Y-STR diversity and sex-biased gene flow among Caribbean populations

In the present study, we report, for the first time, the allele and haplotype frequencies of 17 Y-STR (Y-filer) loci in the populations of Haiti, Jamaica and the Bahamas (Abaco, Eleuthera, Exuma, Grand Bahama, Long Island and New Providence). This investigation was undertaken to assess the paternal genetic structure of the abovementioned Caribbean islands. A total of 607 different haplotypes were identified among the 691 males examined, of which 537 (88.5%) were unique. Haplotype diversities (HD) ranged from 0.989 in Long Island to 1.000 in Grand Bahama, with limited haplotype sharing observed among these Caribbean collections. Discriminatory capacity (DC) values were also high, ranging from 79.1% to 100% in Long Island and Grand Bahama, respectively, illustrating the capacity of this set of markers to differentiate between patrilineal related individuals within each population. Phylogenetic comparison of the Bahamian, Haitian and Jamaican groups with available African, European, East Asian and Native American populations reveals strong genetic ties with the continental African collections, a finding that corroborates our earlier work using autosomal STR and Y-chromosome binary markers. In addition, various degrees of sex-biased gene flow exhibiting disproportionately higher European paternal (as compared to autosomal) influences were detected in all Caribbean islands genotyped except for Abaco and Eleuthera. We attribute the presence or absence of asymmetric gene flow to unique, island specific demographic events and family structures.     

Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS

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Postnatal development in Andersen's leaf-nosed bat Hipposideros pomona: flight, wing shape, and wing bone lengths

Postnatal changes in flight development, wing shape and wing bone lengths of 56 marked neonate Hipposideros pomona were investigated under natural conditions in southwest China. Flight experiments showed that pups began to flutter with a short horizontal displacement at 10 days and first took flight at 19 days, with most achieving sustained flight at 1 month old. Analysis of covariance on wingspan, wing area, and the other seven wing characteristics between ‘pre-flight’ and ‘post-volancy’ periods supports the hypothesis that growth had one ‘pre-flight’ trajectory and a different ‘post-volancy’ trajectory in bats. Wingspan, handwing length and area, armwing length and area, and total wing area increased linearly until the age of first flight, after which the growth rates decreased (all P < 0.001). Wing loading declined linearly until day 19 before ultimately decreasing to adult levels (P < 0.001). Additionally, the relationship of different pairwise combinations of bony components composing span-wise length and chord-wise length was evaluated to test the hypothesis that compensatory growth of wing bones in H. pomona occurred in both ‘pre-flight’ and ‘post-volancy’ periods. The frequency of short-long and long-short pairs was significantly greater than that of short-short, long-long pairs in most pairs of bone elements in adults. The results indicate that a bone ‘shorter than expected’ would be compensated by a bone or bones ‘longer than expected’, suggesting compensatory growth in H. pomona. The pairwise comparisons conducted in adults were also performed in young bats during ‘pre-flight’ and ‘post-volancy’ periods, demonstrating that compensatory growth occurred throughout postnatal ontogeny.     

Paths to last in mixed crop–livestock farming: lessons from an assessment of farm trajectories of change

Mixed crop–livestock systems, combining livestock and cash crops at farm level, are considered to be suitable for sustainable intensification of agriculture. Ensuring the survival of mixed crop–livestock systems is a challenge for European agriculture: the number of European mixed crop–livestock farms has been decreasing since 1970. Analysis of farming system dynamics may elucidate past changes and the forces driving this decline. The objectives of this study were (i) to identify the diversity of paths that allowed the survival of mixed crop–livestock farming and (ii) to elucidate the driving forces behind such survival. We analysed the variety of farm trajectories from 1950 to 2005. We studied the entire farm population of a case study site, located in the ‘Coteaux de Gascogne’ region. In this less favoured area of south-western France, farmers have limited specialisation. Currently, half of the farms use mixed crop–livestock systems. The data set of 20 variables for 50 farms on the basis of six 10-year time steps was collected through retrospective surveys. We used a two-step analysis including (i) a visual assessment of the whole population of individual farm trajectories and (ii) a computer-based typology of farm trajectories on the basis of a series of multivariate analyses followed by automatic clustering. The European Common Agricultural Policy, market globalisation and decreasing workforce availability were identified as drivers of change that favoured the specialisation process. Nevertheless, farmers’ choices and values have opposed against these driving forces, ensuring the survival of some mixed crop–livestock farming systems. The trajectories were clustered into five types, four of which were compatible with mixed crop–livestock systems. The first type was the maximisation of autonomy by combining crops and livestock. The second type was diversification of production to exploit economies of scope and protect the farm against market fluctuations. The other two types involved enlargement and progressive adaptation of the farm to the familial workforce. The survival of mixed crop–livestock systems in these two types is largely dependent on workforce availability. Only one type of trajectory, on the basis of enlargement and economies of scale, did not lead to mixed crop–livestock systems. In view of the current evolution of the driving forces, maximising autonomy and diversification appear to be suitable paths to deal with current challenges and maintain mixed crop–livestock systems in Europe.     

hCLP46 regulates U937 cell proliferation via Notch signaling pathway

Human CAP10-like protein 46 kDa (hCLP46) is the homolog of Rumi, which is the first identified protein O-glucosyltransferase that modifies Notch receptor in Drosophila. Dysregulation of hCLP46 occurs in many hematologic diseases, but the role of hCLP46 remains unclear. Knockdown of hCLP46 by RNA interference resulted in decreased protein levels of endogenous Notch1, Notch intracellular domain (NICD) and Notch target gene Hes-1, suggesting the impairment of the Notch signaling. However, neither cell surface Notch expression nor ligand binding activities were affected. In addition, down-regulated expression of hCLP46 inhibited the proliferation of U937 cells, which was correlated with increased cyclin-dependent kinase inhibitor (CDKI) CDKN1B (p27) and decreased phosphorylation of retinoblastoma (RB) protein. We showed that lack of hCLP46 results in impaired ligand induced Notch activation in mammalian cell, and hCLP46 regulates the proliferation of U937 cell through CDKI-RB signaling pathway, which may be important for the pathogenesis of leukemia.     

Speed-dependent reference joint trajectory generation for robotic gait support

For the control of actuated orthoses, or gait rehabilitation robotics, kinematic reference trajectories are often required. These trajectories, consisting of joint angles, angular velocities and accelerations, are highly dependent on walking-speed. We present and evaluate a novel method to reconstruct body-height and speed-dependent joint trajectories. First, we collected gait kinematics in fifteen healthy (middle) aged subjects (47–68), at a wide range of walking-speeds (0.5–5 kph). For each joint trajectory multiple key-events were selected (among which its extremes). Second, we derived regression-models that predict the timing, angle, angular velocity and acceleration for each key-event, based on walking-speed and the subject?s body-height. Finally, quintic splines were fitted between the predicted key-events to reconstruct a full gait cycle. Regression-models were obtained for hip ab-/adduction, hip flexion/extension, knee flexion/extension and ankle plantar-/dorsiflexion. Results showed that the majority of the key-events were dependent on walking-speed, both in terms of timing and amplitude, whereas the body-height had less effect. The reconstructed trajectories matched the measured trajectories very well, in terms of angle, angular velocity and acceleration. For the angles the RMSE between the reconstructed and measured trajectories was 2.6°. The mean correlation coefficient between the reconstructed and measured angular trajectories was 0.91. The method and the data presented in this paper can be used to generate speed-dependent gait patterns. These patterns can be used for the control of several robotic gait applications. Alternatively they can assist the assessment of pathological gait, where they can serve as a reference for “normal” gait.     

A Fourier transform infrared spectroscopy study of cell membrane domain modifications induced by docosahexaenoic acid

Background

Detergent resistant membranes (DRMs) are a useful model system for the in vitro characterization of cell membrane domains. Indeed, DRMs provide a simple model to study the mechanisms underlying several key cell processes based on the interplay between specific cell membrane domains on one hand, and specific proteins and/or lipids on the other. Considering therefore their biological relevance, the development of methods capable to provide information on the composition and structure of membrane domains and to detect their modifications is highly desirable. In particular, Fourier transform infrared (FTIR) spectroscopy is a vibrational tool widely used for the study not only of isolated and purified biomolecules but also of complex biological systems, including intact cells and tissues. One of the main advantages of this non-invasive approach is that it allows obtaining a molecular fingerprint of the sample under investigation in a rapid and label-free way.

Methods

Here we present an FTIR characterization of DRM fractions purified from the human breast cancer cells MCF-7, before and after treatment with the omega 3 fatty acid docosahexaenoic acid (DHA), which was found to promote membrane microdomain reorganization.

Results and Conclusions

We will show that FTIR spectroscopy coupled with multivariate analysis enables to monitor changes in the composition of DRMs, induced in particular by the incorporation of DHA in cell membrane phospholipids.

General significance

This study paves the way for a new label-free characterization of specific membrane domains within intact cells, which could provide complementary information to the fluorescence approaches presently used.     

A comparison of toxicant-induced succession for five antifouling compounds on marine periphyton in SWIFT microcosms

Five antifouling biocides, chlorothalonile, dichlofluanide, medetomidine, tolylfluanide, and zinc pyrithione, were evaluated regarding their effect on the composition of the periphyton community and the subsequent toxicant-induced succession (TIS). The periphyton communities were exposed in a semi-static setting for 96 h using a SWIFT microcosm. As a measure of community composition, pigment profiles from the exposed communities were used as effect indicators and compared with unexposed parts of the same community using the Bray–Curtis dissimilarity index. Chlorothalonile caused changes in the community starting at 85 μg l^?1 while dichlofluanide had no effect even at the highest concentrations used, 810 μg l^?1. The related substance tolylfluanide only affected the community composition at 2700 μg l^?1. Medetomidine had a different response curve with a small effect on the community composition at 0.8 μg l^?1 which then disappeared only to reappear at 240 μg l^?1. Zinc pyrithione had the largest effect on the periphyton community with changes starting at 10 μg l^?1 and no detectable pigments at 100 μg l^?1. The changes in the community composition for the five substances were also compared using multidimensional scaling. When all substances were analyzed and plotted together, chlorothalonile, dichlofluanide, medetomidine, and tolylfluanide showed surprisingly similar effects compared to zinc pyrithione that gave very different TIS. However, when only chlorothalonile, dichlofluanide, and tolylfluanide were plotted together, clear differences in TIS between the three toxicants were revealed. Dichlofluanide only induced small effects, while concentration-dependent TIS trajectories for chlorothalonile and tolylfluanide took off in opposite directions indicating very different responses of the periphyton communities. This study demonstrates that substances with a similar chemical structure and mechanisms of action can have different effects on the community composition. With the exception of zinc pyrithione, none of the recorded effect levels were at concentrations reported from marine environments so far.     

Individual variation in growth trajectories: phenotypic and genetic correlations in ontogeny of the house finch (Carpodacus mexicanus)

We studied patterns of growth in a recently established natural population of the house finch (Carpodacus mexicanus) to examine whether phenotypic and genetic covariation among age‐specific trait values is likely to constrain morphological change favoured by selection acting on adults. We found variable patterns of allometric relationships during ontogeny, and documented relatively weak covariations among ages or among traits in individual growth trajectories. Frequent compensatory growth largely cancelled out the initial differences among nestlings, potentially enabling house finches to raise offspring under diverse and unpredictable environmental conditions. Moderate levels of additive genetic variance in morphological traits throughout ontogeny, and relatively low and fluctuating phenotypic and genetic covariation among ages imply strong potential for evolutionary change in morphological traits under selection. This conclusion is consistent with the profound population‐level divergence in morphological patterns that accompanied very successful colonization of most of North America by the house finch over the last 50 years.