Nature of KaiB-KaiC binding in the cyanobacterial circadian oscillator

In the cyanobacteria Synechococcus elongatus and Thermosynechococcus elongatus, the KaiA, KaiB and KaiC proteins in the presence of ATP generate a post-translational oscillator (PTO) that can be reconstituted in vitro. KaiC is the result of a gene duplication and resembles a double doughnut with N-terminal CI and C-terminal CII hexameric rings. Six ATPs are bound between subunits in both the CI and CII ring. CI harbors ATPase activity, and CII catalyzes phosphorylation and dephosphorylation at T432 and S431 with a ca. 24-h period. KaiA stimulates KaiC phosphorylation, and KaiB promotes KaiC subunit exchange and sequesters KaiA on the KaiB-KaiC interface in the final stage of the clock cycle. Studies of the PTO protein-protein interactions are convergent in terms of KaiA binding to CII but have led to two opposing models of the KaiB-KaiC interaction. Electron microscopy (EM) and small angle X-ray scattering (SAXS), together with native PAGE using full-length proteins and separate CI and CII rings, are consistent with binding of KaiB to CII. Conversely, NMR together with gel filtration chromatography and denatured PAGE using monomeric CI and CII domains support KaiB binding to CI. To resolve the existing controversy, we studied complexes between KaiB and gold-labeled, full-length KaiC with negative stain EM. The EM data clearly demonstrate that KaiB contacts the CII ring. Together with the outcomes of previous analyses, our work establishes that only CII participates in interactions with KaiA and KaiB as well as with the His kinase SasA involved in the clock output pathway.     

Tracking 20 Years of Compound-to-Target Output from Literature and Patents

The statistics of drug development output and declining yield of approved medicines has been the subject of many recent reviews. However, assessing research productivity that feeds development is more difficult. Here we utilise an extensive database of structure-activity relationships extracted from papers and patents. We have used this database to analyse published compounds cumulatively linked to nearly 4000 protein target identifiers from multiple species over the last 20 years. The compound output increases up to 2005 followed by a decline that parallels a fall in pharmaceutical patenting. Counts of protein targets have plateaued but not fallen. We extended these results by exploring compounds and targets for one large pharmaceutical company. In addition, we examined collective time course data for six individual protease targets, including average molecular weight of the compounds. We also tracked the PubMed profile of these targets to detect signals related to changes in compound output. Our results show that research compound output had decreased 35% by 2012. The major causative factor is likely to be a contraction in the global research base due to mergers and acquisitions across the pharmaceutical industry. However, this does not rule out an increasing stringency of compound quality filtration and/or patenting cost control. The number of proteins mapped to compounds on a yearly basis shows less decline, indicating the cumulative published target capacity of global research is being sustained in the region of 300 proteins for large companies. The tracking of six individual targets shows uniquely detailed patterns not discernible from cumulative snapshots. These are interpretable in terms of events related to validation and de-risking of targets that produce detectable follow-on surges in patenting. Further analysis of the type we present here can provide unique insights into the process of drug discovery based on the data it actually generates.     

Effect of Dietary Selenium Supplementation on Growth and Reproduction of Silkworm Bombyx mori L.

Biological Trace Element Research - The effects of selenium (Se) on the growth and reproduction of the Lepidoptera insect, the silkworm, Bombyx mori L were investigated. Initially, the silkworms...     

Association of resistin (rs3745367) and urotensin II (rs228648 and rs2890565) gene polymorphisms with risk of type 2 diabetes mellitus in Indian population

Molecular Biology Reports - Insulin resistance may become the most powerful predictor of future development of type 2 diabetes mellitus (T2DM) and a therapeutic target for the treatment of the...     

Biological control of phytopathogenic bacteria Pantoea agglomerans and Erwinia chrysanthemi using 100 essential oils

Plants interact with a wide variety of pathogenic organisms by virtue of their sessile lifestyle. The Pantoea agglomerans and Erwinia chrysanthemi are major plant pathogen amongst them. They are known to cause significant losses in many crop plants. In the present study, bacteria isolated from infected Cajanus cajan and Arachis hypogaea seed are identified by 16S rDNA sequencing as P. agglomerans and E. chrysanthemi, respectively. In vitro antimicrobial properties of 100 essential oils (EOs) were evaluated against P. agglomerans and E. chrysanthemi. The chemical composition of most active EOs was investigated by gas chromatography–mass spectral analysis. The potential properties of these EOs as ecofriendly and economical biocontrol in agriculture is discussed.     

Identification and molecular cytogenetic characterization of a novel complex Y chromosome rearrangement in a boy with disorder of sexual development

Ambiguous genitalia or disorder of the sexual development is a birth defect where the external genitals do not have the typical appearance of either a male or female. Here we report a boy with ambiguous genitalia and short stature. The cytogenetic analysis by G-banding revealed a small Y chromosome and an additional material on the 15p arm. Further, molecular cytogenetic analysis by Fluorescence in situ hybridization (FISH) using whole chromosome paint probes showed the presence of Y sequences on the 15p arm, confirming that it is a Y;15 translocation. Subsequent, FISH with centromere probe Y showed two signals depicting the presence of two centromeres and differing with a balanced translocation. The dicentric nature of the derivative 15 chromosome was confirmed by FISH with both 15 and Y centromeric probes. Further, the delineation of the Y chromosomal DNA was also done by quantitative real time PCR. Additional Y-short tandem repeat typing was performed to find out the extent of deletion on small Y chromosome. Fine mapping was carried out with 8 Y specific BAC clones which helped in defining the breakpoint regions. MLPA was performed to check the presence or absence of subtelomeric regions and SHOX regions on Y. Finally array CGH helped us in confirming the breakpoint regions. In our study we identified and characterized a novel complex Y chromosomal rearrangement with a complete deletion of the Yq region and duplication of the Yp region with one copy being translocated onto the15p arm. This is the first report of novel and unique Y complex rearrangement showing a deletion, duplication and a translocation in the same patient. The possible mechanism of the rearrangement and the phenotype–genotype correlation are discussed.     

Variation in leaf photosynthetic characteristics in wild rice species

Variations in leaf gas-exchange characteristics, leaf pigment content, and other important leaf traits were investigated in seven wild Oryza species, five hybrids, and five improved varieties. The significant variations were observed in photosynthetic pigment contents amongst different species of Oryza. The mean chlorophyll (Chl) content was higher in O. sativa (varieties and hybrids), while O. eichengeri showed the lowest Chl content. The mean carotenoid (Car) content in O. sativa (varieties and hybrids) was higher than in other wild rice species. O. eichengeri and O. barthii had significantly lower Car contents than other rice species. Significant differences were noticed in the rate of photosynthesis (P _N), stomatal conductance (g _s), transpiration rate (E), internal CO₂ concentration (C _i), specific leaf mass (SLM), and leaf thickness amongst different Oryza species. The mean P _N was the highest in O. nivara followed by O. eichengeri. The mean P _N was the lowest in O. glumaepatula, which was lower than that of cultivated varieties and hybrids of O. sativa. High rates of photosynthesis were observed in O. nivara (ACC. No. CR 100097), O. rufipogon (ACC.No. CR 100267), and O. nivara (ACC.No. CR 100008). The O. nivara and O. rufipogon genotypes with high P _N might be used in rice improvement programmes for an increase of leaf photosynthesis in rice. Multiple correlations performed between different gas-exchange characteristics and other physiological traits revealed that the rate of photosynthesis was not dependent on the leaf pigment content or the leaf thickness. A strong positive correlation between P _N and the P _N/C_i ratio, which represents the carboxylation efficiency, indicated that the observed variation in P _N was not based on pigment content or other leaf traits.     

PSCA gene variants (rs2294008 and rs2978974) confer increased susceptibility of gallbladder carcinoma in females

Background and aim

PSCA is a tissue specific tumor suppressor or oncogene which has been found to be associated with several human tumors including gallbladder cancer. It is considered to be involved in the cell-proliferation inhibition and/or cell-death induction activity. Therefore, we aimed to investigate the role of PSCA gene polymorphisms in gallbladder cancer risk in North Indian population.

Methodology

A total of 405 gallbladder cancer patients and 247 healthy controls were included in the case–control study for risk prediction. We examined the association of two functional SNPs, rs2294008 and rs2978974 in PSCA gene by genotyping using Taqman allelic discrimination assays. Statistical analysis was done using SPSS software, version 17. Linkage disequilibrium and haplotype analysis was done with the help of SNPstats software. FDR test was used to correct for multiple comparisons.

Results

No significant associations of rs2294008 and rs2978974 genetic variants of the PSCA gene were found with GBC risk at allele, genotype or haplotype levels. Stratifying the subjects on the basis of gallstone also did not show any significant result. However, on gender stratification, we found a significant association of T_rs2294008-G_rs2978974 haplotype with higher risk of GBC in females (FDR Pcorr = 0.021, OR = 1.6). In contrary, T_rs2294008-A _rs2978974 haplotype conferred significant lower risk in males (FDR Pcorr = 0.013; OR = 0.25).

Conclusions

These findings suggest that PSCA genetic variants may have a significant effect on GBC susceptibility in a gender specific manner.     

Unintended consequences of delisting routine eye exams on retinopathy screening for people with diabetes in Ontario,Canada

Background:

Routine eye examinations for healthy adults aged 20–64 years were delisted from the Ontario Health Insurance Plan in 2004, but they continue to be insured for people with diabetes regardless of age. We sought to assess whether the delisting of routine eye examinations for healthy adults had the unintended consequence of decreasing retinopathy screening for adults with diabetes.

Methods:

We used administrative data to calculate eye examinations for people with diabetes ages 40–64 years and 65 years and older in each 2-year period from 1998 to 2010. We examined differences by sex, income, rurality and type of health care provider. We used segmented linear regression to assess the change in trend before and after 2004.

Results:

For people with diabetes aged 65 years and older, eye examinations rose gradually from 1998 to 2010, with no substantial change between 2004 and 2006. For people with diabetes aged 40–65 years, there was an 8.7% (95% confidence interval [CI] 6.3%–11.1%) decrease in eye examinations between 2004 and 2006. Results were similar for all population subgroups. Ophthalmologic examinations decreased steadily for both age groups during the study period, and there was a decline in optometry examinations for people ages 40–65 years after 2004.

Interpretation:

The delisting of routine eye examinations for healthy adults in Ontario had the unintended consequence of reducing publicly funded retinopathy screening for people with diabetes. More research is needed to understand whether patients are being charged for an insured service or to what degree misunderstanding has prevented patients from seeking care.Diabetic retinopathy is the leading cause of new cases of blindness in people of working age.¹ In the United States, about 40% of adults with diabetes aged 40 years and older have retinopathy, and 8% have vision-threatening retinopathy.² Studies suggest that, if untreated, 50% of patients with proliferative diabetic retinopathy become legally blind within 5 years, compared with only 5% of patients who receive early treatment.³ Regular dilated eye examinations are effective for early detection and monitoring of asymptomatic retinopathy in people with diabetes⁴ and are recommended by clinical practice guidelines.^5,6In Ontario, Canada’s most populous province, medically necessary services are covered by the Ontario Health Insurance Plan (OHIP) for all permanent residents and Canadian citizens living in the province.⁷ Under OHIP, routine eye examinations were fully insured for all children and adults until November 1, 2004. At that time, routine eye examinations ceased being insured for healthy adults aged 20–64 years, but continued to be insured for children aged 19 years and younger and for adults aged 65 years and older.⁸ Regardless of age, adults with diabetes and some other medical conditions affecting the eye, as well as adults receiving social assistance, continued to have an annual eye examination covered by OHIP. Insured examinations are at no cost to the patient and are reimbursed to the provider at about Can$40. In contrast, healthy adults aged 20–64 years are required to pay out-of-pocket or through private insurance for a routine eye examination, with fees set at the discretion of the optometrist⁹ or physician.¹⁰Health policy experts suggest that delisting services from insurance schemes can have unpredictable effects.¹¹ Understanding the effect of delisting on care is particularly important as governments face fiscal pressures and contemplate further reductions in what is publicly insured.¹² We sought to assess whether delisting routine eye examinations for healthy middle-aged adults in Ontario had the unintended consequence of decreasing retinopathy screening for middle-aged adults with diabetes, even though eye examinations continued to be insured for this population.