Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages

There is increasing evidence that strain variation in Mycobacterium tuberculosis complex (MTBC) might influence the outcome of tuberculosis infection and disease. To assess genotype-phenotype associations, phylogenetically robust molecular markers and appropriate genotyping tools are required. Most current genotyping methods for MTBC are based on mobile or repetitive DNA elements. Because these elements are prone to convergent evolution, the corresponding genotyping techniques are suboptimal for phylogenetic studies and strain classification. By contrast, single nucleotide polymorphisms (SNP) are ideal markers for classifying MTBC into phylogenetic lineages, as they exhibit very low degrees of homoplasy. In this study, we developed two complementary SNP-based genotyping methods to classify strains into the six main human-associated lineages of MTBC, the "Beijing" sublineage, and the clade comprising Mycobacterium bovis and Mycobacterium caprae. Phylogenetically informative SNPs were obtained from 22 MTBC whole-genome sequences. The first assay, referred to as MOL-PCR, is a ligation-dependent PCR with signal detection by fluorescent microspheres and a Luminex flow cytometer, which simultaneously interrogates eight SNPs. The second assay is based on six individual TaqMan real-time PCR assays for singleplex SNP-typing. We compared MOL-PCR and TaqMan results in two panels of clinical MTBC isolates. Both methods agreed fully when assigning 36 well-characterized strains into the main phylogenetic lineages. The sensitivity in allele-calling was 98.6% and 98.8% for MOL-PCR and TaqMan, respectively. Typing of an additional panel of 78 unknown clinical isolates revealed 99.2% and 100% sensitivity in allele-calling, respectively, and 100% agreement in lineage assignment between both methods. While MOL-PCR and TaqMan are both highly sensitive and specific, MOL-PCR is ideal for classification of isolates with no previous information, whereas TaqMan is faster for confirmation. Furthermore, both methods are rapid, flexible and comparably inexpensive.

Probing the Mechanical Properties of Magnetosome Chains in Living Magnetotactic Bacteria

The mechanical properties of cytoskeletal networks are intimately involved in determining how forces and cellular processes are generated, directed, and transmitted in living cells. However, determining the mechanical properties of subcellular molecular complexes in vivo has proven to be difficult. Here, we combine in vivo measurements by optical microscopy, X-ray diffraction, and transmission electron microscopy with theoretical modeling to decipher the mechanical properties of the magnetosome chain system encountered in magnetotactic bacteria. We exploit the magnetic properties of the endogenous intracellular nanoparticles to apply a force on the filament-connector pair involved in the backbone formation and stabilization. We show that the magnetosome chain can be broken by the application of external field strength higher than 30 mT and suggest that this originates from the rupture of the magnetosome connector MamJ. In addition, we calculate that the biological determinants can withstand in vivo a force of 25 pN. This quantitative understanding provides insights for the design of functional materials such as actuators and sensors using cellular components.

Dimerization of Poly(methyl methacrylate) Chains Using Radical Trap-Assisted Atom Transfer Radical Coupling

End-brominated poly(methyl methacrylate) (PMMABr) was prepared by atom transfer radical polymerization (ATRP) and employed in a series of atom transfer radical coupling (ATRC) and radical trap-assisted ATRC (RTA-ATRG) reactions. When coupling reactions were performed in the absence of a nitroso radical trap-traditional ATRC condition-very little coupling of the PMMA chains was observed, consistent with disproportionation as the major termination pathway for two PMMA chain-end radicals in our reactions. When 2-methyl-2-nitrosopropane (MNP) was used as the radical trap, coupling of the PMMA chains in this attempted RTA-ATRC reaction was again unsuccessful, owing to capping of the PMMA chains with a bulky nitroxide and preventing further coupling. Analogous reactions performed using nitrosobenzene (NBz) as the radical trap showed significant dimerization, as observed by gel permeation chromatography (GPC) by a shift in the apparent molecular weight compared to the PMMABr precursors. The extent of coupling was found to depend on the concentrion of NBz compared to the PMMABr chain ends, as well as the temperature and time of the coupling reaction. To a lesser extent, the concentrations of copper(I) bromide (CuBr), nitrogen ligand (N,N,N',N',N"-pentamethyldiethylenetriamine = PMDETA), and elemental copper (Cu) were also found to play a role in the success of the RTA-ATRC reaction. The highest levels of dimerization were observed when the coupling reaction was carried out at 80 degrees C for 0.5h, with ratio of 1:4:2.5:8:1 equiv of NBz: CuBr:Cu:PMDETA:PMMABr.

Asia Comes to Main Street and May Learn to Speak Spanish: Globalization in a Poor Neighborhood in Worcester

This paper considers how and why an Asian enclave of small businesses has appeared in a poor neighborhood characterized by Puerto Rican and other Latino immigration in the post-industrial city of Worcester, Massachusetts. We begin by examining the role of the US in the world system, and argue that the US hegemonic role and specific political economic aspects of global capitalism (ie. deindustrialization) account for some of the migration stream. Next, using socioeconomic and historical data, interviews, and observations, we outline the history of Worcester’s economy and immigration patterns. We demonstrate that the increasing economic inequality leaves few promising employment options for newcomers to Worcester. Drawing on existing literature on immigrant entrepreneurs and ethnic enclaves, we argue that some aspects of the literature appear to shed light on the Vietnamese enterprises which have so visibly appeared (e.g., ethnic niches), while others, (e.g., middle-man minority theory) are not now reflected in local conflict. We conclude by considering the prospects for immigrants to this neighborhood in light of its political economic context.

The Mediterranean climate: An overview of the main characteristics and issues

The Mediterranean Region has many morphologic, geographical, historical, and societal characteristics, which make its climate scientifically interesting. The concept of Mediterranean climate is characterized by mild wet winters and warm to hot, dry summers and occur on the west side of continents between about 30° and 40° latitude. However, the presence of a relatively large mass of water is unique to the actual Mediterranean region. The Mediterranean Sea is a marginal and semi-enclosed sea; it is located on the western side of a large continental area and is surrounded by Europe to the North, Africa to the South, and Asia to the East. The chapter discusses that the climate of the Mediterranean region is to a large extent forced by planetary scale patterns. The time and space behavior of the regional features associated with such large-scale forcing is complex. Orography and land–sea distribution play an important role establishing the climate at basin scale and its teleconnections with global patterns. Different levels of services of readiness to emergencies, technological, and economic resources are likely to result in very different adaptation capabilities to environmental changes and new problems. The different economic situations and demographic trends are likely to produce contrasts and conflicts in a condition of limited available resources and environmental stress.

rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and OCTN1/2 variants

BACKGROUND: The IL23R gene has been identified as a susceptibility gene for inflammatory bowel disease (IBD) in the North American population. The aim of our study was to test this association in a large German IBD cohort and to elucidate potential interactions with other IBD genes as well as phenotypic consequences of IL23R variants. METHODS: Genomic DNA from 2670 Caucasian individuals including 833 patients with Crohn's disease (CD), 456 patients with ulcerative colitis (UC), and 1381 healthy unrelated controls was analyzed for 10 IL23R SNPs. Genotyping included the NOD2 variants p.Arg702Trp, p.Gly908Arg, and p.Leu1007fsX1008 and polymorphisms in SLC22A4/OCTN1 (1672 C-->T) and SLC22A5/OCTN2 (-207 G-->C). RESULTS: All IL23R gene variants analyzed displayed highly significant associations with CD. The strongest association was found for the SNP rs1004819 [P = 1.92x10(-11); OR 1.56; 95 % CI (1.37-1.78)]. 93.2% of the rs1004819 TT homozygous carriers as compared to 78% of CC wildtype carriers had ileal involvement [P = 0.004; OR 4.24; CI (1.46-12.34)]. The coding SNP rs11209026 (p.Arg381Gln) was protective for CD [P = 8.04x10(-8); OR 0.43; CI (0.31-0.59)]. Similar, but weaker associations were found in UC. There was no evidence for epistasis between the IL23R gene and the CD susceptibility genes CARD15 and SLC22A4/5. CONCLUSION: IL23R is an IBD susceptibility gene, but has no epistatic interaction with CARD15 and SLC22A4/5. rs1004819 is the major IL23R variant associated with CD in the German population, while the p.Arg381Gln IL23R variant is a protective marker for CD and UC.

Elective implantation of sirolimus-eluting stents for bifurcated and non-bifurcated unprotected left main coronary artery lesions: clinical outcomes at one year

AIMS: Recent studies of drug-eluting stents for unprotected left main coronary artery (LMCA) disease have been encouraging. We examined the performance of sirolimus-eluting stents (SES) for this indication. METHODS AND RESULTS: This retrospective study included 228 consecutive patients (mean age = 68 +/- 11 years, 80.6% men, 26.3% diabetics) who underwent implantation of SES for de novo LMCA stenoses. The mean additive and logistic EuroSCOREs were 5.2 +/- 3.9 and 8.2 +/- 13.2, respectively. The main objective of this study was to measure the rate of major adverse cardiac events (MACE), including death, myocardial infarction and target lesion revascularisation (TLR) at 12 months. Other objectives were to measure the rates of in-hospital MACE and 12-month TLR. Outcomes in 143 patients with (BIF+ group), versus 84 patients without (BIF-group) involvement of the bifurcation were compared. The pre-procedural percent diameter stenosis (%DS) was 60.1 +/- 11.2 in the BIF+ versus 54.7 +/- 12.2% in the BIF- group (p=0.008), and decreased to 18.0 +/- 9.7 and 13.9 +/- 11.3%, respectively (ns), after SES implant. The overall in-hospital MACE rate was 3.5%, and similar in both subgroups. The 1-year MACE rate was 14.5% overall, 16.8% in the BIF+ and 10.7% in the BIF- subgroup (ns). CONCLUSIONS: SES implants in high-risk patients with LMCA stenoses were associated with a low 1-year MACE rate. Stenting of the bifurcation was associated with significant increases in neither mortality nor 1-year MACE rate.