Phylogenetic and phylodynamic analyses of hepatitis C virus subtype 1a in Okinawa, Japan.

Okinawa Island, located in Southern Japan, has a higher prevalence rate of hepatitis C virus subtype 1a (HCV-1a) infection than that in mainland Japan. Okinawa has a history of US military occupation after World War II. To elucidate the transmission history of HCV-1a in Okinawa, 26 whole-genome sequences were obtained from 29 patients during 2011-2016. Phylogenetic trees were reconstructed to identify the origin and characteristics of HCV-1a in Okinawa with epidemiological information. A phylogenetic tree based on whole-genome sequencing revealed that all of the samples were located below the US branches. Additionally, we identified one cluster comprised of 17 strains (Okinawa, n = 16; United States, n = 1). The majority of the patients in this cluster were people who inject drugs (PWID), indicating the presence of a people who inject drugs (PWID) cluster. Subsequently, Bayesian analyses were employed to reveal viral population dynamics. Intriguingly, a phylodynamic analysis uncovered a substantial increase in effective population size of HCV-1a from 1965 to 1980 and a slight increase in mid-2000, which were associated with an increase in illicit drug use in Okinawa. The estimated divergence time of the PWID cluster was 1967.6 (1964.2-1971.1). These findings suggest that HCV-1a was introduced into Okinawa from the United States in the late 1960s, coincident with the Vietnam War. Subsequently, HCV-1a might have spread among the Japanese population with the spread of injecting drug use. Our study provides an understanding of HCV transmission dynamics in Okinawa, as well as the key role of PWID in HCV transmission.

Ethnic differences in cross-sectional associations between impaired glucose regulation, identified by oral glucose tolerance test or HbA1c values, and cardiovascular disease in a cohort of European and South Asian origin.

AIMS: We contrasted impaired glucose regulation (prediabetes) prevalence, defined according to oral glucose tolerance test or HbA1c values, and studied cross-sectional associations between prediabetes and subclinical/clinical cardiovascular disease (CVD) in a cohort of European and South Asian origin. METHODS: For 682 European and 520 South Asian men and women, aged 58-85 years, glycaemic status was determined by oral glucose tolerance test or HbA1c thresholds. Questionnaires, record review, coronary artery calcification scores and cerebral magnetic resonance imaging established clinical plus subclinical coronary heart and cerebrovascular disease. RESULTS: Prediabetes was more prevalent in South Asian participants when defined by HbA1c rather than by oral glucose tolerance test criteria. Accounting for age, sex, smoking, systolic blood pressure, triglycerides and waist-hip ratio, prediabetes was associated with coronary heart disease and cerebrovascular disease in European participants, most obviously when defined by HbA1c rather than by oral glucose tolerance test [odds ratios for HbA1c -defined prediabetes 1.60 (95% CI 1.07, 2.39) for coronary heart disease and 1.57 (95% CI 1.00, 2.51) for cerebrovascular disease]. By contrast, non-significant associations were present between oral glucose tolerance test-defined prediabetes only and coronary heart disease [odds ratio 1.41 (95% CI 0.84, 2.36)] and HbA1c -defined prediabetes only and cerebrovascular disease [odds ratio 1.39 (95% CI 0.69, 2.78)] in South Asian participants. Prediabetes defined by HbA1c or oral glucose tolerance test criteria was associated with cardiovascular disease (defined as coronary heart and/or cerebrovascular disease) in Europeans [odds ratio 1.95 (95% CI 1.31, 2.91) for HbA1c prediabetes criteria] but not in South Asian participants [odds ratio 1.00 (95% CI 0.62, 2.66); ethnicity interaction P = 0.04]. CONCLUSIONS: Prediabetes appeared to be less associated with cardiovascular disease in the South Asian than in the European group. These findings have implications for screening, and early cardiovascular prevention strategies in South Asian populations.

Synchronous rectal adenocarcinoma and splenic marginal zone lymphoma.

Synchronous cancers of different primary origin are rare. Here, we describe the case of a patient with concomitant diagnoses of rectal adenocarcinoma and splenic marginal zone lymphoma (smzl). A 57-year-old woman initially presented with abdominal pain. Physical examination and computed tomography demonstrated massive splenomegaly, and a complete blood count revealed microcytic anemia and lymphopenia. During the subsequent evaluation, she presented with hematochezia, melena, and constipation, which prompted gastroenterology referral. Subsequent endoscopic rectal ultrasonography revealed a T3N1 moderately differentiated rectal adenocarcinoma, with computed tomography imaging of chest, abdomen, and pelvis confirming no metastasis. Thus, the cancer was classified as clinical stage T3N1M0, stage iii. Bone marrow biopsy confirmed co-existing marginal zone lymphoma, and with the clinical presentation of massive splenomegaly, a diagnosis of smzl was made. The patient's management was individually tailored for simultaneous optimal treatment of both conditions. Concurrent treatment with neoadjuvant rituximab and 5-fluorouracil chemotherapy, with external-beam radiation therapy to the pelvis, was administered, followed by surgery consisting of en bloc splenectomy and distal pancreatectomy, and low anterior resection. The patient completed a standard course of adjuvant folfox (fluorouracil-leucovorin-oxaliplatin) chemotherapy and has remained disease-free for 7 years. To our knowledge, this report is the first to specifically describe simultaneous diagnoses of locally advanced rectal cancer and smzl. We also describe the successful combined neoadjuvant treatment combination of 5-fluorouracil, rituximab, and pelvic radiation.

miR-675 mediates downregulation of Twist1 and Rb in AFP-secreting hepatocellular carcinoma.

BACKGROUND: Alpha-fetoprotein (AFP)-secreting hepatocellular carcinomas (HCC) represent a genetically distinct subset of tumors often associated with a worse prognosis. However, the molecular mechanisms that underlie these phenotypic differences remain poorly understood. METHODS: HCC tumor samples from 27 patients were profiled using the Affymetrix 133 Plus 2.0 GeneChips. GeneGO Metacore software was used to identify altered biologic pathways. Expression validation was confirmed by RT-PCR. Manipulation of miR-675 by overexpression and antagomir-mediated knockdown was carried out with subsequent evaluation of effects on cell behavior by cell cycle, proliferation, invasion, and growth in soft agar assays. RESULTS: We identified a strong relationship between primary tumor H19 gene expression and elevated serum AFP. H19 has recently been identified to encode microRNA-675 (miR-675), and we confirmed the relationship in an independent sample of patients. Pathway analyses of the effect of miR-675 overexpression in hepatoma cells revealed a predominant upregulation of cell adhesion and cell cycle initiation pathways. We have demonstrated that miR-675 mediates increases in proliferation and an accumulation of cells with tetraploid DNA content associated with a repression of Rb. We also demonstrated that overexpression of miR-675 alters cellular morphology, reduces invasive potential, and increases anchorage-independent growth capacity. These findings are consistent with a mesenchymal-to-epithelial transition, associated with a reduction in the expression of the key EMT mediator, Twist1. CONCLUSIONS: Expression of the miR-675 in hepatocellular carcinoma links a dramatic upregulation of proliferative and growth capacity with inhibition of motility in HCC cells.

Genomic instability in repeated sequences is an early somatic event in colorectal tumorigenesis that persists after transformation.

Genomic instability at simple repeated sequences (SRS) is a landmark for some sporadic and hereditary cancers of the colon. We have identified several human tumour cell lines with up to 1,000-fold increases in mutation rates for endogenous microsatellite sequences, relative to normal cells or tumour cells without the mutator phenotype and show that they are very early events in tumorigenesis. Our in vivo and in vitro results show that the genomic instability persists after transformation and that microsatellite mutations accumulate as consecutive somatic slippage events of a single or a few repeated units. This mechanism may account for the repeat expansions in triplet hereditary diseases and the same defect in replication fidelity in non-polyposis colon cancer could also contribute to the non-mendelian anticipation in these diseases.

Localization of a susceptibility locus for Peutz-Jeghers syndrome to 19p using comparative genomic hybridization and targeted linkage analysis.

Many human cancer susceptibility genes have been successfully mapped by genetic linkage studies. One that has so far eluded researchers is that for Peutz-Jeghers (P-J) syndrome, a condition characterized by intestinal hamartomatous polyposis and melanin spots of the lips, buccal mucosa and digits. A dramatically elevated risk of malignancy has also been documented. Gastrointestinal tumours as well as cancers of the breast, ovary, testis and uterine cervix appear to be overrepresented in families with this syndrome. The nature of hamartomatous polyps is equivicol. Hamartomas are usually considered histologically benign, but in the case of Peutz-Jeghers patients, there are reports of adenomatous and malignant changes in the polyps, and the possibility of a hamartoma-carcinoma sequence has been discussed. A search for a putative tumour suppressor locus was made using comparative genomic hybridization (CGH) of Peutz-Jeghers polyps, combined with loss of heterozygosity (LOH) study. Genetic linkage analysis in 12 families using markers from a deletion site demonstrated the presence of a high-penetrance locus in distal 19p with a multipoint lod score of 7.00 at marker D19S886 without evidence of genetic heterogeneity. The study demonstrates the power of CGH combined with LOH analysis in identifying putative tumour suppressor loci, and provides molecular evidence of malignant potential in hamartomas.

Tumour susceptibility and spontaneous mutation in mice deficient in Mlh1, Pms1 and Pms2 DNA mismatch repair.

Germline mutations in the human MSH2, MLH1, PMS2 and PMS1 DNA mismatch repair (MMR) gene homologues appear to be responsible for most cases of hereditary non-polyposis colorectal cancer (HNPCC; refs 1-5). An important role for DNA replication errors in colorectal tumorigenesis has been suggested by the finding of frequent alterations in the length of specific mononucleotide tracts within genes controlling cell growth, including TGF-beta receptor type II (ref. 6), BAX (ref. 7) and APC (ref. 8). A broader role for MMR deficiency in human tumorigenesis is implicated by microsatellite instability in a fraction of sporadic tumours, including gastric, endometrial and colorectal malignancies. To better define the role of individual MMR genes in cancer susceptibility and MMR functions, we have generated mice deficient for the murine homologues of the human genes MLH1, PMS1 and PMS2. Surprisingly, we find that these mice show different tumour susceptibilities, most notably, to intestinal adenomas and adenocarcinomas, and different mutational spectra. Our results suggest that a general increase in replication errors may not be sufficient for intestinal tumour formation and that these genes share overlapping, but not identical functions.

Somatic microsatellite mutations as molecular tumor clocks.

Microsatellite (MS) mutations can potentially unravel the past of mutator phenotype tumors, with greater genetic diversity expected in older regions. Rapid clonal expansions of xenografts were characterized by relatively homogenous MS alleles, whereas greater diversity was observed in a colorectal cancer with the greatest variation in its adjacent adenoma. A subcutaneous lung cancer metastasis demonstrated diversity consistent with its one-month clinical duration and evidence of active mitosis during dormancy. The genetic legacy inherent to multistep tumorigenesis provides direct estimates of tumor ages, with up to thousands of cell divisions and high death rates necessary to yield the observed diversities. MS molecular tumor clocks have the unique potential to systematically reconstruct the early and occult evolution of individual human mutator phenotype tumors.

Comparison of traditional two-injection dorsal digital block versus transthecal and subcutaneous single-injection digital block: A systematic review and meta-analysis.

Digital nerve block is a common procedure with several techniques, including the traditional digital nerve block, transthecal digital nerve block, and single subcutaneous palmar digital nerve block. This review aimed to evaluate the efficacy of these three methods. A systematic search was performed in the PubMed, Scopus, and Cochrane Library databases. The risk of bias of the studies was assessed using the Cochrane Collaboration's tool for assessing the risk of bias and the Risk of Bias Assessment Tool for Non-Randomized Studies. Fourteen prospective randomized controlled studies and one prospective comparative study were included. The three methods of digital block showed similar onset times, durations, injection pain and incidence of incomplete anesthesia. This review confirmed that all three methods of digital block are equally effective. Considering that patients prefer a single injection and the potential risk of complications, the single subcutaneous digital block could be more widely used.

Detection of human papilloma virus in paraffin-embedded tissue using the polymerase chain reaction.

Human papilloma virus (HPV) DNA sequences have been detected in paraffin-embedded tissue using an enzymatic in vitro amplification technique known as the polymerase chain reaction. Amplification of a HPV DNA sequence before its detection with a cDNA probe significantly increases the rapidity as well as the sensitivity of detection such that a single 5-10-micron thick paraffin-embedded tissue section can be analyzed within 24 h. The assay specifically detected HPV 16 or 18 without crossreactivity with HPV 6 or 11. As few as 20 viral copies could be detected. The rapid and sensitive analysis of HPV in normal and pathological tissues using this technique may contribute significantly to identifying the role of HPV as a risk factor in carcinoma.

Inferring human stem cell behaviour from epigenetic drift.

Although conventional experimental manipulations are impractical, it may be possible to infer human stem cell fates by 'reading' histories recorded within their genomes. Genomes are almost perfect copies of copies, and ancestries may be surreptitiously recorded by replication errors that inevitably accumulate. The greater the number of divisions, the greater the number of replication errors ('a molecular clock hypothesis'). Mutations rarely occur during a lifetime, but DNA methylation patterns are also copied after DNA replication and measurably drift with ageing at certain CpG sites in mitotic tissues, such as the colon. Such passenger methylation pattern variation may effectively function as 'epigenetic' somatic cell mitotic clocks. Replication errors can only accumulate in long-lived stem cell lineages, so methylation pattern drift largely records stem cell behaviour. How methylation patterns may encode stem cell ancestries is illustrated with two types of small reproductive units--colon crypt niches with continuous genealogies, and hair follicles with punctuated genealogies. Potentially, the genealogy of any human cell may be inferred by 'reading' its genome.

Urinary tract infections and reduced risk of bladder cancer in Los Angeles.

We investigated the association between urinary tract infections (UTIs) and transitional cell carcinoma of the bladder in a population-based case-control study in Los Angeles covering 1586 cases and age-, gender-, and race-matched neighbourhood controls. A history of bladder infection was associated with a reduced risk of bladder cancer among women (odds ratio (OR), 0.66; 95% confidence interval (CI), 0.46-0.96). No effect was found in men, perhaps due to power limitations. A greater reduction in bladder cancer risk was observed among women with multiple infections (OR, 0.37; 95% CI, 0.18-0.78). Exclusion of subjects with a history of diabetes, kidney or bladder stones did not change the inverse association. A history of kidney infections was not associated with bladder cancer risk, but there was a weak association between a history of other UTIs and slightly increased risk among men. Our results suggest that a history of bladder infection is associated with a reduced risk of bladder cancer among women. Cytotoxicity from antibiotics commonly used to treat bladder infections is proposed as one possible explanation.

Absorption spectroscopy of gold nanoisland films: optical and structural characterization.

Nanoisland films prepared by annealing thin gold films at high temperatures were imaged using scanning electron microscopy (SEM) and atomic force microscopy, and optically characterized through absorption spectroscopy. Thin gold films of effective thicknesses 2, 5 and 7 nm annealed at 500, 700 and 900 degrees C were fabricated and studied experimentally. The measured absorption characteristics in support of theoretical calculations showed that the shapes of gold islands were partial spheres. The position of the peak absorption wavelength measured with s-polarized light or at normal incidence confirmed that the island shape grew from a near-hemisphere towards a sphere with increasing annealing temperature. The SEM images confirmed that the size of islands increased from 15 nm in diameter to 40 nm in diameter as film thickness increased from 2 to 5 nm. The affect of the index of the substrate material on absorption characteristics were also studied by comparing the absorption spectra of gold island films on quartz and LaSF15 glass substrates. The use of gold nanoisland films for preparing localized surface plasmon resonance substrates was suggested as they held advantages over the gold colloid films.

DNA mismatch repair in mammals: role in disease and meiosis.

The understanding of mammalian mismatch repair (MMR) gene function has been accelerated as a result of progress on several fronts. First, the biochemical analysis of MMR has been advanced by the production of purified human MMR proteins which will eventually allow reconstitution of MMR activity in vitro. Second, a wealth of clinical studies on colon cancer patients have begun to allow correlations to be made among MMR mutations, tumor types, therapeutic approaches and clinical outcomes. Finally, new unexpected meiotic phenotypes have been associated with mutations in certain mouse MMR genes.

Overexpression of the Arabidopsis thaliana EDS5 gene enhances resistance to viruses.

The Arabidopsis thaliana ENHANCED DISEASE SUSCEPTIBILITY 5 gene (EDS5) is required for salicylic acid (SA) synthesis in pathogen-challenged plants. SA and EDS5 have an important role in the Arabidopsis RCY1 gene-conferred resistance against the yellow strain of Cucumber mosaic virus [CMV(Y)], a Bromoviridae, and HRT-conferred resistance against the Tombusviridae, Turnip crinkle virus (TCV). EDS5 expression and SA accumulation are induced in response to CMV(Y) inoculation in the RCY1-bearing ecotype C24. To further discern the involvement of EDS5 in Arabidopsis defence against viruses, we overexpressed the EDS5 transcript from the constitutively expressed Cauliflower mosaic virus 35S gene promoter in ecotype C24. In comparison to the non-transgenic control, the basal level of salicylic acid (SA) was twofold higher in the 35S:EDS5 plant. Furthermore, viral spread and the size of the hypersensitive response associated necrotic local lesions (NLL) were more highly restricted in CMV(Y)-inoculated 35S:EDS5 than in the non-transgenic plant. The heightened restriction of CMV(Y) spread was paralleled by more rapid induction of the pathogenesis-related gene, PR-1, in the CMV(Y)-inoculated 35S:EDS5 plant. The 35S:EDS5 plant also had heightened resistance to the virulent CMV strain, CMV(B2), and TCV. These results suggest that, in addition to R gene-mediated gene-for-gene resistance, EDS5 is also important for basal resistance to viruses. However, while expression of the Pseudomonas putida nahG gene, which encodes the SA-degrading salicylate hydroxylase, completely suppressed 35S:EDS5-conferred resistance against CMV(Y) and TCV, it only partially compromised resistance against CMV(B2), indicating that SA-dependent and -independent mechanisms are associated with 35S:EDS5-conferred resistance against viruses.

Comprehensive resources for tomato functional genomics based on the miniature model tomato micro-tom.

Tomato (Solanum lycopersicum L., Solanaceae) is an excellent model plant for genomic research of solanaceous plants, as well as for studying the development, ripening, and metabolism of fruit. In 2003, the International Solanaceae Project (SOL, www.sgn.cornell.edu ) was initiated by members from more than 30 countries, and the tomato genome-sequencing project is currently underway. Genome sequence of tomato obtained by this project will provide a firm foundation for forthcoming genomic studies such as the comparative analysis of genes conserved among the Solanaceae species and the elucidation of the functions of unknown tomato genes. To exploit the wealth of the genome sequence information, there is an urgent need for novel resources and analytical tools for tomato functional genomics. Here, we present an overview of the development of genetic and genomic resources of tomato in the last decade, with a special focus on the activities of Japan SOL and the National Bio-Resource Project in the development of functional genomic resources of a model cultivar, Micro-Tom.

Differences in brain structure in deaf persons on MR imaging studied with voxel-based morphometry.

BACKGROUND AND PURPOSE: The loss of a major sensory input early in life is known to cause alterations in neuronal connectivity and physiology at the cellular level, but effects on gross anatomy are less well understood. The purpose of this study was to compare volumetric structural brain MR imaging scans of deaf versus hearing subjects by using voxel-based morphometry (VBM). The hypothesis was that the deaf would have relative hypoplasia in the temporal lobe centers involved in hearing and speech. METHODS: T1-weighted volumetric images from 53 prelingually deaf persons and 51 control subjects were analyzed with VBM. Initial segmentations were spatially normalized, and then these deformation parameters were applied to the original images, which were again segmented. Statistic parametric mapping was then applied on a voxel-by-voxel basis to determine group differences and asymmetries. RESULTS: The white matter analysis revealed a statistically significant focal deficit in the deaf persons in the left posterior superior temporal gyrus (STG), corresponding to white matter inferior to auditory cortex. Gray matter asymmetries in the deaf persons were overall similar to that in hearing persons but a focal loss of asymmetry was noted in the posterior STG white matter in the deaf persons. CONCLUSION: These results support the hypothesis that there are gross alterations in brain anatomy as a consequence of early deafness. The white matter deficit in the posterior left superior temporal gyrus may represent hypoplasia of the auditory/speech related tracts. Hemispheric asymmetries however remain largely intact.

Management and outcomes following pancreaticoduodenectomy for ampullary adenocarcinoma.

INTRODUCTION: The purpose of this study was to evaluate outcomes following pancreaticoduodenectomy(PD) for ampullary adenocarcinoma(AAC). METHODS: We evaluated patients having undergone PD for AAC and the impact of clinical/histopathologic factors and adjuvant therapy(AT) on survival. RESULTS: 52 patients underwent potentially curative PD. Perineural and lymphovascular invasion were associated with decreased survival. There was no difference in survival between patients treated with PD vs. PD+AT, however, AT was more often administered to patients with N1 vs. N0 and stage II/III vs. I disease. Among patients receiving AT, we observed a trend towards improved survival when radiation was included. Recurrence occurred in 7/18(39%) stage I patients, only 2(7%) of which received AT. CONCLUSION: AT did not improve survival, however was more commonly administered in advanced disease. Stage I patients had high recurrence rates but rarely received AT. Prospective evaluation of appropriate AT regimens and use in early stage patients should be considered.