Role of DNA replication proteins in double-strand break-induced recombination in Saccharomyces cerevisiae

Mitotic double-strand break (DSB)-induced gene conversion involves new DNA synthesis. We have analyzed the requirement of several essential replication components, the Mcm proteins, Cdc45p, and DNA ligase I, in the DNA synthesis of Saccharomyces cerevisiae MAT switching. In an mcm7-td (temperature-inducible degron) mutant, MAT switching occurred normally when Mcm7p was degraded below the level of detection, suggesting the lack of the Mcm2-7 proteins during gene conversion. A cdc45-td mutant was also able to complete recombination. Surprisingly, even after eliminating both of the identified DNA ligases in yeast, a cdc9-1 dnl4 Delta strain was able to complete DSB repair. Previous studies of asynchronous cultures carrying temperature-sensitive alleles of PCNA, DNA polymerase alpha (Pol alpha), or primase showed that these mutations inhibited MAT switching (A. M. Holmes and J. E. Haber, Cell 96:415-424, 1999). We have reevaluated the roles of these proteins in G(2)-arrested cells. Whereas PCNA was still essential for MAT switching, neither Pol alpha nor primase was required. These results suggest that arresting cells in S phase using ts alleles of Pol alpha-primase, prior to inducing the DSB, sequesters some other component that is required for repair. We conclude that DNA synthesis during gene conversion is different from S-phase replication, involving only leading-strand polymerization.     

Integrating host gene expression and the microbiome to explore disease pathogenesis

In a recent study, rich clinical assessment and longitudinal study design are combined with host gene expression and microbial sequencing analyses to develop a framework for exploring disease etiology and outcomes in the context of human inflammatory disease.See related article: http://dx.doi.org/10.1186/s13059-015-0637-x     

Use of Fixed Dose Combination (FDC) Drugs in India: Central Regulatory Approval and Sales of FDCs Containing Non-Steroidal Anti-Inflammatory Drugs (NSAIDs), Metformin,or Psychotropic Drugs

Background

In 2012, an Indian parliamentary committee reported that manufacturing licenses for large numbers of fixed dose combination (FDC) drugs had been issued by state authorities without prior approval of the Central Drugs Standard Control Organization (CDSCO) in violation of rules, and considered that some ambiguity until 1 May 2002 about states’ powers might have contributed. To our knowledge, no systematic enquiry has been undertaken to determine if evidence existed to support these findings. We investigated CDSCO approvals for and availability of oral FDC drugs in four therapeutic areas: analgesia (non-steroidal anti-inflammatory drugs [NSAIDs]), diabetes (metformin), depression/anxiety (anti-depressants/benzodiazepines), and psychosis (anti-psychotics).

Methods and Findings

This was an ecologic study with a time-trend analysis of FDC sales volumes (2007–2012) and a cross-sectional examination of 2011–2012 data to establish the numbers of formulations on the market with and without a record of CDSCO approval (“approved” and “unapproved”), their branded products, and sales volumes. Data from the CDSCO on approved FDC formulations were compared with sales data from PharmaTrac, a database of national drug sales. We determined the proportions of FDC sales volumes (2011–2012) arising from centrally approved and unapproved formulations and from formulations including drugs banned/restricted internationally. We also determined the proportions of centrally approved and unapproved formulations marketed before and after 1 May 2002, when amendments were made to the drug rules. FDC approvals in India, the United Kingdom (UK), and United States of America (US) were compared.For NSAID FDCs, 124 formulations were marketed, of which 34 (27%) were centrally approved and 90 (73%) were unapproved; metformin: 25 formulations, 20 (80%) approved, five (20%) unapproved; anti-depressants/benzodiazepines: 16 formulations, three (19%) approved, 13 (81%) unapproved; anti-psychotics: ten formulations, three (30%) approved, seven (70%) unapproved. After 1 May 2002, the proportions of approved FDC formulations increased for NSAIDs (26%/28%) and anti-psychotics (0%/38%) and decreased for metformin (100%/75%) and anti-depressants/benzodiazepines (20%/18%), and the overall proportion approved remained similar before and after that date.FDC formulations gave rise to multiple branded products, ranging from 211 anti-psychotic FDC products from ten formulations to 2,739 NSAID FDC products from 124 formulations. The proportions of FDC sales volumes arising from unapproved formulations were as follows: anti-depressants/benzodiazepines, 69%; anti-psychotics, 43%; NSAIDs, 28%; and metformin, 0.4%. Formulations including drugs banned/restricted internationally comprised over 12% of NSAID FDC sales and 53% of anti-psychotic FDC sales. Across the four therapeutic areas, 14 FDC formulations were approved in the UK and 22 in the US.

Conclusions

There was evidence supporting concerns about FDCs. Metformin excepted, substantial numbers of centrally unapproved formulations for NSAID, anti-depressant/benzodiazepine, and anti-psychotic FDCs were marketed; sales volumes were high. The legal need for central approval of new drugs before manufacture has been in place continuously since 1961, including for FDCs meeting the applicable legal test. Proportions of centrally unapproved formulations after 1 May 2002 did not decrease overall, and no ambiguity was found about states’ licensing powers. Unapproved formulations should be banned immediately, prioritising those withdrawn/banned internationally and undertaking a review of benefits and risks for patients in ceasing or switching to other medicines. Drug laws need to be amended to ensure the safety and effectiveness of medicines marketed in India.     

Personality predicts ectoparasite abundance in an asocial sciurid

Parasitism is a consequence of complex interactions between host, parasite, and their shared environment, and host behavior can influence parasite risk. Animal personality (i.e., consistent behavioral differences that are repeatable across time and context) can influence parasitism with more explorative individuals typically hosting greater parasite loads. Host “sociality” is known to impact parasite risk with more social individuals typically at higher risk of acquiring or transmitting parasites, but other behaviors could also be important. We quantified personality in least chipmunks (Tamias minimus), including repeatability of behavioral traits, and determined whether these personality traits affected ectoparasite prevalence and abundance. We measured personality using standardized hole‐board tests and quantified ectoparasitism of 39 least chipmunks over 2 years at a site in southeastern Manitoba, Canada. We found that activity and exploration were repeatable within the context of the hole‐board test for least chipmunks, which suggests that these traits reflect personality. More exploratory individuals hosted a greater abundance of ectoparasites compared to less exploratory individuals. Our results are consistent with past studies implicating personality as a factor in host–parasite dynamics and suggest that exploration may be an important behavioral correlate of parasite acquisition.     

Seed Dispersal of Morus macroura (Moraceae) by Two Frugivorous Bats in Xishuangbanna, SW China

The dispersal of Morus macroura seeds by two species of frugivorous bats ( Rousettus leschenaulti and Cynopterus sphinx ) was studied in a forest at Xishuangbanna Tropical Botanical Garden in Southwest China from March to May 2005. Feeding roosts were identified within 500 m around parent trees and the types and number of seed loads under each roost were recorded. We found feeding roost density decreased with increasing distance from the parent, but found no correlation between distance and seed deposition. The effect of bat digestion on seed germination was investigated, and we found that germination percentage of all treatments involving ingestion by bats was significantly lower than control seeds and some germination parameters of seeds from different treatments changed.     

Changing the substrate specificity of creatine kinase from creatine to glycocyamine: evidence for a highly evolved active site

Eight variants of creatine kinase were created to switch the substrate specificity from creatine to glycocyamine using a rational design approach. Changes to creatine kinase involved altering several residues on the flexible loops that fold over the bound substrates including a chimeric replacement of the guanidino specificity loop from glycocyamine kinase into creatine kinase. A maximal 2,000-fold change in substrate specificity was obtained as measured by a ratio of enzymatic efficiency (k(cat)/K(M).K(d)) for creatine vs. glycocyamine. In all cases, a change in specificity was accompanied by a large drop in enzymatic efficiency. This data, combined with evidence from other studies, indicate that substrate specificity in the phosphagen kinase family is obtained by precise alignment of substrates in the active site to maximize k(cat)/K(M).K(d) as opposed to selective molecular recognition of one guanidino substrate over another. A model for the evolution of the dimeric forms of phosphagen kinases is proposed in which these enzymes radiated from a common ancestor that may have possessed a level of catalytic promiscuity. As mutational events occurred leading to greater degrees of substrate specificity, the dimeric phosphagen kinases became evolutionary separated such that the substrate specificity could not be interchanged by a small number of mutations.     

Seasonal variation of nutritional and antioxidant properties of different Kappaphycus alvarezii strains (Rhodophyta) farmed in Brazil

Journal of Applied Phycology - Antioxidant potential, carbohydrate content, ash, minerals, proteins, and amino acids of Kappaphycus alvarezii farmed along the São Paulo coast, Brazil, were...     

Nitrate boosts anaerobic ethanol production in an acetate-dependent manner in the yeast Dekkera bruxellensis

Journal of Industrial Microbiology & Biotechnology - In the past few years, the yeast Dekkera bruxellensis has gained much of attention among the so-called non-conventional yeasts for its...     

Observations and models of emissions of volatile terpenoid compounds from needles of ponderosa pine trees growing in situ: control by light,temperature and stomatal conductance

Terpenoid emissions from ponderosa pine (Pinus ponderosa subsp. scopulorum) were measured in Colorado, USA over two growing seasons to evaluate the role of incident light, needle temperature, and stomatal conductance in controlling emissions of 2-methyl-3-buten-2-ol (MBO) and several monoterpenes. MBO was the dominant daylight terpenoid emission, comprising on average 87 % of the total flux, and diurnal variations were largely determined by light and temperature. During daytime, oxygenated monoterpenes (especially linalool) comprised up to 75 % of the total monoterpenoid flux from needles. A significant fraction of monoterpenoid emissions was dependent on light and ¹³CO₂ labeling studies confirmed de novo production. Thus, modeling of monoterpenoid emissions required a hybrid model in which a significant fraction of emissions was dependent on both light and temperature, while the remainder was dependent on temperature alone. Experiments in which stomata were forced to close using abscisic acid demonstrated that MBO and a large fraction of the monoterpene flux, presumably linalool, could be limited at the scale of seconds to minutes by stomatal conductance. Using a previously published model of terpenoid emissions, which explicitly accounts for the physico-chemical properties of emitted compounds, we were able to simulate these observed stomatal effects, whether induced experimentally or arising under naturally fluctuation conditions of temperature and light. This study shows unequivocally that, under naturally occurring field conditions, de novo light-dependent monoterpenes comprise a significant fraction of emissions in ponderosa pine. Differences between the monoterpene composition of ambient air and needle emissions imply a significant non-needle emission source enriched in Δ-3-carene.