Genetics,History, and Identity: The Case of the Bene Israel and the Lemba

The paper examines the impact of genetic research on the religious identity of the Bene Israel Indian Jewish community and the Lemba Judaising group of southern Africa. It demonstrates how DNA tests which happened to support the possibility of the communities' legends of origin affected their self-perception, the way they are viewed by their neighbors, and their image in the West. It is argued that in both cases what accounted most for the Bene Israel and Lemba responses to the tests was the way the results were portrayed in the mass media, the history of the development of Judaism in their communities, and the local realities.     

The Seven Daughters of Eve: The Science That Reveals Our Genetic Ancestry

The Seven Daughters of Eve: The Science That Reveals Our Genetic Ancestry. Bryan Sykes. New York: W. W. Norton and Company, Inc., 2001. 306 pp.     

Comparative Genomics of Gardnerella vaginalis Strains Reveals Substantial Differences in Metabolic and Virulence Potential

Background

Gardnerella vaginalis is described as a common vaginal bacterial species whose presence correlates strongly with bacterial vaginosis (BV). Here we report the genome sequencing and comparative analyses of three strains of G. vaginalis. Strains 317 (ATCC 14019) and 594 (ATCC 14018) were isolated from the vaginal tracts of women with symptomatic BV, while Strain 409-05 was isolated from a healthy, asymptomatic individual with a Nugent score of 9.

Principal Findings

Substantial genomic rearrangement and heterogeneity were observed that appeared to have resulted from both mobile elements and substantial lateral gene transfer. These genomic differences translated to differences in metabolic potential. All strains are equipped with significant virulence potential, including genes encoding the previously described vaginolysin, pili for cytoadhesion, EPS biosynthetic genes for biofilm formation, and antimicrobial resistance systems, We also observed systems promoting multi-drug and lantibiotic extrusion. All G. vaginalis strains possess a large number of genes that may enhance their ability to compete with and exclude other vaginal colonists. These include up to six toxin-antitoxin systems and up to nine additional antitoxins lacking cognate toxins, several of which are clustered within each genome. All strains encode bacteriocidal toxins, including two lysozyme-like toxins produced uniquely by strain 409-05. Interestingly, the BV isolates encode numerous proteins not found in strain 409-05 that likely increase their pathogenic potential. These include enzymes enabling mucin degradation, a trait previously described to strongly correlate with BV, although commonly attributed to non-G. vaginalis species.

Conclusions

Collectively, our results indicate that all three strains are able to thrive in vaginal environments, and therein the BV isolates are capable of occupying a niche that is unique from 409-05. Each strain has significant virulence potential, although genomic and metabolic differences, such as the ability to degrade mucin, indicate that the detection of G. vaginalis in the vaginal tract provides only partial information on the physiological potential of the organism.     

The viability of ethnic democracy: Jewish citizens in inter-war Poland and Palestinian citizens in Israel

Ethnic democracies are sustainable only if the two conflicting constitutional principles defining them as such – ethno-nationalism and liberal democracy – are successfully mediated by a third principle, of whatever kind. This is demonstrated through a comparative examination of inter-war Poland (1918–39), where ethnic democracy, while written into the constitution, never really took hold, and Israel (within its pre-1967 borders), where ethnic democracy was stable for thirty-five years (1966–2000) but may now be eroding. In both cases the fate of ethnic democracy is shown to be determined by the existence, lack, or decline of the mediating third principle.     

Proteomic Profiling of Cereal Aphid Saliva Reveals Both Ubiquitous and Adaptive Secreted Proteins

The secreted salivary proteins from two cereal aphid species, Sitobion avenae and Metopolophium dirhodum, were collected from artificial diets and analysed by tandem mass spectrometry. Protein identification was performed by searching MS data against the official protein set from the current pea aphid (Acyrthosiphon pisum) genome assembly and revealed 12 and 7 proteins in the saliva of S. avenae and M. dirhodum, respectively. When combined with a comparable dataset from A. pisum, only three individual proteins were common to all the aphid species; two paralogues of the GMC oxidoreductase family (glucose dehydrogenase; GLD) and ACYPI009881, an aphid specific protein previously identified as a putative component of the salivary sheath. Antibodies were designed from translated protein sequences obtained from partial cDNA sequences for ACYPI009881 and both saliva associated GLDs. The antibodies detected all parent proteins in secreted saliva from the three aphid species, but could only detect ACYPI009881, and not saliva associated GLDs, in protein extractions from the salivary glands. This result was confirmed by immunohistochemistry using whole and sectioned salivary glands, and in addition, localised ACYPI009881 to specific cell types within the principal salivary gland. The implications of these findings for the origin of salivary components and the putative role of the proteins identified are discussed in the context of our limited understanding of the functional relationship between aphid saliva and the plants they feed on. The mass spectrometry data have been deposited to the ProteomeXchange and can be accessed under the identifier PXD000113.     

The good Arab: conditional inclusion and settler colonial citizenship among Palestinian citizens of Israel in Jewish Tel Aviv

Dominant majorities often use idealized categories to validate the ‘goodness’ and deservingness of minority citizens. For Palestinian citizens of Israel, this category is the ‘good Arab’. Since its origins in early Jewish settlement of Palestine, it has become a powerful and controversial metaphor in Israeli public discourse. As an experienced condition of limited inclusion, the ‘good Arab’ exemplifies the Palestinian dilemma of accessing socioeconomic opportunities in Jewish Israeli spaces that stigmatize and fend off their ethnonational identity. Combining a historical genealogy of the ‘good Arab’ with ethnographic research among Palestinians in Tel Aviv, this article shows how a historically evolved logic of settler colonial control and indigenous erasure continues to define liberal frameworks of conditional citizenship and inclusion. Theorized through the emerging concept of conditional inclusion, these insights open up new avenues for analysis and comparison in anthropological debates surrounding indigenous struggles, settler colonialism, urban inclusion, and citizenship.     

Population Genetics of Streptococcus dysgalactiae Subspecies equisimilis Reveals Widely Dispersed Clones and Extensive Recombination

Background

Streptococcus dysgalactiae subspecies equisimilis (SDSE) is an emerging global pathogen that can colonize and infect humans. Although most SDSE isolates possess the Lancefield group G carbohydrate, a significant minority have the group C carbohydrate. Isolates are further sub-typed on the basis of differences within the emm gene. To gain a better understanding of their molecular epidemiology and evolutionary relationships, multilocus sequence typing (MLST) analysis was performed on SDSE isolates collected from Australia, Europe and North America.

Methodology/Principal Findings

The 178 SDSE isolates, representing 37 emm types, segregate into 80 distinct sequence types (STs) that form 17 clonal complexes (CCs). Eight STs recovered from all three continents account for >50% of the isolates. Thus, a small number of STs are highly prevalent and have a wide geographic distribution. Both ST and CC strongly correlate with group carbohydrate. In contrast, eleven STs were associated with >1 emm type, suggestive of recombinational replacements involving the emm gene; furthermore, 35% of the emm types are associated with genetically distant STs. Data also reveal a history of extensive inter- and intra-species recombination involving the housekeeping genes used for MLST. Sequence analysis of single locus variants identified through goeBURST indicates that genetic change mediated by recombination occurred ∼4.4 times more frequently than by point mutation.

Conclusions/Significance

A few genetic lineages with an intercontinental distribution dominate among SDSE causing infections in humans. The distinction between group C and G isolates reflects recent evolution, and no long-term genetic isolation between them was found. Lateral gene transfer and recombination involving housekeeping genes and the emm gene are important mechanisms driving genetic variability in the SDSE population.     

印度北方河流中主要鲤科鱼类卡拉(鱾)的年龄和生长

为了获得印度北部赣达(Ganga)盆地河流中野生卡特拉(鱾)种群的年龄结构和重要生长参数,对该鱼的年龄和生长进行了研究.鳞片取自商业捕捞和实验室饲养的样品.根据研究分析,该鱼最大年龄可达8龄;巴吉拉蒂河(Bhagirathi R.)的种群平均体长为521.51 mm,退算体长为288.9-1132.3 mm;旁遮普邦(Punjab)Satluj河种群平均体长为641.6 mm,退算体长为335.4-1096.08 mm.2龄时,种群线性生长率(Cl)和体重增加率(Cw)表现出迅速下降的趋势.其它生长参数值(Clt)也呈现快速下降.退算体长差异(ANOVA)分析显示,生活在赣达盆地不同流域中的种群,1 -4 龄组的长度差异较明显(P<0.05),高龄组(5 -8 )差异不显著.根据本项研究结果,提出了对印度北部赣达盆地相关河流中生活的野生卡特拉(鱾)种群资源持续利用的对策.     

印度北方河流中主要鲤科鱼类卡拉鲃的年龄和生长

为了获得印度北部赣达（Ganga）盆地河流中野生卡特拉鲃种群的年龄结构和重要生长参数,对该鱼的年龄和生长进行了研究。鳞片取自商业捕捞和实验室饲养的样品。根据研究分析,该鱼最大年龄可达8龄;巴吉拉蒂河（Bhagirathi R.）的种群平均体长为521.51 mm,退算体长为288.9 -1132.3 mm;旁遮普邦（Punjab）Satluj河种群平均体长为641.6 mm,退算体长为335.4 -1096.08 mm。2龄时,种群线性生长率（Cl）和体重增加率（Cw）表现出迅速下降的趋势。其它生长参数值（Clt）也呈现快速下降。退算体长差异（ANOVA）分析显示,生活在赣达盆地不同流域中的种群, 1^＋-4^＋龄组的长度差异较明显（P〈0.05） ,高龄组（5^＋-8^＋）差异不显著。根据本项研究结果,提出了对印度北部赣达盆地相关河流中生活的野生卡特拉鲃种群资源持续利用的对策。     

The diet of Indian foxes in a peri-urban area of eastern India

Urban expansions into natural habitats have forced many carnivores to adapt to the modified areas; however, our understanding of their ecology in such areas is limited. The Indian fox (Vulpes bengalensis) is a small carnivore species that can adapt and exploit urban areas due to its generalist nature, but there is a paucity of data on Indian foxes in these human-modified areas. To understand the resource requirement of Indian foxes in urban habitats, we conducted a diet analysis by examining 119 scats of Indian foxes in a peri-urban habitat of Baripada town, Odisha, eastern India. To determine the diet composition of Indian foxes, we analyzed scat contents by their frequency occurrence (%FO), the relative frequency of occurrence (%RF) and mean percent volume (%Vm). Indian foxes consumed a wide range of food categories, including arthropods, rodents, reptiles, birds, plant parts and anthropogenic resources. In %Vm, rodents showed the highest volume, followed by polythene, Spondias pinnata fruit and Coleoptera. We found anthropogenic foods in considerable quantities, including polythene and paper. The diet of Indian foxes indicates that the species has opportunistic and generalist feeding habits consisting primarily of easily accessible foods. Furthermore, management efforts should focus on the proper management of waste and control of anthropogenic food sources in urban habitats.     

A Reporter Assay in Lamprey Embryos Reveals Both Functional Conservation and Elaboration of Vertebrate Enhancers

The sea lamprey is an important model organism for investigating the evolutionary origins of vertebrates. As more vertebrate genome sequences are obtained, evolutionary developmental biologists are becoming increasingly able to identify putative gene regulatory elements across the breadth of the vertebrate taxa. The identification of these regions makes it possible to address how changes at the genomic level have led to changes in developmental gene regulatory networks and ultimately to the evolution of morphological diversity. Comparative genomics approaches using sea lamprey have already predicted a number of such regulatory elements in the lamprey genome. Functional characterisation of these sequences and other similar elements requires efficient reporter assays in lamprey. In this report, we describe the development of a transient transgenesis method for lamprey embryos. Focusing on conserved non-coding elements (CNEs), we use this method to investigate their functional conservation across the vertebrate subphylum. We find instances of both functional conservation and lineage-specific functional evolution of CNEs across vertebrates, emphasising the utility of functionally testing homologous CNEs in their host species.