Utility of large consanguineous family-based model for investigating the genetics of type 2 diabetes mellitus

Objectives

This study examined the utility of a family-based model for replicating the results of genome-wide association studies (GWAS) of type 2 diabetes (T2D).

Methods and results

In a total of 232 members of a large consanguineous Omani Arab pedigree (age: 16–80 years), there were 27 diabetics and 50 prediabetics (17 with impaired fasting glucose and 33 with impaired glucose tolerance). All 232 individuals underwent anthropometric and biochemical investigations and genotyped for 14 known common gene variants of modest effect on T2D risk. Power analysis at a LOD score of 3, gave 80% power to locate a single specific locus that accounts for 52% of the total phenotypic variation. Measured genotype analysis (MGA) was used to determine heritability of various quantitative traits (QTs) which ranged 25–56%. Using MGA, some common gene variants were found to have little (< 5%) but significant impact on the heritability of T2D related QTs [KCNJ11 (rs5219), p = 0.004]; [IGF2BP2 (rs4402960), p = 0.02]; [SLC30A8 (rs13266634), p = 0.05]; [CAPN10 (rs2975760), p = 0.031]; [FTO (rs8050136), p = 0.023]; [FTO (rs9939609), p = 0.018] and [SLC30A8 (rs13266634), p = 0.05]. Sib-TDT analysis showed that some gene variants were significantly associated with T2D risk but didn't reach the level of significance after Bonferroni correction [KCNJ11 (rs5219), p = 0.047] and [CAPN10 (rs41266971), p = 0.035].

Conclusion

We have demonstrated that, in principle, a family-based model with minor limitations could be used to replicate some of the results of large GWAS case–control studies. This model could successfully be applied for the future discovery, by deep sequencing, of rare gene variants.     

Antibacterial and cytotoxic activity of Brazilian plant extracts--Clusiaceae

Twelve extracts obtained from nine plants belonging to six different genera of Clusiaceae were analyzed against Gram-negative (Escherichia coli and Pseudomonas aeruginosa) and Gram-positive (Staphylococcus aureus and Enterococcus faecalis) bacteria using the microdilution broth assay. Tovomita aff. longifolia, T. brasiliensis, Clusia columnaris, Garcinia madruno, Haploclathra paniculata, and Caraipa grandifolia extracts showed significant results against the bacteria. The organic extract obtained from the leaves of T. aff. longifolia showed minimal inhibitory concentration (MIC) = 70 microg/ml and minimal bactericidal concentration (MBC) = 90 microg/ml against E. faecalis and the organic extract made with the stem of C. columnaris showed MIC = 180 microg/ml and MBC = 270 microg/ml against P. aeruginosa. None of the antibacterial extracts showed lethal activity against brine shrimp nauplii. On the other hand, both aqueous and organic extracts obtained from the aerial organs of Vismia guianensis that were cytotoxic to brine shrimp nauplii did not show a significant antibacterial activity in the assay.     

Tyrosine 537 within the Na+,K+-ATPase alpha-subunit is essential for AP-2 binding and clathrin-dependent endocytosis

In renal epithelial cells endocytosis of Na(+),K(+)-ATPase molecules is initiated by phosphorylation of its alpha(1)-subunit, leading to activation of phosphoinositide 3-kinase and adaptor protein-2 (AP-2)/clathrin recruitment. The present study was performed to establish the identity of the AP-2 recognition domain(s) within the Na(+),K(+)-ATPase alpha(1)-subunit. We identified a conserved sequence (Y(537)LEL) within the alpha(1)-subunit that represents an AP-2 binding site. Binding of AP-2 to the Na(+),K(+)-ATPase alpha(1)-subunit in response to dopamine (DA) was increased in OK cells stably expressing the wild type rodent alpha-subunit (OK-WT), but not in cells expressing the Y537A mutant (OK-Y537A). DA treatment was associated with increased alpha(1)-subunit abundance in clathrin vesicles from OK-WT but not from OK-Y537A cells. In addition, this mutation also impaired the ability of DA to inhibit Na(+),K(+)-ATPase activity. Because phorbol esters increase Na(+),K(+)-ATPase activity in OK cells, and this effect was not affected by the Y537A mutation, the present results suggest that the identified motif is specifically required for DA-induced AP-2 binding and Na(+),K(+)-ATPase endocytosis.     

Patterns of CRISPR/Cas9 activity in plants,animals and microbes

The CRISPR/Cas9 system and related RNA‐guided endonucleases can introduce double‐strand breaks (DSBs) at specific sites in the genome, allowing the generation of targeted mutations in one or more genes as well as more complex genomic rearrangements. Modifications of the canonical CRISPR/Cas9 system from Streptococcus pyogenes and the introduction of related systems from other bacteria have increased the diversity of genomic sites that can be targeted, providing greater control over the resolution of DSBs, the targeting efficiency (frequency of on‐target mutations), the targeting accuracy (likelihood of off‐target mutations) and the type of mutations that are induced. Although much is now known about the principles of CRISPR/Cas9 genome editing, the likelihood of different outcomes is species‐dependent and there have been few comparative studies looking at the basis of such diversity. Here we critically analyse the activity of CRISPR/Cas9 and related systems in different plant species and compare the outcomes in animals and microbes to draw broad conclusions about the design principles required for effective genome editing in different organisms. These principles will be important for the commercial development of crops, farm animals, animal disease models and novel microbial strains using CRISPR/Cas9 and other genome‐editing tools.     

Efficiency of different application methods of biocontrol agents and biocides in control of Fusarium root rot on some citrus rootstocks

Abstract

The efficiency of two biocontrol agents (Trichoderma harzianum NB and Bacillus subtilis NB) and two commercial biocides (Plant Guard and Rhizo-N) in controlling Fusarium root rot disease on some citrus rootstocks was evaluated under artificially infested soil in green house.

Fusrium root rot on citrus rootstocks seedlings i.e. sour orange (SO), volkamer lime (VL), rangpur lime (RP) and cleopatra mandarin (CL) was successfully controlled by dipping the root system of such seedlings in water suspensions of each biological treatment i.e. Trichoderma harzianum (spore suspension 5×10⁶ spore/ml), Bacillus subtilis (cell suspension 8×10⁷ cell/ml), Plant Guard (3 g/l) and Rhizo-N (4 g/l), then transplanted into artificially infested soil with Fusarium solani and drenched with enough water suspension of such biological treatments. Plant Guard (3 g/l) and Rhizo-N (4 g/l) were highly effective treatments in decreasing infection and severity of the disease, Fusarium density in rhizosphere soil and colonization of Fusarium solani in the roots of all tested seedlings.

Meanwhile, root dipping or soil drenching with the same treatments individually gave the least effect in reducing root rot incidenceon all tested rootstocks compared with application of the two methods together.

It should be noted that using biocontrol agents and commercial biocides could be successfully used in controlling root rot pathogens on citrus in commercial greenhouses or under field conditions before transplanting in new reclaimed lands in the desert.     

Breeding ecology of the Little Bittern Ixobrychus minutus in northeast Algeria

Capsule This is the first study of the reproductive ecology of the Little Bittern Ixobrychus minutus in North Africa. During the study period, clutch size exhibited a sharp drop concurrent with a steady human encroachment and 30% habitat loss.

Aim To investigate the status, nest-site selection, breeding parameters, chick development and chick diet of Little Bittern in Algeria, under deteriorating habitat conditions

Methods Data were collected during surveys of all major Algerian wetlands (2002–08) and monitoring of breeding at Boussedra, a freshwater marsh in northeast Algeria, during the years 2005 and 2008.

Results Egg-laying spanned the period of 10 May to 30 June with one recorded case of a double brood in early July (n = 30). The mean clutch size in 2005 was 6.2?±?0.4 sd eggs per nest (n = 6 clutches), which was significantly higher than that of 2008, which amounted to 4.3?±?0.5 sd eggs per nest (n = 6 clutches), and this decline was associated with increased disturbance and loss of habitat. Overall, clutches suffered from a low rate of predation (17.6%) and displayed a high hatching rate (85.7%).

Conclusion Breeding parameters of the Little Bittern in North Africa are similar to elsewhere in Europe.     

Prevalence of antibiotic resistant mastitis pathogens in dairy cows in Egypt and potential biological control agents produced from plant endophytic actinobacteria

Dairy production is threatened by antibiotic resistant pathogens worldwide, and alternative solutions to treat mastitis are not available. The prevalence of antibiotic resistant strains is not well known in less developed countries. The prevalence of pathogenic bacteria and their resistance to 21 commercial antibiotics were studied in milk samples taken from 122 dairy cows suffering from the symptoms of mastitis in Egypt. The bacterial species were identified with molecular methods, and antibiotic resistance was studied with disc diffusion method. The prevalence of Streptococcus aureus, Escherichia coli and Pseudomonas aeruginosa were 30%, 17% and 3.5%, respectively. Most (90%) of the S. aureus strains showed resistance to penicillin whereas only 10% of the strains were resistant to oxacillin. Nearly half (40%) of E. coli strains showed resistance to streptomycin. Six P. aeruginosa strains showed resistance to several antibiotics, including ceftriaxone, enrofloxacin and levofloxacin. This points out that despite P. aeruginosa was not common, it should be followed up carefully. Potential biocontrol agents against antibiotic resistant mastitis bacteria were searched among 30 endophytic actinobacterial strains derived from wild medicinal plants. Three plants, namely Mentha longifolia, Malva parviflora and Pulicaria undulata were chosen for a more detailed study; their endophytic actinobacteria were used to prepare metabolic extracts. The crude metabolites of the actinobacteria were extracted with ethyl acetate. All metabolic extracts inhibited the growth of S. aureus, methicillin-resistant Staphylococcus aureus (MRSA), E. coli and P. aeruginosa in vitro. The 16S rRNA sequence analysis revealed that the most efficient actinobacterial strains were two Micromonospora sp. and one Actinobacteria bacterium. We conclude that the combination of the metabolites of several endophytic actinobacteria derived from several medicinal plants would be the most efficient against pathogens. Different metabolite cocktails should be studied further in order to develop novel biocontrol agents to treat antibiotic resistant mastitis bacteria in dairy cows.     

Effects of Agricultural Management Policies on the Exposure of Black-Winged Stilts (Himantopus himantopus) Chicks to Cholinesterase-Inhibiting Pesticides in Rice Fields

Levels of exposure to pesticides in rice fields can be significant depending on the environmental policies practiced. The aim of European Union integrated management policy is to reduce pesticide use and impact on environment. Rice fields provide an alternative breeding habitat for many waterbirds that are exposed to the pesticides used and therefore can be valuable indicators of their risk for wildlife. To evaluate integrated management success we examined exposure of Black-winged Stilts (Himantopus himantopus) to cholinesterase-inhibiting pesticides in rice fields under different types of management by measuring plasma cholinesterase activity. Cholinesterase activity was lower in birds sampled in (a) 2008 after a period of intense pesticide application, than in (b) 2005-2007 and 2011 in rice fields subject to integrated management in Doñana (SW Spain) and (c) in control natural wetlands in Spain and Morocco. During 2009 and 2010, cholinesterase activity was lower in rice fields in Doñana than in rice fields in Larache and Sidi Allal Tazi (NW Morocco). Our results suggest that integrated management successfully reduced the exposure of Black-winged Stilts to pesticides in most of the years. Care should be taken to implement mosquito and pest crop controls on time and with environmentally friendly products in order to reduce its impact on wildlife.