Genic constraint against nonsynonymous variation across the mouse genome.

BACKGROUND: Selective constraint, the depletion of variation due to negative selection, provides insights into the functional impact of variants and disease mechanisms. However, its characterization in mice, the most commonly used mammalian model, remains limited. This study aims to quantify mouse gene constraint using a new metric called the nonsynonymous observed expected ratio (NOER) and investigate its relationship with gene function. RESULTS: NOER was calculated using whole-genome sequencing data from wild mouse populations (Mus musculus sp and Mus spretus). Positive correlations were observed between mouse gene constraint and the number of associated knockout phenotypes, indicating stronger constraint on pleiotropic genes. Furthermore, mouse gene constraint showed a positive correlation with the number of pathogenic variant sites in their human orthologues, supporting the relevance of mouse models in studying human disease variants. CONCLUSIONS: NOER provides a resource for assessing the fitness consequences of genetic variants in mouse genes and understanding the relationship between gene constraint and function. The study's findings highlight the importance of pleiotropy in selective constraint and support the utility of mouse models in investigating human disease variants. Further research with larger sample sizes can refine constraint estimates in mice and enable more comprehensive comparisons of constraint between mouse and human orthologues.

Modelling the genetic aetiology of complex disease: human-mouse conservation of noncoding features and disease-associated loci.

Understanding the genetic aetiology of loci associated with a disease is crucial for developing preventative measures and effective treatments. Mouse models are used extensively to understand human pathobiology and mechanistic functions of disease-associated loci. However, the utility of mouse models is limited in part by evolutionary divergence in transcription regulation for pathways of interest. Here, we summarize the alignment of genomic (exonic and multi-cell regulatory) annotations alongside Mendelian and complex disease-associated variant sites between humans and mice. Our results highlight the importance of understanding evolutionary divergence in transcription regulation when interpreting functional studies using mice as models for human disease variants.

Disappearance of an ecosystem engineer, the white-lipped peccary (Tayassu pecari), leads to density compensation and ecological release.

Given the rate of biodiversity loss, there is an urgent need to understand community-level responses to extirpation events, with two prevailing hypotheses. On one hand, the loss of an apex predator leads to an increase in primary prey species, triggering a trophic cascade of other changes within the community, while density compensation and ecological release can occur because of reduced competition for resources and absence of direct aggression. White-lipped peccary (Tayassu pecari-WLP), a species that typically co-occurs with collared peccary (Pecari tajacu), undergo major population crashes-often taking 20 to 30-years for populations to recover. Using a temporally replicated camera trapping dataset, in both a pre- and post- WLP crash, we explore how WLP disappearance alters the structure of a Neotropical vertebrate community with findings indicative of density compensation. White-lipped peccary were the most frequently detected terrestrial mammal in the 2006-2007 pre-population crash period but were undetected during the 2019 post-crash survey. Panthera onca (jaguar) camera trap encounter rates declined by 63% following the WLP crash, while collared peccary, puma (Puma concolor), red-brocket deer (Mazama americana) and short-eared dog (Atelocynus microtis) all displayed greater encounter rates (490%, 150%, 280%, and 500% respectively), and increased in rank-abundance. Absence of WLP was correlated with ecological release changes in habitat-use for six species, with the greatest increase in use in the preferred floodplain habitat of the WLP. Surprisingly, community-weighted mean trait distributions (body size, feeding guild and nocturnality) did not change, suggesting functional redundancy in diverse tropical mammal assemblages.

Determinants of spatial behavior of a tropical forest seed predator: The roles of optimal foraging, dietary diversification, and home range defense.

Specialized seed predators in tropical forests may avoid seasonal food scarcity and interspecific feeding competition but may need to diversify their daily diet to limit ingestion of any given toxin. Seed predators may, therefore, adopt foraging strategies that favor dietary diversity and resource monitoring, rather than efficient energy intake, as suggested by optimal foraging theory. We tested whether fine-scale space use by a small-group-living seed predator-the bald-faced saki monkey (Pithecia irrorata)-reflected optimization of short-term foraging efficiency, maximization of daily dietary diversity, and/or responses to the threat of territorial encroachment by neighboring groups. Food patches across home ranges of five adjacent saki groups were widely spread, but areas with higher densities of stems or food species were not allocated greater feeding time. Foraging patterns-specifically, relatively long daily travel paths that bypassed available fruiting trees and relatively short feeding bouts in undepleted food patches-suggest a strategy that maximizes dietary diversification, rather than "optimal" foraging. Travel distance was unrelated to the proportion of seeds in the diet. Moreover, while taxonomically diverse, the daily diets of our study groups were no more species-rich than randomly derived diets based on co-occurring available food species. Sakis preferentially used overlapping areas of their HRs, within which adjacent groups shared many food trees, yet the density of food plants or food species in these areas was no greater than in other HR areas. The high likelihood of depletion by neighboring groups of otherwise enduring food sources may encourage monitoring of peripheral food patches in overlap areas, even if at the expense of immediate energy intake, suggesting that between-group competition is a key driver of fine-scale home range use in sakis.

Enhancing conservation, ecosystem services, and local livelihoods through a wildlife premium mechanism.

We propose the wildlife premium mechanism as an innovation to conserve endangered large vertebrates. The performance-based payment scheme would allow stakeholders in lower-income countries to generate revenue by recovering and maintaining threatened fauna that can also serve as umbrella species (i.e., species whose protection benefits other species with which they co-occur). There are 3 possible options for applying the premium: option 1, embed premiums in a carbon payment; option 2, link premiums to a related carbon payment, but as independent and legally separate transactions; option 3, link premiums to noncarbon payments for conserving ecosystem services (PES). Each option presents advantages, such as incentive payments to improve livelihoods of rural poor who reside in or near areas harboring umbrella species, and challenges, such as the establishment of a subnational carbon credit scheme. In Kenya, Peru, and Nepal pilot premium projects are now underway or being finalized that largely follow option 1. The Kasigau (Kenya) project is the first voluntary carbon credit project to win approval from the 2 leading groups sanctioning such protocols and has already sold carbon credits totaling over $1.2 million since June 2011. A portion of the earnings is divided among community landowners and projects that support community members and has added over 350 jobs to the local economy. All 3 projects involve extensive community management because they occur on lands where locals hold the title or have a long-term lease from the government. The monitoring, reporting, and verification required to make premium payments credible to investors include transparent methods for collecting data on key indices by trained community members and verification of their reporting by a biologist. A wildlife premium readiness fund would enable expansion of pilot programs needed to test options beyond those presented here.

High-resolution forest carbon stocks and emissions in the Amazon.

Efforts to mitigate climate change through the Reduced Emissions from Deforestation and Degradation (REDD) depend on mapping and monitoring of tropical forest carbon stocks and emissions over large geographic areas. With a new integrated use of satellite imaging, airborne light detection and ranging, and field plots, we mapped aboveground carbon stocks and emissions at 0.1-ha resolution over 4.3 million ha of the Peruvian Amazon, an area twice that of all forests in Costa Rica, to reveal the determinants of forest carbon density and to demonstrate the feasibility of mapping carbon emissions for REDD. We discovered previously unknown variation in carbon storage at multiple scales based on geologic substrate and forest type. From 1999 to 2009, emissions from land use totaled 1.1% of the standing carbon throughout the region. Forest degradation, such as from selective logging, increased regional carbon emissions by 47% over deforestation alone, and secondary regrowth provided an 18% offset against total gross emissions. Very high-resolution monitoring reduces uncertainty in carbon emissions for REDD programs while uncovering fundamental environmental controls on forest carbon storage and their interactions with land-use change.

Making sense of the linear genome, gene function and TADs.

BACKGROUND: Topologically associating domains (TADs) are thought to act as functional units in the genome. TADs co-localise genes and their regulatory elements as well as forming the unit of genome switching between active and inactive compartments. This has led to the speculation that genes which are required for similar processes may fall within the same TADs, allowing them to share regulatory programs and efficiently switch between chromatin compartments. However, evidence to link genes within TADs to the same regulatory program is limited. RESULTS: We investigated the functional similarity of genes which fall within the same TAD. To do this we developed a TAD randomisation algorithm to generate sets of "random TADs" to act as null distributions. We found that while pairs of paralogous genes are enriched in TADs overall, they are largely depleted in TADs with CCCTC-binding factor (CTCF) ChIP-seq peaks at both boundaries. By assessing gene constraint as a proxy for functional importance we found that genes which singly occupy a TAD have greater functional importance than genes which share a TAD, and these genes are enriched for developmental processes. We found little evidence that pairs of genes in CTCF bound TADs are more likely to be co-expressed or share functional annotations than can be explained by their linear proximity alone. CONCLUSIONS: These results suggest that algorithmically defined TADs consist of two functionally different groups, those which are bound by CTCF and those which are not. We detected no association between genes sharing the same CTCF TADs and increased co-expression or functional similarity, other than that explained by linear genome proximity. We do, however, find that functionally important genes are more likely to fall within a TAD on their own suggesting that TADs play an important role in the insulation of these genes.

Expression of calretinin by breast carcinoma and the potential for misdiagnosis of mesothelioma.

AIMS: Calretinin and cytokeratin (CK)5/6 are frequently used to differentiate between metastatic breast cancer and primary malignant mesothelioma in pleural biopsies, but both tumours may express these markers. This study was aimed at evaluating the frequency of calretinin expression in primary breast carcinomas, and assessing the characteristics of the calretinin-positive tumours. METHODS AND RESULTS: Fifty-three primary breast adenocarcinomas were analysed for immunohistochemical expression of calretinin. CK5/6 and epidermal growth factor receptor (EGFR) immunostaining were performed on the calretinin-positive subset. Tumours were classified as basal-like if they met standard morphological and immunohistochemical criteria. Fifteen per cent (8/53) of the breast tumours were positive for calretinin. Eighty-eight per cent (7/8) of the calretinin-positive tumours were grade 3, as compared with 20% (9/45) of the calretinin-negative tumours (P<0.001). Only 13% (1/8) of the calretinin-positive tumours were also oestrogen receptor (ER)-positive, as compared with 87% (39/45) of the calretinin-negative tumours (P<0.001). Eleven per cent (6/53) of the tumours were classified as basal-like. Of these, four were positive for calretinin and two were negative (P=0.003). CONCLUSIONS: Fifteen per cent of breast carcinomas stain with calretinin. These tumours are more likely to be high-grade, ER-negative, and display a basal-like phenotype. These tumours may be misdiagnosed as malignant mesothelioma when they metastasize to the pleura.

Taxonomy and remote sensing of leaf mass per area (LMA) in humid tropical forests.

Leaf mass per area (LMA) is a trait of central importance to plant physiology and ecosystem function, but LMA patterns in the upper canopies of humid tropical forests have proved elusive due to tall species and high diversity. We collected top-of-canopy leaf samples from 2873 individuals in 57 sites spread across the Neotropics, Australasia, and Caribbean and Pacific Islands to quantify environmental and taxonomic drivers of LMA variation, and to advance remote-sensing measures of LMA. We uncovered strong taxonomic organization of LMA, with species accounting for 70% of the global variance and up to 62% of the variation within a forest stand. Climate, growth habit, and site conditions are secondary contributors (1-23%) to the observed LMA patterns. Intraspecific variation in LMA averages 16%, which is a fraction of the variation observed between species. We then used spectroscopic remote sensing (400-2500 nm) to estimate LMA with an absolute uncertainty of 14-15 g/m2 (r2 = 0.85), or approximately 10% of the global mean. With radiative transfer modeling, we demonstrated the scalability of spectroscopic remote sensing of LMA to the canopy level. Our study indicates that remotely sensed patterns of LMA will be driven by taxonomic variation against a backdrop of environmental controls expressed at site and regional levels.

Environmental and anthropogenic factors synergistically affect space use of jaguars.

Large terrestrial carnivores have undergone some of the largest population declines and range reductions of any species, which is of concern as they can have large effects on ecosystem dynamics and function.1-4 The jaguar (Panthera onca) is the apex predator throughout the majority of the Neotropics; however, its distribution has been reduced by >50% and it survives in increasingly isolated populations.5 Consequently, the range-wide management of the jaguar depends upon maintaining core populations connected through multi-national, transboundary cooperation, which requires understanding the movement ecology and space use of jaguars throughout their range.6-8 Using GPS telemetry data for 111 jaguars from 13 ecoregions within the four biomes that constitute the majority of jaguar habitat, we examined the landscape-level environmental and anthropogenic factors related to jaguar home range size and movement parameters. Home range size decreased with increasing net productivity and forest cover and increased with increasing road density. Speed decreased with increasing forest cover with no sexual differences, while males had more directional movements, but tortuosity in movements was not related to any landscape factors. We demonstrated a synergistic relationship between landscape-scale environmental and anthropogenic factors and jaguars' spatial needs, which has applications to the conservation strategy for the species throughout the Neotropics. Using large-scale collaboration, we overcame limitations from small sample sizes typical in large carnivore research to provide a mechanism to evaluate habitat quality for jaguars and an inferential modeling framework adaptable to the conservation of other large terrestrial carnivores.

Kikuchi-Fujimoto Disease and Prognostic Implications.

Kikuchi-Fujimoto disease (KFD) is a rare cause of lymphadenitis seen mostly in Asian populations (Kikuchi in Nippon Ketsueki Gakkai Zasshi 35:379-80, 1972). First described in 1972, KFD is a benign and self-limiting disease characterised by lymphadenopathy, mild fever, fatigue, and leukopenia (Fujimoto in Naika 30:920-7, 1972; Lin et al. in Otolaryngol Head Neck Surg 128(5): 650-3, 2003). We present a case of a 38-year-old woman with a 6-week history of cervical lymphadenopathy. Her ultrasound scan and fine needle aspiration cytology results were inconclusive. Excisional biopsy of the lymph node confirmed presence of KFD. The aetiology of KFD is unknown; however, there is strong association with systemic lupus erythematosus (SLE). Kucukardali reported 9% of European KFD patients and 28% of East Asian patients had concomitant SLE (Kucukardali et al. in Clin Rheumatol 26(1):50-4, 2007). We describe a follow-up algorithm for newly diagnosed KFD cases, based on the current literature. KFD is a rare cause of cervical lymphadenopathy. It is associated with increased risk of developing SLE, therefore early diagnosis and long-term follow-up are recommended.

Genomic Mutation Identification in Mice Using Illumina Sequencing and Linux-Based Computational Methods.

Genetically modified mice are an essential tool for modeling disease-causing mechanisms and discovering gene function. SNP genotyping was traditionally used to associate candidate regions with traits in the mouse, but failed to reveal novel variants without further targeted sequencing. Using a robust set of computational protocols, we present a platform to enable scientists to detect variants arising from whole-genome and exome sequencing experiments. This article guides researchers on aligning reads to the mouse genome, quality-assurance strategies, mutation discovery, comparing mutations to previously discovered mouse SNPs, and the annotation of novel variants, in order to predict mutation consequences on the protein level. Challenges unique to the mouse are discussed, and two protocols use self-contained containers to maintain version control and allow users to adapt our approach to new techniques by upgrading container versions. Our protocols are suited for servers or office workstations and are usable by non-bioinformatics specialists. © 2019 by John Wiley & Sons, Inc.

Patterns of growth in the presacral vertebral column of the leopard gecko (Eublepharis macularius).

Postnatal growth patterns within the vertebral column may be informative about body proportions and regionalization. We measured femur length, lengths of all pre-sacral vertebrae, and lengths of intervertebral spaces, from radiographs of a series of 21 Eublepharis macularius, raised under standard conditions and covering most of the ontogenetic body size range. Vertebrae were grouped into cervical, sternal, and dorsal compartments, and lengths of adjacent pairs of vertebrae were summed before analysis. Femur length was included as an index of body size. Principal component analysis of the variance-covariance matrix of these data was used to investigate scaling among them. PC1 explained 94.19% of total variance, interpreted as the variance due to body size. PC1 differed significantly from the hypothetical isometric vector, indicating overall allometry. The atlas and axis vertebrae displayed strong negative allometry; the remainder of the vertebral pairs exhibited weak negative allometry, isometry or positive allometry. PC1 explained a markedly smaller amount of variance for the vertebral pairs of the cervical compartment than for the remainder of the vertebral pairs, with the exception of the final pair. The relative standard deviations of the eigenvalues from the PCAs of the three vertebral compartments indicated that the vertebrae of the cervical compartment were less strongly integrated by scaling than were the sternal or dorsal vertebrae, which did not differ greatly between themselves in their strong integration, suggesting that the growth of the cervical vertebrae is constrained by the mechanical requirements of the head. Regionalization of the remainder of the vertebral column is less clearly defined but may be associated with wave form propagation incident upon locomotion, and by locomotory changes occasioned by tail autotomy and regeneration. Femur length exhibits negative allometry relative to individual vertebral pairs and to vertebral column length, suggesting a change in locomotor requirements over the ontogenetic size range.

Incentives Increase Participation in Mass Dog Rabies Vaccination Clinics and Methods of Coverage Estimation Are Assessed to Be Accurate.

In this study we show that incentives (dog collars and owner wristbands) are effective at increasing owner participation in mass dog rabies vaccination clinics and we conclude that household questionnaire surveys and the mark-re-sight (transect survey) method for estimating post-vaccination coverage are accurate when all dogs, including puppies, are included. Incentives were distributed during central-point rabies vaccination clinics in northern Tanzania to quantify their effect on owner participation. In villages where incentives were handed out participation increased, with an average of 34 more dogs being vaccinated. Through economies of scale, this represents a reduction in the cost-per-dog of $0.47. This represents the price-threshold under which the cost of the incentive used must fall to be economically viable. Additionally, vaccination coverage levels were determined in ten villages through the gold-standard village-wide census technique, as well as through two cheaper and quicker methods (randomized household questionnaire and the transect survey). Cost data were also collected. Both non-gold standard methods were found to be accurate when puppies were included in the calculations, although the transect survey and the household questionnaire survey over- and under-estimated the coverage respectively. Given that additional demographic data can be collected through the household questionnaire survey, and that its estimate of coverage is more conservative, we recommend this method. Despite the use of incentives the average vaccination coverage was below the 70% threshold for eliminating rabies. We discuss the reasons and suggest solutions to improve coverage. Given recent international targets to eliminate rabies, this study provides valuable and timely data to help improve mass dog vaccination programs in Africa and elsewhere.

Primary uterine osteosarcoma presenting synchronously with bilateral breast carcinomas.

Primary uterine sarcomas are infrequent neoplasms and most commonly leiomyosarcomas or endometrial stromal sarcomas. We report a rare case of primary uterine osteosarcoma discovered in a woman in her 60s following staging CT imaging for bilateral breast carcinomas. Examination of the subsequent hysterectomy specimen showed a tumour composed of malignant spindle cells and osteoclast-like giant cells associated with osteoid and neoplastic bone, in keeping with primary uterine osteosarcoma. Distinction of osteosarcoma from the more common carcinosarcoma is important due to the worse prognosis impacting on treatment decisions. In addition, synchronous presentation of this unusual tumour with bilateral breast carcinomas raises the possibility of a mutual genetic pathogenesis.

Anatomy of the crus and pes of neotropical iguanian lizards in relation to habitat use and digitally based grasping capabilities.

Ecomorphological studies of lizards have explored the role of various morphological traits and how these may be associated with, among other things, habitat use. We present an analysis of selected traits of internal morphology of the hind limbs of Neotropical iguanian lizards and their relationship to habitat use. Considering that one of the most widely-held hypotheses relating to the origin of grasping is associated with the exploitation of the narrow-branch arboreal habitat, we include subdivisions of this designation as two of our ecologically defined categories of habitat exploitation for analysis, and compare lizards assigned to these categories to the features displayed by terrestrial lizards. The influence of phylogeny in shaping the morphology of lizards was assessed by using the comparative method. K values were significant for several osteological traits. Most of the K values for the variables based upon muscle and tendon morphometric characters (13 out 21), by contrast, had values <1, suggesting that their variation cannot be explained by phylogeny alone. Results of our phylogenetic and conventional ANCOVA analyses reveal that the characters highlighted through the application of the comparative method are not absolutely related to habitat in terms of the categories considered here. It appears that the bauplan of the lizard pes incorporates a morphological configuration that is sufficiently versatile to enable exploitation of almost all of the available habitats. As unexpected as conservation of internal gross morphology appears, it represents a means of accommodating to environmental challenges by apparently permitting adequacy for all situations examined.

Enterobius vermicularis infection of the ovary.

Enterobius vermicularis is an intestinal parasite, which may occasionally involve extraintestinal sites including the female genital tract. We report a rare case of ovarian involvement, which presented with chronic right iliac fossa pain in a 31-year-old woman. A transvaginal ultrasound scan was suggestive of a right adnexal dermoid cyst; however, histological examination of the subsequent salpingo-oophorectomy specimen showed an abscess containing viable E. vermicularis ova. E. vermicularis is the most prevalent human nematode worldwide. Its ova are ingested, larvae hatch and mature female worms journey to the perianal region where they lay eggs. Female worms may also migrate from the anus along the female genital tract. Although of low pathogenicity, complications such as infertility or peritonitis may arise.

An incidental peri-adrenal cystic lesion.

A 50-year-old man was found to have an incidental peri-adrenal cystic lesion on CT imaging which was removed laparoscopically. Histological examination showed a cystic structure composed of respiratory and cuboidal-type epithelium with underlying smooth muscle, cartilage and seromucinous glands. The differential diagnosis for such a lesion includes bronchogenic cyst or teratoma differentiated. This case report offers an overview of both the conditions and the difficulties encountered in the histological distinction.

Thoraco-pulmonary and hepatic actinomycosis: an autopsy report.

Actinomycosis is now a rare disease and death unheard of. Diagnosis is made challenging by its varied presentations and ability to be a 'great pretender'. This report describes a rare autopsy case of thoraco-pulmonary and hepatic actinomycosis with the preceding clinical presentation.