, Tunisia, Spain and Bolivia). Keywords: soil and water conservation, sustainable land management, policies, approaches, practice

Evaluation of alternative mosquito sampling methods for malaria vectors in Lowland South - East Zambia.

Sampling malaria vectors and measuring their biting density is of paramount importance for entomological surveys of malaria transmission. Human landing catch (HLC) has been traditionally regarded as a gold standard method for surveying human exposure to mosquito bites. However, due to the risk of human participant exposure to mosquito-borne parasites and viruses, a variety of alternative, exposure-free trapping methods were compared in lowland, south-east Zambia. Centres for Disease Control and Prevention miniature light trap (CDC-LT), Ifakara Tent Trap model C (ITT-C), resting boxes (RB) and window exit traps (WET) were all compared with HLC using a 3 × 3 Latin Squares design replicated in 4 blocks of 3 houses with long lasting insecticidal nets, half of which were also sprayed with a residual deltamethrin formulation, which was repeated for 10 rounds of 3 nights of rotation each during both the dry and wet seasons. The mean catches of HLC indoor, HLC outdoor, CDC-LT, ITT-C, WET, RB indoor and RB outdoor, were 1.687, 1.004, 3.267, 0.088, 0.004, 0.000 and 0.008 for Anopheles quadriannulatus Theobald respectively, and 7.287, 6.784, 10.958, 5.875, 0.296, 0.158 and 0.458, for An. funestus Giles, respectively. Indoor CDC-LT was more efficient in sampling An. quadriannulatus and An. funestus than HLC indoor (Relative rate [95% Confidence Interval] = 1.873 [1.653, 2.122] and 1.532 [1.441, 1.628], respectively, P < 0.001 for both). ITT-C was the only other alternative which had comparable sensitivity (RR = 0.821 [0.765, 0.881], P < 0.001), relative to HLC indoor other than CDC-LT for sampling An. funestus. While the two most sensitive exposure-free techniques primarily capture host-seeking mosquitoes, both have substantial disadvantages for routine community-based surveillance applications: the CDC-LT requires regular recharging of batteries while the bulkiness of ITT-C makes it difficult to move between sampling locations. RB placed indoors or outdoors and WET had consistently poor sensitivity so it may be useful to evaluate additional alternative methods, such as pyrethrum spray catches and back packer aspirators, for catching resting mosquitoes