Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications.

BACKGROUND: The evolutionary lineage leading to the teleost fish underwent a whole genome duplication termed FSGD or 3R in addition to two prior genome duplications that took place earlier during vertebrate evolution (termed 1R and 2R). Resulting from the FSGD, additional copies of genes are present in fish, compared to tetrapods whose lineage did not experience the 3R genome duplication. Interestingly, we find that ParaHox genes do not differ in number in extant teleost fishes despite their additional genome duplication from the genomic situation in mammals, but they are distributed over twice as many paralogous regions in fish genomes. RESULTS: We determined the DNA sequence of the entire ParaHox C1 paralogon in the East African cichlid fish Astatotilapia burtoni, and compared it to orthologous regions in other vertebrate genomes as well as to the paralogous vertebrate ParaHox D paralogons. Evolutionary relationships among genes from these four chromosomal regions were studied with several phylogenetic algorithms. We provide evidence that the genes of the ParaHox C paralogous cluster are duplicated in teleosts, just as it had been shown previously for the D paralogon genes. Overall, however, synteny and cluster integrity seems to be less conserved in ParaHox gene clusters than in Hox gene clusters. Comparative analyses of non-coding sequences uncovered conserved, possibly co-regulatory elements, which are likely to contain promoter motives of the genes belonging to the ParaHox paralogons. CONCLUSION: There seems to be strong stabilizing selection for gene order as well as gene orientation in the ParaHox C paralogon, since with a few exceptions, only the lengths of the introns and intergenic regions differ between the distantly related species examined. The high degree of evolutionary conservation of this gene cluster's architecture in particular - but possibly clusters of genes more generally - might be linked to the presence of promoter, enhancer or inhibitor motifs that serve to regulate more than just one gene. Therefore, deletions, inversions or relocations of individual genes could destroy the regulation of the clustered genes in this region. The existence of such a regulation network might explain the evolutionary conservation of gene order and orientation over the course of hundreds of millions of years of vertebrate evolution. Another possible explanation for the highly conserved gene order might be the existence of a regulator not located immediately next to its corresponding gene but further away since a relocation or inversion would possibly interrupt this interaction. Different ParaHox clusters were found to have experienced differential gene loss in teleosts. Yet the complete set of these homeobox genes was maintained, albeit distributed over almost twice the number of chromosomes. Selection due to dosage effects and/or stoichiometric disturbance might act more strongly to maintain a modal number of homeobox genes (and possibly transcription factors more generally) per genome, yet permit the accumulation of other (non regulatory) genes associated with these homeobox gene clusters.

Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India

The aim of the present study was to compare polymerase chain reaction (PCR)-based methods - spoligotyping and mycobacterial interspersed repetitive units (MIRU) typing - with the gold-standard IS6110 restriction fragment length polymorphism (RFLP) analysis in 101 isolates of Mycobacterium tuberculosis to determine the genetic diversity of M. tuberculosis clinical isolates from Delhi, North India. Spoligotyping resulted in 49 patterns (14 clusters); the largest cluster was composed of Spoligotype International Types (SITs)26 [Central-Asian (CAS)1-Delhi lineage], followed by SIT11 [East-African-Indian (EAI) 3-Indian lineage]. A large number of isolates (75%) belonged to genotypic lineages, such as CAS, EAI and Manu, with a high specificity for the Indian subcontinent, emphasising the complex diversity of the phylogenetically coherent M. tuberculosis in North India. MIRU typing, using 11 discriminatory loci, was able to distinguish between all but two strains based on individual patterns. IS6110-RFLP analysis (n = 80 strains) resulted in 67 unique isolates and four clusters containing 13 strains. MIRUs discriminated all 13 strains, whereas spoligotyping discriminated 11 strains. Our results validate the use of PCR-based molecular typing of M. tuberculosis using repetitive elements in Indian isolates and demonstrate the usefulness of MIRUs for discriminating low-IS6110-copy isolates, which accounted for more than one-fifth of the strains in the present study.

The karyotype of Crocidura flavescens (Mammalia, Insectivora) in South Africa

Karyological results give evidence that the South African Crocidura flavescens (Geoffroy, 1827) is not conspecific with the West and East African giant shrews of the taxa spurrelli, manni, kivu and olivieri

Geometric morphometric analyses provide evidence for the adaptive character of the Tanganyikan cichlid fish radiations.

The cichlids of East Africa are renowned as one of the most spectacular examples of adaptive radiation. They provide a unique opportunity to investigate the relationships between ecology, morphological diversity, and phylogeny in producing such remarkable diversity. Nevertheless, the parameters of the adaptive radiations of these fish have not been satisfactorily quantified yet. Lake Tanganyika possesses all of the major lineages of East African cichlid fish, so by using geometric morphometrics and comparative analyses of ecology and morphology, in an explicitly phylogenetic context, we quantify the role of ecology in driving adaptive speciation. We used geometric morphometric methods to describe the body shape of over 1000 specimens of East African cichlid fish, with a focus on the Lake Tanganyika species assemblage, which is composed of more than 200 endemic species. The main differences in shape concern the length of the whole body and the relative sizes of the head and caudal peduncle. We investigated the influence of phylogeny on similarity of shape using both distance-based and variance partitioning methods, finding that phylogenetic inertia exerts little influence on overall body shape. Therefore, we quantified the relative effect of major ecological traits on shape using phylogenetic generalized least squares and disparity analyses. These analyses conclude that body shape is most strongly predicted by feeding preferences (i.e., trophic niches) and the water depths at which species occur. Furthermore, the morphological disparity within tribes indicates that even though the morphological diversification associated with explosive speciation has happened in only a few tribes of the Tanganyikan assemblage, the potential to evolve diverse morphologies exists in all tribes. Quantitative data support the existence of extensive parallelism in several independent adaptive radiations in Lake Tanganyika. Notably, Tanganyikan mouthbrooders belonging to the C-lineage and the substrate spawning Lamprologini have evolved a multitude of different shapes from elongated and Lamprologus-like hypothetical ancestors. Together, these data demonstrate strong support for the adaptive character of East African cichlid radiations.

Transnational private authority and the participation of workers' organizations in the regulatory space surrounding the employment relationship

Most corporate codes of conduct and multi-stakeholder sustainability standards guarantee workers' rights to freedom of association and collective bargaining, but many authors are sceptical about the concrete impact of codes and standards of this kind. In this paper we use Hancher and Moran's (1998) concept of 'regulatory space' to assess the potential of private transnational regulation to support the growth of trade union membership and collective bargaining relationships, drawing on some preliminary case study results from a project on the impact of the International Finance Corporation's (IFC) social conditionality on worker organization and social dialogue. One of the major effects of neoliberal economic and industrial policy has been the routine exclusion of workers' organizations from regulatory processes on the grounds that they introduce inappropriate 'political' motives into what ought to be technical decision-making processes. This, rather than any direct attack on their capacity to take action, is what seems best to explain the global decline in union influence (Cradden 2004; Howell 2007; Howe 2012). The evidence we present in the paper suggests that private labour regulation may under certain conditions contribute to a reversal of this tendency, re-establishing the legitimacy of workers' organizations within regulatory processes and by extension the legitimacy of their use of economic and social power. We argue that guarantees of freedom of association and bargaining rights within private regulation schemes are effective to the extent that they can be used by workers' organizations in support of a claim for access to the regulatory space within which the terms and conditions of the employment relationship are determined. Our case study evidence shows that certain trade unions in East Africa have indeed been able to use IFC and other private regulation schemes as levers to win recognition from employers and to establish collective bargaining relationships. Although they did not attempt to use formal procedures to make a claim for the enforcement of freedom of association rights on behalf of their members, the unions did use enterprises' adherence to private regulation schemes as a normative point of reference in argument and political exchange about worker representation. For these unions, the regulation was a useful addition to the range of arguments that they could deploy as means to justify their demand for recognition by employers. By contrast, the private regulation that helps workers' organizations to win access to regulatory processes does little to ensure that they are able to participate meaningfully, whether in terms of technical capacity or of their ability to mobilize social power as a counterweight to the economic power of employers. To the extent that our East African unions were able to make an impact on terms and conditions of employment via their participation in regulatory space it was solely on the basis of their own capacities and resources and the application of national labour law.

Actitudes hacia el VIH/SIDA, el cáncer y la enfermedad de Alzheimer

Esta revisión de la literatura tuvo como objetivo describir las actitudes hacia el VIH/SIDA, el cáncer y la Enfermedad de Alzheimer desde el modelo tripartito. Se revisaron 109 artículos publicados entre 2005 y 2015 en algunas bases de datos especializadas y herramientas de análisis de impacto. También se incluyeron fuentes secundarias ampliándose la búsqueda a los últimos 20 años (1995-2015). Los resultados mostraron que la mayoría de los estudios realizados sobre las actitudes hacia estas tres enfermedades son de tipo cuantitativo y la información se analizó con base en los componentes del modelo tripartito. Algunos aspectos sociodemográficos como el sexo y la edad están asociados con las actitudes hacia las tres enfermedades y predominan las creencias erróneas sobre ellas respecto a sus causas, curso y tratamiento. También predominan actitudes negativas hacia las tres enfermedades y las conductas e intenciones conductuales son diversas hacia cada una de ellas. No se hallaron antecedentes empíricos del estudio de la estructura de las actitudes propuesta por el modelo tripartito hacia las tres enfermedades. La Salud Pública ha liderado la investigación con base en el modelo de conocimientos, actitudes y prácticas propuesto por la OMS.

Productivity of crossbred dairy cows suckling their calves for 12 or 24 weeks post calving

An experiment on restricted suckling of crossbred dairy cows was conducted at the Livestock Research Centre, Tanga in northeast Tanzania. Thirty-six Bos taurus (Holstein Friesian and Jersey) x Bos indicus (East African Zebu) cows were allocated alternately as they calved to suckling their calves for either 12 or 24 weeks after calving. Cows grazed improved pastures and were offered 4 kg concentrate daily. Milking occurred twice daily by hand; calves were allowed to suck residual milk for 30 min following each milking. Calves were also allowed access to grazing and were offered a maximum of I kg concentrate daily to 24 weeks of age. Weaning age had no significant effect on lactation milk yield for human consumption, the mean (SE) yield being 1806 (102.0) L and 1705 (129. 1) L for 12- and 24-week weaning, respectively. Cows from the two treatments suffered similar losses of live weight and body condition score during lactation and neither group had returned to the original body condition score 40 weeks following calving. Post-partum anoestrous intervals were prolonged. Although not significant, cows suckling calves to 24 weeks had a mean interval to first oestrus extended by 38 days compared with cows suckling calves to 12 weeks. The mean (SE) daily live weight gains of the calves to 52 weeks were 263 (14.1) g/day and 230 (18.1) g/day for calves weaned at 12 and 24 weeks, respectively, such that 12-month weights were 119 (5.6) kg and 110 (7.3) kg, respectively. Twelve-week-weaned calves consumed more concentrate (p < 0.05) from 13 to 24 weeks than did 24-week weaned calves. Calculation of residual milk consumption removed by calves from birth to 12 weeks indicated that it accounted for 28% of total yield. No benefits in cow and calf performance and welfare were found to justify prolonging the suckling period to 24 weeks.

Stress field control of eruption dynamics at a rift volcano: Nyamuragira, D.R.Congo

Using the record of 30 flank eruptions over the last 110 years at Nyamuragira, we have tested the relationship between the eruption dynamics and the local stress field. There are two groups of eruptions based on their duration (< 80days >) that are also clustered in space and time. We find that the eruptions fed by dykes parallel to the East African Rift Valley have longer durations (and larger volumes) than those eruptions fed by dykes with other orientations. This is compatible with a model for compressible magma transported through an elastic-walled dyke in a differential stress field from an over-pressured reservoir (Woods et al., 2006). The observed pattern of eruptive fissures is consistent with a local stress field modified by a northwest-trending, right lateral slip fault that is part of the northern transfer zone of the Kivu Basin rift segment. We have also re-tested with new data the stochastic eruption models for Nyamuragira of Burt et al. (1994). The time-predictable, pressure-threshold model remains the best fit and is consistent with the typically observed declining rate of sulphur dioxide emission during the first few days of eruption with lava emission from a depressurising, closed, crustal reservoir. The 2.4-fold increase in long-term eruption rate that occurred after 1977 is confirmed in the new analysis. Since that change, the record has been dominated by short-duration eruptions fed by dykes perpendicular to the Rift. We suggest that the intrusion of a major dyke during the 1977 volcano-tectonic event at neighbouring Nyiragongo volcano inhibited subsequent dyke formation on the southern flanks of Nyamuragira and this may also have resulted in more dykes reaching the surface elsewhere. Thus that sudden change in output was a result of a changed stress field that forced more of the deep magma supply to the surface. Another volcano-tectonic event in 2002 may also have changed the magma output rate at Nyamuragira.

The resolution sensitivity of the South Asian monsoon and Indo-Pacific in a global 0.35◦ AGCM

The South Asian monsoon is one of the most significant manifestations of the seasonal cycle. It directly impacts nearly one third of the world’s population and also has substantial global influence. Using 27-year integrations of a high-resolution atmospheric general circulation model (Met Office Unified Model), we study changes in South Asian monsoon precipitation and circulation when horizontal resolution is increased from approximately 200 to 40 km at the equator (N96 to N512, 1.9 to 0.35◦). The high resolution, integration length and ensemble size of the dataset make this the most extensive dataset used to evaluate the resolution sensitivity of the South Asian monsoon to date. We find a consistent pattern of JJAS precipitation and circulation changes as resolution increases, which include a slight increase in precipitation over peninsular India, changes in Indian and Indochinese orographic rain bands, increasing wind speeds in the Somali Jet, increasing precipitation over the Maritime Continent islands and decreasing precipitation over the northern Maritime Continent seas. To diagnose which resolution related processes cause these changes we compare them to published sensitivity experiments that change regional orography and coastlines. Our analysis indicates that improved resolution of the East African Highlands results in the improved representation of the Somali Jet and further suggests that improved resolution of orography over Indochina and the Maritime Continent results in more precipitation over the Maritime Continent islands at the expense of reduced precipitation further north. We also evaluate the resolution sensitivity of monsoon depressions and lows, which contribute more precipitation over northeast India at higher resolution. We conclude that while increasing resolution at these scales does not solve the many monsoon biases that exist in GCMs, it has a number of small, beneficial impacts.

Recent observed and simulated changes in precipitation over Africa

Multiple observational data sets and atmosphere-only simulations from the Coupled Model Intercomparison Project Phase 5 are analyzed to characterize recent rainfall variability and trends over Africa focusing on 1983–2010. Data sets exhibiting spurious variability, linked in part to a reduction in rain gauge density, were identified. The remaining observations display coherent increases in annual Sahel rainfall (29 to 43 mm yr−1 per decade), decreases in March–May East African rainfall (−14 to −65 mm yr−1 per decade), and increases in annual Southern Africa rainfall (32 to 41 mm yr−1 per decade). However, Central Africa annual rainfall trends vary in sign (−10 to +39 mm yr−1 per decade). For Southern Africa, observed and sea surface temperature (SST)-forced model simulated rainfall variability are significantly correlated (r~0.5) and linked to SST patterns associated with recent strengthening of the Pacific Walker circulation.

Regional projections of extreme apparent temperature days in Africa and the related potential risk to human health

Regional climate modelling was used to produce high resolution climate projections for Africa, under a “business as usual scenario”, that were translated into potential health impacts utilizing a heat index that relates apparent temperature to health impacts. The continent is projected to see increases in the number of days when health may be adversely affected by increasing maximum apparent temperatures (AT) due to climate change. Additionally, climate projections indicate that the increases in AT results in a moving of days from the less severe to the more severe Symptom Bands. The analysis of the rate of increasing temperatures assisted in identifying areas, such as the East African highlands, where health may be at increasing risk due to both large increases in the absolute number of hot days, and due to the high rate of increase. The projections described here can be used by health stakeholders in Africa to assist in the development of appropriate public health interventions to mitigate the potential health impacts from climate change.

Cathepsin L-like genes of Trypanosoma vivax from Africa and South America - characterization, relationships and diagnostic implications

We characterized sequences from genes encoding cathepsin L-like (CatL-like) cysteine proteases from African and South American isolates of Trypanosoma vivax and T. vivax-like organisms, and evaluated their suitability as genetic markers for population structure analysis and diagnosis. Phylogenetic analysis of sequences corresponding to CatL-like catalytic domains revealed substantial polymorphism, and clades of sequences (TviCatL1-9) were separated by large genetic distances. TviCatL1-4 sequences were from cattle isolates from West Africa (Nigeria and Burkina Faso) and South America (Brazil and Venezuela), which belonged to the same T. vivax genotype. T. vivax-like genotypes from East Africa showed divergent sequences, including TviCatL5-7 for isolates from Mozambique and TviCatL8-9 for an isolate from Kenya. Phylogenetic analysis of CatL-like gene data supported the relationships among trypanosome species reflected in the phylogenies based on the analysis of small subunit (SSU) of ribosomal RNA gene sequence data. The discovery of different CatL-like sequences for each genotype, defined previously by ribosomal DNA data, indicate that these sequences provide useful targets for epidemiological and population genetic studies. Regions in CatL-like sequences shared by all T. vivax genotypes but not by other trypanosomes allowed the establishment of a specific and sensitive diagnostic PCR for epidemiological studies in South America and Africa. (C) 2008 Elsevier Ltd. All rights reserved.

M-PESA mobile money: a case study in Blue ocean strategy

The recent and widespread availability of affordable mobile phone technology in developing countries has paved the way for the development of a number of mobile money and electronic remittance services. One of the most successful of these services is Safaricom’s M-PESA program, launched in the East African nation of Kenya in March 2007. Since then, the program has successfully enrolled over 15.2 million users, transferred more than US$1.4 trillion in electronic funds, and contributed significantly to poverty alleviation and financial inclusion efforts in Kenya. M-Pesa is a mobile phone based money transfer system in Kenya which grew at a blistering pace following its inception in 2007. This case study will analyze the critical factors that make M-PESA such a unique success in Kenya specifically.

Phylogenetic structure of Guinea-Bissau ethnic groups for mitochondrial DNA and Y chromosome genetic systems

The maternal and paternal genetic profile of Guineans is markedly sub-Saharan West African, with the majority of lineages belonging to L0-L3 mtDNA sub-clusters and E3a-M2 and E1-M33 Y chromosome haplogroups. Despite the sociocultural differences among Guinea-Bissau ethnic groups,marked by the supposedly strict admixture barriers, their genetic pool remains largely common. Their extant variation coalesces at distinct timeframes, from the initial occupation of the area to later inputs of people. Signs of recent expansion in mtDNA haplogroups L2a-L2c and NRY E3a-M2 suggest population growth in the equatorial western fringe, possibly supported by an early local agricultural centre, and to which the Mandenka and the Balanta people may relate. Non-West African signatures are traceable in less frequent extant haplogroups, fitting well with the linguistic and historical evidence regarding particular ethnic groups: the Papel and Felupe-Djola people retain traces of their putative East African relatives; U6 and M1b among Guinea-Bissau Bak-speakers indicate partial diffusion to Sahel of North African lineages; U5b1b lineages in Fulbe and Papel represent a link to North African Berbers, emphasizing the great importance of post-glacial expansions; exact matches of R1b-P25 and E3b1-M78 with Europeans likely trace back to the times of the slave trade.

Spoligotypes of Mycobacterium tuberculosis complex isolates from patients residents of 11 states of Brazil

One of the high tuberculosis (TB) incidence countries in the world, Brazil is characterized by considerable differences in TB incidence on regional and state level. In the present study, we describe Brazilian spoligotypes of 1991 Mycobacterium tuberculosis complex (MTC) clinical isolates from patients residents of 11 states from different regions of the country, diagnosed between 1996 and 2005. By performing spoligotyping on a large number of M. tuberculosis clinical isolates, one of the main objectives of this study was to determine the major genotype families causing TB in Brazil and to verify the region-associated genotype distribution. We observed a total of 577 distinct spoligopatterns, 12.6% of these corresponded to orphan patterns while 87.4% belonged to 326 shared-types (SITs). Among the latter, 86 SITs (isolated from 178 patients) had been observed for the first time in this study, the most frequent being SIT2517 which belonged to the T3-ETH lineage and was exclusively found among patients residents of Belem, the capital of the state of Para (n = 8 isolates). Irrespective of shared-type labeling, a total of 19.5% strains were unique (unclustered) in our study as opposed to 80.5% clustered isolates (189 clusters, size range from 2 to 205 isolates). The three largest clusters were SIT42 of the Latin-America & Mediterranean (LAM) 9 clade (10.3%), SIT53 of the T clade (7.6%), and SIT50 of the Haarlem clade (5.4%). The predominant MTC lineages in Brazil in decreasing order belonged to the LAM (46%); the ill-defined T (18.6%); the Haarlem (12.2%), the X (4.7%), the S (1.9%), and the East African Indian (EAI) (0.85%) families. The rest of clades grouped together as Mycobacterium africanum, Mycobacterium bovis, Beijing, Central Asian (CAS), and the Manu types, represented less than 1% of the strains. Finally, about 15% of the isolates showed spoligotype signatures that were not yet classified among well-defined lineages. In conclusion, we provide hereby a first insight into the population structure of MTC isolates in Brazil, showing the predominance of both LAM and T family and the existence of region-associated genotypes. (C) 2011 Elsevier B.V. All rights reserved.