Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.
The green fluorescent protein (GFP) gene offers many advantages as a viability reporter for high-throughput antimicrobial drug screening. However, screening for antituberculosis compounds by using GFP driven by the heat shock promoter, hsp60, has been of limited utility due to the low signal-to-noise ratio. Therefore, an alternative promoter was evaluated for its enhanced fluorescence during microplate-based culture and its response to 18 established antimicrobial agents by using a green fluorescent protein microplate assay (GFPMA). Mycobacterium tuberculosis strains H37Rv, H37Ra, and Erdman were transformed with pFPCA1, which contains a red-shifted gfp gene driven by the acetamidase promoter of M. smegmatis mc 2 155. The pFPCA1 transformants achieved higher levels of GFP-mediated fluorescence than those carrying the hsp60 construct, with signal-to-noise ratios of 20.6 to 27.8 and 3.8 to 4.5, respectively. The MICs of 18 established antimicrobial agents for all strains carrying pFPCA1 in the GFPMA were within 1 to 2 twofold dilutions of those determined by either the fluorometric or the visual microplate Alamar Blue assay (MABA). No significant differences in MICs were observed between wild-type and pFPCA1 transformants by MABA. The optimized GFPMA is sufficiently simple, robust, and inexpensive (no reagent costs) to be used for routine high-throughput screening for antituberculosis compounds.Tuberculosis continues to be a major global public health problem. In addition, the increasing prevalence of multidrugresistant Mycobacterium tuberculosis is of concern (20) and has fostered a sense of urgency with regard to the need to acquire new drugs. Several rapid methods such as the microplate Alamar Blue assay (MABA) (3, 5), the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide-based assay (9), and the luciferase assay (1, 2, 7, 21) have been established for the screening of the antimycobacterial activities of compounds. However, each has one or more drawbacks for high-throughput screening, including the need to add a dye or a substrate to test the viability of the bacteria, a step which both increases labor and decreases safety.Fluorometric assays based on the Aequorea victoria gfp gene encoding a green fluorescent protein (GFP) or its mutants have been used widely in prokaryotes (8,10,11,24) due to several properties of gfp that are advantageous for use as a reporter for bacterial viability and growth, including the low level of toxicity, continuous production during replication, and easy imaging and quantification (11,25). Previous studies with mycobacteria exclusively used the hsp60 promoter, which has been fused to gfp in a variety of investigations (8,11,26). Collins et al. (6) demonstrated that a recombinant M. tuberculosis strain carrying pFPV2, an hsp60::gfp construct, could be used to assess the MICs of known antimycobacterial compounds. However, the low level of the fluorescence signal and the relatively high background autofluorescence of the medium precluded the establishment of a robust assa...
Global Mycobacterium tuberculosis population comprises 7 major lineages. The Beijing strains, particularly the ones classified as Modern groups, have been found worldwide, frequently associated with drug resistance, younger ages, outbreaks and appear to be expanding. Here, we report analysis of whole genome sequences of 1170 M. tuberculosis isolates together with their patient profiles. Our samples belonged to Lineage 1–4 (L1–L4) with those of L1 and L2 being equally dominant. Phylogenetic analysis revealed several new or rare sublineages. Differential associations between sublineages of M. tuberculosis and patient profiles, including ages, ethnicity, HIV (human immunodeficiency virus) infection and drug resistance were demonstrated. The Ancestral Beijing strains and some sublineages of L4 were associated with ethnic minorities while L1 was more common in Thais. L2.2.1.Ancestral 4 surprisingly had a mutation that is typical of the Modern Beijing sublineages and was common in Akha and Lahu tribes who have migrated from Southern China in the last century. This may indicate that the evolutionary transition from the Ancestral to Modern Beijing sublineages might be gradual and occur in Southern China, where the presence of multiple ethnic groups might have allowed for the circulations of various co-evolving sublineages which ultimately lead to the emergence of the Modern Beijing strains.
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