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1.
Artigo em Inglês | MEDLINE | ID: mdl-31446183

RESUMO

BACKGROUND AND AIMS: Little is known about the clinical significance of indefinite dysplasia (IND) in patients with inflammatory bowel diseases (IBD) undergoing colonoscopic surveillance for colorectal neoplasia. METHODS: We conducted a retrospective cohort analysis of 492 patients with colonic IBD for 8 or more years or concomitant primary sclerosing cholangitis, with no history of advanced colorectal neoplasia (high-grade dysplasia or colorectal cancer) or colectomy, undergoing colorectal neoplasia surveillance at tertiary IBD referral center from 2001 through 2017. Subjects received consistent histopathologic grading of dysplasia. We collected data on time to development of (advanced) colorectal neoplasia or colectomy using Kaplan Meier methods. We identified factors independently associated with (advanced) colorectal neoplasia with multivariable Cox regression analysis. RESULTS: After 2149 person-years of follow-up, 53 patients (10.8%) received a diagnosis of IND without prior or synchronous low-grade dysplasia (LGD). Compared to patients without dysplasia, patients with IND had a significantly higher risk of advanced colorectal neoplasia (adjusted hazard ratio, 6.85; 95% CI, 1.78-26.4) and colorectal neoplasia (adjusted hazard ratio, 3.25; 95% CI, 1.50-7.05), but not colectomy (P=.78). Compared to IND, LGD was associated with a significantly higher risk of advanced colorectal neoplasia (P=.05). Following a diagnosis of no dysplasia, IND only, or LGD, the incidence rates of advanced colorectal neoplasia were 0.4% per patient-year, 3.1% per patient-year, and 8.4% per patient-year, respectively. CONCLUSIONS: In a retrospective analysis of patients with IBD undergoing colorectal neoplasia surveillance with consistent histopathologic grading of dysplasia, IND was independently associated with a significant increase in risk of advanced colorectal neoplasia. These findings require validation and if confirmed, a reappraisal of the colorectal neoplasia surveillance guidelines.

2.
Microbiology ; 165(8): 891-904, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31246167

RESUMO

Multidrug-resistant Klebsiella pneumoniae has emerged as one of the deadliest opportunistic nosocomial pathogens that forms biofilm for the establishment of chronic K. pneumoniae infections. Herein, we made an attempt to identify the genes involved in biofilm formation in the strain K. pneumoniae ATCC13883. To achieve this, we constructed mini-Tn5 transposon insertion mutants and screened them for biofilm production. We observed that the biofilm formation was enhanced in the mutant where the wcaJ gene was disrupted. WcaJ is the initiating enzyme of colanic acid synthesis and loads the first sugar (glucose-1-P) on the lipid carrier undecaprenyl phosphate. The absence of this glycosyltransferase results in the absence of colanic acid, which renders a non-mucoid phenotype to the mutant. Further, to determine the effect of mucoidy on antibiotic susceptibility, we tested the sensitivity of the strains towards different groups of antibiotics. Unlike the mucoid strains, the resistance of the non-mucoid cells was greater for polymyxins, but less for quinolones. Capsular polysaccharides are known to have a protective effect against phagocytosis, therefore we assessed the role of colanic acid in virulence by conducting infection studies on murine macrophages. Surprisingly, the ΔwcaJ strain was less efficient in macrophage activation and was not readily phagocytosed. Thus, the presence of colanic acid appeared to increase the immunogenicity of K. pneumoniae. Overall, the results indicate that the presence of colanic acid increases the vulnerability of K. pneumoniae towards both polymyxins and macrophages, implying that the mucoid strains are less threatening as compared to their high biofilm forming non-mucoid counterparts.

3.
Bioinformatics ; 2019 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-30923804

RESUMO

MOTIVATION: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes. We introduce Shouji, a highly-parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator that adopts modern FPGA (Field-Programmable Gate Array) architectures to further boost the performance of our algorithm. RESULTS: Shouji significantly improves the accuracy of pre-alignment filtering by up to two orders of magnitude compared to the state-of-the-art pre-alignment filters, GateKeeper and SHD. Our FPGA-based accelerator is up to three orders of magnitude faster than the equivalent CPU implementation of Shouji. Using a single FPGA chip, we benchmark the benefits of integrating Shouji with five state-of-the-art sequence aligners, designed for different computing platforms. The addition of Shouji as a pre-alignment step reduces the execution time of the five state-of-the-art sequence aligners by up to 18.8x. Shouji can be adapted for any bioinformatics pipeline that performs sequence alignment for verification. Unlike most existing methods that aim to accelerate sequence alignment, Shouji does not sacrifice any of the aligner capabilities, as it does not modify or replace the alignment step. AVAILABILITY: https://github.com/CMU-SAFARI/Shouji. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

4.
Am J Med Genet A ; 179(6): 966-977, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30920161

RESUMO

Phacomatosis pigmentovascularis (PPV) comprises a family of rare conditions that feature vascular abnormalities and melanocytic lesions that can be solely cutaneous or multisystem in nature. Recently published work has demonstrated that both vascular and melanocytic abnormalities in PPV of the cesioflammea and cesiomarmorata subtypes can result from identical somatic mosaic activating mutations in the genes GNAQ and GNA11. Here, we present three new cases of PPV with features of the cesioflammea and/or cesiomarmorata subtypes and mosaic mutations in GNAQ or GNA11. To better understand the risk of potentially occult complications faced by such patients we additionally reviewed 176 cases published in the literature. We report the frequency of clinical findings, their patterns of co-occurrence as well as published recommendations for surveillance after diagnosis. Features assessed include: capillary malformation; dermal and ocular melanocytosis; glaucoma; limb asymmetry; venous malformations; and central nervous system (CNS) anomalies, such as ventriculomegaly and calcifications. We found that ocular findings are common in patients with phacomatosis cesioflammea and cesiomarmorata. Facial vascular involvement correlates with a higher risk of seizures (p = .0066). Our genetic results confirm the role of mosaic somatic mutations in GNAQ and GNA11 in phacomatosis cesioflammea and cesiomarmorata. Their clinical and molecular findings place these conditions on a clinical spectrum encompassing other GNAQ and GNA11 related disorders and inform recommendations for their management.

5.
Gastroenterology ; 156(5): 1333-1344.e3, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30529584

RESUMO

BACKGROUND & AIMS: Patients with inflammatory bowel diseases who have postinflammatory polyps (PIPs) have an increased risk of colorectal neoplasia (CRN). European guidelines propose that patients with PIPs receive more frequent surveillance colonoscopies, despite limited evidence of this increased risk. We aimed to define the risk of CRN and colectomy in patients with inflammatory bowel diseases and PIPs. METHODS: We conducted a multicenter retrospective cohort study of patients with inflammatory bowel diseases who underwent colonoscopic surveillance for CRN, from January 1997 through January 2017, at 5 academic hospitals and 2 large nonacademic hospitals in New York or the Netherlands. Eligible patients had confirmed colonic disease with duration of at least 8 years (or any duration, if they also had primary sclerosing cholangitis) and no history of advanced CRN (high-grade dysplasia or colorectal cancer) or colectomy. The primary outcome was occurrence of advanced CRN according to PIP status; secondary outcomes were occurrence of CRN (inclusive of low-grade dysplasia) and colectomy. RESULTS: Of 1582 eligible patients, 462 (29.2%) had PIPs. PIPs were associated with more severe inflammation (adjusted odds ratio 1.32; 95% confidence interval [CI] 1.13-1.55), greater disease extent (adjusted odds ratio 1.92; 95% CI 1.34-2.74), and lower likelihood of primary sclerosing cholangitis (adjusted odds ratio 0.38; 95% CI 0.26-0.55). During a median follow-up period of 4.8 years, the time until development of advanced CRN did not differ significantly between patients with and those without PIPs. PIPs did not independently increase the risk of advanced CRN (adjusted hazard ratio 1.17; 95% CI 0.59-2.31). The colectomy rate was significantly higher in patients with PIPs (P = .01). CONCLUSIONS: In a retrospective analysis of data from 2 large independent surveillance cohorts, PIPs were associated with greater severity and extent of colon inflammation and higher rates of colectomy, but were not associated with development of any degree of CRN. Therefore, intervals for surveillance should not be shortened based solely on the presence of PIPs.


Assuntos
Colite Ulcerativa/epidemiologia , Pólipos do Colo/epidemiologia , Neoplasias Colorretais/epidemiologia , Doença de Crohn/epidemiologia , Adulto , Biópsia , Colectomia , Colite Ulcerativa/patologia , Colite Ulcerativa/cirurgia , Pólipos do Colo/patologia , Pólipos do Colo/cirurgia , Colonoscopia , Neoplasias Colorretais/patologia , Neoplasias Colorretais/cirurgia , Doença de Crohn/patologia , Doença de Crohn/cirurgia , Detecção Precoce de Câncer/métodos , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Gradação de Tumores , Países Baixos/epidemiologia , Cidade de Nova Iorque/epidemiologia , Prevalência , Estudos Retrospectivos , Medição de Risco , Fatores de Risco , Fatores de Tempo
6.
Gut Liver ; 2018 Oct 18.
Artigo em Inglês | MEDLINE | ID: mdl-30400722

RESUMO

Background/Aims: Statins have been postulated to lower the risk of colorectal neoplasia. No studies have examined any possible chemopreventive effect of statins in patients with inflammatory bowel disease (IBD) undergoing colorectal cancer (CRC) surveillance. This study examined the association of statin exposure with dysplasia and CRC in patients with IBD undergoing dysplasia surveillance colonoscopies. Methods: A cohort of patients with IBD undergoing colonoscopic surveillance for dysplasia and CRC at a single academic medical center were studied. The inclusion criteria were IBD involving the colon for >8 years (or any colitis duration if associated with primary sclerosing cholangitis [PSC]) and at least two colonoscopic surveillance exams. The exclusion criteria were CRC or high-grade dysplasia (HGD) prior to or at enrollment, prior colectomy, or limited (<30%) colonic disease. The primary outcome was the frequency of dysplasia and/or CRC in statin-exposed versus nonexposed patients. Results: A total of 642 patients met the inclusion criteria (57 statin-exposed and 585 nonexposed). The statin-exposed group had a longer IBD duration, longer follow-up period, and more colonoscopies but lower inflammatory scores, less frequent PSC and less use of thiopurines and biologics. There were no differences in low-grade dysplasia, HGD, or CRC development during the follow-up period between the statin-exposed and nonexposed groups (21.1%, 5.3%, and 1.8% vs 19.2%, 2.9% and 2.9%, respectively). Propensity score analysis did not alter the overall findings. Conclusion: In IBD patients undergoing surveillance colonoscopies, statin use was not associated with reduced dysplasia or CRC rates. The role of statins as chemopreventive agents in IBD remains controversial.

7.
J Family Med Prim Care ; 7(1): 162-166, 2018 Jan-Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29915752

RESUMO

Introduction: The study aimed to determine the prevalence of nasal colonization of methicillin-resistant Staphylococcus aureus (MRSA), the minimum inhibitory concentration (MIC) of oxacillin and vancomycin, inducible clindamycin resistance, and antimicrobial resistance pattern of S. aureus among children of Barabanki district, Uttar Pradesh, India. Materials and Methods: School-going children of age group of 5-15 years were identified and selected according to the inclusion and exclusion criteria. Two nasal swabs were collected from each child as per the Centers for Disease Control and Prevention guidelines and transported to laboratory. Swabs were cultured on mannitol salt agar and 5% blood agar and incubated for 18-24 h at 37°C. Identification was done as per routine laboratory protocol. Detection of MRSA was done through cefoxitin 30 µg discs and D-zone test. Antibiotic susceptibility pattern of S. aureus by Kirby-Bauer disc diffusion method along with MIC for oxacillin and vancomycin was performed simultaneously according to Clinical Laboratory Standards Institute guidelines. Results: Out of 300 children, 140 (46.67%) were found to be nasal carriage for S. aureus, among which MRSA was found to be 23 (7.67%). All S. aureus and MRSA isolates were sensitive to vancomycin with MIC <2 µg/ml, whereas 23 S. aureus were found resistant to oxacillin with MIC value >4 µg/ml. Resistance to penicillin and co-trimoxazole was highest, whereas all were sensitive to linezolid. MRSA showed 100% susceptibility to linezolid, followed by gentamicin (91.4%) and tetracycline (87%). Conclusion: With the risk involved in transmission of infection, steps for identifying the carriers and its eradication should be carried out. Rational use of antibiotics should be given preference too.

8.
Gut ; 2018 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-29720408

RESUMO

OBJECTIVES: Surveillance colonoscopy is thought to prevent colorectal cancer (CRC) in patients with long-standing colonic IBD, but data regarding the frequency of surveillance and the findings thereof are lacking. Our aim was to determine whether consecutive negative surveillance colonoscopies adequately predict low neoplastic risk. DESIGN: A multicentre, multinational database of patients with long-standing IBD colitis without high-risk features and undergoing regular CRC surveillance was constructed. A 'negative' surveillance colonoscopy was predefined as a technically adequate procedure having no postinflammatory polyps, no strictures, no endoscopic disease activity and no evidence of neoplasia; a 'positive' colonoscopy was a technically adequate procedure that included at least one of these criteria. The primary endpoint was advanced colorectal neoplasia (aCRN), defined as high-grade dysplasia or CRC. RESULTS: Of 775 patients with long-standing IBD colitis, 44% (n=340) had >1 negative colonoscopy. Patients with consecutive negative surveillance colonoscopies were compared with those who had at least one positive colonoscopy. Both groups had similar demographics, disease-related characteristics, number of surveillance colonoscopies and time intervals between colonoscopies. No aCRN occurred in those with consecutive negative surveillance, compared with an incidence rate of 0.29 to 0.76/100 patient-years (P=0.02) in those having >1 positive colonoscopy on follow-up of 6.1 (P25-P75: 4.6-8.2) years after the index procedure. CONCLUSION: Within this large surveillance cohort of patients with colonic IBD and no additional high-risk features, having two consecutive negative colonoscopies predicted a very low risk of aCRN occurrence on follow-up. Our findings suggest that longer surveillance intervals in this selected population may be safe.

9.
Clin Lymphoma Myeloma Leuk ; 18(6): e249-e254, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29680411

RESUMO

BACKGROUND: The purpose of our study was to evaluate the clinical, cytogenetic, and molecular features, and survival outcomes in patients with acute myeloid leukemia (AML) with myeloid sarcoma (MS) and compare them with patients with AML without MS. PATIENTS AND METHODS: This was a retrospective analysis of de novo pediatric AML patients with or without MS diagnosed at our cancer center between June 2003 and June 2016. RESULTS: MS was present in 121 of 570 (21.2%), the most frequent site being the orbit. Patients with MS had a younger median age (6 years vs. 10 years) and presented with higher hemoglobin and platelet but lower white blood cell count compared with patients without MS. Further, t (8; 21) (P < .01), loss of Y chromosome (P < .01), and deletion 9q (P = .03) were significantly higher in patients with AML with MS. Event-free survival (EFS; P = .003) and overall survival (OS; P = .001) were better among patients with AML with MS (median EFS 21.0 months and median OS 37.1 months) compared with those with AML without MS (median EFS 11.2 months and median OS 16.2 months). The t (8; 21) was significantly associated with MS (odds ratio, 3.92). In a comparison of the 4 groups divided according to the presence or absence of MS and t (8; 21), the subgroup of patients having MS without concomitant t (8; 21) was the only group to have a significantly better OS (hazard ratio, 0.53; 95% confidence interval, 0.34-0.82; P = .005). CONCLUSION: Although t (8; 21) was more frequently associated with MS, it did not appear to be the reason for better outcome.

10.
3 Biotech ; 8(3): 142, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29484281

RESUMO

Impact of second-generation ethanol (2G) use in transportation sector mainly depends upon energy efficiency of entire production process. The objective of present study was to determine energy efficiency of a potential lignocellulosic feedstock; wheat straw and its conversion into cellulosic ethanol in Indian scenario. Energy efficiency was determined by calculating Net energy ratio (NER), i.e. ratio of output energy obtained by ethanol and input energy used in ethanol production. Energy consumption and generation at each step is calculated briefly (11,837.35 MJ/ha during Indian dwarf irrigated variety of wheat crop production and 7.1148 MJ/kg straw during ethanol production stage). Total energy consumption is calculated as 8.2988 MJ/kg straw whereas energy generation from ethanol is 15.082 MJ/kg straw; resulting into NER > 1. Major portion of agricultural energy input is contributed by diesel and fertilisers whereas refining process of wheat straw feedstock to ethanol and by-products require mainly in the form of steam and electricity. On an average, 1671.8 kg water free ethanol, 930 kg lignin rich biomass (for combustion), and 561 kg C5-molasses (for fodder) per hectare are produced. Findings of this study, net energy ratio (1.81) and figure of merit (14.8028 MJ/nil kg carbon) proves wheat straw as highest energy efficient lignocellulosic feedstock for the country.

11.
Indian J Pediatr ; 84(9): 709-714, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28687950

RESUMO

The timing and role of chemotherapy in the management of Wilms' tumor has long been the matter of debate, with different groups showing equally comparable and encouraging results. Over the last decade, however, both the ideol-ogies seem to be converging and the attempt has been to identify groups benefitting with pre-operative chemotherapy, as well as those, where upfront resection should be attempted. In this article authors intend to discuss pros and cons of both the strategies and their applicability in a resource poor setting in developing countries like India.


Assuntos
Neoplasias Renais/cirurgia , Tumor de Wilms/cirurgia , Criança , Terapia Combinada , Países em Desenvolvimento , Humanos , Índia , Neoplasias Renais/tratamento farmacológico , Tumor de Wilms/tratamento farmacológico
13.
Gut Liver ; 10(4): 569-73, 2016 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-27021501

RESUMO

BACKGROUND/AIMS: Optimal bowel preparation is essential for successful screening or for surveillance colonoscopy (SC). Inadequate bowel preparation is associated with older age, the male gender, and the presence of certain comorbidities. However, the association between patients' functional status and bowel preparation quality has not been studied. We prospectively examined the relationship between functional status, namely, the ability to perform activities of daily living (ADLs) and ambulate, and the quality of bowel preparation in elderly patients undergoing SC. METHODS: Before undergoing SC, 88 elderly patients were surveyed regarding their functional status, specifically regarding their ability to perform ADLs and ambulate a quarter of a mile. Gastroenterologists then determined the quality of the bowel preparation, which was classified as either adequate or inadequate. Then, the frequency of inadequate bowel preparation in patients who did or did not experience difficulty performing ADLs and ambulating was calculated. RESULTS: Difficulty ambulating (unadjusted odds ratio [OR], 4.83; p<0.001), difficulty performing ADLs (OR, 2.93; p=0.001), and history of diabetes (OR, 2.88; p=0.007) were significant univariate predictors of inadequate bowel preparation. After adjusting for the above variables, only difficulty ambulating (adjusted OR, 5.78; p=0.004) was an independent predictor of inadequate bowel preparation. CONCLUSIONS: Difficulty with ambulation is a strong predictor of inadequate bowel preparation in elderly patients undergoing SC.


Assuntos
Catárticos/efeitos adversos , Colonoscopia , Avaliação Geriátrica/métodos , Cuidados Pré-Operatórios/efeitos adversos , Atividades Cotidianas , Idoso , Idoso de 80 Anos ou mais , Feminino , Humanos , Masculino , Razão de Chances , Cuidados Pré-Operatórios/métodos , Estudos Prospectivos , Fatores de Risco , Resultado do Tratamento , Caminhada
14.
Nat Med ; 22(4): 369-78, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26928463

RESUMO

Tumor heterogeneity may reduce the efficacy of molecularly guided systemic therapy for cancers that have metastasized. To determine whether the genomic alterations in a single metastasis provide a reasonable assessment of the major oncogenic drivers of other dispersed metastases in an individual, we analyzed multiple tumors from men with disseminated prostate cancer through whole-exome sequencing, array comparative genomic hybridization (CGH) and RNA transcript profiling, and we compared the genomic diversity within and between individuals. In contrast to the substantial heterogeneity between men, there was limited diversity among metastases within an individual. The number of somatic mutations, the burden of genomic copy number alterations and aberrations in known oncogenic drivers were all highly concordant, as were metrics of androgen receptor (AR) activity and cell cycle activity. AR activity was inversely associated with cell proliferation, whereas the expression of Fanconi anemia (FA)-complex genes was correlated with elevated cell cycle progression, expression of the E2F transcription factor 1 (E2F1) and loss of retinoblastoma 1 (RB1). Men with somatic aberrations in FA-complex genes or in ATM serine/threonine kinase (ATM) exhibited significantly longer treatment-response durations to carboplatin than did men without defects in genes encoding DNA-repair proteins. Collectively, these data indicate that although exceptions exist, evaluating a single metastasis provides a reasonable assessment of the major oncogenic driver alterations that are present in disseminated tumors within an individual, and thus may be useful for selecting treatments on the basis of predicted molecular vulnerabilities.


Assuntos
Proteínas Mutadas de Ataxia Telangiectasia/genética , Fator de Transcrição E2F1/biossíntese , Neoplasias da Próstata/genética , Receptores Androgênicos/biossíntese , Proteína do Retinoblastoma/genética , Adulto , Idoso , Carboplatina/administração & dosagem , Proliferação de Células/efeitos dos fármacos , Hibridização Genômica Comparativa , Variações do Número de Cópias de DNA/genética , Fator de Transcrição E2F1/genética , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Variação Genética , Genoma Humano , Humanos , Masculino , Pessoa de Meia-Idade , Metástase Neoplásica , Neoplasias da Próstata/tratamento farmacológico , Neoplasias da Próstata/patologia , Receptores Androgênicos/genética
15.
Genes Chromosomes Cancer ; 55(3): 278-87, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26650888

RESUMO

Investigation of the genetic lesions underlying classical Hodgkin lymphoma (CHL) has been challenging due to the rarity of Hodgkin and Reed-Sternberg (HRS) cells, the pathognomonic neoplastic cells of CHL. In an effort to catalog more comprehensively recurrent copy number alterations occurring during oncogenesis, we investigated somatic alterations involved in CHL using whole-genome sequencing-mediated copy number analysis of purified HRS cells. We performed low-coverage sequencing of small numbers of intact HRS cells and paired non-neoplastic B lymphocytes isolated by flow cytometric cell sorting from 19 primary cases, as well as two commonly used HRS-derived cell lines (KM-H2 and L1236). We found that HRS cells contain strikingly fewer copy number abnormalities than CHL cell lines. A subset of cases displayed nonintegral chromosomal copy number states, suggesting internal heterogeneity within the HRS cell population. Recurrent somatic copy number alterations involving known factors in CHL pathogenesis were identified (REL, the PD-1 pathway, and TNFAIP3). In eight cases (42%) we observed recurrent copy number loss of chr1:2,352,236-4,574,271, a region containing the candidate tumor suppressor TNFRSF14. Using flow cytometry, we demonstrated reduced TNFRSF14 expression in HRS cells from 5 of 22 additional cases (23%) and in two of three CHL cell lines. These studies suggest that TNFRSF14 dysregulation may contribute to the pathobiology of CHL in a subset of cases.


Assuntos
Doença de Hodgkin/genética , Membro 14 de Receptores do Fator de Necrose Tumoral/genética , Linhagem Celular Tumoral , Separação Celular , Citometria de Fluxo , Doença de Hodgkin/metabolismo , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , Membro 14 de Receptores do Fator de Necrose Tumoral/biossíntese , Membro 14 de Receptores do Fator de Necrose Tumoral/deficiência , Células de Reed-Sternberg
16.
FEMS Microbiol Lett ; 362(15): fnv112, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-26187746

RESUMO

Bacterial surface components have a major role in the development of biofilms. In the present study, the effect of Escherichia coli O8-antigen on biofilms was investigated using two E. coli K-12 derived strains that differed only in the O8-antigen biosynthesis. In the presence of O8-antigen both bacterial adhesion and biofilm formation slightly decreased under static conditions whereas a substantial increase in adhesion and biofilm formation was observed under agitated conditions. It was noted that, irrespective of the O8-antigen status, the hydrophobic interactions played an important role in bacterial adhesion under both static and agitated conditions. However, under agitated conditions, the extent of bacterial adhesion in the O8-antigen bearing strain was predominantly determined by the electrostatic interactions. Results showed that the presence of O8-antigen decreases the surface hydrophobicity and surface charge. Moreover, O8-antigen facilitates adhesion on hydrophilic and hydrophobic surfaces as revealed through tests with modified substrata. Our results indicate that O8-antigen, which appears dispensable for biofilm formation under static conditions, actually enhances E. coli biofilm formation under agitated conditions.


Assuntos
Biofilmes/crescimento & desenvolvimento , Escherichia coli K12/fisiologia , Antígenos O/fisiologia , Aderência Bacteriana , Escherichia coli K12/genética , Escherichia coli K12/imunologia , Escherichia coli K12/ultraestrutura , Interações Hidrofóbicas e Hidrofílicas , Lipopolissacarídeos/fisiologia , Antígenos O/química , Antígenos O/genética , Propriedades de Superfície
17.
Genome Med ; 7(1): 35, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26019723

RESUMO

BACKGROUND: Preimplantation genetic diagnosis (PGD) enables profiling of embryos for genetic disorders prior to implantation. The majority of PGD testing is restricted in the scope of variants assayed or by the availability of extended family members. While recent advances in single cell sequencing show promise, they remain limited by bias in DNA amplification and the rapid turnaround time (<36 h) required for fresh embryo transfer. Here, we describe and validate a method for inferring the inherited whole genome sequence of an embryo for preimplantation genetic diagnosis (PGD). METHODS: We combine haplotype-resolved, parental genome sequencing with rapid embryo genotyping to predict the whole genome sequence of a day-5 human embryo in a couple at risk of transmitting alpha-thalassemia. RESULTS: Inheritance was predicted at approximately 3 million paternally and/or maternally heterozygous sites with greater than 99% accuracy. Furthermore, we successfully phase and predict the transmission of an HBA1/HBA2 deletion from each parent. CONCLUSIONS: Our results suggest that preimplantation whole genome prediction may facilitate the comprehensive diagnosis of diseases with a known genetic basis in embryos.

18.
World J Gastrointest Endosc ; 7(5): 573-4, 2015 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-25992198

RESUMO

We report an unexpected, previously unreported complication of Bravo pH capsule dislodgement. During Bravo pH testing of a 44-year-old man with gastroesophageal reflux disease, we were unable to endoscopically visualize the capsule attached to the esophageal wall after deployment. After multiple attempts to detect the capsule, it was visualized in the left pyriform sinus. As there was significant risk for pulmonary dislodgement, ENT and pulmonary physicians were immediately consulted to review options for safe removal. Ultimately, ENT successfully retrieved the capsule with a foreign body removal forceps. The Bravo pH test is generally a well-tolerated diagnostic tool used to confirm the presence of abnormal esophageal acid reflux. While few complications have been reported, technical difficulties can occur, including poor data reception, misplacement, and early dislodgement. Rarely, more serious complications can occur, ranging from esophageal wall trauma to capsule aspiration. Gastroenterologists performing this procedure should be aware of the low, but non-trivial, risk of complications.

19.
Curr Microbiol ; 70(2): 228-34, 2015 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-25292249

RESUMO

The silkworm forms cocoon to protect its pupa that survives for months inside the cocoon without being affected by various environmental stresses. To understand the possible mode of pupal survival within the cocoon encasement, we investigate the cause that protects the cocoon. During the end of the spinning process, we have isolated different bacterial species from the cocoon surface. These are identified using molecular techniques and checked for their abilities to form biofilm in vitro. The bacteria are able to form biofilm either individually or in consortia. Of which, Bacillus and Erwinia species are prominent biofilm formers. Interestingly, these bacteria have the ability to form biofilm on the cocoon mimetic surface of the silk protein Sericin Hope that contains only sericin. The origin and the behavior of the bacteria lead us to hypothesize the possible role of biofilm layer on the cocoon surface, which provides protection from adverse environmental conditions.


Assuntos
Fenômenos Fisiológicos Bacterianos , Biofilmes , Bombyx/fisiologia , Meio Ambiente , Seda , Estresse Fisiológico , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/ultraestrutura , Pupa , RNA Ribossômico 16S/genética
20.
Genome Res ; 24(12): 2041-9, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-25327137

RESUMO

We describe a method that exploits contiguity preserving transposase sequencing (CPT-seq) to facilitate the scaffolding of de novo genome assemblies. CPT-seq is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to > 1 megabase. These pools are "subhaploid," in that the lengths of fragments contained in each pool sums to ∼5% to 10% of the full genome. The scaffolding approach described here, termed fragScaff, leverages coincidences between the content of different pools as a source of contiguity information. Specifically, CPT-seq data is mapped to a de novo genome assembly, followed by the identification of pairs of contigs or scaffolds whose ends disproportionately co-occur in the same indexed pools, consistent with true adjacency in the genome. Such candidate "joins" are used to construct a graph, which is then resolved by a minimum spanning tree. As a proof-of-concept, we apply CPT-seq and fragScaff to substantially boost the contiguity of de novo assemblies of the human, mouse, and fly genomes, increasing the scaffold N50 of de novo assemblies by eight- to 57-fold with high accuracy. We also demonstrate that fragScaff is complementary to Hi-C-based contact probability maps, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps. Finally, we demonstrate CPT-seq as a means of anchoring unplaced novel human contigs to the reference genome as well as for detecting misassembled sequences.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Transposases/metabolismo , Animais , Biologia Computacional/métodos , Biblioteca Gênica , Genômica/métodos , Humanos , Camundongos , Software
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