The agonist binding site of the M1 muscarinic acetylcholine receptors probed by scanning mutagenesis

The anchor point for the binding of the quaternary ammonium headgroup of acetylcholine to muscarinic acetylcholine receptors is known, but less is known about the interaction of other important moieties, particularly the side-chain of acetylcholine. The aim of this project was to identify residues in the M1 muscarinic acetylcholine receptor that may contact the side-chain methyl group of acetylcholine. Receptor models predict that residues in the sequence between Ile188 and Ala196 may be at a suitable distance from the aspartate residue which binds the headgroup. Substitution mutants were constructed of these residues. Mutation to Cys allowed probing with sulphydryl reagents including the alkylating acetylcholine analogue bromoacetylcholine and the group specific methanethiosulphonate (MTS) derivatives. Mutation to Ala or Gly allowed a complementary ligand side-chain / amino acid side-chain deletion strategy. Mutation of residues Ile188, Thr189, Thr192 and Ala196 caused significant decreases in acetylcholine binding. This led to a reduction in the potency of the functional response. There were small decreases in the binding of acetylcholine analogues carbachol and oxotremorine-M, but no significant effect on the affinity of the des-methyl analogue formylcholine. Interestingly, mutation of Phe190 to Cys resulted in a constitutively active receptor. The environment of this residue may change during receptor activation. The positively-charged MTSET reacted strongly with F190C, T192C and A193C, identifying these residues as accessible within the binding site crevice. Bromoacetylcholine interacted specifically with the T192C mutant receptor confirming the importance of this position. These results indicate that Ile188, Thr189, Thr192 and Ala196 contribute to the acetylcholine binding pocket, and that this section of TM V is α-helical. Ala193 is accessible in the binding pocket but not involved in acetylcholine binding. In addition to any involvement in a network of hydrogen bonds Thr192 is predicted to contact the acetylmethyl group of acetylcholine

Distribution, Abundance, and Age Structure of Red Snapper (Lutjanus campechanus) Caught on Research Longlines in U.S. Gulf of Mexico

Two pilot surveys were conducted in the northern Gulf of Mexico (Gulf) to determine the feasibility of sampling red snapper (Lutjanus campechanus) populations in offshore waters with bottom longline gear. The first pilot survey off Mississippi-Alabama was conducted in May 1999 and yielded a total of seven snapper from 60 stations. The second pilot survey was off Texas in June 2000 and yielded a total of 76 snapper from 44 stations. The catch per unit effort was 0.12 red snapper/100 hook hr [coefficient of variation (CV) = 0.54] in 1999 and 1.73 red snapper/100 hook hr (CV = 0.21) in 2000. Otoliths were removed from all collected red snapper, and ages were assigned with an average percent error of 3.71%. Red snapper from the 1999 survey ranged from 405 to 873 mm total length (TL) (545 mm TL median) and from 3 to 19 yr (median age 5 yr). The red snapper from Texas ranged in size from 380 to 903 mm TL (755 mm TL median) and ranged in age from 3 to 53 yr (median age 11 yr). Based on the results of the pilot surveys, expanded longline surveys targeting red snapper were conducted in 2001 and 2002; these surveys yielded 86 snapper and 75 snapper, respectively. The 2001 snapper ranged from 427 to 950 mm TL (770 mm TL median) and from 3 to 37 yr (median age 12 yr). The 2002 snapper ranged from 409 to 950 mm TL (815 mm TL median) and from 4 to 44 yr (median age 13 yr). Twelve red snapper were captured in the eastern Gulf (east of the Mississippi River), and their ages ranged from 3 to 19 yr (median age 6 yr). The 232 red snapper that were caught in the western Gulf ranged in age from 3 to 53 yr (median age 12 yr). A difference in catch rates by depth was also noted with most red snapper captures occurring in the 55-92 m depth range

DSC Prize shortlisting: reflections on South Asian literature

On 26 November, the DSC Prize for South Asian literature shortlist was announced at LSE for the third year in a row. The novels selected were Family Life by Akhil Sharma (Faber & Faber, UK); Sleeping on Jupiter by Anuradha Roy (Hachette, India); Hangwoman by K.R. Meera (Translated by J Devika; Penguin, India); The Book of Gold Leaves by Mirza Waheed (Viking/Penguin India); The Lives of Others by Neel Mukherjee (Vintage/Penguin Random House, UK); and She Will Build Him A City by Raj Kamal Jha (Bloomsbury, India). After the announcement, Sonali Campion caught up with the five members of the jury about why they accepted the invitation to participate on the panel and their experiences of judging the novels

Phylesystem: a git-based data store for community-curated phylogenetic estimates

Motivation: Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. As the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work and making errors introduced during curation easier to correct. Results: Here, we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git’s version control features. Hosting this data store on GitHub (http://github.com/) provides open access to the data store using tools familiar to many developers. We have deployed a server running the ‘phylesystem-api’, which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements

The Fossil Calibration Database—A New Resource for Divergence Dating

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important—often least appreciated—step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as a key pipeline for peer-reviewed calibrations to enter the databas

Skunk River Fall 1998

https://openspace.dmacc.edu/skunkriver/1019/thumbnail.jp

Impact of Carnivory on Human Development and Evolution Revealed by a New Unifying Model of Weaning in Mammals

Our large brain, long life span and high fertility are key elements of human evolutionary success and are often thought to have evolved in interplay with tool use, carnivory and hunting. However, the specific impact of carnivory on human evolution, life history and development remains controversial. Here we show in quantitative terms that dietary profile is a key factor influencing time to weaning across a wide taxonomic range of mammals, including humans. In a model encompassing a total of 67 species and genera from 12 mammalian orders, adult brain mass and two dichotomous variables reflecting species differences regarding limb biomechanics and dietary profile, accounted for 75.5%, 10.3% and 3.4% of variance in time to weaning, respectively, together capturing 89.2% of total variance. Crucially, carnivory predicted the time point of early weaning in humans with remarkable precision, yielding a prediction error of less than 5% with a sample of forty-six human natural fertility societies as reference. Hence, carnivory appears to provide both a necessary and sufficient explanation as to why humans wean so much earlier than the great apes. While early weaning is regarded as essentially differentiating the genus Homo from the great apes, its timing seems to be determined by the same limited set of factors in humans as in mammals in general, despite some 90 million years of evolution. Our analysis emphasizes the high degree of similarity of relative time scales in mammalian development and life history across 67 genera from 12 mammalian orders and shows that the impact of carnivory on time to weaning in humans is quantifiable, and critical. Since early weaning yields shorter interbirth intervals and higher rates of reproduction, with profound effects on population dynamics, our findings highlight the emergence of carnivory as a process fundamentally determining human evolution

Increased Infarct Wall Thickness by a Bio-Inert Material Is Insufficient to Prevent Negative Left Ventricular Remodeling after Myocardial Infarction

Several injectable materials have been shown to preserve or improve cardiac function as well as prevent or slow left ventricular (LV) remodeling post-myocardial infarction (MI). However, it is unclear as to whether it is the structural support or the bioactivity of these polymers that lead to beneficial effects. Herein, we examine how passive structural enhancement of the LV wall by an increase in wall thickness affects cardiac function post-MI using a bio-inert, non-degradable synthetic polymer in an effort to better understand the mechanisms by which injectable materials affect LV remodeling.Poly(ethylene glycol) (PEG) gels of storage modulus G' = 0.5±0.1 kPa were injected and polymerized in situ one week after total occlusion of the left coronary artery in female Sprague Dawley rats. The animals were imaged using magnetic resonance imaging (MRI) at 7±1 day(s) post-MI as a baseline and again post-injection 49±4 days after MI. Infarct wall thickness was statistically increased in PEG gel injected vs. control animals (p<0.01). However, animals in the polymer and control groups showed decreases in cardiac function in terms of end diastolic volume, end systolic volume and ejection fraction compared to baseline (p<0.01). The cellular response to injection was also similar in both groups.The results of this study demonstrate that passive structural reinforcement alone was insufficient to prevent post-MI remodeling, suggesting that bioactivity and/or cell infiltration due to degradation of injectable materials are likely playing a key role in the preservation of cardiac function, thus providing a deeper understanding of the influencing properties of biomaterials necessary to prevent post-MI negative remodeling