Effects of tillage and cropping systems on yield and nitrogen fixation of cowpea intercropped with maize in northern Guinea savanna zone of Ghana

Published information is scanty on the response of crops in mixed cropping systems to the various tillage systems practised by farmers in the northern savanna zone of Ghana. A field experiment assessed the yield and nitrogen (N) fixation of cowpea (Vigna unguiculata (L.) Walp) intercropped with maize (Zea mays L.) on four different tillage systems at Nyankpala in the Northern Region of Ghana. The experiment was laid in a split-plot design with four replications. The main factor was tillage systems comprising conventional (Con), bullock plough (BP), hand hoe (HH) and zero tillage (ZT). The sub-factor was cropping systems (CRPSYT) which consisted of sole maize, sole cowpea, maize/cowpea inter-row cropping system, and bare fallow in 2000. The last-named was replaced by maize/cowpea intra-row cropping system in 2001. The results showed that Con and BP, which produced over 10 cm plough depth, significantly reduced soil bulk density that favoured significant (

Accounting for data heterogeneity in integrative analysis and prediction methods: An application to Chronic Obstructive Pulmonary Disease

Epidemiologic and genetic studies in chronic obstructive pulmonary disease (COPD) and many complex diseases suggest subgroup disparities (e.g., by sex). We consider this problem from the standpoint of integrative analysis where we combine information from different views (e.g., genomics, proteomics, clinical data). Existing integrative analysis methods ignore the heterogeneity in subgroups, and stacking the views and accounting for subgroup heterogeneity does not model the association among the views. To address analytical challenges in the problem of our interest, we propose a statistical approach for joint association and prediction that leverages the strengths in each view to identify molecular signatures that are shared by and specific to males and females and that contribute to the variation in COPD, measured by airway wall thickness. HIP (Heterogeneity in Integration and Prediction) accounts for subgroup heterogeneity, allows for sparsity in variable selection, is applicable to multi-class and to univariate or multivariate continuous outcomes, and incorporates covariate adjustment. We develop efficient algorithms in PyTorch. Our COPD findings have identified several proteins, genes, and pathways that are common and specific to males and females, some of which have been implicated in COPD, while others could lead to new insights into sex differences in COPD mechanisms

2014-2021, 8 years without bottom-reaching deep water formation in the Western Mediterranean. Probably, the longest known period

Deep Water Formation (DWF) appeared almost regularly every year, during central winter months, in an area located offshore the Gulf of Lions in the NW Mediterranean Sea. Since the early 1960s, the processes involved in the DWF have been monitored, more or less intensively by regular hydrographic surveys or by moored instruments. It is worth noting the international efforts carried out in late 60s-early 70s by the so-called MEDOC Group to obtain a quite precise description of the whole process. Although the intensity of the DWF, as well as the amount of the newly formed Western Mediterranean Deep Water (WMDW), have shown high interanual variability, those years when the DWF was absent were exceptional, e.g. 1990, and those not reaching the bottom were scarce, e.g. 1997. Typically, they were years with almost no cold northerly winds during winter. By contrast, in some years the amount of newly formed WMDW was exceptional, e.g. 1987, and in some cases, an extra amount of this water came from dense shelf cascading, e.g. 1999. Moreover, in some years, the so-called variable Bottom Water, a slightly warm and salty layer, appeared near the bottom. It was a layer not thicker than 300 m, attributed to a large area affected by DWF which caused an extra amount of Levantine Intermediate Water (LIW) involved in the process, e.g. 1973. Other concomitant conditions that contributed to the DWF variability across the years was the presence of a blocking anticyclone in the Balearic Sea, that would play a role in intensifying the exposure of surface water to the northerlies, e.g. 1999. In winter 2005, all the factors contributing to an intense DWF process acted simultaneously, resulting in a new structure within the WMDW. The amount of newly formed WMDW, with higher density, T and S, was so extraordinary that affected the entire western Mediterranean basin, and it was identified as the Western Mediterranean Transition (WMT). The remnants of the WMDW previous to the WMT have been uplifted as to being available for a relevant contribution to the Mediterranean Outlfow Water (MOW) through the Gibraltar sill. After the WMT, the MOW showed both lower T and S than previously recorded up to around 2015, indicating that the old WMDW has been almost completely lost by leakage and diffusion. After the 2005 episode, the WMDW has evolved, changing its TS shape and increasing both T and S at the bottom, but still maintaining a deep layer with higher stratification than before 2005. In a previous work, we attributed the long period (2014-2018) without DWF to a combination of mild winters, the absence of the old WMDW, and the deep stratification. Such a process would be similar to the recovery of the Eastern Mediterranean Transient. In the present communication we incorporate 3 new years of data to the series, discuss the current situation and try to identify the requirements for a successful bottom-reaching DWF

Long-term continuous administration of a hydro-ethanolic extract of Synedrella nodiflora (L) Gaertn in male Sprague-Dawley rats: biochemical, haematological and histopathological changes

Background: Conflicting reports about the toxicity of Synedrella nodiflora (L) Gaertn (family Asteraceae), a plant traditionally used in Ghana for the management of epilepsy, abound in literature. The present study evaluates the effect of a 90-day continuous oral administration of a hydro-ethanolic whole plant extract of Synedrella nodiflora (SNE) in male Sprague-Dawley rats.Methods: The toxicological evaluation of the extract (100, 300 and 1000 mgkg-1) was focused on haematological, serum biochemical parameters and histopathological changes of some isolated organs.Results: The extract produced no mortality in the rats treated during the study period. Only SNE 100 mgkg-1 produced significant decrease in white blood cell and neutrophil counts and an increase in albumin, globulin, total bilirubin, total protein and potassium levels. The higher doses (SNE 300 and 1000 mgkg-1) had no significant effect on all the haematological and biochemical parameters measured. Histopathological assessment of the liver, kidney and heart revealed no abnormalities in rats treated with the extracts. Only the SNE 1000 mgkg-1 produced distortions of the branching arrangements of the myocardial fibres and a congested vessel which indicates a healed infarction.Conclusions: The findings suggest hydro-ethanolic extract of Synedrella nodiflora (L) Gaertn generally has a low toxicity profile following a 90-day continuous oral administration in male Sprague-Dawley rats under the present laboratory conditions. However patients with renal or cardiac problems should use the plant with caution.Funding: Jointly supported by the International Foundation for Science, Stockholm, Sweden, through a grant (# F/5191-1) to Dr. Patrick Amoateng and the Office of Research, Innovation and Development (ORID), University of Ghana, Accra, Ghana, grant awarded to Dr. Patrick Amoateng (reference number: URF/6/ILG-002/2012-2013)Keywords: : Synedrella nodiflora, Sprague-Dawley rats, histopathological, haematologica

Quantitative isotope-dilution high-resolution-mass-apectrometry analysis of multiple intracellular metabolites in Clostridium autoethanogenum with uniformly 13C-labeled standards derived from Spirulina

We have investigated the applicability of commercially available lyophilized spirulina (Arthrospira platensis), a microorganism uniformly labeled with 13C, as a readily accessible source of multiple 13C-labeled metabolites suitable as internal standards for the quantitative determination of intracellular bacterial metabolites. Metabolites of interest were analyzed by hydrophilic-interaction liquid chromatography coupled with high-resolution mass spectrometry. Multiple internal standards obtained from uniformly (U)-13C-labeled extracts from spirulina were used to enable isotope-dilution mass spectrometry (IDMS) in the identification and quantification of intracellular metabolites. Extraction of the intracellular metabolites of Clostridium autoethanogenum using 2:1:1 chloroform/methanol/water was found to be the optimal method in comparison with freeze–thaw, homogenization, and sonication methods. The limits of quantification were ≤1 μM with excellent linearity for all of the calibration curves (R2 ≥ 0.99) for 74 metabolites. The precision and accuracy were found to be within relative standard deviations (RSDs) of 15% for 49 of the metabolites and within RSDs of 20% for all of the metabolites. The method was applied to study the effects of feeding different levels of carbon monoxide (as a carbon source) on the central metabolism and Wood–Ljungdahl pathway of C. autoethanogenum grown in continuous culture over 35 days. Using LC-IDMS with U-13C spirulina allowed the successful quantification of 52 metabolites in the samples, including amino acids, carboxylic acids, sugar phosphates, purines, and pyrimidines. The method provided absolute quantitative data on intracellular metabolites that was suitable for computational modeling to understand and optimize the C. autoethanogenum metabolic pathways active in gas fermentation

Role of the Subunits Interactions in the Conformational Transitions in Adult Human Hemoglobin: an Explicit Solvent Molecular Dynamics Study

Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present study, the dynamical and quaternary structural changes occurring in two unligated (deoxy-) T structures, and two fully ligated (oxy-) R, R2 structures of adult human hemoglobin were investigated with molecular dynamics. It is shown that, in the sub-microsecond time scale, there is no marked difference in the global dynamics of the amino acids residues in both the oxy- and the deoxy- forms of the individual structures. In addition, the R, R2 are relatively stable and do not present quaternary conformational changes within the time scale of our simulations while the T structure is dynamically more flexible and exhibited the T\rightarrow R quaternary conformational transition, which is propagated by the relative rotation of the residues at the {\alpha}1{\beta}2 and {\alpha}2{\beta}1 interface.Comment: Reprinted (adapted) with permission from J. Phys. Chem. B DOI:10.1021/jp3022908. Copyright (2012) American Chemical Societ

Ocean Circulation over Formigas and Ormonde Seamounts

Seamounts constitute an obstacle to the free ocean flow, modifying the patter of circulation. As a result of these alterations, a variety of hydrodynamical processes and phenomena may take place in seamounts, among others, Taylor columns/caps. These oceanographic effects may turn seamounts into very productive ecosystems with high biodiversity. Under these conditions seamounts provide a particularly good environment for the settle of some organisms, acting as stepping stones and contributing to its dispersal. In this study, we verify if these oceanographic effects explain the presence of cold-water corals of Mediterranean origin in the Atlantic. To achieve this, three seamounts in the path of the Mediterranean Outflow Water (MOW) through the Eastern North Atlantic were selected: the Gazul mud volcano, and the Ormonde and Formigas seamounts. In order to determine the hydrographic and dynamical conditions in each one of the three locations, CTD, LADPC and biochemical observations were carried out. Taylor columns were not observed in any of the three sampled areas. Although we found suggestions of upwelling/downwelling systems, their effect was barely noticed in the circulation pattern. The oceanographic processes in those areas are more influenced by the vertical distribution of water masses, which determine the stability of the water column. Moreover, the high values of the Brunt-Väisälä frequency around the MOW halocline can lead to the formation of internal waves. These perturbations in the water column can enhance the vertical mixing, producing suspension, which, in turn, could affect the vertical distribution of cold-water corals

Human immunotypes impose selection on viral genotypes through viral epitope specificity

BACKGROUND: Understanding the genetic interplay between human hosts and infectious pathogens is crucial for how we interpret virulence factors. Here, we tested for associations between HIV and host genetics, and interactive genetic effects on viral load (VL) in HIV+ ART-naive clinical trial participants. METHODS: HIV genomes were sequenced and the encoded amino acid (AA) variants were associated with VL, human single nucleotide polymorphisms (SNPs) and imputed HLA alleles, using generalized linear models with Bonferroni correction. RESULTS: Human (388,501 SNPs) and HIV (3,010 variants) genetic data was available for 2,122 persons. Four HIV variants were associated with VL (p-values<1.66×10 -5). Twelve HIV variants were associated with a range of 1-512 human SNPs (p-value<4.28×10 -11). We found 46 associations between HLA alleles and HIV variants (p-values<1.29×10 -7). We found HIV variants and immunotypes when analyzed separately, were associated with lower VL, whereas the opposite was true when analyzed in concert. Epitope binding prediction showed HLA alleles to be weaker binders of associated HIV AA variants relative to alternative variants on the same position. CONCLUSIONS: Our results show the importance of immunotype specificity on viral antigenic determinants, and the identified genetic interplay puts emphasis that viral and human genetics should be studied in the context of each other

Engineering improved ethylene production: Leveraging systems Biology and adaptive laboratory evolution

Ethylene is a small hydrocarbon gas widely used in the chemical industry. Annual worldwide production currently exceeds 150 million tons, producing considerable amounts of CO2 contributing to climate change. The need for a sustainable alternative is therefore imperative. Ethylene is natively produced by several different microorganisms, including Pseudomonas syringae pv. phaseolicola via a process catalyzed by the ethylene forming enzyme (EFE), subsequent heterologous expression of EFE has led to ethylene production in non-native bacterial hosts including E. coli and cyanobacteria. However, solubility of EFE and substrate availability remain rate limiting steps in biological ethylene production. We employed a combination of genome scale metabolic modelling, continuous fermentation, and protein evolution to enable the accelerated development of a high efficiency ethylene producing E. coli strain, yielding a 49-fold increase in production, the most significant improvement reported to date. Furthermore, we have clearly demonstrated that this increased yield resulted from metabolic adaptations that were uniquely linked to the EFE enzyme (WT vs mutant). Our findings provide a novel solution to deregulate metabolic bottlenecks in key pathways, which can be readily applied to address other engineering challenges

Ocean Circulation over North Atlantic underwater features in the path of the Mediterranean Outflow Water: Ormonde and Formigas seamounts, and the Gazul mud volcano

Seamounts constitute an obstacle to the ocean circulation, modifying it. As a result, a variety of hydrodynamical processes and phenomena may take place over seamounts, among others, flow intensification, current deflection, upwelling, Taylor caps, and internal waves. These oceanographic effects may turn seamounts into very productive ecosystems with high species diversity, and in some cases, are densely populated by benthic organisms, such corals, gorgonians, and sponges. In this study, we describe the oceanographic conditions over seamounts and other underwater features in the path of the Mediterranean Outflow Water (MOW), where populations of benthic suspensions feeders have been observed. Using CTD, LADPC and biochemical measurements carried out in the Ormonde and Formigas seamounts and the Gazul mud volcano (Northeast Atlantic), we show that Taylor caps were not observed in any of the sampled features. However, we point out that the relatively high values of the Brunt–Väisälä frequency in the MOW halocline, in conjunction with the slope of the seamount flanks, set up conditions for the breakout of internal waves and amplification of the currents. This may enhance the vertical mixing, resuspending the organic material deposited on the seafloor and, therefore, increasing the food availability for the communities dominated by benthic suspension feeders. Thus, we hypothesize that internal waves could be improving the conditions for benthic suspension feeders to grow on the slope of seamounts.En prens