Potential impact of primate‐specific SVA retrotransposons during the evolution of human cognitive function.

The SVA family of hominid-specific non-LTR retrotransposon comprises the youngest group of transposable elements in the human genome. The propagation of the most ancient SVA subfamily took place about 13.5 million years ago, and the youngest SVA subfamily appeared in the human genome after the human/chimpanzee divergence. Functional analysis of genes associated with SVA insertions demonstrated their link to multiple ontological categories, with one of the major categories being attributed to brain function. Further analysis of this subset demonstrated that SVA elements expanded their presence in the human genome at different stages of hominoid evolution and were associated with progressively evolving behavioral features that indicate a potential impact of SVA propagation on the cognitive ability of a modern human. Our analysis suggests a potential role of SVAs in the evolution of human central nervous system and especially in the emergence of functional trends relevant to social and parental behavior. Coevolution of behavioral features and reproductive functions are suggested by our analysis and discussed

A TOMM40 poly-T variant modulates gene expression and is associated with vocabulary ability and decline in nonpathologic aging

The Translocase of Outer Mitochondrial Membrane 40 Homolog and Apolipoprotein E (TOMM40-APOE) locus has been associated with a number of age-related phenotypes in humans including nonpathologic cognitive aging, late-onset Alzheimer's disease, and longevity. Here, we investigate the influence of the TOMM40 intron 6 poly-T variant (rs10524523) on TOMM40 gene expression and cognitive abilities and decline in a cohort of 1613 community-dwelling elderly volunteers who had been followed for changes in cognitive functioning over a period of 14 years (range = 12–18 years). We showed that the shorter length poly-T variants were found to act as a repressor of luciferase gene expression in reporter gene constructs. Expression was reduced to approximately half of that observed for the very long variant. We further observed that the shorter poly-T variant was significantly associated with reduced vocabulary ability and a slower rate of vocabulary decline with age compared to the very long poly-T variants. No significant associations were observed for memory, fluid intelligence or processing speed, although the direction of effect, where the short variant was correlated with reduced ability and slower rate of decline was observed for all tests. Our results indicate that the poly-T variant has the ability to interact with transcription machinery and differentially modulate reporter gene expression and influence vocabulary ability and decline with age

CRISPR Deletion of a SVA Retrotransposon Demonstrates Function as a cis-Regulatory Element at the TRPV1/TRPV3 Intergenic Region

SINE-VNTR-Alu (SVA) retrotransposons are a subclass of transposable elements (TEs) that exist only in primate genomes. TE insertions can be co-opted as cis-regulatory elements (CREs); however, the regulatory potential of SVAs has predominantly been demonstrated using bioinformatic approaches and reporter gene assays. The objective of this study was to demonstrate SVA cis-regulatory activity by CRISPR (clustered regularly interspaced short palindromic repeats) deletion and subsequent measurement of direct effects on local gene expression. We identified a region on chromosome 17 that was enriched with human-specific SVAs. Comparative gene expression analysis at this region revealed co-expression of TRPV1 and TRPV3 in multiple human tissues, which was not observed in mouse, highlighting key regulatory differences between the two species. Furthermore, the intergenic region between TRPV1 and TRPV3 coding sequences contained a human specific SVA insertion located upstream of the TRPV3 promoter and downstream of the 3' end of TRPV1, highlighting this SVA as a candidate to study its potential cis-regulatory activity on both genes. Firstly, we generated SVA reporter gene constructs and demonstrated their transcriptional regulatory activity in HEK293 cells. We then devised a dual-targeting CRISPR strategy to facilitate the deletion of this entire SVA sequence and generated edited HEK293 clonal cell lines containing homozygous and heterozygous SVA deletions. In edited homozygous ∆SVA clones, we observed a significant decrease in both TRPV1 and TRPV3 mRNA expression, compared to unedited HEK293. In addition, we also observed an increase in the variability of mRNA expression levels in heterozygous ∆SVA clones. Overall, in edited HEK293 with SVA deletions, we observed a disruption to the co-expression of TRPV1and TRPV3. Here we provide an example of a human specific SVA with cis-regulatory activity in situ, supporting the role of SVA retrotransposons as contributors to species-specific gene expression

Mitochondria function associated genes contribute to Parkinson’s Disease risk and later age at onset

Mitochondrial dysfunction has been implicated in the etiology of monogenic Parkinson’s disease (PD). Yet the role that mitochondrial processes play in the most common form of the disease; sporadic PD, is yet to be fully established. Here, we comprehensively assessed the role of mitochondrial function-associated genes in sporadic PD by leveraging improvements in the scale and analysis of PD GWAS data with recent advances in our understanding of the genetics of mitochondrial disease. We calculated a mitochondrial-specific polygenic risk score (PRS) and showed that cumulative small effect variants within both our primary and secondary gene lists are significantly associated with increased PD risk. We further reported that the PRS of the secondary mitochondrial gene list was significantly associated with later age at onset. Finally, to identify possible functional genomic associations we implemented Mendelian randomization, which showed that 14 of these mitochondrial function-associated genes showed functional consequence associated with PD risk. Further analysis suggested that the 14 identified genes are not only involved in mitophagy, but implicate new mitochondrial processes. Our data suggests that therapeutics targeting mitochondrial bioenergetics and proteostasis pathways distinct from mitophagy could be beneficial to treating the early stage of P

Medial patellofemoral ligament injury patterns and associated pathology in lateral patella dislocation: an MRI study

BACKGROUND: Lateral Patella dislocations are common injuries seen in the active and young adult populations. Our study focus was to evaluate medial patellofemoral ligament (MPFL) injury patterns and associated knee pathology using Magnetic Resonance Imaging studies. METHODS: MRI studies taken at one imaging site between January, 2007 to January, 2008 with the final diagnosis of patella dislocation were screened for this study. Of the 324 cases that were found, 195 patients with lateral patellar dislocation traumatic enough to cause bone bruises on the lateral femoral trochlea and the medial facet of the patella were selected for this study. The MRI images were reviewed by three independent observers for location and type of MPFL injury, osteochondral defects, loose bodies, MCL and meniscus tears. The data was analyzed as a single cohort and by gender. RESULTS: This study consisted of 127 males and 68 females; mean age of 23 yrs. Tear of the MPFL at the patellar attachment occurred in 93/195 knees (47%), at the femoral attachment in 50/195 knees (26%), and at both the femoral and patella attachment sites in 26/195 knees (13%). Attenuation of the MPFL without rupture occurred in 26/195 knees (13%). Associated findings included loose bodies in 23/195 (13%), meniscus tears 41/195 (21%), patella avulsion/fracture in 14/195 (7%), medial collateral ligament sprains/tears in 37/195 (19%) and osteochondral lesions in 96/195 knees (49%). Statistical analysis showed females had significantly more associated meniscus tears than the males (27% vs. 17%, p = 0.04). Although not statistically significant, osteochondral lesions were seen more in male patients with acute patella dislocation (52% vs. 42%, p = 0.08). CONCLUSION: Patients who present with lateral patella dislocation with the classic bone bruise pattern seen on MRI will likely rupture the MPFL at the patellar side. Females are more likely to have an associated meniscal tear than males; however, more males have underlying osteochondral lesions. Given the high percentage of associated pathology, we recommend a MRI of the knee in all patients who present with acute patella dislocation

Genome-Wide Analysis of Structural Variants in Parkinson Disease

OBJECTIVE: Identification of genetic risk factors for Parkinson disease (PD) has to date been primarily limited to the study of single nucleotide variants, which only represent a small fraction of the genetic variation in the human genome. Consequently, causal variants for most PD risk are not known. Here we focused on structural variants (SVs), which represent a major source of genetic variation in the human genome. We aimed to discover SVs associated with PD risk by performing the first large-scale characterization of SVs in PD. METHODS: We leveraged a recently developed computational pipeline to detect and genotype SVs from 7,772 Illumina short-read whole genome sequencing samples. Using this set of SV variants, we performed a genome-wide association study using 2,585 cases and 2,779 controls and identified SVs associated with PD risk. Furthermore, to validate the presence of these variants, we generated a subset of matched whole-genome long-read sequencing data. RESULTS: We genotyped and tested 3,154 common SVs, representing over 412 million nucleotides of previously uncatalogued genetic variation. Using long-read sequencing data, we validated the presence of three novel deletion SVs that are associated with risk of PD from our initial association analysis, including a 2 kb intronic deletion within the gene LRRN4. INTERPRETATION: We identified three SVs associated with genetic risk of PD. This study represents the most comprehensive assessment of the contribution of SVs to the genetic risk of PD to date. ANN NEUROL 202

Patchiness and Co-Existence of Indigenous and Invasive Mussels at Small Spatial Scales: The Interaction of Facilitation and Competition

Ecological theory predicts that two species with similar requirements will fail to show long-term co-existence in situations where shared resources are limiting, especially at spatial scales that are small relative to the size of the organisms. Two species of intertidal mussels, the indigenous Perna perna and the invasive Mytilus galloprovincialis, form mixed beds on the south coast of South Africa in a situation that has been stable for several generations of these species, even though these populations are often limited by the availability of space. We examined the spatial structure of these species where they co-exist at small spatial scales in the absence of apparent environmental heterogeneity at two sites, testing: whether conspecific aggregation of mussels can occur (using spatial Monte-Carlo tests); the degree of patchiness (using Korcak B patchiness exponent), and whether there was a relationship between percent cover and patchiness. We found that under certain circumstances there is non-random conspecific aggregation, but that in other circumstances there may be random distribution (i.e. the two species are mixed), so that spatial patterns are context-dependent. The relative cover of the species differed between sites, and within each site, the species with higher cover showed low Korcak B values (indicating low patchiness, i.e. the existence of fewer, larger patches), while the less abundant species showed the reverse, i.e. high patchiness. This relationship did not hold for either species within sites. We conclude that co-existence between these mussels is possible, even at small spatial scales because each species is an ecological engineer and, while they have been shown to compete for space, this is preceded by initial facilitation. We suggest that a patchy pattern of co-existence is possible because of a balance between direct (competitive) and indirect (facilitative) interactions

Infant feeding counselling in Uganda in a changing environment with focus on the general population and HIV-positive mothers - a mixed method approach

<p>Abstract</p> <p>Background</p> <p>Health workers' counselling practices are essential to improve infant feeding practices. This paper will assess how infant feeding counselling was done and experienced by counsellors and mothers in Eastern Uganda in the context of previous guidelines. This has implications for implementation of the new infant feeding guidelines from 2009.</p> <p>Methods</p> <p>This paper combines qualitative and quantitative data from Mbale District in Eastern Uganda. Data was collected from 2003 to 2005 in a mixed methods approach. This includes: key-informant interviews among eighteen health workers in the public hospital, health clinics and non-governmental organisations working with people living with HIV, fifteen focus group discussions in the general population and among clients from an HIV clinic, two cross-sectional surveys including 727 mothers from the general population and 235 HIV-positive mothers.</p> <p>Results</p> <p>The counselling sessions were often improvised. Health workers frequently had pragmatic approaches to infant feeding as many clients struggled with poverty, stigma and non-disclosure of HIV. The feasibility of the infant feeding recommendations was perceived as challenging among health workers, both for HIV-positive mothers and in the general population. Group counselling with large groups was common in the public health service. Some extra infant feeding teaching capacities were mobilised for care-takers of undernourished children. A tendency to simplify messages giving one-sided information was seen. Different health workers presented contradicting simplified perspectives in some cases. Outdated training was a common concern with many health workers not being given courses or seminars on infant feeding since professional graduation. Other problems were minimal staffing, lack of resources, and programs being started and subsequently stopped abruptly. Many of the HIV-counsellors in the non-governmental organisations got extended training in counselling which seemed to be beneficial.</p> <p>Conclusions</p> <p>Health workers were faced with challenges related to workload, resources, scientific updating, and also a need to adjust to frequent changes in programs, recommendations and guidelines. The clients were faced with difficult choices, poverty, lack of education and stigma. Feasibility of the recommendations was a major concern. Systematic approaches to update health workers should be a priority.</p

A cluster randomised controlled trial of the community effectiveness of two interventions in rural Malawi to improve health care and to reduce maternal, newborn and infant mortality

<p>Abstract</p> <p>Background</p> <p>The UN Millennium Development Goals call for substantial reductions in maternal and child mortality, to be achieved through reductions in morbidity and mortality during pregnancy, delivery, postpartum and early childhood. The MaiMwana Project aims to test community-based interventions that tackle maternal and child health problems through increasing awareness and local action.</p> <p>Methods/Design</p> <p>This study uses a two-by-two factorial cluster-randomised controlled trial design to test the impact of two interventions. The impact of a community mobilisation intervention run through women's groups, on home care, health care-seeking behaviours and maternal and infant mortality, will be tested. The impact of a volunteer-led infant feeding and care support intervention, on rates of exclusive breastfeeding, uptake of HIV-prevention services and infant mortality, will also be tested. The women's group intervention will employ local female facilitators to guide women's groups through a four-phase cycle of problem identification and prioritisation, strategy identification, implementation and evaluation. Meetings will be held monthly at village level. The infant feeding intervention will select local volunteers to provide advice and support for breastfeeding, birth preparedness, newborn care and immunisation. They will visit pregnant and new mothers in their homes five times during and after pregnancy.</p> <p>The unit of intervention allocation will be clusters of rural villages of 2500-4000 population. 48 clusters have been defined and randomly allocated to either women's groups only, infant feeding support only, both interventions, or no intervention. Study villages are surrounded by 'buffer areas' of non-study villages to reduce contamination between intervention and control areas. Outcome indicators will be measured through a demographic surveillance system. Primary outcomes will be maternal, infant, neonatal and perinatal mortality for the women's group intervention, and exclusive breastfeeding rates and infant mortality for the infant feeding intervention.</p> <p>Structured interviews will be conducted with mothers one-month and six-months after birth to collect detailed quantitative data on care practices and health-care-seeking. Further qualitative, quantitative and economic data will be collected for process and economic evaluations.</p> <p>Trial registration</p> <p>ISRCTN06477126</p

Preschool hyperactivity specifically elevates long-term mental health risks more strongly in males than females: a prospective longitudinal study through to young adulthood

Evidence of continuities between preschool hyperactivity and adult mental health problems highlight the potential value of targeting early identification and intervention strategies. However, specific risk factors are currently unclear. This large-scale prospective longitudinal study aimed to identify which hyperactive preschoolers are at greatest long-term risk of poor mental health. One hundred and seventy children (89 females) rated as hyperactive by their parents and 88 non-hyperactive controls (48 females) were identified from a community sample of 4,215 3 year-olds. Baseline data relating to behavioral/emotional problems and background characteristics were collected. Follow-up mental health and functional impairment outcomes were collected between 14 and 25 years of age. At age 3 years, males and females in the hyperactive group had similarly raised levels of hyperactivity and other behavior problems. In adolescence/young adulthood, these individuals showed elevated symptoms of ADHD, conduct disorder, mood disorder, anxiety and autism, as well as functional impairment. Preschool hyperactivity was strongly predictive of poor adolescent/adult outcomes for males across domains with effects being specifically driven by hyperactivity. For females, the effects of preschool hyperactivity were smaller and dropped to non-significant levels when other preschool problems were taken into account. Environmental risk factors also differed between the sexes, although these may also have been mediated by genetic risk. In conclusion, these results demonstrate marked sex differences in preschool predictors of later adolescent/adult mental health problems. Future research should include a measure of preschool inattention as well hyperactivity. The findings highlight the potential value of tailored approaches to early identification strategies