Comparative analysis of multiple protein-sequence alignment methods [published erratum appears in Mol Biol Evol 1994 Sep;11(5):811]

We have analyzed a total of 12 different global and local multiple protein-sequence alignment methods. The purpose of this study is to evaluate each method's ability to correctly identify the ordered series of motifs found among all members of a given protein family. Four phylogenetically distributed sets of sequences from the hemoglobin, kinase, aspartic acid protease, and ribonuclease H protein families were used to test the methods. The performance of all 12 methods was affected by (1) the number of sequences in the test sets, (2) the degree of similarity among the sequences, and (3) the number of indels required to produce a multiple alignment. Global methods generally performed better than local methods in the detection of motif patterns.      

Cool and Crazy: Anthropological Film at the Point of Convergence between Humanities and Social Science

ABSTRACT

The use of film as a tool in anthropological fieldwork is a challenge to traditional ways of thinking about scientific research. Nevertheless, documentary filming of the informants in their own context has proved to be an interesting supplement in the exploration of what the anthropological research field actually covers. Furthermore, film work confronts the researchers with aesthetic aspects of mediation that have not been epistemically well attended to within social science. This article highlights pivotal problems in the professional no-man's-land where visual culture studies take place, as exemplified by the film Cool and Crazy.     

Wearing the veil: hijab,Islam and job qualifications as determinants of social attitudes towards immigrant women in Norway

Immigrant women are a particularly vulnerable part of the immigrant population. In this paper we analyse negative attitudes towards immigrant women in Norway. We focus on immigrant women’s formal job qualifications, their religious background and wearing of hijab – the headscarf sometimes used by Muslim women. Using survey-embedded experiments we are able to analyse the net effects on attitudes of job qualifications, Islamic religious background and the hijab. The results show that native population frequently has more negative views of Muslim women who wear a hijab. The negative effects of a hijab do not seem to be strongly reduced if a woman wearing it has higher education. With a single exception, the results also show that Muslim background in itself (i.e. without the hijab) does not have any strong effect on attitudes of the native population towards immigrant women.     

Bucking the trend: the African Black Oystercatcher as a recent conservation success story

The African Black Oystercatcher Haematopus moquini is a charismatic, southern African near-endemic, wader species, that is often seen as a flagship species for coastal bird conservation, as it was recently down-listed regionally to Least Concern on the IUCN Red List of Threatened Species. To celebrate this rare conservation success story, BirdLife South Africa named it the 2018 Bird of the Year and ran a year-long programme in collaboration with the Nature’s Valley Trust highlighting aspects of the species’ biology, current threats, and conservation success. We used data collected by the Southern African Bird Atlas Project (SABAP1 and SABAP2) to examine changes in the species’ range and relative abundance, both in the records between the two projects, as well as trends within the SABAP2 sampling period (2008–2017). This case study enabled us to assess whether such metrics can accurately reflect abundance and distributional changes in a species. We found increases in the reported range and the reporting rates between the two Atlas projects, and that the SABAP2 reporting rate was stable. Regionally, across four coastal categories, the reporting rate was lowest in KwaZulu-Natal, though this region also showed an increase in the probability of reporting during the SABAP2 period. While corroborating the recent change in the species’ conservation status, we also provide good evidence that the long-term SABAP data can be used successfully to assess population trends and range changes over time.     

Developmental effects of testosterone on behavior in male and female green anoles (Anolis carolinensis)

This study addressed the role of testosterone (T) in the development of sexually dimorphic behavior in the green anole lizard, Anolis carolinensis. We documented the pattern of endogenous T concentrations during ontogeny and we determined the behavioral effects of experimentally elevated T in juvenile males and females. T concentrations were measured in the plasma of hatchlings from eggs incubated in the laboratory, in juveniles of all sizes sampled in the field, and in the yolks of freshly laid eggs in the laboratory and were compared to plasma T in adult females (measured in this study) and adult males. There were no sex differences in plasma T in hatchling and small juvenile (<26-mm snout-vent length, SVL; <14 days old) males and females, concentrations of which in both sexes tended to decline over the 14-day posthatching period. Plasma T sharply increased in juvenile males, but not females, after approximately 14 days posthatching (>25-mm SVL), and it became significantly higher after approximately 38 days posthatching (>30-mm SVL). Plasma T for juvenile males was within the range detected in breeding adult females, but it was 20- to 45-fold lower than that of adult males, breeding or postbreeding. All eggs contained detectable yolk T, but eggs that gave rise to males contained nearly twice as much yolk T as those that gave rise to females. We do not know whether this yolk T comes from the mother, embryo, or both. In behavior trials conducted in the laboratory, juveniles (36- to 42-mm SVL) with T implants, regardless of whether they were male or female, had increased activity levels compared to juveniles with blank implants, due to increased rates of nearly every behavior monitored. These results are discussed in the context of the organization-activation theory of sexual differentiation and the particular life history of A. carolinensis.     

Induction of homologous recombination in the hprt gene of V79 Chinese hamster cells in response to low- and high-LET irradiation

Dense ionization tracks from high linear energy transfer (LET) radiations form multiple damaged sites (MDS), which involve several types of DNA lesions in close vicinity. The primary DNA damage triggers sensor proteins that activate repair processes, cell cycle control or eventually apoptosis in subsequent cellular responses. The question how homologous recombination (HR) and non-homologous end joining (NHEJ) interact in the repair of radiation-induced DNA damage of MDS type has been addressed in different model systems but several questions remain to be answered. We have therefore challenged cells with treatments of ionizing radiation of different qualities to investigate whether primary DNA damages of different complexity are reflected in the processes of repair by HR as well as cell survival. We used the V79 derived SPD8 cell line to determine the induction of HR in the hprt exon 7 and clonogenic assay for survival in response to radiation. SPD8 cells were irradiated with gamma-rays (137Cs 0.5 keV/microm), boron ions (40 and 80 keV/microm) and nitrogen ions (140 keV/microm), with doses up to 5 Gy. Analysis of clonogenic survival showed that B-ions (80 keV/microm) and N-ions were more toxic than gamma-rays, 4.1 and 5.0 times respectively, while B-ions at 40 keV/microm were 2.0 times as toxic as gamma-rays. Homologous recombination in the cells exposed to B-ions (80 keV/microm) increased 2.9 times, a significant response as compared to cells exposed to gamma-rays, while for B-ions (40 keV/microm) and N-ions a nonsignificant increase in HR of 1.2 and 1.4, respectively, was observed. We hypothesize that the high-LET generated formation of MDS is responsible for the enhanced cytotoxicity as well as for the mobilization of the HR machinery.