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.

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.

Differences in catalytic activity between rat testicular and ovarian carbonyl reductases are due to two amino acids

The sequences of rat testis carbonyl reductase (rCR1) and rat ovary carbonyl reductase (rCR2) are 98% identical, differing only at amino acids 140, 141, 143, 235 and 238. Despite such strong sequence identity, we find that rCR1 and rCR2 have different catalytic constants for metabolism of menadione and 4-benzoyl-pyridine. Compared to rCR1, rCR2 has a 20-fold lower K(m) and 5-fold lower k(cat) towards menadione and a 7-fold lower K(m) and 7-fold lower k(cat) towards 4-benzoyl-pyridine. We constructed hybrids of rCR1 and rCR2 that were changed at either residues 140, 141 and 143 or residues 235 and 238. rCR1 with residues 140, 141 and 143 of rCR2 has similar catalytic efficiency for menadione and 4-benzoyl-pyridine as rCR1. rCR1 with Thr-235 and Glu-238 of rCR2 has the catalytic constants of rCR2, indicating that it is this part of rCR2 that contributes to its lower K(m) for menadione and 4-benzoyl-pyridine. Comparisons of three-dimensional models of rCR1 and rCR2 show how Thr-235 and Glu-238 stabilize rCR2 binding of NADPH and menadione.

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.

Acute testicular torsion in children: the role of sonography in the diagnostic workup

Acute testicular torsion in children is an emergency and has to be diagnosed urgently. Doppler sonography is increasingly used in imaging the acute scrotum. Nevertheless, in uncertain cases, surgical exploration is required. In this study, we attempted to define the role of Doppler sonography in the diagnostic workup of the acutely painful scrotum. All patients admitted between 1999 and 2005 with acute scrotal pain were included. After clinical assessment, patients were imaged by Doppler sonography with a ''high-end'' instrument. In cases of absent arterial perfusion of the testis in Doppler sonography, surgical exploration was carried out. Patients with unaffected perfusion were followed clinically by ultrasound for up to 2 years. Sixty-one infants and children aged 1 day to 17 years (median: 7.9 years) were included. In 14 cases, sonography demonstrated absent central perfusion, with abnormal parenchymal echogenicity in six. Absence of venous blood flow together with reduction of central arterial perfusion was found in one infant. In these 15 patients, surgical exploration confirmed testicular torsion. Among the other 46 patients, we found four cases with increased testicular perfusion and 27 with increased perfusion of the epididymis. In one infant, a testicular tumour was found sonographically, and orchiectomy confirmed diagnosis of a teratoma. Follow-up examinations of the conservatively treated patients showed good clinical outcome with physiologic central perfusion as well as normal echogenic pattern of both testes. No case of testicular torsion was missed. By means of Doppler sonography, an unequivocal statement regarding testicular perfusion was possible in all cases. The initial Doppler diagnosis was confirmed by operative evaluation and follow-up ultrasound. Testicular torsion can therefore be excluded by correctly performed ultrasound with modern equipment.

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.

Impact of drug-eluting stent selection on long-term clinical outcomes in patients treated for unprotected left main coronary artery disease: the sirolimus vs paclitaxel drug-eluting stent for left main registry (SP-DELFT)

AIM: To compare the long-term relative efficacy and safety of SES and PES in patients undergoing percutaneous coronary intervention (PCI) for unprotected left main coronary artery (ULMCA) disease and to evaluate the role of lesion location and stenting technique in determining outcomes. METHODS AND RESULTS: From April 2002 to April 2004, 288 consecutive patients who underwent elective PCI with DES implantation for de novo lesions on ULMCA have been retrospectively selected and analyzed in seven European and US tertiary care centers. All patients had a minimum follow-up of 3 years. SES was used in 152 patients while 136 received PES. Isolated ostial-shaft disease was present in 27% of patients. Distal LM disease (73%) was treated with single and double stent approach in 29.5% and 43.4% of patients respectively. After 3 years, rates of survival free from any of the events investigated, were independent from lesion location and stenting approach and did not differ significantly between SES and PES groups. Freedom from MACE (SES vs. PES) was 76.3% vs. 83.1% in the ostial/shaft group, 80.3% vs. 72.8% in the distal-single stent group and 67.1% vs. 66.2% in the distal-double stent group. Definite stent thrombosis occurred only in 1(0.3%) patient at 439 days. CONCLUSIONS: In elective patients who underwent PCI for de novo lesions in the ostium, shaft or distal ULMCA, long-term clinical outcomes with SES and PES use were similar independently of lesion location and stenting technique.