Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays

MOTIVATION: Single nucleic polymorphisms (SNPs) are one of the most abundant genetic variations in the human genome. Recently, several platforms for high-throughput SNP analysis have become available, capable of measuring thousands of SNPs across the genome. Tools for analysing and visualizing these large genetic data sets in biologically relevant manner are rare. This hinders effective use of the SNP-array data in research on complex diseases, such as cancer. RESULTS: We describe a computational framework to analyse and visualize SNP-array data, and link the results in relevant databases. Our major objective is to develop methods for identifying DNA regions that likely harbour recessive mutations. Thus, the algorithms are designed to have high sensitivity and the identified regions are ranked using a scoring algorithm. We have also developed annotation tools that automatically query gene IDs, exon counts, microarray probe IDs, etc. In our case study, we apply the methods for identifying candidate regions for recessively inherited colorectal cancer predisposition and suggest directions for wet-lab experiments. AVAILABILITY: R-package implementation is available at http://www.ltdk.helsinki.fi/sysbio/csb/downloads/CohortComparator/     

Patients with a non-dysferlin Miyoshi myopathy have a novel membrane repair defect

Two autosomal recessive muscle diseases, limb girdle muscular dystrophy type 2B (LGMD2B) and Miyoshi myopathy (MM), are caused by mutations in the dysferlin gene. These mutations result in poor ability to repair cell membrane damage, which is suggested to be the cause for this disease. However, many patients who share clinical features with MM-type muscular dystrophy do not carry mutations in dysferlin gene. To understand the basis of MM that is not due to mutations in dysferlin gene, we analyzed cells from patients in one such family. In these patients, we found no defects in several potential candidates - annexin A2, caveolin-3, myoferlin and the MMD2 locus on chromosome 10p. Similar to dysferlinopathy, these cells also exhibit membrane repair defects and the severity of the defect correlated with severity of their disease. However, unlike dysferlinopathy, none of the conventional membrane repair pathways are defective in these patient cells. These results add to the existing evidence that cell membrane repair defect may be responsible for MM-type muscular dystrophy and indicate that a previously unsuspected genetic lesion that affects cell membrane repair pathway is responsible for the disease in the non-dysferlin MM patients.     

Quantitative trait loci on chromosome 5 for susceptibility to frequency-specific effects on hearing in DBA/2J mice

The DBA/2J strain is a model for early-onset, progressive hearing loss in humans, as confirmed in the present study. DBA/2J mice showed progression of hearing loss to low-frequency sounds from ultrasonic-frequency sounds and profound hearing loss at all frequencies before 7 months of age. It is known that the early-onset hearing loss of DBA/2J mice is caused by affects in the ahl (Cdh23^ahl) and ahl8 (Fscn2^ahl8) alleles of the cadherin 23 and fascin 2 genes, respectively. Although the strong contributions of the Fscn2^ahl8 allele were detected in hearing loss at 8- and 16-kHz stimuli with LOD scores of 5.02 at 8 kHz and 8.84 at 16 kHz, hearing loss effects were also demonstrated for three new quantitative trait loci (QTLs) for the intervals of 50.3–54.5, 64.6–119.9, and 119.9–137.0 Mb, respectively, on chromosome 5, with significant LOD scores of 2.80–3.91 for specific high-frequency hearing loss at 16 kHz by quantitative trait loci linkage mapping using a (DBA/2J × C57BL/6J) F₁ × DBA/2J backcross mice. Moreover, we showed that the contribution of Fscn2^ahl8 to early-onset hearing loss with 32-kHz stimuli is extremely low and raised the possibility of effects from the Cdh23^ahl allele and another dominant quantitative trait locus (loci) for hearing loss at this ultrasonic frequency. Therefore, our results suggested that frequency-specific QTLs control early-onset hearing loss in DBA/2J mice.     

Autologous embryo-cumulus cells co-culture and blastocyst transfer in repeated implantation failures: a collaborative prospective randomized study

In repeated implantation failure, the co-culture of human embryos with somatic cells has been reported to promote the improvement of embryos quality, implantation and pregnancy rate. It was reported that feeder cells can be more beneficial to the oocyte and embryo by detoxifying the culture medium and supporting embryo development via different pathways. In this study, 432 patients, each with a minimum of three repeated implantation failures, were accepted for a prospective randomized study with or without autologous cumulus cell embryo co-culture and transfer at day 3 or day 5-6. We also investigated the expression of leukaemia inhibitor factor (LIF) and platelet activating factor receptor (PAF-R) on day 3 confluent cumulus cells. The statistic analysis of the data showed significant difference of implantation and clinical pregnancy rates between classical culture and day 3 compared with co-culture and day 5-6 transfer. The molecular analysis showed that cumulus cells express the LIF and the PAF-R genes and confirmed the possible positive role of growth factors and cytokines in early embryo development. Embryo co-culture systems with autologous cells can be beneficial in routine in vitro fertilization for embryo selection and implantation improvement. More molecular investigations need to be done to improve elucidation of the complex dialogue between the embryo and feeder cells prior to implantation and to understand the involved biological function and molecular process during embryo development.     

Plasma copeptin in the assessment of febrile neutropenia

Copeptin, the surrogate marker of arginine vasopressin (AVP), has been suggested to be a useful biomarker in monitoring sepsis reflecting hemodynamic imbalance and stress state. This prospective study conducted at a hematology ward in a Finnish University Hospital aimed to investigate whether plasma copeptin predicts the development of complicated course of neutropenic fever (bacteremia or need for treatment at intensive care unit) in 100 hematological patients experiencing their first neutropenic fever episode after intensive chemotherapy for hematological malignancy. Contrary to study presumptions, not elevated copeptin but the lack of a proper initial increase of plasma copeptin (<0.02 ng/mL from day 0 to day 1) predicted blood culture positive sepsis (p=0.023) and gram-negative bacteremia (p=0.045). No correlation was observed with plasma sodium, blood pressure or evaluated osmolality. Plasma copeptin correlated inversely with the same day pentraxin 3 on day 0-day 2 (all p-values <0.001) and with C-reactive protein on day 1 (p=0.015). In conclusion, copeptin did not correlate with disease severity, but the lack of a proper initial increase was associated with bacteremic complications of febrile neutropenia in hematological patients. The findings suggest the possibility of central dysregulation of AVP release and do not support the use of copeptin as a biomarker of septic complications in this patient group.     

Nasal cytobrush cytology: evaluation of the hyperchromatic supranuclear stria

OBJECTIVE: To evaluate the hyperchromatic supranuclear stria (SNS) in various types of rhinopathies. STUDY DESIGN: The study included 42 patients with rhinopathies and a control group consisting of 28 healthy adults. The rhinopathy group was categorized into 4 subgroups, including allergic rhinitis, infective rhinitis, vasomotor rhinitis and mixed group. Cytologic samples were obtained by cytobrush from the middle one third of the inferior turbinate. RESULTS: The hyperchromatic SNS was present in the majority of ciliated cells in a high percentage in the control group (91.7%), whereas in the pathologic group it was 40%. The difference is significant (p = 0.0000). CONCLUSION: Nasal cytology is a simple, reliable tool for the diagnosis of rhinopathies.     

Effect of n-3 and n-6 polyunsaturated fatty acids on lymphocyte proliferation, interleukin production and phospholipid fatty acids composition in type 2 diabetic and healthy subjects in Jordan people

Dietary lipid manipulation may affect a great number of immune parameters, such as lymphocyte proliferation, cytokine synthesis. In this study, lymphocytes of diabetic type 2 were incubated with different polyunsaturated fatty acid (docosahexaenoic, eicosapentaenoic, arachidonic acid) for investigated their effect on lymphoproliferation response, the concentration of interleukin 2 produced in each essay and phospholipid fatty acid composition of lymphocyte membrane. Our results found that the concanavalin A and insulin increase significantly the proliferative response while eicosapentaenoic, arachidonic and docosahexaenoic acid inhibited that by different degrees: 47%, 37% and 19%, respectively, for healthy subjects and 39%, 29% and 13% for diabetes. However, the concentration of IL-2 produced in presence of either docosahexaenoic, eicosapentaenoic or arachidonic acid was significantly reduced by 36%, 32% and 39%, respectively, in controls while 16%, 15% and 23%, respectively, in diabetics. On the other hand, the tested fatty acids demonstrated a major impact on the fatty acid composition of different phospholipid fractions of lymphocyte membrane but these fractions were different in their response to each fatty acid examined. For instance, the addition of docosahexaenoic acid to culture media was accompanied with a predominant composition of docosahexaenoic acid in phospholipid fractions. Also, our results showed a notable increased proportion of arachidonic, eicosapentaenoic and docosahexaenoic acids in control phospholipid fractions than those of diabetic.     

Starch storage in the stems of wheat plants: localization and temporal changes

Background and Aims

Carbohydrate temporarily accumulates in wheat stems during the early reproductive growth phase, predominantly as water soluble carbohydrate (WSC), and is subsequently remobilized during grain filling. Starch has also been reported as a minor storage carbohydrate component in wheat stems, but the details are lacking.

Methods

The accumulation and localization of starch in wheat stem and leaf sheath tissue over a developmental period from 6 d before anthesis to 35 d after anthesis was investigated.

Key Results

The region of the peduncle enclosed by the flag-leaf sheath, and the penultimate internode were the main tissues identified as containing starch, in which the starch grains localized to the storage parenchyma cells. In contrast, the exposed peduncle lacked starch grains. Starch grains were also found in the flag-leaf and second-leaf sheath. Plants grown in low-nitrogen conditions exhibited increased storage of both starch and WSC compared with plants grown in high-nitrogen supply.

Conclusions

The major accumulation and decrease of starch occurred temporally independently to that for WSC, suggesting a different functional role for starch in wheat stems. Starch reutilization concomitant with peduncle growth, and the early development of the reproductive structures, suggested a role in provision of energy and/or carbon scaffolds for these growth processes.Key words: Carbohydrate partitioning, peduncle, starch, wheat stem, storage parenchyma, Triticum aestivum