Multiple mitochondrial introgression events and heteroplasmy in trypanosoma cruzi revealed by Maxicircle MLST and next generation sequencing

Background Mitochondrial DNA is a valuable taxonomic marker due to its relatively fast rate of evolution. In Trypanosoma cruzi, the causative agent of Chagas disease, the mitochondrial genome has a unique structural organization consisting of 20–50 maxicircles (∼20 kb) and thousands of minicircles (0.5–10 kb). T. cruzi is an early diverging protist displaying remarkable genetic heterogeneity and is recognized as a complex of six discrete typing units (DTUs). The majority of infected humans are asymptomatic for life while 30–35% develop potentially fatal cardiac and/or digestive syndromes. However, the relationship between specific clinical outcomes and T. cruzi genotype remains elusive. The availability of whole genome sequences has driven advances in high resolution genotyping techniques and re-invigorated interest in exploring the diversity present within the various DTUs. Methodology/Principal Findings To describe intra-DTU diversity, we developed a highly resolutive maxicircle multilocus sequence typing (mtMLST) scheme based on ten gene fragments. A panel of 32 TcI isolates was genotyped using the mtMLST scheme, GPI, mini-exon and 25 microsatellite loci. Comparison of nuclear and mitochondrial data revealed clearly incongruent phylogenetic histories among different geographical populations as well as major DTUs. In parallel, we exploited read depth data, generated by Illumina sequencing of the maxicircle genome from the TcI reference strain Sylvio X10/1, to provide the first evidence of mitochondrial heteroplasmy (heterogeneous mitochondrial genomes in an individual cell) in T. cruzi. Conclusions/Significance mtMLST provides a powerful approach to genotyping at the sub-DTU level. This strategy will facilitate attempts to resolve phenotypic variation in T. cruzi and to address epidemiologically important hypotheses in conjunction with intensive spatio-temporal sampling. The observations of both general and specific incidences of nuclear-mitochondrial phylogenetic incongruence indicate that genetic recombination is geographically widespread and continues to influence the natural population structure of TcI, a conclusion which challenges the traditional paradigm of clonality in T. cruzi

Short-term progression of cardiometabolic risk factors in relation to age at type 2 diabetes diagnosis: a longitudinal observational study of 100,606 individuals from the Swedish National Diabetes Register

Aims/hypothesis: The reasons underlying a greater association of premature mortality with early-onset type 2 diabetes relative to late-onset disease are unclear. We evaluated the clinical characteristics at type 2 diabetes diagnosis and the broad trajectories in cardiometabolic risk factors over the initial years following diagnosis in relation to age at diagnosis. Methods: Our cohort consisted of 100,606 individuals with newly diagnosed type 2 diabetes enrolled in the Swedish National Diabetes Register from 2002 to 2012. The average follow-up time was 2.8 years. Analyses were performed using a linear mixedeffects model for continuous risk factors and a mixed generalised linear model with a logistic link function for dichotomous risk factors. Results: The individuals diagnosed at the youngest age (18–44 years) were more often male and had the highest BMI (mean of 33.4 kg/m2 ) at diagnosis and during follow-up compared with all other groups (those diagnosed at 45–59 years, 60–74 years and ≥75 years; p < 0.05), being ~5 kg/m2 higher than the oldest group. Although HbA1c patterns were similar between all age groups, there was a difference of about 5 mmol/mol (0.45%) between the two groups at 8 years post-diagnosis (p < 0.05). Additionally, individuals diagnosed younger had ~0.7 mmol/l higher triacylglycerol, and ~0.2 mmol/l lower HDL-cholesterol levels at diagnosis relative to the oldest group. Such differences continued for several years post diagnosis. Yet, although more of these younger individuals were receiving oral glucose-lowering agents, other cardioprotective therapies were prescribed less often in this group. Differences in BMI, blood glucose and lipid levels remained with adjustment for potential confounders, including marital status, education and country of birth, and, where relevant, differential treatments by age, and in those with at least 5 years of follow-up. Conclusions/interpretation: Individuals who develop type 2 diabetes at a younger age are more frequently obese, display a more adverse lipid profile, have higher HbA1c and a faster deterioration in glycaemic control compared with individuals who develop diabetes later in life. These differences largely remain for several years after diagnosis and support the notion that early-onset type 2 diabetes may be a more pathogenic condition than late-onset disease

Increase in mast cells and hyaluronic acid correlates to radiation-induced damage and loss of serous acinar cells in salivary glands: the parotid and submandibular glands differ in radiation sensitivity.

The detailed mechanisms which can explain the inherent radiosensitivity of salivary glands remain to be elucidated. Although DNA is the most plausible critical target for the lethal effects of irradiation, interactions with other constituents, such as cell membrane and neuropeptides, have been suggested to cause important physiological changes. Moreover, mast cells seem to be closely linked to radiation-induced pneumonitis. Therefore, in the present study the effects of fractionated irradiation on salivary glands have been assessed with special regard to the appearance of mast cells and its correlation with damage to gland parenchyma. Sprague-Dawley strain rats were unilaterally irradiated to the head and neck with the salivary glands within the radiation field. The irradiation was delivered once daily for 5 days to a total dose of 20, 35 and 45 Gy. The contralateral parotid and submandibular glands served as intra-animal controls and parallel analysis of glands was performed 2, 4, 10 or 180 days following the last radiation treatment. Morphological analysis revealed no obvious changes up to 10 days after the irradiation. At 180 days a radiation dose-dependent loss of gland parenchyma was seen, especially with regard to serious acinar cells in parotid gland and acinar cells and serous CGT (convoluted granular tubule) cells in the submandibular gland. These changes displayed a close correlation with a concomitant dose-dependent enhanced density of mast cells and staining for hyaluronic acid. This cell population seems to conform with the features of the connective tissue mast cell type. The parotid seems to be more sensitive to irradiation than the submandibular gland. Thus, the present results further strengthen the role of and the potential interaction of mast cells with radiation-induced tissue injury and alterations in normal tissue integrity

Sperm design and variation in the New World blackbirds (Icteridae)

Post-copulatory sexual selection (PCSS) is thought to be one of the evolutionary forces responsible for the rapid and divergent evolution of sperm design. However, whereas in some taxa particular sperm traits are positively associated with PCSS, in other taxa, these relationships are negative, and the causes of these different patterns across taxa are poorly understood. In a comparative study using New World blackbirds (Icteridae), we tested whether sperm design was influenced by the level of PCSS and found significant positive associations with the level of PCSS for all sperm components but head length. Additionally, whereas the absolute length of sperm components increased, their variation declined with the intensity of PCSS, indicating stabilizing selection around an optimal sperm design. Given the diversity of, and strong selection on, sperm design, it seems likely that sperm phenotype may influence sperm velocity within species. However, in contrast to other recent studies of passerine birds, but consistent with several other studies, we found no significant link between sperm design and velocity, using four different species that vary both in sperm design and PCSS. Potential reasons for this discrepancy between studies are discussed

Molecular abnormalities in autopsied brain tissue from the inferior horn of the lateral ventricles of nonagenarians and Alzheimer disease patients

Background The ventricular system plays a vital role in blood-cerebrospinal fluid (CSF) exchange and interstitial fluid-CSF drainage pathways. CSF is formed in the specialized secretory tissue called the choroid plexus, which consists of epithelial cells, fenestrated capillaries and the highly vascularized stroma. Very little is currently known about the role played by the ventricles and the choroid plexus tissue in aging and Alzheimer's disease (AD). MethodsIn this study, we used our state-of-the-art proteomic platform, a liquid chromatography/mass spectrometry (LC-MS/MS) approach coupled with Tandem Mass Tag isobaric labeling to conduct a detailed unbiased proteomic analyses of autopsied tissue isolated from the walls of the inferior horn of the lateral ventricles in AD (77.2 ± 0.6 yrs), age-matched controls (77.0 ± 0.5 yrs), and nonagenarian cases (93.2 ± 1.1 yrs). ResultsIngenuity pathway analyses identified phagosome maturation, impaired tight-junction signaling, and glucose/mannose metabolism as top significantly regulated pathways in controls vs nonagenarians. In matched-control vs AD cases we identified alterations in mitochondrial bioenergetics, oxidative stress, remodeling of epithelia adherens junction, macrophage recruitment and phagocytosis, and cytoskeletal dynamics. Nonagenarian vs AD cases demonstrated augmentation of oxidative stress, changes in gluconeogenesis-glycolysis pathways, and cellular effects of choroidal smooth muscle cell vasodilation. Amyloid plaque score uniquely correlated with remodeling of epithelial adherens junctions, Fc γ-receptor mediated phagocytosis, and alterations in RhoA signaling. Braak staging was uniquely correlated with altered iron homeostasis, superoxide radical degradation and phagosome maturation. Conclusions These changes provide novel insights to explain the compromise to the physiological properties and function of the ventricles/choroid plexus system in nonagenarian aging and AD pathogenesis. The pathways identified could provide new targets for therapeutic strategies to mitigate the divergent path towards AD

Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate

<p>Abstract</p> <p>Background</p> <p><it>Giardia intestinalis </it>is a protozoan parasite that causes diarrhea in a wide range of mammalian species. To further understand the genetic diversity between the <it>Giardia intestinalis </it>species, we have performed genome sequencing and analysis of a wild-type <it>Giardia intestinalis </it>sample from the assemblage E group, isolated from a pig.</p> <p>Results</p> <p>We identified 5012 protein coding genes, the majority of which are conserved compared to the previously sequenced genomes of the WB and GS strains in terms of microsynteny and sequence identity. Despite this, there is an unexpectedly large number of chromosomal rearrangements and several smaller structural changes that are present in all chromosomes. Novel members of the VSP, NEK Kinase and HCMP gene families were identified, which may reveal possible mechanisms for host specificity and new avenues for antigenic variation. We used comparative genomics of the three diverse <it>Giardia intestinalis </it>isolates P15, GS and WB to define a core proteome for this species complex and to identify lineage-specific genes. Extensive analyses of polymorphisms in the core proteome of <it>Giardia </it>revealed differential rates of divergence among cellular processes.</p> <p>Conclusions</p> <p>Our results indicate that despite a well conserved core of genes there is significant genome variation between <it>Giardia </it>isolates, both in terms of gene content, gene polymorphisms, structural chromosomal variations and surface molecule repertoires. This study improves the annotation of the <it>Giardia </it>genomes and enables the identification of functionally important variation.</p

Fifteen new risk loci for coronary artery disease highlight arterial-wall-specific mechanisms

Coronary artery disease (CAD) is a leading cause of morbidity and mortality worldwide. Although 58 genomic regions have been associated with CAD thus far, most of the heritability is unexplained, indicating that additional susceptibility loci await identification. An efficient discovery strategy may be larger-scale evaluation of promising associations suggested by genome-wide association studies (GWAS). Hence, we genotyped 56,309 participants using a targeted gene array derived from earlier GWAS results and performed meta-analysis of results with 194,427 participants previously genotyped, totaling 88,192 CAD cases and 162,544 controls. We identified 25 new SNP-CAD associations (P &lt; 5 × 10(-8), in fixed-effects meta-analysis) from 15 genomic regions, including SNPs in or near genes involved in cellular adhesion, leukocyte migration and atherosclerosis (PECAM1, rs1867624), coagulation and inflammation (PROCR, rs867186 (p.Ser219Gly)) and vascular smooth muscle cell differentiation (LMOD1, rs2820315). Correlation of these regions with cell-type-specific gene expression and plasma protein levels sheds light on potential disease mechanisms

Species-Area Relationships Are Controlled by Species Traits

The species-area relationship (SAR) is one of the most thoroughly investigated empirical relationships in ecology. Two theories have been proposed to explain SARs: classical island biogeography theory and niche theory. Classical island biogeography theory considers the processes of persistence, extinction, and colonization, whereas niche theory focuses on species requirements, such as habitat and resource use. Recent studies have called for the unification of these two theories to better explain the underlying mechanisms that generates SARs. In this context, species traits that can be related to each theory seem promising. Here we analyzed the SARs of butterfly and moth assemblages on islands differing in size and isolation. We tested whether species traits modify the SAR and the response to isolation. In addition to the expected overall effects on the area, traits related to each of the two theories increased the model fit, from 69% up to 90%. Steeper slopes have been shown to have a particularly higher sensitivity to area, which was indicated by species with restricted range (slope  = 0.82), narrow dietary niche (slope  = 0.59), low abundance (slope  = 0.52), and low reproductive potential (slope  = 0.51). We concluded that considering species traits by analyzing SARs yields considerable potential for unifying island biogeography theory and niche theory, and that the systematic and predictable effects observed when considering traits can help to guide conservation and management actions

Shared and distinct pathways and networks genetically linked to coronary artery disease between human and mouse

Mouse models have been used extensively to study human coronary artery disease (CAD) or atherosclerosis and to test therapeutic targets. However, whether mouse and human share similar genetic factors and pathogenic mechanisms of atherosclerosis has not been thoroughly investigated in a data-driven manner. We conducted a cross-species comparison study to better understand atherosclerosis pathogenesis between species by leveraging multiomics data. Specifically, we compared genetically driven and thus CAD-causal gene networks and pathways, by using human GWAS of CAD from the CARDIoGRAMplusC4D consortium and mouse GWAS of atherosclerosis from the Hybrid Mouse Diversity Panel (HMDP) followed by integration with functional multiomics human (STARNET and GTEx) and mouse (HMDP) databases. We found that mouse and human shared >75% of CAD causal pathways. Based on network topology, we then predicted key regulatory genes for both the shared pathways and species-specific pathways, which were further validated through the use of single cell data and the latest CAD GWAS. In sum, our results should serve as a much-needed guidance for which human CAD-causal pathways can or cannot be further evaluated for novel CAD therapies using mouse models

Quality of life and functionality after total hip arthroplasty: a long-term follow-up study

<p>Abstract</p> <p>Background</p> <p>There is a lack of data on the long-term outcome of total hip arthroplasty procedures, as assessed by validated tools.</p> <p>Methods</p> <p>We conducted a follow-up study to evaluate the quality of life and functionality of 250 patients an average of 16 years (range: 11-23 years) after total hip arthroplasty using a validated assessment set including the SF-36 questionnaire, Harris Hip Score, WOMAC score, Functional Comorbidity Index, and a study specific questionnaire. Models of multiple stepwise linear and logistic regression analysis were constructed to evaluate the relationships between several explanatory variables and these functional outcomes.</p> <p>Results</p> <p>The SF-36 physical indexes of these patients compared negatively with the normative values but positively with the results obtained in untreated subjects with severe hip osteoarthritis. Similar results were detected for the Harris Hip Score and WOMAC score. There was a 96% rate of post-surgical satisfaction. Hip functionality and comorbidities were the most important determinants of physical measures on the SF-36.</p> <p>Conclusions</p> <p>Patients who had undergone total hip arthroplasty have impaired long-term self-reported physical quality of life and hip functionality but they still perform physically better than untreated patients with advanced hip osteoarthritis. However, the level of post-surgical satisfaction is high.</p