A revised metric for quantifying body shape in vertebrates

Vertebrates exhibit tremendous diversity in body shape, though quantifying this variation has been challenging. In the past, researchers have used simplified metrics that either describe overall shape but reveal little about its anatomical basis or that characterize only a subset of the morphological features that contribute to shape variation. Here, we present a revised metric of body shape, the vertebrate shape index (VSI), which combines the four primary morphological components that lead to shape diversity in vertebrates: head shape, length of the second major body axis (depth or width), and shape of the precaudal and caudal regions of the vertebral column. We illustrate the usefulness of VSI on a data set of 194 species, primarily representing five major vertebrate clades: Actinopterygii, Lissamphibia, Squamata, Aves, and Mammalia. We quantify VSI diversity within each of these clades and, in the course of doing so, show how measurements of the morphological components of VSI can be obtained from radiographs, articulated skeletons, and cleared and stained specimens. We also demonstrate that head shape, secondary body axis, and vertebral characteristics are important independent contributors to body shape diversity, though their importance varies across vertebrate groups. Finally, we present a functional application of VSI to test a hypothesized relationship between body shape and the degree of axial bending associated with locomotor modes in ray-finned fishes. Altogether, our study highlights the promise VSI holds for identifying the morphological variation underlying body shape diversity as well as the selective factors driving shape evolution.     

An efficient algorithm for protein structure comparison using elastic shape analysis

Background

Protein structure comparison play important role in in silico functional prediction of a new protein. It is also used for understanding the evolutionary relationships among proteins. A variety of methods have been proposed in literature for comparing protein structures but they have their own limitations in terms of accuracy and complexity with respect to computational time and space. There is a need to improve the computational complexity in comparison/alignment of proteins through incorporation of important biological and structural properties in the existing techniques.

Results

An efficient algorithm has been developed for comparing protein structures using elastic shape analysis in which the sequence of 3D coordinates atoms of protein structures supplemented by additional auxiliary information from side-chain properties are incorporated. The protein structure is represented by a special function called square-root velocity function. Furthermore, singular value decomposition and dynamic programming have been employed for optimal rotation and optimal matching of the proteins, respectively. Also, geodesic distance has been calculated and used as the dissimilarity score between two protein structures. The performance of the developed algorithm is tested and found to be more efficient, i.e., running time reduced by 80–90 % without compromising accuracy of comparison when compared with the existing methods. Source codes for different functions have been developed in R. Also, user friendly web-based application called ProtSComp has been developed using above algorithm for comparing protein 3D structures and is accessible free.

Conclusions

The methodology and algorithm developed in this study is taking considerably less computational time without loss of accuracy (Table 2). The proposed algorithm is considering different criteria of representing protein structures using 3D coordinates of atoms and inclusion of residue wise molecular properties as auxiliary information.

     

A new body shape index predicts mortality hazard independently of body mass index

Background

Obesity, typically quantified in terms of Body Mass Index (BMI) exceeding threshold values, is considered a leading cause of premature death worldwide. For given body size (BMI), it is recognized that risk is also affected by body shape, particularly as a marker of abdominal fat deposits. Waist circumference (WC) is used as a risk indicator supplementary to BMI, but the high correlation of WC with BMI makes it hard to isolate the added value of WC.

Methods and Findings

We considered a USA population sample of 14,105 non-pregnant adults () from the National Health and Nutrition Examination Survey (NHANES) 1999–2004 with follow-up for mortality averaging 5 yr (828 deaths). We developed A Body Shape Index (ABSI) based on WC adjusted for height and weight: ABSI had little correlation with height, weight, or BMI. Death rates increased approximately exponentially with above average baseline ABSI (overall regression coefficient of per standard deviation of ABSI [95% confidence interval: –]), whereas elevated death rates were found for both high and low values of BMI and WC. (–) of the population mortality hazard was attributable to high ABSI, compared to (–) for BMI and (–) for WC. The association of death rate with ABSI held even when adjusted for other known risk factors including smoking, diabetes, blood pressure, and serum cholesterol. ABSI correlation with mortality hazard held across the range of age, sex, and BMI, and for both white and black ethnicities (but not for Mexican ethnicity), and was not weakened by excluding deaths from the first 3 yr of follow-up.

Conclusions

Body shape, as measured by ABSI, appears to be a substantial risk factor for premature mortality in the general population derivable from basic clinical measurements. ABSI expresses the excess risk from high WC in a convenient form that is complementary to BMI and to other known risk factors.     

A neurobiophysical interpretation of certain aspects of the problem of risks

A situation is considered in which an individual is given an opportunity to risk a certain amount of money or goods in order to gain a larger amount, providing the result of some uncertain event proves favorable. A neural mechanism is introduced in which the probability of success can be ordered according to its value. The response to a situation thus becomes dependent upon the probability. An expression is then derived for the amount that would be risked in terms of the probability and of the amount that would be gained in the event of a successful outcome. Similar expressions are obtained for the case of insurance against loss. Results of questionnaires indicate that individuals can be classified according to their pattern of behavior in the situation considered. The various types can be most easily recognized when a plot is made of the relative amount risked against the probability of success. In a general way, these types can be understood in terms of the equations derived.     

A comparison of deoxynivalenol intake and urinary deoxynivalenol in UK adults

The relationship between deoxynivalenol (DON) intake and first morning urinary DON was examined in UK adults to validate the latter as a biomarker of human exposure. DON was assessed in first morning samples collected during a period of normal diet, a wheat-restriction intervention diet, and partial wheat-restriction intervention in which bread was allowed. During the partial intervention duplicate bread portions were collected for DON analysis. During the normal diet, partial intervention and full intervention, urinary DON was detected in 198/210 (geometric mean 10.1?ng DON mg^?1 creatinine, 95% confidence interval (CI) 8.6–11.6?ng mg^?1; range nd–70.7?ng mg^?1), in 94/98 (5.9?ng mg^?1, 95% CI 4.8–7.0?ng mg^?1; range nd–28.4?ng mg^?1), and 17/40 (0.5?ng mg^?1, 95% CI 0.3–0.7?ng mg^?1; range nd–3.3?ng mg^?1) volunteers, respectively. A strong correlation between DON intake and the urinary biomarker was observed (p <0.001, adjusted r²?=?0.83) in models adjusting for age, sex and body mass index. These data demonstrate a quantitative correlation between DON exposure and urinary DON, and serve to validate the use of urinary DON as an exposure biomarker.     

Mechanical aspects of cell shape regulation and signaling

Physical forces play a critical role in cell integrity and development, but little is known how cells convert mechanical signals into biochemical responses. This mini-review examines potential molecular mediators like integrins, focal adhesion proteins, and the cytoskeleton in the context of a complex cell structure. These molecules-when activated by cell binding to the extracellular matrix-associate with the skeletal scaffold via the focal adhesion complex. Vinculin is presented as a mechanical coupling protein that contributes to the integrity of the cytoskeleton and cell shape control, and examples are given of how mechanical signals converge into biochemical responses through force-dependent changes in cell geometry and molecular mechanics.     

Transgenesis changes body and head shape in Pacific salmon

Insertion of a pOnMTGH1 gene construct into coho salmon altered centroid size significantly (P<0·05). The dorsal caudal peduncle and abdominal regions were also distinctly enhanced in transgenic fish when compared to controls. Shape change patterns of both whole body and syncranium were prominent.     

Determination of hair structure and shape

The hair follicle attracted significant attention as a model for the investigation of diverse biological problems. Whereas its morphology and the structure of the hair shaft are known in detail, the molecular biology of this miniorgan is significantly less characterised. Many efforts focussed on the development of the hair follicle and its stem cell reservoir; by contrast, the follicular product, the hair, which is interesting not only in terms of cosmetics was neglected. This review highlights our current knowledge of the control of hair structure and shape with emphasis on mouse hair follicle biology and discusses continuing problems.     

Genetics of body shape and armour variation in threespine sticklebacks

Patterns of genetic variation and covariation can influence the rate and direction of phenotypic evolution. We explored the possibility that the parallel morphological evolution seen in threespine stickleback (Gasterosteus aculeatus) populations colonizing freshwater environments is facilitated by patterns of genetic variation and covariation in the ancestral (marine) population. We estimated the genetic (G) and phenotypic (P) covariance matrices and directions of maximum additive genetic (g(max) ) and phenotypic (p(max) ) covariances of body shape and armour traits. Our results suggest a role for the ancestral G in explaining parallel morphological evolution in freshwater populations. We also found evidence of genetic constraints owing to the lack of variance in the ancestral G. Furthermore, strong genetic covariances and correlations among traits revealed that selective factors responsible for threespine stickleback body shape and armour divergence may be difficult to disentangle. The directions of g(max) and p(max) were correlated, but the correlations were not high enough to imply that phenotypic patterns of trait variation and covariation within populations are very informative of underlying genetic patterns.