Mitogenome assembly from genomic multiplex libraries: comparison of strategies and novel mitogenomes for five species of frogs.

Next-generation sequencing continues to revolutionize biodiversity studies by generating unprecedented amounts of DNA sequence data for comparative genomic analysis. However, these data are produced as millions or billions of short reads of variable quality that cannot be directly applied in comparative analyses, creating a demand for methods to facilitate assembly. We optimized an in silico strategy to efficiently reconstruct high-quality mitochondrial genomes directly from genomic reads. We tested this strategy using sequences from five species of frogs: Hylodes meridionalis (Hylodidae), Hyloxalus yasuni (Dendrobatidae), Pristimantis fenestratus (Craugastoridae), and Melanophryniscus simplex and Rhinella sp. (Bufonidae). These are the first mitogenomes published for these species, the genera Hylodes, Hyloxalus, Pristimantis, Melanophryniscus and Rhinella, and the families Craugastoridae and Hylodidae. Sequences were generated using only half of one lane of a standard Illumina HiqSeq 2000 flow cell, resulting in fewer than eight million reads. We analysed the reads of Hylodes meridionalis using three different assembly strategies: (1) reference-based (using bowtie2); (2) de novo (using abyss, soapdenovo2 and velvet); and (3) baiting and iterative mapping (using mira and mitobim). Mitogenomes were assembled exclusively with strategy 3, which we employed to assemble the remaining mitogenomes. Annotations were performed with mitos and confirmed by comparison with published amphibian mitochondria. In most cases, we recovered all 13 coding genes, 22 tRNAs, and two ribosomal subunit genes, with minor gene rearrangements. Our results show that few raw reads can be sufficient to generate high-quality scaffolds, making any Illumina machine run using genomic multiplex libraries a potential source of data for organelle assemblies as by-catch.

Outcomes and Mortality in Renal Transplant Recipients Admitted to the Intensive Care Unit.

INTRODUCTION: In the intensive care unit (ICU), mortality is considered higher among renal transplant recipients than among nontransplantation patients. However, data regarding severe complications after kidney transplantation are scarce. MATERIALS AND METHODS: In this study, we evaluated all consecutive renal transplant recipients admitted to our ICU between July 2012 and July 2013 (n = 70), comparing their outcomes with those of a control group of nontransplantation patients admitted during the same period (n = 153). Among the transplant recipients, we compared survivors and nonsurvivors to identify predictors of ICU mortality. RESULTS: The mean age of the transplant recipients was 52 ± 13 years. Of the 70 transplant recipients, 18 (25%) required mechanical ventilation, 28 (40%) required inotropic support, and 27 (39%) required hemodialysis, all of which are factors that worsen the prognosis significantly. Twenty-two (31%) of the transplant recipients died in the ICU and 17 (24%) died within 30 days after ICU discharge, rates similar to those observed for the control group. CONCLUSIONS: We observed similar mortality between recipient and control groups, albeit the mortality was higher in the clinical group. In the multivariate model, the need for mechanical ventilation and the need for hemodialysis were independently associated with mortality.

De novo thrombotic microangiopathy after kidney transplantation: clinical features, treatment, and long-term patient and graft survival.

INTRODUCTION: Posttransplant thrombotic microangiopathy (TMA)/hemolytic uremic syndrome (HUS) can occur as a recurrent or de novo disease. METHODS: A retrospective single-center observational study was applied in order to examine the incidence and outcomes of de novo TMA/HUS among transplantations performed between 2000 and 2010. Recurrent HUS or antibody-mediated rejections were excluded. RESULTS: Seventeen (1.1%) among 1549 kidney transplant recipients fulfilled criteria for de novo TMA. The mean follow-up was 572 days (range, 69-1769). Maintenance immunosuppression was prednisone, tacrolimus (TAC), and mycophenolic acid in 14 (82%) patients. Mean age at onset was 40 ± 15 years, and serum creatinine was 6.1 ± 4.1 mg/dL. TMA occurred at a median of 25 days (range, 1-1755) after transplantation. Nine (53%) patients developed TMA within 1 month of transplantation and only 12% after 1 year. Clinical features were anemia (hemoglobin < 10 g/dL) in 9 (53%) patients, thrombocytopenia in 7 (41%), and increased lactate dehydrogenase in 12 (70%). Decreased haptoglobin was observed in 64% and schistocytes in 35%. Calcineurin inhibitor (CNI) withdrawal or reduction was the first step in the management of 10/15 (66%) patients, and 6 (35%) received fresh frozen plasma (FFP) and/or plasmapheresis. TAC was successfully reintroduced in six patients after a median of 17 days. Eight (47%) patients needed dialytic support after TMA diagnosis and 75% remained on dialysis. At 4 years of follow-up, death-censored graft survival was worse for TMA group (43.0% versus 85.6%, log-rank = 0.001; hazard ratio = 3.74) and there was no difference in patient survival (53.1% versus 82.2%, log-rank = 0.24). CONCLUSION: De novo TMA after kidney transplantation is a rare but severe condition with poor graft outcomes. This syndrome may not be fully manifested, and clinical suspicion is essential for early diagnosis and treatment, based mainly in CNI withdrawal and FFP infusions and/or plasmapheresis.

[Analysis of incidence of ocular surface disease index with objective tests and treatment for dry eye]. / Relación de índice de enfermedad de la superficie ocular con pruebas objetivas y tratamiento del ojo seco.

OBJECTIVE: To correlate ocular surface disease index (OSDI) with objective tests on patients with dry eye on first consultation and evaluate the efficiency of topical medication administered depending on severity of symptoms reported by patients who were evaluated at 3 months. MATERIALS AND METHODS: We studied a sample of 144 patients with dry eye who were evaluated with OSDI and basic diagnostic tests at first consultation: Height of lacrimal meniscus, Schirmer II test (with anesthetic), Break-up time test (BUT), and lissamine green staining. The sample was divided into four groups depending on clinical severity, taking into account results of OSDI questionnaire. Treatment was determined for each group taking into account lubricant viscosity properties: OSDI (mild) = carboxymethylcelullose, OSDI (moderate) = hidroxypropylmethylcelullose, OSDI (severe) = polyethyleneglycol and OSDI (very severe) = polyethyleneglycol + cyclosporine A 0.05%. Final OSDI was established for 56 patients who were assessed at 3 months. RESULTS: Results of objective tests at first consult showed a correlation between the severity of symptoms and the grade of lissamine green staining (p = 0.0421). We found significant improvement in OSDI values after topical treatment was administered in all groups of patients (p = 0.0066) at three months post treatment. CONCLUSIONS: Conjuntival lissamine green staining is a useful guideline that could be routinely used to confirm diagnosis in subjective evaluations and patient follow-up. Patients with dry eye show a decrease in OSDI after being treated with the appropriate medication prescribed for each particular group, depending on severity.

Acute renal failure due to abdominal compartment syndrome: report on four cases and literature review.

We report on 4 cases of abdominal compartment syndrome complicated by acute renal failure that were promptly reversed by different abdominal decompression methods. Case 1: A 57-year-old obese woman in the post-operative period after giant incisional hernia correction with an intra-abdominal pressure of 24 mm Hg. She was sedated and curarized, and the intra-abdominal pressure fell to 15 mm Hg. Case 2: A 73-year-old woman with acute inflammatory abdomen was undergoing exploratory laparotomy when a hypertensive pneumoperitoneum was noticed. During the surgery, enhancement of urinary output was observed. Case 3: An 18-year-old man who underwent hepatectomy and developed coagulopathy and hepatic bleeding that required abdominal packing, developed oliguria with a transvesical intra-abdominal pressure of 22 mm Hg. During reoperation, the compresses were removed with a prompt improvement in urinary flow. Case 4: A 46-year-old man with hepatic cirrhosis was admitted after incisional hernia repair with intra-abdominal pressure of 16 mm Hg. After paracentesis, the intra-abdominal pressure fell to 11 mm Hg.

Hyperhomocyst(e)inemia in chronic stable renal transplant patients.

PURPOSE: Hyperhomocyst(e)inaemia is an important risk factor for atherosclerosis, which is currently a major cause of death in renal transplant patients. The aim of this study was to assess the influence of immunosuppressive therapy on homocyst(e)inemia in renal transplant recipients. METHODS: Total serum homocysteine (by high performance liquid chromatography), creatinine, lipid profile, folic acid (by radioimmunoassay-RIA) and vitamin B12 (by RIA) concentrations were measured in 3 groups. Group I patients (n=20) were under treatment with cyclosporine, azathioprine, and prednisone; group II (n=9) were under treatment with azathioprine and prednisone; and group III (n=7) were composed of renal graft donors for groups I and II. Creatinine, estimated creatinine clearance, cyclosporine trough level, lipid profile, folic acid, and vitamin B12 concentrations and clinical characteristics of patients were assessed with the aim of ascertaining determinants of hyperhomocyst(e)inemia. RESULTS: Patient ages were 48.8 +/- 15.1 yr (group I), 43.3 +/- 11.3 yr (group II); and 46.5 +/- 14.8 yr (group III). Mean serum homocyst(e)ine (tHcy) concentrations were 18.07 +/- 8.29 mmol/l in renal transplant recipients; 16.55 +/- 5.6 mmol/l and 21.44 +/- 12.1 mmol/l respectively for group I (with cyclosporine) and group II (without cyclosporine) (NS). In renal donors, tHcy was significantly lower (9.07 +/- 3.06 mmol/l; group I + group II vs. group III, p<0.008). There was an unadjusted correlation (p<0.10) between age (r=0.427; p<0.005) body weight (r=0.412; p<0.05), serum creatinine (r=0.427; p<0.05), estimated creatinine clearance (r=0.316; p<0.10), and tHcy in renal recipients (group I +II). Independent regressors (r2=0.46) identified in the multiple regression model were age (coefficient= 0.253; p=0.009) and serum creatinine (coefficient=8.07; p=0.045). We found no cases of hyperhomocyst(e)inemia in the control group. In contrast, 38% of renal recipients had hyperhomocyst(e)inemia: 7 cases (35%) on cyclosporine and 4 (45%) without cyclosporine, based on serum normal levels. CONCLUSIONS: Renal transplant recipients frequently have hyperhomocyst(e)inemia. Hyperhomocyst(e)inemia in renal transplant patients is independent of the scheme of immunosuppression they are taking. The older the patients are and the higher are their serum creatinine levels, the more susceptible they are to hyperhomocyst(e)inemia following renal transplantation.