41 research outputs found

    Hybrid gene misregulation in multiple developing tissues within a recent adaptive radiation of Cyprinodon pupfishes.

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    Genetic incompatibilities constitute the final stages of reproductive isolation and speciation, but little is known about incompatibilities that occur within recent adaptive radiations among closely related diverging populations. Crossing divergent species to form hybrids can break up coadapted variation, resulting in genetic incompatibilities within developmental networks shaping divergent adaptive traits. We crossed two closely related sympatric Cyprinodon pupfish species-a dietary generalist and a specialized molluscivore-and measured expression levels in their F1 hybrids to identify regulatory variation underlying the novel craniofacial morphology found in this recent microendemic adaptive radiation. We extracted mRNA from eight day old whole-larvae tissue and from craniofacial tissues dissected from 17-20 day old larvae to compare gene expression between a total of seven F1 hybrids and 24 individuals from parental species populations. We found 3.9% of genes differentially expressed between generalists and molluscivores in whole-larvae tissues and 0.6% of genes differentially expressed in craniofacial tissue. We found that 2.1% of genes were misregulated in whole-larvae hybrids whereas 19.1% of genes were misregulated in hybrid craniofacial tissues, after correcting for sequencing biases. We also measured allele specific expression across 15,429 heterozygous sites to identify putative compensatory regulatory mechanisms underlying differential expression between generalists and molluscivores. Together, our results highlight the importance of considering misregulation as an early indicator of genetic incompatibilities in the context of rapidly diverging adaptive radiations and suggests that compensatory regulatory divergence drives hybrid gene misregulation in developing tissues that give rise to novel craniofacial traits

    Self-driving cameras: automated camera capture for biological imaging

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    Efficient quantitative analysis of plant traits is critical to keep pace with advances in molecular and genetic plant breeding tools. Machine learning has shown impressive results in automating a lot of these analytical processes however, many of the algorithms rely on a surplus of high-quality biological imagery. This data is currently collected in labs via static camera systems, which provide consistent images but are challenging to tailor to individual plants, species, or tasks. Current research in autonomous camera systems use object detection or tracking methods to control the camera. Unfortunately, this quickly falls apart for static biological imagery as large inter- and intra-species variations, even within the same specimen, make object detection less robust and stationary targets make tracking unusable. Inspired by the success of deep learning in the autonomous driving space, we apply an end-to-end learned approach to directly map saliency-augmented input frames from an RGB monocular camera to a pan-tilt-zoom (PTZ) actuation. Our results show our model correctly classifies which direction to move the camera in 87% of instances and has an average offset error of 250 and 140 pixels for a 1920x1080 image, respectively. Results on a much smaller, plant-only dataset demonstrates the applicability of the model to biological imagery and we demonstrate saliency’s effectiveness in improving accuracy by up to 4%

    Case series of elective instrumented posterior lumbar spinal fusions demonstrating a low incidence of venous thromboembolism

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    Introduction: Venous thromboembolism (VTE) is a significant cause of morbidity and mortality in orthopaedic surgery. While specific guidelines exist for hip and knee arthroplasty, there is wide variation in VTE prophylaxis in complex spinal surgery. This study sought to determine the incidence of VTE, and risk factors associated with VTE, in patients undergoing elective instrumented posterior lumbar spinal fusion. Methods: In a single-centre case series study, 107 consecutive patients undergoing elective lumbar spinal fusion were evaluated for VTE by lower limb duplex ultrasonography and/or clinical observation, and where indicated, computed tomography pulmonary angiogram (CTPA). The Caprini model for thrombosis risk factor assessment was retrospectively applied to grade levels of VTE risk, which were compared with overall VTE incidence. Results: All patients were operated on a spinal frame and received mechanical prophylaxis (thromboembolic deterrent stockings and sequential calf-compression devices). Thirty-seven percent also received chemoprophylaxis with low molecular weight heparin (LMWH). There was no significant relationship between LMWH use and protection from VTE. Risk scores ³3 (high/highest risk categories) were observed in 96.2% of patients. Four (3.7%) patients encountered a VTE complication (all with no chemoprophylaxis), either deep vein thrombosis (1.9%) or pulmonary embolism (1.9%). No patient sustained an epidural haematoma. Conclusion: Although patients undergoing elective instrumental posterior lumbar spinal fusion are at high risk of developing VTE, the actual incidence of VTE in these patients is low. Our data support the use of mechanical prophylaxis with thromboembolic deterrent stockings and sequential calf-compression devices to prevent VTE in these patients

    Eye trauma epidemiology in regional Australia

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    Purpose: To describe the epidemiology of eye trauma presenting to a regional referral health service in New South Wales, Australia. Methods: A two-stage retrospective and prospective case series study was conducted. Patients who presented with eye trauma to Wagga Wagga Base Hospital (WWBH) emergency department (ED) during a one year review period formed the retrospective case series (RCS). Patient inclusion was determined using SNOMED CT and ICD-10 codes applied to medical records. Patients presenting with eye trauma to the WWBH ED or its ophthalmology service over a prospective 80 day study period formed the prospective case series (PCS). The main outcome measures were patient demographics, eye trauma incidence for Wagga Wagga and the Murrumbidgee region and injury details. Results: Four hundred and eleven and 117 eye injuries were identified for the RCS and PCS, respectively. Mean age was 35.5 years ± 18.6 (RCS) and 34.1 years ± 17.1 (PCS), with male predominance, 77.9% (RCS) and 89.7% (PCS). The incidence of eye trauma in Wagga Wagga and Murrumbidgee was estimated from the PCS at 537.1 and 334.4 per 100,000 person-years, respectively. A large proportion of injuries were work-related, 40.2% (RCS) and 45.8% (PCS). Protective eyewear use in work-related injuries was low, 27.6% (RCS) and 39.0% (PCS). Conclusions: Eye trauma remains a significant public health concern with a high incidence in Wagga Wagga and the Murrumbidgee region. Protective eyewear compliance is low in work-related eye injuries. Patient demographic and occupational factors may be targeted to reduce the burden of disease

    Novel candidate genes underlying extreme trophic specialization in Caribbean pupfishes

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    The genetic changes responsible for evolutionary transitions from generalist to specialist phenotypes are poorly understood. Here we examine the genetic basis of craniofacial traits enabling novel trophic specialization in a sympatric radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist species and two novel specialists: a small-jawed "snail-eater" and a large-jawed "scale-eater." We genotyped 12 million single nucleotide polymorphisms (SNPs) by whole-genome resequencing of 37 individuals of all three species from nine populations and integrated genome-wide divergence scans with association mapping to identify divergent regions containing putatively causal SNPs affecting jaw size-the most rapidly diversifying trait in this radiation. A mere 22 fixed variants accompanied extreme ecological divergence between generalist and scale-eater species. We identified 31 regions (20 kb) containing variants fixed between specialists that were significantly associated with variation in jaw size which contained 11 genes annotated for skeletal system effects and 18 novel candidate genes never previously associated with craniofacial phenotypes. Six of these 31 regions showed robust signs of hard selective sweeps after accounting for demographic history. Our data are consistent with predictions based on quantitative genetic models of adaptation, suggesting that the effect sizes of regions influencing jaw phenotypes are positively correlated with distance between fitness peaks on a complex adaptive landscape