Cyclic AMP and Calcium in Relaxation in Intestinal Smooth Muscle

WE have studied the role of cyclic AMP in relaxation of smooth muscle and elucidated the mechanism of its action.     

Accuracy of genomic selection to predict maize single-crosses obtained through different mating designs

Key message

Testcross is the worst mating design to use as a training set to predict maize single-crosses that would be obtained through full diallel or North Carolina design II.

Abstract

Even though many papers have been published about genomic prediction (GP) in maize, the best mating design to build the training population has not been defined yet. Such design must maximize the accuracy given constraints on costs and on the logistics of the crosses to be made. Hence, the aims of this work were: (1) empirically evaluate the effect of the mating designs, used as training set, on genomic selection to predict maize single-crosses obtained through full diallel and North Carolina design II, (2) and identify the possibility of reducing the number of crosses and parents to compose these training sets. Our results suggest that testcross is the worst mating design to use as a training set to predict maize single-crosses that would be obtained through full diallel or North Carolina design II. Moreover, North Carolina design II is the best training set to predict hybrids taken from full diallel. However, hybrids from full diallel and North Carolina design II can be well predicted using optimized training sets, which also allow reducing the total number of crosses to be made. Nevertheless, the number of parents and the crosses per parent in the training sets should be maximized.

     

Severity of drug resistance and co-existence of <Emphasis Type="Italic">Enterococcus faecalis</Emphasis> in diabetic foot ulcer infections

The genes encoding aminoglycoside resistance in Enterococcus faecalis may promote collateral aminoglycoside resistance in polymicrobial wounds. We studied a total of 100 diabetic foot ulcer samples for infection and found 60 samples to be polymicrobial, 5 to be monomicrobial, and 35 samples to be culture negative. A total of 65 E. faecalis isolates were screened for six genes coding for aminoglycoside resistance, antibiotic resistance patterns, and biofilm production. Infectious Diseases Society of America/International Working Group on the Diabetic Foot system was used to classify the wound ulcers. Majority of the subjects with culture-positive wound were recommended conservative management, while 14 subjects underwent amputation. Enterococcal isolates showed higher resistance for erythromycin, tetracycline, and ciprofloxacin. Isolates from grade 3 ulcer showed higher frequency of aac(6′)-Ie-aph(2″)-Ia, while all the isolates were negative for aph(2″)-Ib, aph(2″)-Ic, and aph(2″)-Id. The isolates from grade 3 ulcers showed higher resistance to aminoglycosides as well as teicoplanin and chloramphenicol. All the 39 biofilm producers were obtained from polymicrobial wound and showed higher resistance when compared to biofilm non-producers. Higher frequency of isolates carrying aac(6′)-Ie-aph(2″)-Ia in polymicrobial community showing resistance to key antibiotics suggests widespread distribution of aminoglycoside-resistant E. faecalis and their role in worsening diabetic foot ulcers.     

Effect of hyperbaric air on endotoxin from <Emphasis Type="Italic">Bacteroides fragilis</Emphasis> strains

The aim of the project was to determine any effect of hyperbaric air on Bacteroides fragilis strains cultivated under hyperbaric conditions. Previously, it was hypothesized that there was a correlation between the presence of Bacteroides bacteria in patients preferring a meaty diet and cancer of the small intestine, and particularly of the large intestine and rectum. With respect to the fact that Bacteroides fragilis (BAFR) group are important producers of endotoxins, measurement and statistical evaluation of endotoxin production by individual strains of isolated Bacteroides species were used to compare bacteria isolated from various clinical samples from patients with colon and rectum cancer in comparison with strains isolated from other non-cancer diagnoses. Endotoxin production was proven by quantitative detection using the limulus amebocyte lysate (LAL) test in EU/mL. Production of endotoxins in these bacteria cultured under hyperbaric air conditions was higher than those strains cultured under normobaric anaerobic conditions. But these differences in endotoxin production were not statistically significant (t test with log-transformed data, p value = 0.0910). Based on a two-tier t test for lognormal data, it is possible to cautiously conclude that a statistically significant difference was found between endotoxin production by Bacteroides fragilis strains isolated from non-carcinoma diagnoses (strains (1–6) and strains isolated from colorectal carcinoma diagnoses (strains 7–8; Wilcoxon non-parametric test p = 0.0132; t test = 0.1110; t test with log-transformed data, p value = 0.0294).     

Twenty-seven modes of reproduction in the obligate lichen symbiosis

Fungi exhibit some of the greatest reproductive diversity across Eukaryotes. In addition to sexual and asexual reproduction, fungi engage in parasexual (mitotic recombinatorial) processes to acquire new genetic variation. Reproduction has been studied extensively in numerous free-living fungi but comparatively less knowledge exists for lichenized fungi, which are assumed to reproduce only through sexual spores, asexual conidia, and specialized asexual lichen propagules. We present a new conceptual framework describing reproductive modes in lichens that includes sexual and asexual processes as well as accommodating the possibility of parasexual reproduction. To support the plausibility of some of these modes of reproduction, we reviewed data spanning more than 200 years of anatomical investigation. We recovered evidence supporting the possibility of 22 of 27 possible modes of reproduction and found no counter-evidence to suggest the remaining five do not occur in nature. This conceptual framework allows for a greater plurality of reproductive processes than previously acknowledged in lichens, exceeding that of their non-lichenized relatives.     

Enhanced Production of β-D-glycosidase and α-L-arabinofuranosidase in Recombinant <Emphasis Type="Italic">Escherichia coli</Emphasis> in Fed-batch Culture for the Biotransformation of Ginseng Leaf Extract to Ginsenoside Compound K

Ginsenoside compound K is an essential ingredient in nutritional supplements, cosmetics, and traditional medicines. However, cultivation for the production of enzymes involved in ginsenoside biotransformation has not been attempted in a fermenter. The host strain Escherichia coli ER2566 and the constitutive pHCE vector were selected for the efficient production of β-D-glycosidase, and expression medium composition to produce Sulfolobus solfataricus β-glycosidase expressed in E. coli was optimized in flask and batch cultures. The total activity of β-Dglycosidase in fed-batch culture using a fermenter increased 14-fold before optimization. S. solfataricus β-D-glycosidase and Thermotoga petrophila α-L-arabinofuranosidase were produced in a fed-batch culture. These two enzymes completely converted protopanaxadiol-type ginsenosides in ginseng leaf extract obtained from discarded ginseng leaves as a renewable substrate to compound K. The effective bioprocess for compound K production developed here will contribute to the industrial biological production of compound K.     

Sequence and Structural Features of Subsite Residues in GH10 and GH11 Xylanases

Xylanases are the enzymes that breakdown complex plant cell wall polysaccharide xylan into xylose by hydrolysing the β-(1→4) glycosidic linkage between xylosides. They mainly belong to the families GH10 and GH11 of the glycoside hydrolase claβs of enzymes. GH10 xylanases have (α/β)₈-barrel type of fold whereas GH11 xylanases have β-jelly roll type of fold. Both enzymes have several substrate binding subsites. This study analysed in detail the sequence and structural conservation of subsites residues by examining their 3D structures crystallized with homoxylan or its non-hydrolysable form as substrate. A total of 19 structures from GH10 and 6 structures from GH11 were analysed. It was found that in GH10 the subsites -3 to -1 consisted of conserved residues, whereas in GH11 subsites -1, -3 and +1 were found to be conserved. The substrate and subsite interaction analysed based on the presence of h-bonds and CH-π interactions showed that Face-to-Face or Edge-to-Face CH-π interactions are formed in the subsites of GH10, whereas such specific CH-π interactions were no at all observed in case of GH11 xylanases. The spatial conservation of subsite residues was also analysed using a distance matrix based approach. It was found that in GH10 xylanases conserved residues have conserved spatial position of those residues as opposed to GH11 enzymes where in subsites -2 and +2 conserved residues showed non-conservation in their spatial positions. The results presented in this study can be used in discovering new xylanases and in the engineering highly efficient xylanases.     

Isolation and characterization of <Emphasis Type="Italic">Aspergillus flavus</Emphasis> strains in China

Important staple foods (peanuts, maize and rice) are susceptible to contamination by aflatoxin (AF)-producing fungi such as Aspergillus flavus. The objective of this study was to explore non-aflatoxin-producing (atoxigenic) A. flavus strains as biocontrol agents for the control of AFs. In the current study, a total of 724 A. flavus strains were isolated from different regions of China. Polyphasic approaches were utilized for species identification. Non-aflatoxin and non-cyclopiazonic acid (CPA)-producing strains were further screened for aflatoxin B₁ (AFB₁) biosynthesis pathway gene clusters using a PCR assay. Strains lacking an amplicon for the regulatory gene aflR were then analyzed for the presence of the other 28 biosynthetic genes. Only 229 (32%) of the A. flavus strains were found to be atoxigenic. Smaller (S) sclerotial phenotypes were dominant (51%) compared to large (L, 34%) and non-sclerotial (NS, 15%) phenotypes. Among the atoxigenic strains, 24 strains were PCR-negative for the fas-1 and aflJ genes. Sixteen (67%) atoxigenic A. flavus strains were PCRnegative for 10 or more of the biosynthetic genes. Altogether, 18 new PCR product patterns were observed, indicating great diversity in the AFB₁ biosynthesis pathway. The current study demonstrates that many atoxigenic A. flavus strains can be isolated from different regions of China. In the future laboratory as well as field based studies are recommended to test these atoxigenic strains as biocontrol agents for aflatoxin contamination.     

Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant

The increased antibiotic resistance among microorganisms has resulted into growing interest for investigating the wastewater treatment plants (WWTPs) as they are reported to be the major source in the dissemination of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment. In this study, we investigated the prevalence and persistence of ARGs and HMRGs as well as bacterial diversity and mobile genetic elements (MGEs) in influent and effluent at the WWTP in Gwangju, South Korea, using high-throughput sequencing based metagenomic approach. A good number of broad-spectrum of resistance genes (both ARG and HMRG) were prevalent and likely persistent, although large portion of them were successfully removed at the wastewater treatment process. The relative abundance of ARGs and MGEs was higher in effluent as compared to that of influent. Our results suggest that the resistance genes with high abundance and bacteria harbouring ARGs and MGEs are likely to persist more through the treatment process. On analyzing the microbial community, the phylum Proteobacteria, especially potentially pathogenic species belonging to the genus Acinetobacter, dominated in WWTP. Overall, our study demonstrates that many ARGs and HMRGs may persist the treatment processes in WWTPs and their association to MGEs may contribute to the dissemination of resistance genes among microorganisms in the environment.     

Redox metabolic and molecular parameters for screening drought tolerant indigenous aromatic rice cultivars

The present work makes an effort to assess and standardize some redox metabolic and molecular parameters for screening drought tolerant indigenous aromatic rice cultivars of West Bengal, India. PEG-induced dehydration stress during early germination caused disruption of redox-homeostasis and oxidative damage in four IARVs (Jamainadu, Tulaipanji, Sitabhog and Badshabhog) by enhancing the accumulation of pro-oxidants [assessed in terms of oxidation of 2′,7′-dichlorofluorescindiacetate (DCFDA), accumulation of \({\text{O}}_{2}^{ \cdot - }\) and H₂O₂ and in situ staining of reactive oxygen species (ROS) in germinating tissue], significant reduction of antioxidative defence (total antioxidant and radical scavenging capacity, total thiol content and activities of antioxidative defence enzymes) and aggravating protein oxidation and lipid peroxidation (assessed in terms of free carbonyl content and accumulation of thiobarbituric acid reactive substances). When compared between the indigenous aromatic rice cultivars, a clear trend in differential redox regulatory properties in which ROS-antioxidant interaction acts at metabolic interface for redox homeostasis was observed in the order Badshabhog > Tulaipanji > Sitabhog > Jamainadu. Moreover, when the efficacy of ascorbate–glutathione cycle for scavenging H₂O₂ generated during dehydration stress was assessed and compared between the landraces exposed to PEG-induced dehydration stress in germinating tissue, it also exhibited almost the same trend with the landrace Tulaipanji and Badsabhog exhibiting maximum and Jamainadu the minimum efficiencies of the redox cycle. The indigenous aromatic rice cultivars Tulaipanji and Badsabhog resist dehydration stress better than the other two landraces due to its early preparedness to combat oxidative stress by up-regulating expression of genes of some enzymes of ascorbate–glutathione cycle along with some other antioxidative enzymes. A model of redox homeostasis in which ROS-antioxidant (ascorbate–glutathione system) acts at metabolic interface for up-regulation of antioxidative gene expression necessary for differential drought stress tolerance among the indigenous aromatic rice varieties is suggested.