Scapula form and locomotion in chimpanzee evolution

A number of primatologists have followed Coolidge (Am. J. Phys. Anthropol. 18:1–57, 1933) in suggesting that 1) there are significant shape differences in scapula form between pygmy and common chimpanzees, 2) scapulae of P. paniscus resemble those of hylobatids more than do those of P. troglodytes, and 3) therefore pygmy chimpanzees may exhibit a greater component of arm-swinging and other arboreal behaviors than common chimpanzees. In this paper I utilize a comparative analysis of ontogenetic allometries of linear dimensions to determine shape differences in the scapulae of adult pygmy and common chimpanzees and to clarify size-related changes in shape resulting from ontogenetic scaling, i.e., the differential extension of common patterns of growth allometry. Results demonstrate that the scapulae of adult P. paniscus are relatively narrower (in a direction approximately perpendicular to the scapula spine) than those of P. troglodytes, supporting Coolidge's original claim. The allometric analysis further demonstrates, however, that the two chimpanzee species exhibit ontogenetic scaling for all proportions of the scapula examined. Thus, adult pygmy chimpanzees have the scapula proportions observed in small adult and subadult P. troglodytes of comparable scapula size. The implications of this finding for past claims concerning differences in locomotor behavior between the species are discussed. This work lends additional support to previous studies that have demonstrated a high frequency of ontogenetic scaling within the genus Pan and a pedomorphic or juvenilized morphology in the pygmy chimpanzee.     

Coarse-grained models for protein aggregation

The aggregation of soluble proteins into fibrillar species is a complex process that spans many lengths and time scales, and that involves the formation of numerous on-pathway and off-pathway intermediate species. Despite this complexity, several elements underlying the aggregation process appear to be universal. The kinetics typically follows a nucleation-growth process, and proteins with very different sequences aggregate to form similar fibril structures, populating intermediates with sufficient structural similarity to bind to a common antibody. This review focuses on a computational approach that exploits the common features of aggregation to simplify or 'coarse-grain' the representation of the protein. We highlight recent developments in coarse-grained modeling and illustrate how these models have been able to shed new light into the mechanisms of protein aggregation and the nature of aggregation intermediates. The roles of aggregation prone conformations in the monomeric state and the influence of inherent β-sheet and aggregation propensities in modulating aggregation pathways are discussed.     

Sex chromosome mosaicism and hybrid speciation among tiger swallowtail butterflies

Hybrid speciation, or the formation of a daughter species due to interbreeding between two parental species, is a potentially important means of diversification, because it generates new forms from existing variation. However, factors responsible for the origin and maintenance of hybrid species are largely unknown. Here we show that the North American butterfly Papilio appalachiensis is a hybrid species, with genomic admixture from Papilio glaucus and Papilio canadensis. Papilio appalachiensis has a mosaic phenotype, which is hypothesized to be the result of combining sex-linked traits from P. glaucus and P. canadensis. We show that P. appalachiensis' Z-linked genes associated with a cooler thermal habitat were inherited from P. canadensis, whereas its W-linked mimicry and mitochondrial DNA were inherited from P. glaucus. Furthermore, genome-wide AFLP markers showed nearly equal contributions from each parental species in the origin of P. appalachiensis, indicating that it formed from a burst of hybridization between the parental species, with little subsequent backcrossing. However, analyses of genetic differentiation, clustering, and polymorphism based on molecular data also showed that P. appalachiensis is genetically distinct from both parental species. Population genetic simulations revealed P. appalachiensis to be much younger than the parental species, with unidirectional gene flow from P. glaucus and P. canadensis into P. appalachiensis. Finally, phylogenetic analyses, combined with ancestral state reconstruction, showed that the two traits that define P. appalachiensis' mosaic phenotype, obligatory pupal diapause and mimicry, evolved uniquely in P. canadensis and P. glaucus, respectively, and were then recombined through hybridization to form P. appalachiensis. These results suggest that natural selection and sex-linked traits may have played an important role in the origin and maintenance of P. appalachiensis as a hybrid species. In particular, ecological barriers associated with a steep thermal cline appear to maintain the distinct, mosaic genome of P. appalachiensis despite contact and occasional hybridization with both parental species.     

PAX6 haplotypes are associated with high myopia in Han chinese

Background

The paired box 6 (PAX6) gene is considered as a master gene for eye development. Linkage of myopia to the PAX6 region on chromosome 11p13 was shown in several studies, but the results for association between myopia and PAX6 were inconsistent so far.

Methodology/Principal Findings

We genotyped 16 single nucleotide polymorphisms (SNPs) in the PAX6 gene and its regulatory regions in an initial study for 300 high myopia cases and 300 controls (Group 1), and successfully replicated the positive results with another independent group of 299 high myopia cases and 299 controls (Group 2). Five SNPs were genotyped in the replication study. The spherical equivalent of subjects with high myopia was ≤−8.0 dioptres. The PLINK package was used for genetic data analysis. No association was found between each of the SNPs and high myopia. However, exhaustive sliding-window haplotype analysis highlighted an important role for rs12421026 because haplotypes containing this SNP were found to be associated with high myopia. The most significant results were given by the 4-SNP haplotype window consisting of rs2071754, rs3026393, rs1506 and rs12421026 (P = 3.54×10⁻¹⁰, 4.06×10⁻¹¹ and 1.56×10⁻¹⁸ for Group 1, Group 2 and Combined Group, respectively) and the 3-SNP haplotype window composed of rs3026393, rs1506 and rs12421026 (P = 5.48×10⁻¹⁰, 7.93×10⁻¹² and 6.28×10⁻²³ for the three respective groups). The results remained significant after correction for multiple comparisons by permutations. The associated haplotyes found in a previous study were also successfully replicated in this study.

Conclusions/Significance

PAX6 haplotypes are associated with susceptibility to the development of high myopia in Chinese. The PAX6 locus plays a role in high myopia.     

The composite insect trap: an innovative combination trap for biologically diverse sampling

Documentation of insect diversity is an important component of the study of biodiversity, community dynamics, and global change. Accurate identification of insects usually requires catching individuals for close inspection. However, because insects are so diverse, most trapping methods are specifically tailored to a particular taxonomic group. For scientists interested in the broadest possible spectrum of insect taxa, whether for long term monitoring of an ecosystem or for a species inventory, the use of several different trapping methods is usually necessary. We describe a novel composite method for capturing a diverse spectrum of insect taxa. The Composite Insect Trap incorporates elements from four different existing trapping methods: the cone trap, malaise trap, pan trap, and flight intercept trap. It is affordable, resistant, easy to assemble and disassemble, and collects a wide variety of insect taxa. Here we describe the design, construction, and effectiveness of the Composite Insect Trap tested during a study of insect diversity. The trap catches a broad array of insects and can eliminate the need to use multiple trap types in biodiversity studies. We propose that the Composite Insect Trap is a useful addition to the trapping methods currently available to ecologists and will be extremely effective for monitoring community level dynamics, biodiversity assessment, and conservation and restoration work. In addition, the Composite Insect Trap will be of use to other insect specialists, such as taxonomists, that are interested in describing the insect taxa in a given area.     

The lysophosphatidic acid receptor LPA1 links pulmonary fibrosis to lung injury by mediating fibroblast recruitment and vascular leak

Aberrant wound-healing responses to injury have been implicated in the development of pulmonary fibrosis, but the mediators directing these pathologic responses have yet to be fully identified. We show that lysophosphatidic acid levels increase in bronchoalveolar lavage fluid following lung injury in the bleomycin model of pulmonary fibrosis, and that mice lacking one of its receptors, LPA1, are markedly protected from fibrosis and mortality in this model. The absence of LPA1 led to reduced fibroblast recruitment and vascular leak, two responses that may be excessive when injury leads to fibrosis rather than to repair, whereas leukocyte recruitment was preserved during the first week after injury. In persons with idiopathic pulmonary fibrosis, lysophosphatidic acid levels in bronchoalveolar lavage fluid were also increased, and inhibition of LPA1 markedly reduced fibroblast responses to the chemotactic activity of this fluid. LPA1 therefore represents a new therapeutic target for diseases in which aberrant responses to injury contribute to fibrosis, such as idiopathic pulmonary fibrosis.     

A dynamic pathway for calcium-independent activation of CaMKII by methionine oxidation

tRNAs are synthesized as immature precursors, and on their way to functional maturity, extra nucleotides at their 5' ends are removed by an endonuclease called RNase P. All RNase P enzymes characterized so far are composed of an RNA plus one or more proteins, and tRNA 5' end maturation is considered a universal ribozyme-catalyzed process. Using a combinatorial purification/proteomics approach, we identified the components of human mitochondrial RNase P and reconstituted the enzymatic activity from three recombinant proteins. We thereby demonstrate that human mitochondrial RNase P is a protein enzyme that does not require a trans-acting RNA component for catalysis. Moreover, the mitochondrial enzyme turns out to be an unexpected type of patchwork enzyme, composed of a tRNA methyltransferase, a short-chain dehydrogenase/reductase-family member, and a protein of hitherto unknown functional and evolutionary origin, possibly representing the enzyme's metallonuclease moiety. Apparently, animal mitochondria lost the seemingly ubiquitous RNA world remnant after reinventing RNase P from preexisting components.     

Dietary Supplementation with S-Adenosyl Methionine was Associated with Protracted Reduction of Seizures in a Line of Transgenic Mice

Transgenic mice, although useful for analyses of gene function, can present unanticipated phenotypic manifestations, including behavioral problems, that may not be directly associated with the gene of interest but rather due to the complex interplay inherent in genomes. These unexpected events can present unique insight into gene function, leading to an advantage in some situations, yet in others can confound interpretation and compromise usefulness of the transgenic line. Here we document that short-term supplementation with S-adenosyl methionine (SAM)—a nutriceutical known to regulate neurotransmitter levels, improve working memory, and reduce aggression—reduced handling- and startling-induced seizures that otherwise precluded behavioral analyses in a transgenic line. This effect lasted for at least 1 mo after withdrawal of SAM and allowed mice to be used in standard maze analyses. These findings suggest that short-term administration of a neurotropic nutriceutical may provide a functional rescue for behavioral studies in an otherwise intractable transgenic mouse line as well as improve the welfare of similar lines.Abbreviations: SAH, S-adenosyl homocysteine; SAM, S-adenosyl methionineSite-directed mutagenesis, gene deletion, and the insertion of exogenous genes present powerful tools for genetic analyses. Incorporation of such genetic alterations into the murine germline, and the resultant generation of transgenic strains of mice, has provided novel insight into the roles of genes, and their interaction with other genes, at all stages of life. However, transgenic mice can present unanticipated behavioral problems that may not be associated directly with the gene of interest but rather are due to the complex interplay inherent in genomes.²⁰ This unexpected outcome can present unique insight into gene function, leading to an advantage in some situations, yet in others can confound interpretation and compromise usefulness of the transgenic line. Genetic variability of inbred strains can confound interpretation of behavior,¹⁸ especially if behavioral analyses are part of the regimen to be studied.²⁶The presence of 1 or more ApoE4 alleles is associated with an increased risk of Alzheimer disease.¹³ Transgenic mice in which the single murine ApoE allele has been ablated and replaced with human apolipoprotein E isoforms have been useful models for studying the impact of ApoE on age-related cognitive decline and Alzheimer disease. In addition to impaired cognition, mice lacking murine ApoE and expressing human ApoE4 (ApoE4 mice) display increased aggression as compared with normal mice, mice lacking murine ApoE, or mice lacking murine ApoE and expressing other human ApoE alleles.^5,6 These behavioral manifestations of ApoE4 mice are useful in that Alzheimer disease is often accompanied by behavioral trauma, including pyschosis and agitation,⁷ and ApoE4 has been associated with an increase psychotic symptoms in humans.²⁷Recent shipments of ApoE4 mice displayed violent spontaneous and handling-induced convulsions (hereafter referred to as seizures for the sake of simplicity), which included jumping and eventual prostration due to overt exhaustion. These seizures occurred regardless of how quietly or slowly the handler or caregiver moved. These seizures, which persisted for more than 1 mo, had not previously been observed in ApoE4 mice or other mice in our facility and precluded the intended use of the ApoE4 mice in standard maze trials.⁵In our ongoing studies, we had observed that dietary supplementation with the nutriceutical S-adenosyl methionine (SAM) reduced aggressive behavior in ApoE4 mice.⁵ SAM also restores neurotransmitter balance, increases working memory, and modulates neuronal activity.^6,8,17,19 We therefore hypothesized that SAM supplementation would reduce or alleviate handling-induced seizures. Here we document that short-term administration of SAM reduced of seizures for extended periods, to the extent that these mice could be used in behavioral studies. We discuss the possibility that such an approach may be useful for habituation of other mouse lines displaying similar behavior difficulties.     

The Irish DAFNE Study Protocol: A cluster randomised trial of group versus individual follow-up after structured education for Type 1 diabetes

Background

Subgroup analyses in randomized trials examine whether effects of interventions differ between subgroups of study populations according to characteristics of patients or interventions. However, findings from subgroup analyses may be misleading, potentially resulting in suboptimal clinical and health decision making. Few studies have investigated the reporting and conduct of subgroup analyses and a number of important questions remain unanswered. The objectives of this study are: 1) to describe the reporting of subgroup analyses and claims of subgroup effects in randomized controlled trials, 2) to assess study characteristics associated with reporting of subgroup analyses and with claims of subgroup effects, and 3) to examine the analysis, and interpretation of subgroup effects for each study's primary outcome.

Methods

We will conduct a systematic review of 464 randomized controlled human trials published in 2007 in the 118 Core Clinical Journals defined by the National Library of Medicine. We will randomly select journal articles, stratified in a 1:1 ratio by higher impact versus lower impact journals. According to 2007 ISI total citations, we consider the New England Journal of Medicine, JAMA, Lancet, Annals of Internal Medicine, and BMJ as higher impact journals. Teams of two reviewers will independently screen full texts of reports for eligibility, and abstract data, using standardized, pilot-tested extraction forms. We will conduct univariable and multivariable logistic regression analyses to examine the association of pre-specified study characteristics with reporting of subgroup analyses and with claims of subgroup effects for the primary and any other outcomes.

Discussion

A clear understanding of subgroup analyses, as currently conducted and reported in published randomized controlled trials, will reveal both strengths and weaknesses of this practice. Our findings will contribute to a set of recommendations to optimize the conduct and reporting of subgroup analyses, and claim and interpretation of subgroup effects in randomized trials.