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1.
Environ Microbiol ; 23(7): 3710-3726, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-33350070

RESUMEN

Geothermal springs are essentially unaffected by environmental conditions aboveground as they are continuously supplied with subsurface water with little variability in chemistry. Therefore, changes in their microbial community composition and function, especially over a long period, are expected to be limited but this assumption has not yet been rigorously tested. Toward closing this knowledge gap, we applied whole metagenome sequencing to 17 water samples collected between 2010 and 2016 from the Thermopyles sulfur-rich geothermal springs in central Greece. As revealed by 16S rRNA gene fragments recovered in the metagenomes, Epsilonproteobacteria-related operational taxonomic units (OTUs) dominated most samples and grouping of samples based on OTU abundances exhibited no apparent seasonal pattern. Similarities between samples regarding functional gene content were high, with all samples sharing >70% similarity in functional pathways. These community-wide patterns were further confirmed by analysis of metagenome-assembled genomes (MAGs), which showed that novel species and genera of the chemoautotrophic Campylobacterales order dominated the springs. These MAGs carried different pathways for thiosulfate or sulfide oxidation coupled to carbon fixation pathways. Overall, our study showed that even in the long term, functions of microbial communities in a moderately hot terrestrial spring remain stable, presumably driving the corresponding stability in community structure.


Asunto(s)
Manantiales de Aguas Termales , Microbiota , Bacterias/genética , Grecia , Metagenoma , Microbiota/genética , Oxidación-Reducción , Filogenia , ARN Ribosómico 16S/genética , Azufre
2.
Nat Commun ; 15(1): 3607, 2024 Apr 29.
Artículo en Inglés | MEDLINE | ID: mdl-38684658

RESUMEN

Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfur-oxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes.


Asunto(s)
Fijación del Nitrógeno , Oxidación-Reducción , Raíces de Plantas , Poaceae , Azufre , Humedales , Azufre/metabolismo , Raíces de Plantas/metabolismo , Raíces de Plantas/microbiología , Poaceae/metabolismo , Filogenia , Simbiosis , Bacterias/metabolismo , Bacterias/genética , Bacterias/clasificación , Metagenoma , Sulfatos/metabolismo , Nitrógeno/metabolismo
3.
mBio ; 15(4): e0342223, 2024 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-38488359

RESUMEN

Diarrheagenic Escherichia coli, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality E. coli metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent E. coli (DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance. IMPORTANCE: Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.


Asunto(s)
Infecciones por Escherichia coli , Escherichia coli , Niño , Humanos , Escherichia coli/genética , Metagenoma , Infecciones por Escherichia coli/epidemiología , Diarrea/diagnóstico , Diarrea/epidemiología , Virulencia/genética
4.
Appl Environ Microbiol ; 78(19): 7023-31, 2012 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-22843538

RESUMEN

The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites.


Asunto(s)
Biota , Microbiología Ambiental , Compuestos Orgánicos/análisis , Suelo/química , Agua/química , Carbono/análisis , Concentración de Iones de Hidrógeno , Lacasa/metabolismo , Minnesota , Datos de Secuencia Molecular , Nitrógeno/análisis , Peroxidasas/metabolismo , Análisis de Secuencia de ADN
5.
Colorectal Dis ; 13(6): e137-44, 2011 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-21564466

RESUMEN

AIM: The detection rate of adenomas is one of the current quality indicators in high-quality colonoscopy. We compared the performance of colonoscopy for the detection of polyps in patients sedated with deep and moderate sedation. Secondary objectives included the patient's and the endoscopist's satisfaction, recovery time and the adverse events related to sedation between the two groups. METHOD: Five hundred and twenty patients submitted for colonoscopy were prospectively randomized into a deep sedation group (DS group, n = 258) and a moderate sedation (MS group, n = 262) group. In both, sedation and analgesia were performed using midazolam with pethidine. RESULTS: There were no differences between the two groups in the following three areas: (1) The overall detection of polyps (DS, 1 [0-20]; MS, 1 [0-15]; P = 0.67), (2): polyp size ≥ 10 mm (DS, 0.00 [0-7]; MS, 0.00 [0-6]; P = 0.30), and (3) polyp size < 10 mm (DS, 0.00 [0-20]; MS, 0.00 [0-13]; P = 0.83). There was no significant difference in the rate of adenoma detection (DS, 1 [0-10]; MS, 1 [0-9]; P = 0.99). CONCLUSION: The study demonstrated no difference in the detection of polyps by colonoscopy using deep or moderate sedation.


Asunto(s)
Pólipos del Colon/diagnóstico , Colonoscopía , Sedación Consciente , Sedación Profunda , Anciano , Anciano de 80 o más Años , Analgesia , Analgésicos Opioides/administración & dosificación , Periodo de Recuperación de la Anestesia , Actitud del Personal de Salud , Pólipos del Colon/patología , Sedación Consciente/efectos adversos , Sedación Profunda/efectos adversos , Femenino , Humanos , Hipnóticos y Sedantes/administración & dosificación , Masculino , Meperidina/administración & dosificación , Midazolam/administración & dosificación , Persona de Mediana Edad , Satisfacción del Paciente , Factores de Tiempo
6.
Colorectal Dis ; 13(10): e345-8, 2011 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-21689363

RESUMEN

AIM: Polypectomy techniques in the removal of polyps in the 3-8 mm size range are inconsistent. The aim of our study was to compare cold (CSP) with hot snare polypectomy (HSP) in the occurrence of postpolypectomy bleeding in small colonic polyps 3-8 mm in size. METHOD: In all, 414 consecutive patients with small colorectal polyps 3-8 mm in size were prospectively randomized into the CSP group and the HSP group. RESULTS: There was no early or late postpolypectomy bleeding in either group. Intraprocedural bleeding was significantly more frequent in the CSP group than the HSP group (CSP, 19/208; HSP, 2/206; P<0.001) but resolved spontaneously without any intervention in both groups. CONCLUSION: The data show that the CSP technique is safe, effective and quicker than HSP for patients and it could be considered the ideal procedure for small polyp removal.


Asunto(s)
Pólipos del Colon/cirugía , Colonoscopía , Electrocoagulación , Hemorragia Posoperatoria , Femenino , Humanos , Masculino , Persona de Mediana Edad
7.
Colorectal Dis ; 12(10 Online): e260-6, 2010 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-19930146

RESUMEN

AIM: We sought to compare the performance of colonoscopy using a high-definition, wide-angle endoscope vs a standard colonoscope for the detection of polyps. METHOD: A total of 390 patients were prospectively randomized into high-definition colonoscopy group (HD, n = 193) and standard colonoscopy group (SC, n = 197). RESULTS: Analysis demonstrated that there were significant differences between the two groups, as far as the overall rate of polyps (SC, 1.31 ± 1.90; HD, 1.76 ± 2.31; P = 0.03) and the rate of small hyperplastic polyps (size < 5 mm; SC, 0.10 ± 0.36; HD, 0.25 ± 0.61; P = 0.003) were concerned. No significant differences between the two groups were observed, regarding large polyps (size ≥ 10 mm; SC, 0.39 ± 0.89; HD, 0.48 ± 0.80; P = 0.10), medium polyps (10 mm > size ≥ 5 mm; SC, 0.60 ± 1.46; HD, 0.58 ± 1.25; P = 0.31) and small polyps (size < 5 mm; SC, 0.32 ± 0.86; HD, 0.71 ± 1.65; P = 0.09). Similarly, no significant differences were demonstrated in the detection rate of adenomas and hyperplastic polyps, large adenomas, medium adenomas, small adenomas and large and medium hyperplastic polyps. CONCLUSION: High-definition colonoscopy led to a significant increase in the polyp detection.


Asunto(s)
Adenoma/diagnóstico , Neoplasias del Colon/diagnóstico , Pólipos del Colon/diagnóstico , Colonoscopios , Neoplasias del Recto/diagnóstico , Adenoma/patología , Anciano , Neoplasias del Colon/patología , Pólipos del Colon/patología , Colonoscopía/métodos , Femenino , Humanos , Masculino , Persona de Mediana Edad , Neoplasias del Recto/patología , Factores de Tiempo , Estudios de Tiempo y Movimiento
8.
mBio ; 11(6)2020 11 17.
Artículo en Inglés | MEDLINE | ID: mdl-33203758

RESUMEN

Norovirus infections take a heavy toll on worldwide public health. While progress has been made toward understanding host responses to infection, the role of the gut microbiome in determining infection outcome is unknown. Moreover, data are lacking on the nature and duration of the microbiome response to norovirus infection, which has important implications for diagnostics and host recovery. Here, we characterized the gut microbiomes of subjects enrolled in a norovirus challenge study. We analyzed microbiome features of asymptomatic and symptomatic individuals at the genome (population) and gene levels and assessed their response over time in symptomatic individuals. We show that the preinfection microbiomes of subjects with asymptomatic infections were enriched in Bacteroidetes and depleted in Clostridia relative to the microbiomes of symptomatic subjects. These compositional differences were accompanied by differences in genes involved in the metabolism of glycans and sphingolipids that may aid in host resilience to infection. We further show that microbiomes shifted in composition following infection and that recovery times were variable among human hosts. In particular, Firmicutes increased immediately following the challenge, while Bacteroidetes and Proteobacteria decreased over the same time. Genes enriched in the microbiomes of symptomatic subjects, including the adenylyltransferase glgC, were linked to glycan metabolism and cell-cell signaling, suggesting as-yet unknown roles for these processes in determining infection outcome. These results provide important context for understanding the gut microbiome role in host susceptibility to symptomatic norovirus infection and long-term health outcomes.IMPORTANCE The role of the human gut microbiome in determining whether an individual infected with norovirus will be symptomatic is poorly understood. This study provides important data on microbes that distinguish asymptomatic from symptomatic microbiomes and links these features to infection responses in a human challenge study. The results have implications for understanding resistance to and treatment of norovirus infections.


Asunto(s)
Bacteroidetes/crecimiento & desarrollo , Infecciones por Caliciviridae/prevención & control , Firmicutes/crecimiento & desarrollo , Microbioma Gastrointestinal , Norovirus/inmunología , Proteobacteria/crecimiento & desarrollo , Enfermedades Asintomáticas , Bacteroidetes/genética , Infecciones por Caliciviridae/inmunología , Infecciones por Caliciviridae/virología , Susceptibilidad a Enfermedades , Firmicutes/genética , Humanos , Metagenómica , Proteobacteria/genética
9.
Endoscopy ; 41(12): 1046-51, 2009 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-19967620

RESUMEN

BACKGROUND AND STUDY AIMS: We sought to determine whether bispectral index (BIS) monitoring is a useful adjunct to the administration of propofol titrated to deep sedation, as measured by reductions of doses of propofol administered during endoscopic retrograde cholangiopancreatography (ERCP). PATIENTS AND METHODS: 90 consecutive patients undergoing ERCP were randomized to receive propofol titrated to deep sedation, with the BIS value either visible (BIS group, n = 46) or invisible (control group, n = 44) to the anesthesiologist. In the BIS group, the anesthesiologist was instructed to use the BIS value as the primary end point for titration of sedation, and to target BIS values between 40 and 60. For the control group, the anesthesiologist was instructed to titrate propofol according to routine practice in the unit using the modified Observer's Assessment of Alertness/Sedation (MOAA/S) Scale (MOAA/S score 0). RESULTS: The mean (SD) propofol doses (mg/min per kg weight) were 0.139 (0.02) and 0.193 (0.02) for the BIS and control groups, respectively (P < 0.001). Mean (SD) BIS values throughout the procedure were 61.68 (7.5) and 56.93 (4.77) for the BIS and control groups, respectively (P = 0.001). During the maintenance phase of sedation (MOAA/S score 0), the mean (SD) BIS values were 53.73 (8.67) and 45.65 (4.39) for the BIS and control groups, respectively (P < 0.001). CONCLUSIONS: Our data suggest that BIS monitoring led to a reduction in the mean propofol dose when the BIS value was used as the primary target for sedation in ERCP procedures.


Asunto(s)
Colangiopancreatografia Retrógrada Endoscópica , Monitores de Conciencia , Sedación Profunda , Hipnóticos y Sedantes/administración & dosificación , Propofol/administración & dosificación , Anciano , Sedación Profunda/efectos adversos , Electroencefalografía , Femenino , Humanos , Bombas de Infusión , Inyecciones Intravenosas , Masculino , Satisfacción del Paciente
11.
Obes Surg ; 26(4): 882-90, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-26843083

RESUMEN

BACKGROUND: Type 2 diabetic obese patients present with a normalization of plasma glucose levels shortly after most bariatric procedures, before any significant weight loss takes place. There is only scarce literature in the new field of metabolic surgery, with most experiments being performed on small animal models. AIM: Our aim is to develop a reliable large animal model for assessment of surgical correction of diabetes. METHOD: Titrated doses of streptozotocin (STZ) were used for induction of diabetes mellitus. After standardization of the surgical technique to avoid any restrictive component, three groups were created, a duodenojejunal bypass (DJB; n = 4), a gastroileal conduit (GIC; n = 3) near the ileocecal valve, and a sham (control; n = 5) group. Preoperative and postoperative glycemic curves were recorded by means of intravenous glucose tolerance tests. Body weight fluctuations were recorded as well. RESULTS: Diabetes was successfully induced with the use of STZ in all cases. Animals in the sham group remained diabetic for 3 weeks after operation. There was normalization of blood glucose levels in the operative groups during the 3-week postoperative follow-up, without significant body weight changes. The duodenojejunal group resulted in stronger positive response of glycemia. CONCLUSION: STZ-induced diabetes in swine leads to a reliable large animal model for assessment of metabolic surgical procedures. STZ is an effective but highly toxic means for inducing stable diabetes in the sensitive porcine model. Duodenojejunal bypass, although less invasive, seems to exert better antidiabetic effects than gastroileal conduit.


Asunto(s)
Diabetes Mellitus Experimental/cirugía , Diabetes Mellitus Tipo 2/cirugía , Procedimientos Quirúrgicos del Sistema Digestivo , Modelos Animales de Enfermedad , Anastomosis Quirúrgica , Animales , Cirugía Bariátrica , Glucemia/análisis , Diabetes Mellitus Experimental/sangre , Diabetes Mellitus Tipo 2/sangre , Duodeno/cirugía , Femenino , Gastroenterostomía , Íleon/cirugía , Yeyuno/cirugía , Estómago/cirugía , Porcinos
14.
Angiology ; 55(6): 669-78, 2004.
Artículo en Inglés | MEDLINE | ID: mdl-15547653

RESUMEN

In contrast to the well-recognized salutary effects of angiotensin-converting enzyme inhibition, the value of angiotensin II type I (ATl)-receptor blockade on left ventricular hypertrophy (LVH) is controversial. In addition, the data on the influence of this therapy on cardiac diastolic function are scarce. Thirty-nine patients with moderate primary hypertension, LVH, and normal systolic function received losartan, 50 to 100 mg daily. Transthoracic echocardiography was performed at baseline and after 6 months of treatment. Thirty-one patients completed and were included in the study (16 males, 61.1 +/- 1.0 years). The patients were divided into responders if mean blood pressure (BP) decreased > 5 mm Hg at the end of the study (20 patients) and non-responders (mean BP decrease < or = 5 mm Hg, 11 patients). The BP and the LVH were significantly reduced (systolic BP by 10.0%, diastolic BP 6.5%, mean BP 8.2%, left ventricular mass index [LVMI] 6.2%, interventricular septum 5.8%, posterior wall 3.0%) (p< or =0.02), attributed to the reduction of BP and LVH in responders; the LVH in non-responders did not alter with treatment. A significant correlation was noted between changes in BP and LVMI (r=0.60, p<0.001). The systolic cardiac function remained normal. The Doppler parameters usually used to assess the diastolic function of the LV (early diastolic filling velocity [E wave], late diastolic filling velocity [A wave], ratio of E/A waves, isovolumic relaxation time), which were abnormal at baseline, did not change with treatment. The size of the left atrium increased (p<0.05) at the end of the study. In conclusion, a 6-month course with losartan decreased BP and LVH. However, the LVH regression was rather associated with the reduction of the hemodynamic stimulus per se, than any trophic effect of the drug in the myocardium. The diastolic cardiac function remained abnormal with treatment.


Asunto(s)
Antihipertensivos/uso terapéutico , Diástole/efectos de los fármacos , Hipertensión/tratamiento farmacológico , Hipertrofia Ventricular Izquierda/tratamiento farmacológico , Losartán/uso terapéutico , Presión Sanguínea/efectos de los fármacos , Ecocardiografía , Ecocardiografía Doppler , Femenino , Humanos , Hipertensión/fisiopatología , Masculino , Persona de Mediana Edad , Estudios Prospectivos , Factores de Tiempo
15.
Urologe A ; 28(3): 152-7, 1989 May.
Artículo en Alemán | MEDLINE | ID: mdl-2741262

RESUMEN

From 1982 to December 1987, 71 with incomplete (C4 by Rocco) and 37 with complete (C5 by Rocco) staghorn calculi underwent anatrophic nephrolithotomy (AN; n = 29), or combined percutaneous nephrostolithotomy and ESWL (PCNL + ESWL; n = 21), or ESWL monotherapy without or with preoperative JJ stenting (n = 37/21). The patients with incomplete staghorn calculi (C4) and preoperative ureteral stenting were free of stones after 6 months in 15 of 17 cases (88%), which is comparable to our results with AN (90%) and combined PCNL + ESWL (85%). ESWL without JJ stenting were free of stones in only 52%. The treatment of infected C4 calculi with JJ stenting was especially successful (92%). Complete staghorn calculi (C5) represented the best results after AN (78%) and combined PCNL + ESWL (75%), in contrast to ESWL without JJ stenting (44%). Four patients with C5 calculi were treated with ESWL and preoperative stenting, three of them were free of stones after 6 months. For incomplete staghorn calculi (C4), ESWL monotherapy with JJ stenting seems to be a justifiable noninvasive method which offers excellent results in stone elimination (88%), with lower costs than AN or PCNL + ESWL. More invasive procedures should be reserved for complete staghorn calculi.


Asunto(s)
Cálculos Renales/terapia , Litotricia/métodos , Nefrostomía Percutánea/métodos , Terapia Combinada , Femenino , Humanos , Masculino , Persona de Mediana Edad
16.
mBio ; 5(3): e01193-14, 2014 Jun 03.
Artículo en Inglés | MEDLINE | ID: mdl-24895307

RESUMEN

UNLABELLED: Microbial activities in soils, such as (incomplete) denitrification, represent major sources of nitrous oxide (N2O), a potent greenhouse gas. The key enzyme for mitigating N2O emissions is NosZ, which catalyzes N2O reduction to N2. We recently described "atypical" functional NosZ proteins encoded by both denitrifiers and nondenitrifiers, which were missed in previous environmental surveys (R. A. Sanford et al., Proc. Natl. Acad. Sci. U. S. A. 109:19709-19714, 2012, doi:10.1073/pnas.1211238109). Here, we analyzed the abundance and diversity of both nosZ types in whole-genome shotgun metagenomes from sandy and silty loam agricultural soils that typify the U.S. Midwest corn belt. First, different search algorithms and parameters for detecting nosZ metagenomic reads were evaluated based on in silico-generated (mock) metagenomes. Using the derived cutoffs, 71 distinct alleles (95% amino acid identity level) encoding typical or atypical NosZ proteins were detected in both soil types. Remarkably, more than 70% of the total nosZ reads in both soils were classified as atypical, emphasizing that prior surveys underestimated nosZ abundance. Approximately 15% of the total nosZ reads were taxonomically related to Anaeromyxobacter, which was the most abundant genus encoding atypical NosZ-type proteins in both soil types. Further analyses revealed that atypical nosZ genes outnumbered typical nosZ genes in most publicly available soil metagenomes, underscoring their potential role in mediating N2O consumption in soils. Therefore, this study provides a bioinformatics strategy to reliably detect target genes in complex short-read metagenomes and suggests that the analysis of both typical and atypical nosZ sequences is required to understand and predict N2O flux in soils. IMPORTANCE: Nitrous oxide (N2O) is a potent greenhouse gas with ozone layer destruction potential. Microbial activities control both the production and the consumption of N2O, i.e., its conversion to innocuous dinitrogen gas (N2). Until recently, consumption of N2O was attributed to bacteria encoding "typical" nitrous oxide reductase (NosZ). However, recent phylogenetic and physiological studies have shown that previously uncharacterized, functional, "atypical" NosZ proteins are encoded in genomes of diverse bacterial groups. The present study revealed that atypical nosZ genes outnumbered their typical counterparts, highlighting their potential role in N2O consumption in soils and possibly other environments. These findings advance our understanding of the diversity of microbes and functional genes involved in the nitrogen cycle and provide the means (e.g., gene sequences) to study N2O fluxes to the atmosphere and associated climate change.


Asunto(s)
Metagenoma , Oxidorreductasas/genética , Microbiología del Suelo , Suelo/química , Algoritmos , Biología Computacional/métodos , Ciclo del Nitrógeno , Óxido Nitroso , Filogenia
17.
Int Angiol ; 31(4): 386-92, 2012 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-22801405

RESUMEN

AIM: The treatment of ruptured abdominal aortic aneurysms is a constant challenge for vascular surgeons and can be achieved either by endovascular repair or by an open surgical technique. Endovascular repair presents a higher 30-day survival rate. The aim of this study was to compare the clinical and anatomical characteristics and the outcomes of these two treatment techniques. METHODS: Our study sample comprised patients who presented at the emergency department of a General Regional Hospital with rupture of an abdominal aortic aneurysm between January 2003 and December 2008. Of the 43 patients who were treated, 23 underwent open surgical repair and 20 underwent endovascular repair. RESULTS: Comorbidities, age, clinical presentation and anatomical characteristics didn't present statistically significant differences in the two groups. Patients in the endovascular repair group were transfused with less units of blood and fresh frozen plasma (P=0.001) and had shorter stay in the intensive care unit (P=0.042). The 30-day mortality rate was 43% for open surgical repair and 35% for endovascular treatment (P=0.627), while the overall in-hospital mortality rate was 61% and 50% (P=0.474), respectively. CONCLUSION: When certain anatomical characteristics are present and the hemodynamic condition of the patient allows it, endovascular treatment appears to be associated with better survival rates, both 30-day and overall.


Asunto(s)
Aneurisma de la Aorta Abdominal/cirugía , Rotura de la Aorta/cirugía , Implantación de Prótesis Vascular , Procedimientos Endovasculares , Anciano , Anciano de 80 o más Años , Aneurisma de la Aorta Abdominal/complicaciones , Aneurisma de la Aorta Abdominal/mortalidad , Aneurisma de la Aorta Abdominal/fisiopatología , Rotura de la Aorta/etiología , Rotura de la Aorta/mortalidad , Rotura de la Aorta/fisiopatología , Transfusión Sanguínea , Implantación de Prótesis Vascular/efectos adversos , Implantación de Prótesis Vascular/mortalidad , Distribución de Chi-Cuadrado , Procedimientos Endovasculares/efectos adversos , Procedimientos Endovasculares/mortalidad , Femenino , Hemodinámica , Mortalidad Hospitalaria , Hospitales Generales , Humanos , Estimación de Kaplan-Meier , Tiempo de Internación , Masculino , Persona de Mediana Edad , Selección de Paciente , Polonia , Complicaciones Posoperatorias/etiología , Complicaciones Posoperatorias/mortalidad , Complicaciones Posoperatorias/cirugía , Reoperación , Estudios Retrospectivos , Medición de Riesgo , Factores de Riesgo , Factores de Tiempo , Resultado del Tratamiento
18.
mBio ; 3(3)2012.
Artículo en Inglés | MEDLINE | ID: mdl-22589287

RESUMEN

UNLABELLED: Spirochaetes is one of a few bacterial phyla that are characterized by a unifying diagnostic feature, namely, the helical morphology and motility conferred by axial periplasmic flagella. Their unique morphology and mode of propulsion also represent major pathogenicity factors of clinical spirochetes. Here we describe the genome sequences of two coccoid isolates of the recently described genus Sphaerochaeta which are members of the phylum Spirochaetes based on 16S rRNA gene and whole-genome phylogenies. Interestingly, the Sphaerochaeta genomes completely lack the motility and associated signal transduction genes present in all sequenced spirochete genomes. Additional analyses revealed that the lack of flagella is associated with a unique, nonrigid cell wall structure hallmarked by a lack of transpeptidase and transglycosylase genes, which is also unprecedented in spirochetes. The Sphaerochaeta genomes are highly enriched in fermentation and carbohydrate metabolism genes relative to other spirochetes, indicating a fermentative lifestyle. Remarkably, most of the enriched genes appear to have been acquired from nonspirochetes, particularly clostridia, in several massive horizontal gene transfer events (>40% of the total number of genes in each genome). Such a high level of direct interphylum genetic exchange is extremely rare among mesophilic organisms and has important implications for the assembly of the prokaryotic tree of life. IMPORTANCE: Spiral shape and motility historically have been the unifying hallmarks of the phylum Spirochaetes. These features also represent important virulence factors of highly invasive pathogenic spirochetes such as the causative agents of syphilis and Lyme disease. Through the integration of genome sequencing, microscopy, and physiological studies, we conclusively show that the spiral morphology and motility of spirochetes are not universal morphological properties. In particular, we found that the genomes of the members of the recently described genus Sphaerochaeta lack the genes encoding the characteristic flagellar apparatus and, in contrast to most other spirochetes, have acquired many metabolic and fermentation genes from clostridia. These findings have major implications for the isolation and study of spirochetes, the diagnosis of spirochete-caused diseases, and the reconstruction of the evolutionary history of this important bacterial phylum. The Sphaerochaeta sp. genomes offer new avenues to link ecophysiology with the functionality and evolution of the spirochete flagellar apparatus.


Asunto(s)
Genoma Bacteriano , Spirochaeta/citología , Spirochaeta/genética , Spirochaetales/genética , Transferencia de Gen Horizontal , Humanos , Enfermedad de Lyme/microbiología , Datos de Secuencia Molecular , Filogenia , Spirochaeta/clasificación , Spirochaeta/aislamiento & purificación , Spirochaetales/clasificación , Spirochaetales/aislamiento & purificación , Infecciones por Spirochaetales/microbiología
20.
Int J Med Robot ; 7(4): 375-92, 2011 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-21815238

RESUMEN

BACKGROUND: Autonomous control of surgical robotic platforms may offer enhancements such as higher precision, intelligent manoeuvres, tissue-damage avoidance, etc. Autonomous robotic systems in surgery are largely at the experimental level. However, they have also reached clinical application. METHODS: A literature review pertaining to commercial medical systems which incorporate autonomous and semi-autonomous features, as well as experimental work involving automation of various surgical procedures, is presented. Results are drawn from major databases, excluding papers not experimentally implemented on real robots. RESULTS: Our search yielded several experimental and clinical applications, describing progress in autonomous surgical manoeuvres, ultrasound guidance, optical coherence tomography guidance, cochlear implantation, motion compensation, orthopaedic, neurological and radiosurgery robots. CONCLUSION: Autonomous and semi-autonomous systems are beginning to emerge in various interventions, automating important steps of the operation. These systems are expected to become standard modality and revolutionize the face of surgery.


Asunto(s)
Inteligencia Artificial , Predicción , Robótica/métodos , Cirugía Asistida por Computador/métodos , Diseño de Equipo , Robótica/instrumentación , Robótica/tendencias , Cirugía Asistida por Computador/instrumentación , Cirugía Asistida por Computador/tendencias
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