Peripartum Cardiomyopathy Presenting With Ventricular Tachycardia: A Rare Presentation

A 25-year-old previously asymptomatic pregnant woman at 36 weeks'' gestation was noticed to have repetitive monomorphic ventricular tachycardia. A dilated left ventricle with moderately reduced systolic function was found on echocardiographic examination. This is a very rare presentation of peripartum cardiomyopathy (PPCMP) presenting with repetitive monomorphic ventricular tachycardia.     

Inferring copy number and genotype in tumour exome data

Background

Using whole exome sequencing to predict aberrations in tumours is a cost effective alternative to whole genome sequencing, however is predominantly used for variant detection and infrequently utilised for detection of somatic copy number variation.

Results

We propose a new method to infer copy number and genotypes using whole exome data from paired tumour/normal samples. Our algorithm uses two Hidden Markov Models to predict copy number and genotypes and computationally resolves polyploidy/aneuploidy, normal cell contamination and signal baseline shift. Our method makes explicit detection on chromosome arm level events, which are commonly found in tumour samples. The methods are combined into a package named ADTEx (Aberration Detection in Tumour Exome). We applied our algorithm to a cohort of 17 in-house generated and 18 TCGA paired ovarian cancer/normal exomes and evaluated the performance by comparing against the copy number variations and genotypes predicted using Affymetrix SNP 6.0 data of the same samples. Further, we carried out a comparison study to show that ADTEx outperformed its competitors in terms of precision and F-measure.

Conclusions

Our proposed method, ADTEx, uses both depth of coverage ratios and B allele frequencies calculated from whole exome sequencing data, to predict copy number variations along with their genotypes. ADTEx is implemented as a user friendly software package using Python and R statistical language. Source code and sample data are freely available under GNU license (GPLv3) at http://adtex.sourceforge.net/.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-732) contains supplementary material, which is available to authorized users.     

The induction of allophanate lyase during the vegetative cell cycle in light-synchronized cultures of Chlamydomonas reinhardi.

Allophanate lyase can be induced by urea or acetamide 20-40-fold within 4 h in NH4 + -deprived cultures of Chlamydomonas reinhardi. In light-synchronized cultures, allophanate lyase induction appeared to be limited to the light phase of the cell cycle, provided that culture samples were induced under ongoing illumination conditions (i.e. light induction of light phase cells and dark induction of dark phase cells). However, when culture samples were induced under constant light conditions this cell cycle pattern was abolished. Light was found to be required for allophanate lyase induction and this was shown to be due, in part, to the light requirement for inducer uptake. The relationship between allophanate lyase induction and gametogenesis is discussed.     

Efficiency and establishment of three introduced parasitoids of the mealybug Paracoccus marginatus (Hemiptera: Pseudococcidae)

Three introduced parasitoids Acerophagus papayae, Anagyrus loecki, and Pseudleptomastix mexicana of the mealybug Paracoccus marginatus have been released in Miami-Dade and Broward counties (Florida) in 2003. Efficiency and establishment of these previously introduced parasitoids to control P. marginatus were measured in 2005 and 2006, at three locations in Homestead (Miami-Dade). Mealybug populations were initially established on three branches (per plant) of 10 hibiscus plants inside closed-sleeve cages. The three treatments, closed, open, and no-cage environments were applied to the three established mealybug populations on each plant. The number of mealybugs and natural enemies was monitored in all treatments. After 72 h, the number of P. marginatus in the open-sleeve cage was higher than in the no-cage treatment but both were lower than the number in the closed-sleeve cage. Efficiency of parasitoids was evaluated by their percentage parasitism. Percentage parasitism (=recovery) was also used as an indicator for parasitoid establishment. Two of the three previously released parasitoids (A. papayae and A. loecki) were recovered in this study. Acerophagus papayae had a higher percentage parasitism than A. loecki in both the open-sleeve cage (31.0% vs 2.3%) and the no-cage treatments (21.4% vs 1.6%) and caused the most mortality of P. marginatus. There was no recovery of P. mexicana in either of the treatments. Although both A. papayae and A. loecki were established in tested areas, A. papayae was more efficient in controlling P. marginatus than A. loecki. The reasons for not recovering P. mexicana in release areas is yet unknown.     

Host instar susceptibility and selection and interspecific competition of three introduced parasitoids of the mealybug Paracoccus marginatus (Hemiptera: Pseudococcidae)

Three previously introduced parasitoids (Acerophagus papayae Noyes and Schauff, Anagyrus loecki Noyes and Menezes, and Pseudleptomastix mexicana Noyes and Schauff [Hymenoptera: Encyrtidae]) of the mealybug Paracoccus marginatus Williams and Granara de Willink (Hemiptera: Pseudococcidae) were studied for their host instar susceptibility and sex ratio, host instar selection, and interspecific competition in the laboratory. All three parasitoids were able to develop in the second instars, third-instar females, and adult females of P. marginatus. No progeny emerged from first-instar mealybugs. The proportion of female emergence was increased with increasing host size. Parasitoids selected their host instars for oviposition when they had a choice. Between second- and third-instar hosts, A. papayae and P. mexicana had significantly higher parasitism in second-instar mealybugs, whereas A. loecki had higher parasitism in the third-instar mealybugs. When competed with either one or two parasitoid species, A. papayae was significantly more successful in second-instar hosts and A. loecki was significantly more successful in third-instar mealybugs. P. mexicana was significantly less competitive when with A. papayae in both second and third instars, with A. loecki in third instars and with both A. papayae and A. loecki in second and third instars. Overall, A. papayae provided a better control of the host, when present singly or with the other two parasitoids. This information is important in evaluating the efficiency of A. papayae, A. loecki, and P. mexicana and understanding the outcome of their recovery and establishment in field studies conducted in Florida.     

Activities of enzymes of fermentation pathways in the leaves and roots of contrasting cultivars of sorghum (Sorghum Bicolor L.) during flooding

Flooding evoked a differential response in the activities of enzymes of fermentation pathway in leaves and roots of flood sensitive (S-308) and flood-tolerant (SSG-59-3) cultivars of sorghum. Activities of alcohol dehydrogenase (ADH), lactate dehydrogenase (LDH) and alanine aminotransferase (AlaAT) enhanced in roots of SSG-59-3 during 72 h of flooding. In contrast, a transient increase in the activities was discerned in roots of S-308 up to 24 h flooding followed by a decline in activities of these enzymes. In leaves of SSG-59-3, the activities of ADH and LDH increased to about three fold during flooding stress as compared to that in the non-flooded control plants. Though elevation in activities of these enzymes was observed in leaves of S-308 up to 48 h of flooding, the magnitude of enhancement was much lower than that in SSG-59-3. Alanine aminotranferase activity depressed in leaves of both the cultivars but the level of decline was more pronounced in sensitive cultivar S-308 as compare to tolerant SSG-59-3. The amount of alcohol, lactic acid and alanine were higher in both roots and leaves of SSG-59-3 than that in S-308 during flooding stress. It is thus apparent that roots and leaves of flood tolerant variety tends to attain greater capacity to perform reactions of various fermentation pathways to sustain production of ATP under flooded conditions.     

Young patients with colorectal cancer have poor survival in the first twenty months after operation and predictable survival in the medium and long-term: Analysis of survival and prognostic markers

Introduction

Male breast cancer (MBC) is a rare, yet potentially aggressive disease. Although literature regarding female breast cancer (FBC) is extensive, little is known about the etiopathogenesis of male breast cancer. Studies from our laboratory show that MBCs have a distinct immunophenotypic profile, suggesting that the etiopathogenesis of MBC is different from FBCs. The aim of this study was to evaluate and correlate the immunohistochemical expression of cell cycle proteins in male breast carcinoma to significant clinico-biological endpoints.

Methods

75 cases of MBC were identified using the records of the Saskatchewan Cancer Agency over 26 years (1970-1996). Cases were reviewed and analyzed for the immunohistochemical expression of PCNA, Ki67, p27, p16, p57, p21, cyclin-D1 and c-myc and correlated to clinico-biological endpoints of tumor size, node status, stage of the disease, and disease free survival (DFS).

Results

Decreased DFS was observed in the majority of tumors that overexpressed PCNA (98%, p = 0.004). The overexpression of PCNA was inversely correlated to the expression of Ki67 which was predominantly negative (78.3%). Cyclin D1 was overexpressed in 83.7% of cases. Cyclin D1 positive tumors were smaller than 2 cm (55.6%, p = 0.005), had a low incidence of lymph node metastasis (38.2%, p = 0.04) and were associated with increased DFS of >150 months (p = 0.04). Overexpression of c-myc (90%) was linked with a higher incidence of node negativity (58.3%, p = 0.006) and increased DFS (p = 0.04). p27 over expression was associated with decreased lymph node metastasis (p = 0.04). P21 and p57 positive tumors were related to decreased DFS (p = 0.04). Though p16 was overexpressed in 76.6%, this did not reach statistical significance with DFS (p = 0.06) or nodal status (p = 0.07).

Conclusion

Aberrant cell cycle protein expression supports our view that these are important pathways involved in the etiopathogenesis of MBC. Tumors with overexpression of Cyclin D1 and c-myc had better outcomes, in contrast to tumors with overexpression of p21, p57, and PCNA with significantly worse outcomes. P27 appears to be a predictive marker for lymph nodal status. Such observation strongly suggests that dysregulation of cell cycle proteins may play a unique role in the initiation and progression of disease in male breast cancer. Such findings open up new avenues for the treatment of MBC as a suitable candidate for novel CDK-based anticancer therapies in the future.     

Molecular systematics and paleobiogeography of the South American sigmodontine rodents [published erratum appears in Mol Biol Evol 1998 Feb;15(2):224]

The murid rodent subfamily Sigmodontinae contains 79 genera which are distributed throughout the New World. The time of arrival of the first sigmodontines in South America and the estimated divergence time(s) of the different lineages of South American sigmodontines have been controversial due to the lack of a good fossil record and the immense number of extant species. The "early-arrival hypothesis" states that the sigmodontines must have arrived in South America no later than the early Miocene, at least 20 MYA, in order to account for their vast present-day diversity, whereas the "late-arrival hypothesis" includes the sigmodontines as part of the Plio-Pleistocene Great American Interchange, which occurred approximately 3.5 MYA. The phylogenetic relationships among 33 of these genera were reconstructed using mitochondrial DNA (mtDNA) sequence data from the ND3, ND4L, arginine tRNA, and ND4 genes, which we show to be evolving at the same rate. A molecular clock was calibrated for these genes using published fossil dates, and the genetic distances were estimated from the DNA sequences in this study. The molecular clock was used to estimate the dates of the South American sigmodontine origin and the main sigmodontine radiation in order to evaluate the "early-" and "late-arrival" scenarios. We estimate the time of the sigmodontine invasion of South America as between approximately 5 and 9 MYA, supporting neither of the scenarios but suggesting two possible models in which the invading lineage was either (1) ancestral to the oryzomyines, akodonts, and phyllotines or (2) ancestral to the akodonts and phyllotines and accompanied by the oryzomyines. The sigmodontine invasion of South America provides an example of the advantage afforded to a lineage by the fortuitous invasion of a previously unexploited habitat, in this case an entire continent.      

Urgent need for consistent standards in functional enrichment analysis

Gene set enrichment tests (a.k.a. functional enrichment analysis) are among the most frequently used methods in computational biology. Despite this popularity, there are concerns that these methods are being applied incorrectly and the results of some peer-reviewed publications are unreliable. These problems include the use of inappropriate background gene lists, lack of false discovery rate correction and lack of methodological detail. To ascertain the frequency of these issues in the literature, we performed a screen of 186 open-access research articles describing functional enrichment results. We find that 95% of analyses using over-representation tests did not implement an appropriate background gene list or did not describe this in the methods. Failure to perform p-value correction for multiple tests was identified in 43% of analyses. Many studies lacked detail in the methods section about the tools and gene sets used. An extension of this survey showed that these problems are not associated with journal or article level bibliometrics. Using seven independent RNA-seq datasets, we show misuse of enrichment tools alters results substantially. In conclusion, most published functional enrichment studies suffered from one or more major flaws, highlighting the need for stronger standards for enrichment analysis.