Mutation of Arabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS1 Causes Circadian Clock Defects

The circadian clock plays a crucial role in coordinating plant metabolic and physiological functions with predictable environmental variables, such as dusk and dawn, while also modulating responses to biotic and abiotic challenges. Much of the initial characterization of the circadian system has focused on transcriptional initiation, but it is now apparent that considerable regulation is exerted after this key regulatory step. Transcript processing, protein stability, and cofactor availability have all been reported to influence circadian rhythms in a variety of species. We used a genetic screen to identify a mutation within a putative RNA binding protein (SPLICEOSOMAL TIMEKEEPER LOCUS1 [STIPL1]) that induces a long circadian period phenotype under constant conditions. STIPL1 is a homolog of the spliceosomal proteins TFP11 (Homo sapiens) and Ntr1p (Saccharomyces cerevisiae) involved in spliceosome disassembly. Analysis of general and alternative splicing using a high-resolution RT-PCR system revealed that mutation of this protein causes less efficient splicing of most but not all of the introns analyzed. In particular, the altered accumulation of circadian-associated transcripts may contribute to the observed mutant phenotype. Interestingly, mutation of a close homolog of STIPL1, STIP-LIKE2, does not cause a circadian phenotype, which suggests divergence in function between these family members. Our work highlights the importance of posttranscriptional control within the clock mechanism. © 2012 American Society of Plant Biologists. All rights reserved

Functional characterization of an alkaline exonuclease and single strand annealing protein from the SXT genetic element of Vibrio cholerae

<p>Abstract</p> <p>Background</p> <p>SXT is an integrating conjugative element (ICE) originally isolated from <it>Vibrio cholerae</it>, the bacterial pathogen that causes cholera. It houses multiple antibiotic and heavy metal resistance genes on its ca. 100 kb circular double stranded DNA (dsDNA) genome, and functions as an effective vehicle for the horizontal transfer of resistance genes within susceptible bacterial populations. Here, we characterize the activities of an alkaline exonuclease (S066, SXT-Exo) and single strand annealing protein (S065, SXT-Bet) encoded on the SXT genetic element, which share significant sequence homology with Exo and Bet from bacteriophage lambda, respectively.</p> <p>Results</p> <p>SXT-Exo has the ability to degrade both linear dsDNA and single stranded DNA (ssDNA) molecules, but has no detectable endonuclease or nicking activities. Adopting a stable trimeric arrangement in solution, the exonuclease activities of SXT-Exo are optimal at pH 8.2 and essentially require Mn²⁺or Mg²⁺ions. Similar to lambda-Exo, SXT-Exo hydrolyzes dsDNA with 5'- to 3'-polarity in a highly processive manner, and digests DNA substrates with 5'-phosphorylated termini significantly more effectively than those lacking 5'-phosphate groups. Notably, the dsDNA exonuclease activities of both SXT-Exo and lambda-Exo are stimulated by the addition of lambda-Bet, SXT-Bet or a single strand DNA binding protein encoded on the SXT genetic element (S064, SXT-Ssb). When co-expressed in <it>E. coli </it>cells, SXT-Bet and SXT-Exo mediate homologous recombination between a PCR-generated dsDNA fragment and the chromosome, analogous to RecET and lambda-Bet/Exo.</p> <p>Conclusions</p> <p>The activities of the SXT-Exo protein are consistent with it having the ability to resect the ends of linearized dsDNA molecules, forming partially ssDNA substrates for the partnering SXT-Bet single strand annealing protein. As such, SXT-Exo and SXT-Bet may function together to repair or process SXT genetic elements within infected <it>V. cholerae </it>cells, through facilitating homologous DNA recombination events. The results presented here significantly extend our general understanding of the properties and activities of alkaline exonuclease and single strand annealing proteins of viral/bacteriophage origin, and will assist the rational development of bacterial recombineering systems.</p

Factors associated with dog ownership and contact with dogs in a UK community

BACKGROUND: Dogs are popular pets in many countries. Identifying differences between those who own dogs or have contact with dogs, and those who do not, is useful to those interested in the human-animal bond, human health and for provision of veterinary services. This census-based, epidemiological study aimed to investigate factors associated with dog ownership and contact with dogs, in a semi-rural community of 1278 households in Cheshire, UK. RESULTS: Twenty-four percent of households were identified as dog-owning and 52% owned a pet of some type. Multivariable logistic regression suggested that households were more likely to own a dog if they had more occupants (five or more); if they had an adult female household member; or if they owned a horse. The age structure of the households was also associated with dog ownership, with households containing older children (between six and 19 years of age) and young adults (between 20 and 29 years of age), more likely to own dogs. We also found that dog owning households were more likely to be multi-dog households than single-dog if they also owned a cat or a bird, or if the household contained a person of 20–29 years old. Dog owners reported increased contact with dogs, other than their own, compared to those that did not own dogs and this contact appeared to be mainly through walking. CONCLUSION: Some household types are more likely to own a dog than others. This study supports the suggestion that dogs are more common in families who have older children (6–19 years), as has been generally observed in other countries. Dog owners are also more likely to have contact with dogs other than their own, compared with those not owning a dog

Effects on Oxygen Consumption and Metabolic Gene Expression when Determining Experimental Exercise Intensity Based on Exercise Capacity Tests Conducted in Hypoxic and Normoxic Environments

Abstract: Exercise intensity can be set relative to VO2 max measured during hypoxic or control conditions in studies investigating exercise in hypoxic environments. It currently is not clear which is the most appropriate method. Objective: The objective of this brief report is to determine the response to 1 hour of cycling at 60% of peak power when measured in either normoxic or hypoxic conditions. Methods: Eleven recreationally active male participants (24 ± 4 yrs, 173 ± 20 cm, 82 ± 12 kg, 15.2 ± 7.1% fat, 4.0 ± 0.6 L x min-1 VO2 max) completed two 1 hour cycling exercise trials at 60% of peak power followed by 4 hours of recovery in ambient environmental conditions (975 m) and at normobaric hypoxic conditions simulating 3000 m in a randomized counter balanced order. Results: VO2 max was not different between trials in relative (p=0.272) or absolute terms (p=0.105) but peak power at VO2 max was higher in the 975 m trial (288 ± 17 watts) than the 3000 m trial (262 ± 12 watts, p=0.003) corresponding to differences at 60% of VO2 max power. Gene expression of HIF-1α, COX, PGC-1α, HK, and PFK increased with exercise (p\u3c0.05) but did not differ between trials. There was a trend (p=0.072) toward increased muscle glycogen use in 975m. Conclusions: Although there were not statistical differences for muscle markers in the current study, these data should be considered when determining exercise intensity in hypoxia related research

Border Screening for SARS

Screening at national borders may not be effective in controlling SARS spread

Bilateral Assessment of Functional Tasks for Robot-assisted Therapy Applications

This article presents a novel evaluation system along with methods to evaluate bilateral coordination of arm function on activities of daily living tasks before and after robot-assisted therapy. An affordable bilateral assessment system (BiAS) consisting of two mini-passive measuring units modeled as three degree of freedom robots is described. The process for evaluating functional tasks using the BiAS is presented and we demonstrate its ability to measure wrist kinematic trajectories. Three metrics, phase difference, movement overlap, and task completion time, are used to evaluate the BiAS system on a bilateral symmetric (bi-drink) and a bilateral asymmetric (bi-pour) functional task. Wrist position and velocity trajectories are evaluated using these metrics to provide insight into temporal and spatial bilateral deficits after stroke. The BiAS system quantified movements of the wrists during functional tasks and detected differences in impaired and unimpaired arm movements. Case studies showed that stroke patients compared to healthy subjects move slower and are less likely to use their arm simultaneously even when the functional task requires simultaneous movement. After robot-assisted therapy, interlimb coordination spatial deficits moved toward normal coordination on functional tasks

Subfamily specific conservation profiles for proteins based on n-gram patterns

<p>Abstract</p> <p>Background</p> <p>A new algorithm has been developed for generating conservation profiles that reflect the evolutionary history of the subfamily associated with a query sequence. It is based on n-gram patterns (NP{<it>n,m</it>}) which are sets of <it>n </it>residues and <it>m </it>wildcards in windows of size <it>n+m</it>. The generation of conservation profiles is treated as a signal-to-noise problem where the signal is the count of n-gram patterns in target sequences that are similar to the query sequence and the noise is the count over all target sequences. The signal is differentiated from the noise by applying singular value decomposition to sets of target sequences rank ordered by similarity with respect to the query.</p> <p>Results</p> <p>The new algorithm was used to construct 4,248 profiles from 120 randomly selected Pfam-A families. These were compared to profiles generated from multiple alignments using the consensus approach. The two profiles were similar whenever the subfamily associated with the query sequence was well represented in the multiple alignment. It was possible to construct subfamily specific conservation profiles using the new algorithm for subfamilies with as few as five members. The speed of the new algorithm was comparable to the multiple alignment approach.</p> <p>Conclusion</p> <p>Subfamily specific conservation profiles can be generated by the new algorithm without aprioi knowledge of family relationships or domain architecture. This is useful when the subfamily contains multiple domains with different levels of representation in protein databases. It may also be applicable when the subfamily sample size is too small for the multiple alignment approach.</p