DNA marker haplotype association with pancreatic sufficiency in cystic fibrosis.

Patients with cystic fibrosis (CF) generally suffer from chronic obstructive lung disease, pancreatic insufficiency (PI), and a number of other exocrine malfunctions. Approximately 15% of CF patients are, however, pancreatic sufficient. To investigate whether the two clinical subgroups, PI and pancreatic sufficiency (PS), are caused by different CF mutant alleles, we have performed linkage disequilibrium and haplotype association analysis with three DNA markers that are tightly linked to the CF locus. The study showed that the allelic and haplotype distributions for these RFLPs are significantly different between the two groups. The data suggest that most of the CF-PI patients are probably descendants of a single mutational event at the CF locus and that the CF-PS patients resulted from multiple, different mutations. While final interpretation of these data awaits molecular cloning of the CF gene, the information on haplotype association in CF may be useful in genetic counseling and disease prognosis, in identifying the gene itself, and in defining the mutations.     

Density dependence: an ecological Tower of Babel

The concept of density dependence represents the effect of changing population size on demographic rates and captures the demographic role of social and trophic mechanisms (e.g. competition, cooperation, parasitism or predation). Ecologists have coined more than 60 terms to denote different statistical and semantic properties of this concept, resulting in a formidable lexicon of synonymies and polysemies. We have examined the vocabulary of density dependence used in the modern ecological literature from the foundational lexicon developed by Smith, Allee, Haldane, Neave and Varley. A few simple rules suffice to abate terminological inconsistency and to enhance the biological meaning of this important concept. Correct citation of original references by ecologists and research journals could ameliorate terminological standards in our discipline and avoid linguistic confusion of mathematically and theoretically complex patterns.     

Which Biomarkers Reveal Neonatal Sepsis?

We address the identification of optimal biomarkers for the rapid diagnosis of neonatal sepsis. We employ both canonical correlation analysis (CCA) and sparse support vector machine (SSVM) classifiers to select the best subset of biomarkers from a large hematological data set collected from infants with suspected sepsis from Yale-New Haven Hospital''s Neonatal Intensive Care Unit (NICU). CCA is used to select sets of biomarkers of increasing size that are most highly correlated with infection. The effectiveness of these biomarkers is then validated by constructing a sparse support vector machine diagnostic classifier. We find that the following set of five biomarkers capture the essential diagnostic information (in order of importance): Bands, Platelets, neutrophil CD64, White Blood Cells, and Segs. Further, the diagnostic performance of the optimal set of biomarkers is significantly higher than that of isolated individual biomarkers. These results suggest an enhanced sepsis scoring system for neonatal sepsis that includes these five biomarkers. We demonstrate the robustness of our analysis by comparing CCA with the Forward Selection method and SSVM with LASSO Logistic Regression.     

Suprathreshold Heat Pain Response Predicts Activity-Related Pain,but Not Rest-Related Pain,in an Exercise-Induced Injury Model

Exercise-induced injury models are advantageous for studying pain since the onset of pain is controlled and both pre-injury and post-injury factors can be utilized as explanatory variables or predictors. In these studies, rest-related pain is often considered the primary dependent variable or outcome, as opposed to a measure of activity-related pain. Additionally, few studies include pain sensitivity measures as predictors. In this study, we examined the influence of pre-injury and post-injury factors, including pain sensitivity, for induced rest and activity-related pain following exercise induced muscle injury. The overall goal of this investigation was to determine if there were convergent or divergent predictors of rest and activity-related pain. One hundred forty-three participants provided demographic, psychological, and pain sensitivity information and underwent a standard fatigue trial of resistance exercise to induce injury of the dominant shoulder. Pain at rest and during active and resisted shoulder motion were measured at 48- and 96-hours post-injury. Separate hierarchical models were generated for assessing the influence of pre-injury and post-injury factors on 48- and 96-hour rest-related and activity-related pain. Overall, we did not find a universal predictor of pain across all models. However, pre-injury and post-injury suprathreshold heat pain response (SHPR), a pain sensitivity measure, was a consistent predictor of activity-related pain, even after controlling for known psychological factors. These results suggest there is differential prediction of pain. A measure of pain sensitivity such as SHPR appears more influential for activity-related pain, but not rest-related pain, and may reflect different underlying processes involved during pain appraisal.     

Forelimb Kinematics of Rats Using XROMM,with Implications for Small Eutherians and Their Fossil Relatives

The earliest eutherian mammals were small-bodied locomotor generalists with a forelimb morphology that strongly resembles that of extant rats. Understanding the kinematics of the humerus, radius, and ulna of extant rats can inform and constrain hypotheses concerning typical posture and mobility in early eutherian forelimbs. The locomotion of Rattus norvegicus has been extensively studied, but the three-dimensional kinematics of the bones themselves remains under-explored. Here, for the first time, we use markerless XROMM (Scientific Rotoscoping) to explore the three-dimensional long bone movements in Rattus norvegicus during a normal, symmetrical gait (walking). Our data show a basic kinematic profile that agrees with previous studies on rats and other small therians: rats maintain a crouched forelimb posture throughout the step cycle, and the ulna is confined to flexion/extension in a parasagittal plane. However, our three-dimensional data illuminate long-axis rotation (LAR) movements for both the humerus and the radius for the first time. Medial LAR of the humerus throughout stance maintains an adducted elbow with a caudally-facing olecranon process, which in turn maintains a cranially-directed manus orientation (pronation). The radius also shows significant LAR correlated with manus pronation and supination. Moreover, we report that elbow flexion and manus orientation are correlated in R. norvegicus: as the elbow angle becomes more acute, manus supination increases. Our data also suggest that manus pronation and orientation in R. norvegicus rely on a divided system of labor between the ulna and radius. Given that the radius follows the flexion and extension trajectory of the ulna, it must rotate at the elbow (on the capitulum) so that during the stance phase its distal end lies medial to ulna, ensuring that the manus remains pronated while the forelimb is supporting the body. We suggest that forelimb posture and kinematics in Juramaia, Eomaia, and other basal eutherians were grossly similar to those of rats, and that humerus and radius LAR may have always played a significant role in forelimb and manus posture in small eutherian mammals.     

The Longin SNARE VAMP7/TI-VAMP Adopts a Closed Conformation

SNARE protein complexes are key mediators of exocytosis by juxtaposing opposing membranes, leading to membrane fusion. SNAREs generally consist of one or two core domains that can form a four-helix bundle with other SNARE core domains. Some SNAREs, such as syntaxin target-SNAREs and longin vesicular-SNAREs, have independent, folded N-terminal domains that can interact with their respective SNARE core domains and thereby affect the kinetics of SNARE complex formation. This autoinhibition mechanism is believed to regulate the role of the longin VAMP7/TI-VAMP in neuronal morphogenesis. Here we use nuclear magnetic resonance spectroscopy to study the longin-SNARE core domain interaction for VAMP7. Using complete backbone resonance assignments, chemical shift perturbations analysis, and hydrogen/deuterium exchange experiments, we conclusively show that VAMP7 adopts a preferentially closed conformation in solution. Taken together, the closed conformation of longins is conserved, in contrast to the syntaxin family of SNAREs for which mixtures of open and closed states have been observed. This may indicate different regulatory mechanisms for SNARE complexes containing syntaxins and longins, respectively.     

Relative need for conservation assessments of vascular plant species among ecoregions

Aim (1) To determine the relative need for conservation assessments of vascular plant species among the world’s ecoregions given under‐assessed species distributions; (2) to evaluate the challenge posed by the lack of financial resources on species assessment efforts; and (3) to demonstrate the utility of nonlinear mixed‐effects models with both homoscedastic and heteroscedastic error structures in the identification of species‐rich ecoregions. Location Global. Methods We identified the world’s ecoregions that contain the highest vascular plant species richness after controlling for area using species–area relationship (SAR) models built within a mixed‐effects multi‐model framework. Using quantitative thresholds, ecoregions with the highest plant species richness, historical habitat loss and projected increase in human population density were deemed to be most in need of conservation assessments of plant species. We used generalized linear models to test if countries that overlap with highly important ecoregions are poorer compared with others. Results We classed ecoregions into nine categories based on the relative need for conservation assessments of vascular plant species. Ecoregions of highest relative need are found mostly in the tropics, particularly Southeast Asia, Central America, Tropical Andes and the Cerrado of South America, and the East African montane region and its surrounding areas. Countries overlapping with ecoregions deemed important for conservation assessments are poorer as measured by their capita gross national income than the other countries. The nonlinear mixed modelling framework was effective in reducing residual spatial autocorrelation compared with nonlinear models comprised of only fixed effects. In contrasting multiple SAR models to identify species‐rich ecoregions, there was not one SAR model that fitted best across all biomes. Not all SAR models displayed homoscedastic errors; therefore it is important to consider models with both homoscedastic and heteroscedastic error structures. Main conclusions We propose that conservation assessments should be conducted first in ecoregions with the greatest predicted species richness, historical habitat loss and future human population increase. As ecoregions deemed to be important for conservation assessments are located in the poorest countries, we urge international aid agencies and botanic gardens to cooperate with both local and international scientists to fund and implement conservation assessment programmes there.     

A first step in understanding an invasive weed through its genes: an EST analysis of invasive <Emphasis Type="Italic">Centaurea maculosa</Emphasis>

Background  

The economic and biological implications of plant invasion are overwhelming; however, the processes by which plants become successful invaders are not well understood. Limited genetic resources are available for most invasive and weedy species, making it difficult to study molecular and genetic aspects that may be associated with invasion.