Genome-wide scans identify known and novel regions associated with prolificacy and reproduction traits in a sub-Saharan African indigenous sheep (Ovis aries)

Maximizing the number of offspring born per female is a key functionality trait in commercial- and/or subsistence-oriented livestock enterprises. Although the number of offspring born is closely associated with female fertility and reproductive success, the genetic control of these traits remains poorly understood in sub-Saharan Africa livestock. Using selection signature analysis performed on Ovine HD BeadChip data from the prolific Bonga sheep in Ethiopia, 41 candidate regions under selection were identified. The analysis revealed one strong selection signature on a candidate region on chromosome X spanning BMP15, suggesting this to be the primary candidate prolificacy gene in the breed. The analysis also identified several candidate regions spanning genes not reported before in prolific sheep but underlying fertility and reproduction in other species. The genes associated with female reproduction traits included SPOCK1 (age at first oestrus), GPR173 (mediator of ovarian cyclicity), HB-EGF (signalling early pregnancy success) and SMARCAL1 and HMGN3a (regulate gene expression during embryogenesis). The genes involved in male reproduction were FOXJ1 (sperm function and successful fertilization) and NME5 (spermatogenesis). We also observed genes such as PKD2L2, MAGED1 and KDM3B, which have been associated with diverse fertility traits in both sexes of other species. The results confirm the complexity of the genetic mechanisms underlying reproduction while suggesting that prolificacy in the Bonga sheep, and possibly African indigenous sheep is partly under the control of BMP15 while other genes that enhance male and female fertility are essential for reproductive fitness.

     

Comparative proteomic network signatures in seminal plasma of infertile men as a function of reactive oxygen species

Background

Reactive oxygen species (ROS) plays a major role in the pathology of male infertility. It is an independent biomarker of sperm function. Seminal plasma is a natural reservoir of antioxidants responsible for the nourishment, protection, capacitation, and motility of sperm within the female reproductive tract resulting in successful fertilization and implantation of the embryo. A comparative proteomic analysis of seminal plasma proteins from fertile men and infertile men with varying levels of ROS was carried out to identify signature proteins involved in ROS-mediated reproductive dysfunction.

Methods

A total of 42 infertile men presenting with infertility and 17 proven fertile donors were enrolled in the study. ROS levels were measured in the seminal ejaculates by chemiluminescence assay. Infertile men were subdivided into Low ROS (0–<93 RLU/s/10⁶ sperm; n = 11), Medium ROS (>93–500 RLU/s/10⁶ sperm; n = 17) and High ROS (>500 RLU/s/10⁶ sperm; n = 14) groups and compared with fertile men (4–50 RLU/s/10⁶ sperm). 4 subjects from fertile group and 4 each from the Low, Medium and High ROS were pooled. 1D gel electrophoresis followed by in-gel digestion and LC/MS–MS in a LTQ-Orbitrap Elite hybrid mass spectrometer system was used for proteome analysis. Identification of differentially expressed proteins (DEPs), their cellular localization and involvement in different pathways were examined utilizing bioinformatics tools.

Results

The results indicate that proteins involved in biomolecule metabolism, protein folding and protein degradation are differentially modulated in all three infertile patient groups in comparison to fertile controls. Membrane metallo-endopeptidase (MME) was uniformly overexpressed (>2 fold) in all infertile groups. Pathway involving 35 focus proteins in post-translational modification of proteins, protein folding (heat shock proteins, molecular chaperones) and developmental disorder was overexpressed in the High ROS group compared with fertile control group. MME was one of the key proteins in the pathway. FAM3D was uniquely expressed in fertile group.

Conclusion

We have for the first time demonstrated the presence of 35 DEPs of a single pathway that may lead to impairment of sperm function in men with Low, Medium or High ROS levels by altering protein turn over. MME and FAM3D along with ROS levels in the seminal plasma may serve as good markers for diagnosis of male infertility.

Electronic supplementary material

The online version of this article (doi:10.1186/s12014-015-9094-5) contains supplementary material, which is available to authorized users.     

Functional interaction of CD154 protein with α5β1 integrin is totally independent from its binding to αIIbβ3 integrin and CD40 molecules

In addition to its classical CD40 receptor, CD154 also binds to αIIbβ3, α5β1, and αMβ2 integrins. Binding of CD154 to these receptors seems to play a key role in the pathogenic processes of chronic inflammation. This investigation was aimed at analyzing the functional interaction of CD154 with CD40, αIIbβ3, and α5β1 receptors. We found that the binding affinity of CD154 for αIIbβ3 is ～4-fold higher than for α5β1. We also describe the generation of sCD154 mutants that lost their ability to bind CD40 or αIIbβ3 and show that CD154 residues involved in its binding to CD40 or αIIbβ3 are distinct from those implicated in its interaction to α5β1, suggesting that sCD154 may bind simultaneously to different receptors. Indeed, sCD154 can bind simultaneously to CD40 and α5β1 and biologically activate human monocytic U937 cells expressing both receptors. The simultaneous engagement of CD40 and α5β1 activates the mitogen-activated protein kinases, p38, and extracellular signal-related kinases 1/2 and synergizes in the release of inflammatory mediators MMP-2 and -9, suggesting a cross-talk between these receptors.     

Binding of 2CA1P (nocturnal inhibitor) to the active site of RubisCO using Genetic Algorithm (GA)

Ribulose-1, 5- Bisphosphate carboxylase/ oxygenase (RubisCO) catalyzes the first step in net photosynthetic assimilation and photorespiratory carbon oxidation. The activity of this enzyme is modulated in response to changes in light intensity as suggested in a number of early reports. Several studies found that the natural inhibitor 2CA1P is involved in the inhibition of the enzyme under reduced light intensity in rice (Oryza sativa). Due to the lack of studies and information on the interaction between this inhibitor and the active site of the enzyme, we attempted to predict the interaction between the amino acids in the active site and the inhibitor using both Hyperchem7.5 and GOLD software. After the docking; three possibilities having the highest fitness score were found (65.71, 64.72, 62.04), in these possibilities the inhibitor was bound to the enzyme, the phosphate and carboxylate groups in the same positions with a clear difference in the position of OH. In order to confirm the accuracy of the genetic algorithm, the artificial inhibitor 2CABP was docked back in the active site of the enzyme using the same parameters used in the case of the 2CA1P and the algorithm''s predictions were compared with the experimentally observed binding mode. The results showed that the difference in the active sites before and after the docking was in the range of 0.93 Å which indicated that the results were very accurate. Depending on this result it was concluded that the results obtained in the case of the 2CA1P were close to the experimental results.     

Assessing the environmental profile of orange production in Brazil

Background, aim, and scope

Brazil is the world’s largest orange producing country, with a total planted area of more than 820,000 hectares. The bulk of the oranges produced in Brazil (70%) is processed into frozen concentrated orange juice (FCOJ) by large processing companies. Exports represent around 97% of the total FCOJ produced, making Brazil the largest world producer and exporter of FCOJ. The Brazilian citrus sector accounts for half of the world’s supply of orange juice and for 80% of the juice traded on the international market. The goal of this study is to characterize the Brazilian orange producers in terms of farm size, cultivated varieties, watering system and tillage practices. In addition, the study presents some aspects of the LCI of oranges grown specifically for the production of FCOJ in the two major orange-growing areas in Brazil (the Northern and Southern regions of the State of São Paulo) during reference crop year 2002/03 in order to generate detailed production inventory data and identify the potential environmental impacts of tillage, both of which are key to enable the formulation of sustainability parameters for the production of FCOJ in Brazil.

Methods

This study was performed in compliance with the guidelines and requirements of the ISO 14040 standard series. All information and data considered and evaluated in this study (the use of water, energy, fertilizers, pesticides and soil correctors) were gathered through in-depth questionnaires either filled in directly by the farm manager or completed by the farm manager and sent in by mail. The data cover a total of 367,200 metric tons of oranges produced by 4 million plants in commercial production from a total evaluated area that accounts for 19.5% of the overall production of oranges in the State of São Paulo. The two major orange-producing areas in Brazil located respectively in the Northern and Southern regions of the State of São Paulo were evaluated. Only the inputs and outputs associated with tillage practices and technology were considered in this paper. The environmental aspects of the production of fertilizers and pesticides were not included within the boundaries. The functional unit selected for this study was 1,000 kg of oranges for FCOJ. Farm-specific data have been combined with agricultural production data to construct an orange cultivation model.

Results

The orange varieties for the production of FCOJ evaluated in this study were Pêra, Valência and Natal. The farms investigated had a cultivated area varying from 22 to 7,000 ha, with a plant density ranging from 170 to 500 plants/ha and an average yield of 30,500 kg/ha for mature trees. Depending on the region, the production of 1,000 kg of oranges requires approx. 120 to 4,400 MJ of energy; 0.3 to 36 kg of diesel; 1,100 to 54,500 kg of water for irrigation; 0.3 to 65 kg of fertilizers (NPK); 0.1 to 13.5 kg of pesticides; 8 to 650 kg of soil correctors. The distribution of some inputs across the farms located in the two main Brazilian orange-producing regions is presented, in addition to the total weighted average.

Discussion

In addition to the variations among the regions evaluated, it was generally observed that there were very considerable differences in order of magnitude between the data collected from farms located in the same region. Although the inputs are directly related to the specific characteristics of each farm and the climatic and topographic conditions of its location, this study has identified some farms that are in a good position to reduce the amounts of some inputs and enhance their environmental and economical performance.

Conclusions

Taking into account the aspects evaluated in this study, only 21% of the orange growers showed good performance, i.e., consumption of pesticides, fertilizers and soil correction compounds equal to or lower than the weighted averages, except for “land use”, which was above the average for the majority of these farms. This study provided important results that allow for a better understanding of the agricultural practices involved and the potential environmental impacts of this product.

Recommendation and perspective

The authors would like to suggest that the five best-performing farms average values be set as the maximum allowable level and point of departure for the discussion on the good environmental performance of Brazilian FCOJ. Besides the total inputs, the role of good agricultural practices to achieve good yields and, at the same time, improve the sustainability of orange growing should also be taken into consideration. Future updates of this study will show the evolution of natural resource management as a result of improved land use, new agricultural practices, reduced use of fertilizers and agrochemicals.     

Cancer de la prostate et masses abdominopelviennes fixant le 99mTc-HDP. Apport de la tomographie d’émission monophotonique couplée à la tomodensitométrie (TEMP–TDM)

We report the case of a 63-year-old man, investigated for staging of a prostatic cancer, diagnosed by biopsy, following a rise in the prostatic specific antigen (PSA) on a systematic assessment. The interrogation before examination revealed signs of beginning right crural neuropathy. The hydroxymethylene diphosphonate technetium 99m-labeled (^99mTc-HDP) whole-body bone scintigraphy highlighted two extraosseous uptake images, the first of moderated intensity in the right iliac area, the second milder, in the abdominal median area. Osseous metastases were not visualized. The single photon emission computerized tomography guided by computerized tomography (SPECT/CT) identified the median abdominal mass which corresponded to a bulky aneurysm of the under renal abdominal aorta. The right iliac mass could be accurately analyzed and differentiated from the various organs of the abdominopelvic cavity. Its lymphatic origin was hypothetised, but the diagnosis of lymphatic metastasis of the prostatic cancer was obtained by the pathologic examination of CT scan-guided biopsy.     

Impact of hypoxia on the growth and alkaloid accumulation in <Emphasis Type="Italic">Catharanthus roseus</Emphasis> cell suspension

The Madagascar periwinkle (Catharanthus roseus) produces numerous indole alkaloids, several of which have an important pharmaceutical uses such as ajmalicine, vinblastine and vincristine. The relationship between hypoxia and ajmalicine production in a cell suspension culture of C. roseus were investigated during the cycle of cell culture, in correlation with the effects on growth. The results show that the lack of oxygenation in C20D cells provokes a very strong inhibition in accumulation of the alkaloids and of other possible substances. Moreover, the addition of loganin, a metabolic intermediate of the biosynthetic pathway, in the culture medium of cells subjected to hypoxia restored the alkaloid production. Also, the results showed that the addition of benzyladenine (BA) to the culture medium increased the ajmalicine production and that the inhibitory effect of hypoxia was almost absent in these conditions. Therefore, it could be suggested that BA can without doubt decrease the effects of the hypoxia and increase the ajmalicine production in periwinkle cell suspensions.     

Radial basis function neural networks for modeling growth rates of the basidiomycetes Physisporinus vitreus and Neolentinus lepideus

A radial basis function (RBF) neural network was developed and compared against a quadratic response surface (RS) model for predicting the specific growth rates of the biotechnologically important basidiomycetous fungi, Physisporinus vitreus and Neolentinus lepideus, under three environmental conditions: temperature (10–30 °C), water activity (0.950–9.998), and pH (4–6). Both the RBF network and polynomial RS model were mathematically evaluated against experimental data using graphical plots and several statistical indices. The evaluation showed that both models gave reasonably good predictions, but the performance of the RBF neural network was superior to that of the classical statistical method for all three data sets used (training, testing, full). Sensitivity analysis revealed that of the three experimental factors the most influential on the growth rate of P. vitreus was water activity, followed by temperature and pH to a lesser extent. In contrast, temperature in particular and then water activity were the key determinants of the development of N. lepideus. RBF neural networks could be a powerful technique for modeling fungal growth behavior under certain parameters and an alternative to time-consuming, traditional microbiological techniques.     

Efficacy of some oils and chemical compounds on Insignorthezia insignis (Browne) (Hemiptera: Ortheziidae) infesting Lantana camara in Alexandria, Egypt

Field and laboratory experiments were conducted in March, 2008 in El-Nouzha garden, Alexandria governorate. Pre-and post treatment inspections of the insects were examined and recorded before and after (2,4,8, and 12 weeks). Spraying was applied to evaluate the efficiency of the tested compounds, [Mineral oils (KZ oil and Star oil); IGRs (Chlorfluazuron, lufenuron and pyriproxyfen); Neem oil; emamectin benzoate and thiamethoxam]. Percentages of reduction were calculated. The ensign scale insects Insignorthezia insignis (Browne) were collected from treated Lantana camara shrubs to investigate the effect of the tested chemicals on Aspartate transferase (AST), Alanine transferase (ALT) and Alkaline-phosphatase (ALPK) of the insect enzymes activities. From the obtained results, it could be concluded that the tested materials gave good results for controlling both adult and immature stages of the ensign scale insect Insignorthezia insignis (Browne) that infested Lantana camara shrubs, through affecting enzymes activities of the assigned insect pest.