A new method for ecologists to estimate heterozygote excess and deficit for multi-locus gene families.

The fixation index, F IS, has been a staple measure to detect selection, or departures from random mating in populations. However, current Next Generation Sequencing (NGS) cannot easily estimate F IS, in multi-locus gene families that contain multiple loci having similar or identical arrays of variant sequences of ≥1 kilobase (kb), which differ at multiple positions. In these families, high-quality short-read NGS data typically identify variants, but not the genomic location, which is required to calculate F IS (based on locus-specific observed and expected heterozygosity). Thus, to assess assortative mating, or selection on heterozygotes, from NGS of multi-locus gene families, we need a method that does not require knowledge of which variants are alleles at which locus in the genome. We developed such a method. Like F IS, our novel measure, 1 H IS, is based on the principle that positive assortative mating, or selection against heterozygotes, and some other processes reduce within-individual variability relative to the population. We demonstrate high accuracy of 1 H IS on a wide range of simulated scenarios and two datasets from natural populations of penguins and dolphins. 1 H IS is important because multi-locus gene families are often involved in assortative mating or selection on heterozygotes. 1 H IS is particularly useful for multi-locus gene families, such as toll-like receptors, the major histocompatibility complex in animals, homeobox genes in fungi and self-incompatibility genes in plants.

Optimizing Nervous System-Specific Gene Targeting with Cre Driver Lines: Prevalence of Germline Recombination and Influencing Factors.

The Cre-loxP system is invaluable for spatial and temporal control of gene knockout, knockin, and reporter expression in the mouse nervous system. However, we report varying probabilities of unexpected germline recombination in distinct Cre driver lines designed for nervous system-specific recombination. Selective maternal or paternal germline recombination is showcased with sample Cre lines. Collated data reveal germline recombination in over half of 64 commonly used Cre driver lines, in most cases with a parental sex bias related to Cre expression in sperm or oocytes. Slight differences among Cre driver lines utilizing common transcriptional control elements affect germline recombination rates. Specific target loci demonstrated differential recombination; thus, reporters are not reliable proxies for another locus of interest. Similar principles apply to other recombinase systems and other genetically targeted organisms. We hereby draw attention to the prevalence of germline recombination and provide guidelines to inform future research for the neuroscience and broader molecular genetics communities.

Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping.

Decoding the functional connectivity of the nervous system is facilitated by transgenic methods that express a genetically encoded reporter or effector in specific neurons; however, most transgenic lines show broad spatiotemporal and cell-type expression. Increased specificity can be achieved using intersectional genetic methods which restrict reporter expression to cells that co-express multiple drivers, such as Gal4 and Cre. To facilitate intersectional targeting in zebrafish, we have generated more than 50 new Cre lines, and co-registered brain expression images with the Zebrafish Brain Browser, a cellular resolution atlas of 264 transgenic lines. Lines labeling neurons of interest can be identified using a web-browser to perform a 3D spatial search (zbbrowser.com). This resource facilitates the design of intersectional genetic experiments and will advance a wide range of precision circuit-mapping studies.

Risks to carbon dynamics in semi-arid woodlands of eastern Australia under current and future climates.

Extreme disturbance events, such as wildfire and drought, have large impacts on carbon storage and sequestration of forests and woodlands globally. Here, we present a modelling approach that assesses the relative impact of disturbances on carbon storage and sequestration, and how this will alter under climate change. Our case study is semi-arid Australia where large areas of land are managed to offset over 122 million tonnes of anthropogenic carbon emissions over a 100-year period. These carbon offsets include mature vegetation that has been protected from clearing and regenerating vegetation on degraded agricultural land. We use a Bayesian Network model to combine multiple probabilistic models of the risk posed by fire, drought, grazing and recruitment failure to carbon dynamics. The model is parameterised from a review of relevant literature and additional quantitative analyses presented here. We found that the risk of vegetation becoming a net source of carbon due to a mortality event, or failing to realise maximum sequestration potential, through recruitment failure in regenerating vegetation, was primarily a function of rainfall in this semi-arid environment. However, the relative size of an emissions event varied across vegetation communities depending on plant attributes, specifically resprouting capacity. Modelled climate change effects were variable, depending on the climate change projection used. Under 'best-case' or 'most-likely' climate scenarios for 2050, similar or increased projections of mean annual precipitation, associated with a build-up of fuel, were expected to drive an increase in fire activity (a 40-160% increase), but a decrease in drought (a 20-35% decrease). Under a 'worst-case' climate scenario, fire activity was expected to decline (a 37% decrease), but drought conditions remain similar (a 5% decrease). These projected changes to the frequency of drought and fire increase the risk that vegetation used for carbon offsetting will fail to provide anticipated amounts of carbon abatement over their lifetime.

Biophysical risks to carbon sequestration and storage in Australian drylands.

Carbon abatement schemes that reduce land clearing and promote revegetation are now an important component of climate change policy globally. There is considerable potential for these schemes to operate in drylands which are spatially extensive. However, projects in these environments risk failure through unplanned release of stored carbon to the atmosphere. In this review, we identify factors that may adversely affect the success of vegetation-based carbon abatement projects in dryland ecosystems, evaluate their likelihood of occurrence, and estimate the potential consequences for carbon storage and sequestration. We also evaluate management strategies to reduce risks posed to these carbon abatement projects. Identified risks were primarily disturbances, including unplanned fire, drought, and grazing. Revegetation projects also risk recruitment failure, thereby failing to reach projected rates of sequestration. Many of these risks are dependent on rainfall, which is highly variable in drylands and susceptible to further variation under climate change. Resprouting vegetation is likely to be less vulnerable to disturbance and have faster recovery rates upon release from disturbance. We conclude that there is a strong impetus for identifying management strategies and risk reduction mechanisms for carbon abatement projects. Risk mitigation would be enhanced by effective co-ordination of mitigation strategies at scales larger than individual abatement project boundaries, and by implementing risk assessment throughout project planning and implementation stages. Reduction of risk is vital for maximising carbon sequestration of individual projects and for reducing barriers to the establishment of new projects entering the market.

Search strategy is regulated by somatostatin signaling and deep brain photoreceptors in zebrafish.

BACKGROUND: Animals use sensory cues to efficiently locate resources, but when sensory information is insufficient, they may rely on internally coded search strategies. Despite the importance of search behavior, there is limited understanding of the underlying neural mechanisms in vertebrates. RESULTS: Here, we report that loss of illumination initiates sophisticated light-search behavior in larval zebrafish. Using three-dimensional tracking, we show that at the onset of darkness larvae swim in a helical trajectory that is spatially restricted in the horizontal plane, before gradually transitioning to an outward movement profile. Local and outward swim patterns display characteristic features of area-restricted and roaming search strategies, differentially enhancing phototaxis to nearby and remote sources of light. Retinal signaling is only required to initiate area-restricted search, implying that photoreceptors within the brain drive the transition to the roaming search state. Supporting this, orthopediaA mutant larvae manifest impaired transition to roaming search, a phenotype which is recapitulated by loss of the non-visual opsin opn4a and somatostatin signaling. CONCLUSION: These findings define distinct neuronal pathways for area-restricted and roaming search behaviors and clarify how internal drives promote goal-directed activity.

Vitamin D status predicts 30 day mortality in hospitalised cats.

Vitamin D insufficiency, defined as low serum concentrations of the major circulating form of vitamin D, 25 hydroxyvitamin D (25(OH)D), has been associated with the development of numerous infectious, inflammatory, and neoplastic disorders in humans. In addition, vitamin D insufficiency has been found to be predictive of mortality for many disorders. However, interpretation of human studies is difficult since vitamin D status is influenced by many factors, including diet, season, latitude, and exposure to UV radiation. In contrast, domesticated cats do not produce vitamin D cutaneously, and most cats are fed a commercial diet containing a relatively standard amount of vitamin D. Consequently, domesticated cats are an attractive model system in which to examine the relationship between serum 25(OH)D and health outcomes. The hypothesis of this study was that vitamin D status would predict short term, all-cause mortality in domesticated cats. Serum concentrations of 25(OH)D, together with a wide range of other clinical, hematological, and biochemical parameters, were measured in 99 consecutively hospitalised cats. Cats which died within 30 days of initial assessment had significantly lower serum 25(OH)D concentrations than cats which survived. In a linear regression model including 12 clinical variables, serum 25(OH)D concentration in the lower tertile was significantly predictive of mortality. The odds ratio of mortality within 30 days was 8.27 (95% confidence interval 2.54-31.52) for cats with a serum 25(OH)D concentration in the lower tertile. In conclusion, this study demonstrates that low serum 25(OH)D concentration status is an independent predictor of short term mortality in cats.

The monitoring of longer term prescriptions of antidepressants: observational study in a primary care setting.

BACKGROUND: There is little evidence to guide the frequency of review for patients taking antidepressants in the longer term. OBJECTIVES: To measure the frequency with which patients on longer term courses of antidepressants have their treatment monitored in primary care and to identify patient characteristics associated with the frequency of monitoring. METHODS: A cohort of patients who were receiving antidepressants continuously for at least two years was identified from four general practices. Data were collected from patients' general medical records. The dates of all GP consultations and whether they included a documented review of antidepressant therapy were recorded, along with patient characteristics hypothesized to influence the frequency of monitoring. RESULTS: The frequency of antidepressant review consultations and proportion of participants being reviewed during a specific year of antidepressant therapy decreased with increasing year of antidepressant therapy. Individuals who receive antidepressants for an overt mental health reason; undergo more dose and drug changes; and who are referred to the community mental health team have their antidepressant therapy reviewed more often during the first five years of antidepressant therapy. CONCLUSION: As many patients on longer term courses of antidepressants are not being appropriately reviewed, a 'chronic disease management approach' to depression in primary care is advocated.

Health maintenance in the inflammatory bowel disease patient.

Gastroenterologists are in a unique position to make very positive differences in the lives of their IBD patients. We understand that IBD patients do not receive preventive services at the same rate as general medical patients. Because these individuals are at increased risk for complications from preventable diseases, we have a valuable opportunity to protect this population (Table 1). Establishing a close working relationship with PCPs can facilitate delivering quality care, but it is important to note that some of these patients rely solely on their GI clinician for the majority of their care. In such a vulnerable population, it is important to be aggressive with vaccine recommendations, monitoring for depression, tobacco cessation, and in performing the appropriate cancer screening examinations. As professional societies and health care system increase their focus on quality measures, incorporating these important issues into routine practice will ultimately result in addressing quality standards; perhaps more important, it should provide our patients with the best individual care possible.

Pseudohypopyon as a clinical manifestation in metastatic lung carcinoma.

Pseudohypopyon is a rare clinical presentation of meta-static disease in the eye. The authors report a case of anterior chamber pseudohypopyon in a 74-year-old man with a history of primary central nervous system and spleen lymphoma, as well as lung, prostate, and bladder carcinoma. A diagnostic vitrectomy and anterior chamber paracentesis of the involved eye was performed that confirmed non-small-cell carcinoma of lung primary.

Bilateral choroidal metastases from primary esophageal melanoma: a rare case.

PURPOSE: The purpose of this case report is to report a rare, bilateral, choroidal metastases from a primary esophageal melanoma. CASE REPORT: A 44-year-old white female presented to the ocular oncology clinic in February 2010 on urgent referral from her ophthalmologist for evaluation of an elevated mass in each eye. The patient presented with best-corrected visual acuities of 20/25 in both eyes. Fundus examination displayed creamy white choroidal infiltrates located in the superior temporal arcade of the right eye and temporally in the left eye. The patient was diagnosed with bilateral choroidal metastatic melanoma from known primary esophageal melanoma. External beam radiation therapy was administered and complete resolution of the lesions occurred. Final visual outcome was 20/20 in both eyes. Nine months after diagnosis of choroidal metastases, the patient died from complications related to the extensive systemic metastatic involvement. CONCLUSIONS: Choroidal metastases are the most common intraocular malignancy. However, metastatic melanoma is a rare finding and has only been reported from cutaneous and primary choroidal melanoma. Therefore, to the best of the authors' knowledge, this is the first reported case of bilateral choroidal metastasis from a primary esophageal malignant melanoma.

Glucose-dependent insulinotropic polypeptide stimulates the proliferation of colorectal cancer cells.

Although numerous epidemiological studies have provided convincing evidence for an increase in the prevalence of colorectal cancer (CRC) in obese individuals, the precise mechanisms involved have not been elucidated. Glucose-dependent insulinotropic polypeptide (GIP) is a gastrointestinal regulatory peptide whose primary physiologic role is to stimulate postprandial pancreatic insulin secretion. Like insulin, GIP has been linked to enhanced nutrient efficiency, which occurred during the course of evolution. Its expression is increased in obesity, and we thus initiated studies to examine whether GIP might contribute to the pathogenesis of obesity-related CRC. RT-PCR and Western analysis demonstrated the presence of the GIP receptor (GIPR) in several human CRC cell lines. GIP stimulated the proliferation of MC-26 cells, a mouse CRC cell line, in a concentration-dependent manner. Western analysis showed that GIP induced the activity of several downstream signaling molecules known to be involved in cellular proliferation in a concentration- and time-dependent manner. These studies indicate that the presence of GIP receptors in CRC may enable ligand binding and, in so doing, stimulate CRC cell proliferation. The overexpression of GIP, which occurs in obesity, might thereby be contributing to the enhanced rate of carcinogenesis observed in obesity.

Which patients receive advice on diet and exercise? Do certain characteristics affect whether they receive such advice?

OBJECTIVE: To examine whether patients' characteristics, familiarity with the clinic, or perspectives on the quality of their care predict whether they receive advice from physicians regarding diet and exercise. DESIGN: Secondary data analysis of responses to the Primary Care Practice Survey. SETTING: Capital District Health Authority in Nova Scotia. PARTICIPANTS: Residents of the Capital District Health Authority 18 years old and older (N = 1562). MAIN OUTCOME MEASURES: Percentage of patients who reported frequently receiving advice from their family physicians regarding diet and exercise. RESULTS: Almost 38% of respondents reported frequently receiving advice from their physicians on diet. Those more likely to receive advice on diet were male (adjusted odds ratio [AOR] 1.6, 95% confidence interval [CI] 1.2 to 2.1), were 35 to 54 years old (compared with those aged 18 to 34) (AOR 1.5, 95% CI 1.1 to 2.2), had more chronic illnesses (AOR 1.3, 95% CI 1.2 to 1.6), had good relationships with their health care providers (AOR 2.3, 95% CI 1.8 to 3.1), or reported higher scores on an enablement scale (AOR 2.2, 95% CI 1.6 to 3.1). Respondents who reported their health status as excellent were less likely to receive advice on diet (AOR 0.5, 95% CI 0.3 to 0.9). About 42% of respondents reported frequently receiving advice on exercise. Men (AOR 1.7, 95% CI 1.3 to 2.2), those older than 35 years (AOR 1.7, 95% CI 1.2 to 2.4 for those aged 35 to 54; AOR 1.6, 95% CI 1.1 to 2.3 for those 55 and older), those rating their health as good (AOR 1.6, 95% CI 1.1 to 2.4), those with more chronic illnesses (AOR 1.3, 95% CI 1.1 to 1.5), and those reporting higher scores on communication (AOR 3.2, 95% CI 2.3 to 4.4) and enablement (AOR 1.8, 95% CI 1.3 to 2.4) scales were more likely to receive advice on exercise. CONCLUSION: Strategies to increase the number of patients who receive advice on diet and exercise would likely include enhancing communication between patients and their physicians, improving relationships between patients and their physicians, and improving physicians' ability to help their patients feel enabled to act on advice and cope with their illnesses. Physicians should be aware of their counseling practices and consider discussing healthy behaviour with patients with no obvious risk factors. This would be practising true primary prevention.

Health visitors' role in newborn blood spot screening.

New national policies and standards for newborn blood spot screening for some uncommon but serious conditions indicate that health visitors may have an increasingly important role in supporting parents. This may include offering support and guidance through times of uncertainty and hearing bad news about their baby's screening result. The U.K. Newborn Screening Programme Centre (UKNSPC) has developed resources for health professionals to support them in communicating with parents about newborn blood spot screening at different times in the screening pathway. In an era of informed choice in health care, including screening, effective communication and the provision of evidence-based information are increasingly highlighted. This paper draws attention to the importance of effective communication between health professionals and parents, and describes the resources developed specifically to support this. It outlines the communication guidelines developed by the UKNSPC, paying particular attention to the role of health visitors at critical times in parents' screening journey.