ParseCNV integrative copy number variation association software with quality tracking

A number of copy number variation (CNV) calling algorithms exist; however, comprehensive software tools for CNV association studies are lacking. We describe ParseCNV, unique software that takes CNV calls and creates probe-based statistics for CNV occurrence in both case–control design and in family based studies addressing both de novo and inheritance events, which are then summarized based on CNV regions (CNVRs). CNVRs are defined in a dynamic manner to allow for a complex CNV overlap while maintaining precise association region. Using this approach, we avoid failure to converge and non-monotonic curve fitting weaknesses of programs, such as CNVtools and CNVassoc, and although Plink is easy to use, it only provides combined CNV state probe-based statistics, not state-specific CNVRs. Existing CNV association methods do not provide any quality tracking information to filter confident associations, a key issue which is fully addressed by ParseCNV. In addition, uncertainty in CNV calls underlying CNV associations is evaluated to verify significant results, including CNV overlap profiles, genomic context, number of probes supporting the CNV and single-probe intensities. When optimal quality control parameters are followed using ParseCNV, 90% of CNVs validate by polymerase chain reaction, an often problematic stage because of inadequate significant association review. ParseCNV is freely available at http://parsecnv.sourceforge.net.     

Molecular characterisation of Fusarium oxysporum causing rot diseases in small cardamom (Elettaria cardamomum Maton)

Incidence of root rot and foliar yellowing, rhizome rot, panicle wilt and stem rot diseases of small cardamom (Elettaria cardamomum Maton) are caused by Fusarium oxysporum Schlecht., and were surveyed in the high ranges of Idukki district, Kerala during 2010–2011. The diseases were noticed in different areas to varying degrees. Root rot was found to be most severe, followed by pseudostem rot, rhizome rot and panicle wilt. The Fusarium infections were prevalent throughout the year (January–December) and varied from 1.5 to 10.6%. Even though the pathogen was isolated from different plant parts, during pathogenicity studies, all the isolates could cross-infect other plant parts too. Twenty different isolates of F. oxysporum were obtained from diseased samples, and five morphologically distinct isolates were analysed with Randomly Amplified Polymorphic DNA (RAPD) markers to study the genetic variability, if any, among them. PCR amplification of total genomic DNA with random oligonucleotide primers generated unique banding patterns, depending upon primers and isolates. Nine oligunucleotide primers were selected for the RAPD assays, which resulted in 221 bands for the five isolates of F. oxysporum. The number of bands obtained was entered into an NTSYS, and the results showed moderate genetic variability among F. oxysporum isolates causing root rot, rhizome rot, panicle wilt and pseudostem rot, collected from different locations. The dendrogram of different isolates into groups resulted in one major cluster at 0.61 similarity index comprising of four isolates (CRT 3, CRR 3, CPW 2 and CSR 1) and one isolate (CRT 5) formed in a separate cluster. Among the five isolates of F. oxysporum, CRT 5 was entirely different from the other four isolates. The isolates also differ according to the geographical area, as revealed from the genetic variability observed in different root rot isolates (CRT 3 and CRT 5). It is inferred that despite moderate variability, F. oxysporum, infecting small cardamom in Idukki district of Kerala, consists of a single clonal lineage.     

B lymphocyte inhibition of anti-tumor response depends on expansion of Treg but is independent of B-cell IL-10 secretion

The mechanisms by which B lymphocytes inhibit anti-tumor immunity remain poorly understood. Murine EMT-6 mammary tumors grow readily in immune competent mice (BALB/c), but poorly in B-cell-deficient μ^?/? BALB/c mice (BCDM). T regulatory cell (Treg) expansion and function were impaired in BCDM compared with BALB/c. In this study, we compared tumor growth, Treg cell proliferation, tumor lymphocyte infiltration and cytolytic T cell activity in BALB/c, BCDM and BCDM partially reconstituted with B cells by adoptive transfer (BCDM+B). Partial reconstitution of BCDM with adoptively transferred B cells restored EMT-6 tumor growth, which was independent of IL-10 secretion by B cells. Instead, high frequencies of intratumoral B cells were associated with increased recruitment and proliferation of Treg cells within the tumor microenvironment. The B-cell-dependent accumulation of Treg within the tumor microenvironment was associated with reduced tumor infiltration by CD49+ NK and CD8+ T cells and reduced cytotoxic T cell activity against EMT-6 targets. Our studies indicate that tumor-dependent immunosuppression of T-cell-mediated anti-tumor immunity is coordinated within the tumor microenvironment by B-cell-dependent cross talk with Treg cells, which does not require production of IL-10 by B cells.     

The new sequencer on the block: comparison of Life Technology’s Proton sequencer to an Illumina HiSeq for whole-exome sequencing

We assessed the performance of the new Life Technologies Proton sequencer by comparing whole-exome sequence data in a Centre d’Etude du Polymorphisme Humain trio (family 1463) to the Illumina HiSeq instrument. To simulate a typical user’s results, we utilized the standard capture, alignment and variant calling methods specific to each platform. We restricted data analysis to include the capture region common to both methods. The Proton produced high quality data at a comparable average depth and read length, and the Ion Reporter variant caller identified 96 % of single nucleotide polymorphisms (SNPs) detected by the HiSeq and GATK pipeline. However, only 40 % of small insertion and deletion variants (indels) were identified by both methods. Usage of the trio structure and segregation of platform-specific alleles supported this result. Further comparison of the trio data with Complete Genomics sequence data and Illumina SNP microarray genotypes documented high concordance and accurate SNP genotyping of both Proton and Illumina platforms. However, our study underscored the problem of accurate detection of indels for both the Proton and HiSeq platforms.     

Major vault protein (MVP) gene polymorphisms and drug resistance in mesial temporal lobe epilepsy with hippocampal sclerosis

The human major vault protein (MVP) has been implicated in the development of drug resistance in cancer cells. Over expression of MVP has also been reported in brain tissue samples from antiepileptic drug (AED)-resistant human focal epilepsies. To investigate the relationship between single nucleotide polymorphisms (SNPs) involving the MVP gene and AED-resistance, we compared the distribution of three SNPs in the MVP gene, rs4788187, rs3815824 and rs3815823, among 220 patients with mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS) (prototype of AED-resistant epilepsy syndrome), 201 patients with juvenile myoclonic epilepsy (JME) (prototype of AED-responsive epilepsy syndrome) and 213 ethnically matched non-epilepsy controls. All the patients and controls were residents of the South Indian state of Kerala for more than three generations. We did not find any significant difference in allele and genotypic frequencies of the studied SNPs between AED-resistant and AED-responsive cohorts, and between AED-resistant and AED-responsive cohorts independently and pooled together when compared with the controls. We conclude that rs4788187, rs3815824, rs3815823 variants of the MVP gene are associated neither with predisposition for epilepsy nor with AED-resistance in the population that we have studied. Our results suggest the need for further research into the link between MVP and AED-resistance.     

The bryophyte flora of northern Iturup (north-west Pacific): between the circumboreal and East Asian floristic regions

Introduction. The Kuril Islands Chain demarcates the boundary between the circumpolar and East Asian floras in the amphi-Pacific and is a trans-Oceanic migration route from warm-temperate insular East Asia to north-east Asia and Beringia. This paper reviews the flora of the northern part of Iturup Island in regards to its bryogeography and taxonomic diversity, as well as its relative position among other bryophyte floras of north-east and East Asia.

Methods. The paper uses morphological methods to identify the species composition and detrended correspondence analysis to identify the position of the northern Iturup Island in the system of local floras of the eastern, extra-tropical, Pacific.

Key results. The flora is closely related to the bryophyte floras of the southern Kurils and Hokkaido Island, but has been found to be distinctly distant from the ‘true’ cool-temperate East Asian floras, as well as from the boreal and hemiarctic floras of north-east Asia. Instead, the floras of the south Kurils and northern Hokkaido Island belong to a peculiar intermediate phytogeographic province that cannot be unambiguously placed in either the East Asian or circumboreal floristic regions. The hemiboreal character of the bryophyte flora of northern Iturup Island is in contrast to the general appearance of many of the dominant vegetation communities on the island, which are more characteristic of the hemiarctic.

Conclusion. There is no robust evidence to refer the bryophyte flora of northern Iturup either to the circumboreal or East Asian Floristic Region, the flora belongs to a unique intermediate province between the two regions.     

Genome reduction as the dominant mode of evolution

A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron‐rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification.     

Defective Autophagy and mTORC1 Signaling in Myotubularin Null Mice

Autophagy is a vesicular trafficking pathway that regulates the degradation of aggregated proteins and damaged organelles. Initiation of autophagy requires several multiprotein signaling complexes, such as the ULK1 kinase complex and the Vps34 lipid kinase complex, which generates phosphatidylinositol 3-phosphate [PtdIns(3)P] on the forming autophagosomal membrane. Alterations in autophagy have been reported for various diseases, including myopathies. Here we show that skeletal muscle autophagy is compromised in mice deficient in the X-linked myotubular myopathy (XLMTM)-associated PtdIns(3)P phosphatase myotubularin (MTM1). Mtm1-deficient muscle displays several cellular abnormalities, including a profound increase in ubiquitin aggregates and abnormal mitochondria. Further, we show that Mtm1 deficiency is accompanied by activation of mTORC1 signaling, which persists even following starvation. In vivo pharmacological inhibition of mTOR is sufficient to normalize aberrant autophagy and improve muscle phenotypes in Mtm1 null mice. These results suggest that aberrant mTORC1 signaling and impaired autophagy are consequences of the loss of Mtm1 and may play a primary role in disease pathogenesis.