The dual behavior of heat shock protein 70 and asymmetric dimethylarginine in relation to serum CRP levels in type 2 diabetes

Background

Experimental evidence suggests that heat shock proteins (HSP) and asymmetric dimethylarginine (ADMA) are induced in the state of chronic inflammation and stress conditions. They are both inhibitors of nitric oxide synthase (NOS). The aim of this study was to evaluate the correlation between ADMA and HSP70, in patients with type 2 diabetes with respect to serum levels of C reactive protein (CRP).

Methods

We quantified serum HSP70, ADMA and CRP in 80 newly-diagnosed patients with type 2 diabetes plus 80 age-, sex and BMI-matched healthy controls. The patients and controls were also stratified into groups of high and low CRP levels (cut-point: 2.5 mg/ml).

Results

Patients with type 2 diabetes had significantly higher serum HSP70 (0.52 [0.51–0.66] vs. 0.27 [0.26–0.36], p < 0.001), ADMA (0.86 [0.81–0.92] vs. 0.72 [0.71–0.85], p < 0.05) and CRP (2.9 [1.7–3.4] vs. 1.6[1.2–2.3], p < 0.05) compared with healthy controls. Serum HSP70 and ADMA levels were significantly correlated in patients with high CRP levels (r = 0.89, p < 0.01), whereas there were no correlation in patients with low CRP (r = − 0.37, p = 0.07) and controls. This correlation was significant (r = 0.77, p < 0.001) in patients with high CRP and also in patients with low CRP levels (r = − 0.51, p < 0.05), after multiple adjustments for LDL and HDL levels.

Discussion

We showed that, in a state of high inflammation; serum levels of ADMA parallel the HSP70 levels. However in low inflammation, they are negatively correlated. The duality in HSP70 and ADMA correlation may be related to the duality of NOS function in low and high CRP levels.     

Logistic Bayesian LASSO for identifying association with rare haplotypes and application to age-related macular degeneration

Rare variants have been heralded as key to uncovering "missing heritability" in complex diseases. These variants can now be genotyped using next-generation sequencing technologies; nonetheless, rare haplotypes may also result from combination of common single nucleotide polymorphisms available from genome-wide association studies (GWAS). The National Eye Institute's data on age-related macular degeneration (AMD) is such an example. Studies on AMD had identified potential rare variants; however, due to lack of appropriate statistical tools, effects of individual rare haplotypes were never studied. Here we develop a method for identifying association with rare haplotypes for case-control design. A logistic regression based retrospective likelihood is formulated and is regularized using logistic Bayesian LASSO (LBL). In particular, we penalize the regression coefficients using appropriate priors to weed out unassociated haplotypes, making it possible for the rare associated ones to stand out. We applied LBL to the AMD data and identified common and rare haplotypes in the complement factor H gene, gaining insights into rare variants' contributions to AMD beyond the current literature. This analysis also demonstrates the richness of GWAS data for mapping rare haplotypes-a potential largely unexplored. Additionally, we conducted simulations to investigate the performance of LBL and compare it with Hapassoc. Our results show that LBL is much more powerful in identifying rare associated haplotypes when the false positive rates for both approaches are kept the same.     

Beyond barcoding: A mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117–200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.     

Gynodioecy in structured populations: understanding fine-scale sex ratio variation in Beta vulgaris ssp. maritima

Natural selection, random processes and gene flow are known to generate sex ratio variations among sexually polymorphic plant populations. In gynodioecious species, in which hermaphrodites and females coexist, the relative effect of these processes on the maintenance of sex polymorphism is still up for debate. The aim of this study was to document sex ratio and cytonuclear genetic variation at a very local scale in wind-pollinated gynodioecious Beta vulgaris ssp. maritima and attempt to elucidate which processes explained the observed variation. The study sites were characterized by geographically distinct patches of individuals and appeared to be dynamic entities, with recurrent establishment of distinct haplotypes through independent founder events. Along with substantial variation in sex ratio and unexpectedly low gene flow within study sites, our results showed a high genetic differentiation among a mosaic of genetically distinct demes, with isolation by distance or abrupt genetic discontinuities taking place within a few tens of metres. Overall, random founder events with restricted gene flow could be primary determinants of sex structure, by promoting the clumping of sex-determining genes. Such high levels of sex structure provide a landscape for differential selection acting on sex-determining genes, which could modify the conditions of maintenance of gynodioecy in structured populations.     

Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing

Background

The detailed study of breakpoints associated with copy number variants (CNVs) can elucidate the mutational mechanisms that generate them and the comparison of breakpoints across species can highlight differences in genomic architecture that may lead to lineage-specific differences in patterns of CNVs. Here, we provide a detailed analysis of Drosophila CNV breakpoints and contrast it with similar analyses recently carried out for the human genome.

Results

By applying split-read methods to a total of 10x coverage of 454 shotgun sequence across nine lines of D. melanogaster and by re-examining a previously published dataset of CNVs detected using tiling arrays, we identified the precise breakpoints of more than 600 insertions, deletions, and duplications. Contrasting these CNVs with those found in humans showed that in both taxa CNV breakpoints fall into three classes: blunt breakpoints; simple breakpoints associated with microhomology; and breakpoints with additional nucleotides inserted/deleted and no microhomology. In both taxa CNV breakpoints are enriched with non-B DNA sequence structures, which may impair DNA replication and/or repair. However, in contrast to human genomes, non-allelic homologous-recombination (NAHR) plays a negligible role in CNV formation in Drosophila. In flies, non-homologous repair mechanisms are responsible for simple, recurrent, and complex CNVs, including insertions of de novo sequence as large as 60 bp.

Conclusions

Humans and Drosophila differ considerably in the importance of homology-based mechanisms for the formation of CNVs, likely as a consequence of the differences in the abundance and distribution of both segmental duplications and transposable elements between the two genomes.     

Transposable elements: not as quiet as a mouse

In this issue of Genome Biology, Nellåker et al. show massive purging of deleterious transposable element variants, through negative selection, in 18 mouse strains.     

The Curation of Genetic Variants: Difficulties and Possible Solutions

The curation of genetic variants from biomedical articles is required for various clinical and research purposes. Nowadays, establishment of variant databases that include overall information about variants is becoming quite popular. These databases have immense utility, serving as a user-friendly information storehouse of variants for information seekers. While manual curation is the gold standard method for curation of variants, it can turn out to be time-consuming on a large scale thus necessitating the need for automation. Curation of variants described in biomedical literature may not be straightforward mainly due to various nomenclature and expression issues. Though current trends in paper writing on variants is inclined to the standard nomenclature such that variants can easily be retrieved, we have a massive store of variants in the literature that are present as non-standard names and the online search engines that are predominantly used may not be capable of finding them. For effective curation of variants, knowledge about the overall process of curation, nature and types of difficulties in curation, and ways to tackle the difficulties during the task are crucial. Only by effective curation, can variants be correctly interpreted. This paper presents the process and difficulties of curation of genetic variants with possible solutions and suggestions from our work experience in the field including literature support. The paper also highlights aspects of interpretation of genetic variants and the importance of writing papers on variants following standard and retrievable methods.     

急性早幼粒细胞白血病患者小孢根霉变种感染1例

报道1例由小孢根霉变种导致的皮肤毛霉病.患者女,30岁.因患急性早幼粒细胞白血病,化疗后继发口腔颌面部小孢根霉变种感染,表现为发热、右侧颊黏膜水肿,皮损中央溃疡、焦痂,周边组织炎性水肿,以面颊部、颌下区为中心明显肿胀,逐渐累及右侧颈部及右下颌,进行性加重.坏死组织涂片镜检显示有粗大、无分隔直角菌丝,真菌学检查鉴定为小孢根霉,分子测序证实为小孢根霉变种.给予两性霉素B、伊曲康唑静脉滴注和手术清创,坏死组织连续3次真菌培养均未培养出小孢根霉变种,患者体温逐渐恢复正常,治疗2周后颔面部肿胀明显减退,浅表淋巴结未触及肿大,4周后额部及右眼睑肿胀已完全消退,伤口结痂愈合.随访2 a,右侧颌下可见长约2 cm手术疤痕,未见皮肤毛霉病复发.     

Flexible migration of Japanese freshwater gobies Rhinogobius spp. as revealed by otolith Sr:Ca ratios

The migratory histories of six Rhinogobius spp., the cross‐band type (R. sp. CB), the large‐dark type (R. sp. LD), the dark type (R. sp. DA), the cobalt type (R. sp. CO), the orange type (R. sp. OR) and R. flumineus, were studied by examining strontium (Sr) and calcium (Ca) concentrations in their otoliths using wavelength dispersive X‐ray spectrometry on an electron microprobe. The Sr:Ca ratios in the otoliths changed both with the ontogenetic development and with the salinity level of the habitat. Most fishes had high Sr:Ca ratios around the otolith core in spite of the fact that those fishes live most of their lives in a freshwater environment. The high ratios in the otoliths were thought to be a physiological effect in those fishes. Thereafter, the Sr:Ca ratios changed remarkably along the life‐history transect, showing intraspecies and interspecies variations. The otolith Sr:Ca ratios of Rhinogobius sp. CB, R. sp. LD and R. sp. CO collected from three rivers connected to the sea were low around the core, subsequently increased sharply to the points 180–345 μm from the core and then decreased again towards the edge. They were thought to reflect the typical amphidromous life history. The R. sp. CO, however, remain in a brackish‐water environment after migration from the sea, while the other species showed typical amphidromous lives with complete freshwater residence after migration from the sea. The five species (R. sp. CB, R. sp. LD, R. sp. CO, R. sp. DA and R. sp. OR) collected above dams had never migrated to the sea, spending their whole life in a freshwater environment, although Rhinogobius species, except for the fluvial type, were thought to have an amphidromous life history according to previous studies. These species are thought to have a landlocked life cycle. The otolith Sr:Ca ratios of R. flumineus showed consistently low ratios towards the edge except for only around the core, although they were collected from a river connected to the sea. These species could have a fluvial life history corresponding to a previous study. The present study clearly suggests that the migratory histories of Rhinogobius spp. are highly different both within and between species and that they have flexible migratory patterns allowing them to utilize the full range of salinity during their life history.