Synteny and collinearity in plant genomes

Correlated gene arrangements among taxa provide a valuable framework for inference of shared ancestry of genes and for the utilization of findings from model organisms to study less-well-understood systems. In angiosperms, comparisons of gene arrangements are complicated by recurring polyploidy and extensive genome rearrangement. New genome sequences and improved analytical approaches are clarifying angiosperm evolution and revealing patterns of differential gene loss after genome duplication and differential gene retention associated with evolution of some morphological complexity. Because of variability in DNA substitution rates among taxa and genes, deviation from collinearity might be a more reliable phylogenetic character.     

Retrieval of irrigated and rainfed crop data using a general maximum entropy approach

This paper presents a method to separate harvested area and yield for irrigated crops from rainfed crops in a region, given gross harvested area and yield, and climatic, agronomic and economic data for crops. The method is based on the principle of general maximum entropy, which combines incomplete data, empirical knowledge and a priori information to derive desired information. The model is applied to three large basins with aggregated climatic and agricultural conditions, and to five counties in Texas and California. The modeled results and assessed values in these study areas are compared. While the dependability of model outputs relies on empirical knowledge and judicious parameter estimation, the model remains reliable even for the significant level of uncertainty produced by subjectively predetermined major parameters. The model can be applied to retriving historical data for irrigated and rainfed crops; it can also be used for irrigated and rainfed agriculture planning based on climatic and technological projections. Moreover, the model provides other useful information, including water allocation by crop, water use efficiency and the impact of other agricultural inputs.     

Arsenic chemistry in a groundwater aquifer from the Eastern Province of Saudi Arabia

Groundwater samples were collected from shallow aquifers underneath an industrial complex in the Eastern Province of Saudi Arabia. Arsenic (As) concentrations in the groundwater samples varied between 10^?8.6 and 10^?6.8 M (0.18 and 11.14 µg L^?1), with an average of 10^?7.5 M (2.19 μ L^?1). The analysis of variance for the analytical data showed that sampling locations had significantly affected As concentrations in the groundwater samples. Analytical and thermodynamic calculations showed that H₂ASO₄ ^? was the most predominant As species in acidic groundwater samples, and HAsO₄ ^2? was the most abundant species in alkaline groundwater samples. Concentrations of H₃AsO₄° and AsO₄ ^3? were too low to be important in this study. Reduced As chemical forms were also expected to be very low. All the groundwater samples were undersaturated with respect to the thermodynamic solubility isotherms of Ca₃(AsO₄)₂(c), Fe₃(AsO₄)₂(c), and Mn₃(AsO₄)₂(c) minerals. Lack of reliable thermodynamic data for these arsenates could be responsible for differences between the theoretical and measured concentrations of As in the shallow groundwater samples. The general trend in the distribution of HAsO₄ ^2? activities in the groundwater samples was parallel to that of the Ca₃(AsO₄)₂ solubility isotherm but different from those of Fe₃(AsO₄)₂(c), and Mn₃(AsO₄)₂(c). These data suggest that As concentrations in the groundwater samples were probably controlled by the precipitation and dissolution of Ca₃(AsO₄)₂ type mineral. A three step hypothesis for As interactions in groundwater/soil system is proposed that combines both solid phase formation and adsorption of As onto the solid colloidal surfaces. This hypothesis is expected to better represent As behavior in groundwater/soil environment.     

Assessment of some soil thermal conductivity models via variations in temperature and bulk density at low moisture range

Simulation of heat transfer in soil under steady and unsteady situations requires reliable estimate of soil thermal conductivity (λ) at varying environmental conditions. In the current work several soil thermal conductivity predicting models including I) de Vries, II) Campbell, III) combined de Vries and Campbell and IV) de Vries-Nobre were evaluated for the four soils of coarse sand, sandy loam, loam and clay loam textured at varying in temperature and bulk density at low moisture range. Thermal conductivities measured by the cylindrical probe method served as the reference for models assessment. Results showed that approximately same thermal conductivities obtained by the five methods at low moisture range (θ ≤ 0.05 m³/m³). Also the de Vries and de Vries-Campbell models produced accurate than Campbell and de vries-Nobre models. The accuracy of the two models increased with soil compaction but decreased with temperature rise. Campbell model showed more reliability at higher (311.16 and 321.16 K) temperatures; but its accuracy declined with soil compaction in current work. It seems that assuming needle shape for the soil particles is far away from the reality whereas assuming spherical shapes may be more realistic and produced more satisfactory prediction of thermal conductivity. The compaction would alter particle arrangement and may increase the contact area of particles; and then make them behave more or less spherical shape.it seems thermal conductivity in solid particles increase via increasing in temperature. Since a modified mineral shape factor, g_m, was developed as a combination between sphere and needle according to geometric mean particle diameter as well as bulk density and temperature as modifying factors. This factor increased the accuracy of de Vries-Nobre model up to 10.37%. Regarding nonlinear regression model, moisture content, bulk density, temperature and quartz content demonstrated significant effect on soil thermal conductivity in our investigation.     

Phenotypic diversity of durum wheat (<Emphasis Type="Italic">Triticum durum</Emphasis> Desf.) from Jordan

Durum wheat landrace genotypes are disappearing from the main wheat areas in Jordan, because of spreading of new uniform cultivars and the serious reduction in wheat cultivation. This study was conducted to evaluate genetic diversity in durum wheat landraces from Jordan and to identify desirable agronomic traits. Landraces were collected from two target areas: Ajloun and Karak. The collected material was grown under rainfed conditions using an augmented design with five blocks and four repeated check cultivars. Data were collected for 14 morphological and agronomic traits. Phenotypic diversity index (H′) was estimated, and the relationships among accessions were measured using cluster analysis and dendrogram similarity matrix. The results revealed the presence of a wide range of variability among landraces., which possess high levels of variability for biological yield, fertile tillers, number of seeds per spike, seed weight per spike and weight of 1000 seeds. These landraces must be considered as a reservoir of genes that plant breeders need in their wheat improvement programs and should be conserved both ex situ and in situ.     

Replacement of soybean meal with levels of inclusion of soya waste in the diet of growing goats

An experiment was conducted to investigate the effect of replacing soybean meal with soya waste at different levels on intake, digestibility and growth in goats. Eighteen male goat kids with initial body weight (BW) of 13.0 kg were distributed equally to three dietary groups. They were fed Napier grass (Pennisetum purpureum) and concentrate mixture, and each goat was assigned to an individual pen. Soybean meal in the concentrate mixture was replaced with soya waste at 0% (T1), 50% (T2) and 100% (T3) levels in respective dietary groups. These diets were isocaloric and isonitrogenous. Results showed that animals fed T3 diet exhibited higher Napier grass intake than those fed T1 or T2 diet. There was no influence on total intakes of dry matter (DM), organic matter (OM), crude protein (CP), metabolic BW, per cent BW and metabolisable energy by the dietary groups. However, there was an increasing trend on intake and digestibility of neutral detergent fibre (NDF) with increasing levels of soya waste in the diets. Animals fed T3 diet showed higher intake and digestibility of NDF than those fed T1 diet. There was no influence of the dietary groups on digestibilities of DM, OM and CP. Similarly, there was no effect of them on the final BW, total BW gain, daily BW gain, feed conversion ratio and feed cost. Soya waste can replace 100% soybean meal in diets for growing goats, because no change was observed in nutrient intake, digestibility and growth performance; inclusion of soya waste enhanced the intake and digestibility of NDF.

     

Use of egg custard augmented with cod liver oil and Moina micrura on production of freshwater prawn postlarvae

Use of egg custard augmented with cod liver oil (CLO) fed during the day, and of an overnight feed with Moina micrura, were evaluated in terms of its effects on production of freshwater prawn (Macrobrachium rosenbergii) postlarvae (PL). Four levels of CLO (0, 1,3 and 5%) were tested. Significantly higher mean (sd) productions, ranging from 11.27 (1.16) to 13.02 (1.70) PL l^–1, were obtained for larvae fed egg custard enriched with CLO compared with that of 7.83 (1.58) PLl^–1 for larvae fed egg custard without CLO. The development and survival of larval stages were also higher for the CLO diets. The -3 highly unsaturated fatty acid (HUFA) in egg custard increased with increasing CLO level (0–5%). The fatty acid composition of postlarvae reflected the composition of the diet.     

Influence of different dietary amino acid patterns on growth and body composition of juvenile Japanese flounder, Paralichthys olivaceus

A feeding trial using five semi-purified diets (50% crude protein) was conducted to investigate the effects of different dietary amino acid patterns on growth and body composition of juvenile Japanese flounder. The control diet contained casein and gelatin as intact protein sources and four other diets contained 30% casein–gelatin (2:1, w/w) and 20% crystalline amino acids (CAA). CAA were added to the diets to simulate the amino acid pattern found in red sea bream egg protein (REP), Japanese flounder larvae whole body protein (FLP), Japanese flounder juvenile whole body protein (FJP), and brown fish meal protein (BFP), respectively. The test diets were fed to triplicate groups of juveniles (2.75±0.05 g) twice a day for 40 days to evaluate weight gain, survival, feed conversion efficiency (FCE), protein efficiency ratio (PER), and apparent protein utilization (APU). The apparent retention of total dietary amino acids in the whole body and A/E ratios of the whole body were also evaluated. The highest weight gain was observed in fish fed the diet containing the dietary amino acid pattern of BFP followed by fish fed the control, FJP, FLP and the REP diets. Percent survival, FCE, PER and APU were also significantly (P<0.05) affected by the amino acid pattern in the diets, indicating the highest value in fish fed the BFP diet. Except for a few amino acids, the amino acid composition of the whole body did not show marked differences with different dietary amino acid pattern. Results suggest that BFP could be more suitable as a reference amino acid pattern in the diet of juvenile Japanese flounder compared to the amino acid pattern of FLP, FJP or REP.     

High prevalence of antibiotic resistance in pathogenic Escherichia coli from large- and small-scale poultry farms in Bangladesh

Antibiotic resistance in avian bacterial pathogens is a common problem in the Bangladesh poultry industry. The aim of the present study was to provide information on the present status of antibiotic resistance patterns in avian pathogenic Escherichia coli in Bangladesh. Of 279 dead or sick poultry of different ages, 101 pathogenic E coli strains isolated from broilers and layer hens with colibacillosis infections were screened to determine phenotypic expression of antimicrobial resistance against 13 antibiotics used in both veterinary and human medicine in Bangladesh. Of 101 pathogenic E. coli isolates, more than 55% were resistant to at least one or more of the tested compounds, and 36.6% of the isolates showed multiple-drug-resistant phenotypes. The most common resistances observed were against tetracycline (45.5%), trimethoprim-sulphamethoxazole (26.7%), nalidixic acid (25.7%), ampicillin (25.7%), and streptomycin (20.8%). Resistance to ciprofloxacin (12.9%), chlormaphenicol (8.9%), nitrofurantoin (2%), and gentamicin (2%) was also observed, and none of the isolates were resistant to tigecycline as well as extended spectrum beta-lactamase (ESBL) producers. One isolate was resistant to cefuroxime (1%), cefadroxil (1%), and mecillinam (1%) but was not an ESBL producer. Resistance rates, although significant in Bangladeshi isolates, were found to be lower than those reported for avian isolates from the Republic of Korea and clinical, avian, and environmental isolates from Bangladesh. The high level of antibiotic resistance in avian pathogens from Bangladesh is worrisome and indicates that widespread use of antibiotics as feed additives for growth promotion and disease prevention could have negative implications for human and animal health and the environment.     

Biomarkers for identifying the early phases of osteoarthritis secondary to medial patellar luxation in dogs

The levels of tartrate resistant acid phosphatase (TRAP), matrix metalloproteinase-2 (MMP-2), and tissue inhibitor of matrix metalloproteinase-2 (TIMP-2) in synovial fluid (SF) and serum in cases of canine osteoarthritis (OA) were measured. OA was induced by a surgically-created medial patellar luxation in the left stifle of 24 dogs. SF and blood samples were collected at 1.5- and 3-month intervals, respectively. Every 3 months, one dog was euthanatized to collect tissue samples from both stifles. TRAP levels in SF and serum were measured using a spectrophotometer, and TRAP-positive cells in joint tissues were identified by enzyme histochemistry. MMP-2 and TIMP-2 in SF and serum were detected by Western blotting and ELISA, respectively. TRAP in SF from the stifles and serum was significantly increased (p < 0.05) after 3 months. TIMP-2 in SF and serum was significantly decreased (p < 0.05), whereas MMP-2 in SF was significantly increased (p < 0.05) during the progression of OA. Histochemistry revealed an increased number of TRAP-positive cells in tissues from OA-affected joints. Assays measuring TRAP, MMP-2, and TIMP-2 in SF and serum, and methods that detect increased numbers of TRAP-positive cells in the joint tissues can play an important role in identifying the early phases of degenerative changes in canine joint components.