UNIFICATION OF REGRESSION‐BASED METHODS FOR THE ANALYSIS OF NATURAL SELECTION

Regression analyses are central to characterization of the form and strength of natural selection in nature. Two common analyses that are currently used to characterize selection are (1) least squares–based approximation of the individual relative fitness surface for the purpose of obtaining quantitatively useful selection gradients, and (2) spline‐based estimation of (absolute) fitness functions to obtain flexible inference of the shape of functions by which fitness and phenotype are related. These two sets of methodologies are often implemented in parallel to provide complementary inferences of the form of natural selection. We unify these two analyses, providing a method whereby selection gradients can be obtained for a given observed distribution of phenotype and characterization of a function relating phenotype to fitness. The method allows quantitatively useful selection gradients to be obtained from analyses of selection that adequately model nonnormal distributions of fitness, and provides unification of the two previously separate regression‐based fitness analyses. We demonstrate the method by calculating directional and quadratic selection gradients associated with a smooth regression‐based generalized additive model of the relationship between neonatal survival and the phenotypic traits of gestation length and birth mass in humans.     

The netrin receptor DCC focuses invadopodia-driven basement membrane transmigration in vivo

Though critical to normal development and cancer metastasis, how cells traverse basement membranes is poorly understood. A central impediment has been the challenge of visualizing invasive cell interactions with basement membrane in vivo. By developing live-cell imaging methods to follow anchor cell (AC) invasion in Caenorhabditis elegans, we identify F-actin–based invadopodia that breach basement membrane. When an invadopodium penetrates basement membrane, it rapidly transitions into a stable invasive process that expands the breach and crosses into the vulval tissue. We find that the netrin receptor UNC-40 (DCC) specifically enriches at the site of basement membrane breach and that activation by UNC-6 (netrin) directs focused F-actin formation, generating the invasive protrusion and the cessation of invadopodia. Using optical highlighting of basement membrane components, we further demonstrate that rather than relying solely on proteolytic dissolution, the AC’s protrusion physically displaces basement membrane. These studies reveal an UNC-40–mediated morphogenetic transition at the cell–basement membrane interface that directs invading cells across basement membrane barriers.     

Estimating minke whale (Balaenoptera acutorostrata) boing sound density using passive acoustic sensors

Density estimation for marine mammal species is performed primarily using visual distance sampling or capture‐recapture. Minke whales in Hawaiian waters are very difficult to sight; however, they produce a distinctive “boing” call, making them ideal candidates for passive acoustic density estimation. We used an array of 14 bottom‐mounted hydrophones, distributed over a 60 × 30 km area off Kauai, Hawaii, to estimate density during 12 d of recordings in early 2006. We converted the number of acoustic cues (i.e., boings) detected using signal processing software into a cue density by accounting for the false positive rate and probability of detection. The former was estimated by manual validation, the latter by applying spatially explicit capture‐recapture (SECR) methods to a subset of data where we had determined which hydrophones detected each call. Estimated boing density was 130 boings per hour per 10,000 km² (95% CI 104–163). Little is known about the population's acoustic behavior, so conversion from boing to animal density is difficult. As a demonstration of the method, we used a tentative boing rate of 6.04 boings per hour, from a single animal tracked in 2009, to give an estimate of 21.5 boing‐calling minke whales per 10,000 km².     

Amphibian swimming traces from the Lower Permian of southern New Mexico

Fossilised traces of swimming amphibians, assigned to Batrachichnus delicatulus and Serpentichnus robledoensis igen. et isp. nov., are described from the Lower Permian of the Robledo Mountains, southern New Mexico. The B. delicatulus specimen is interpreted as a trackway of a small 'amphibian' (temnospondyl, nectridean, microsaur or juvenile embolomere) swimming straight ahead. S. robledoensis consists of repeated pes imprints separated by discontinuous, L-shaped imprints (body traces). It is interpreted as a trackway of an 'amphibian' swimming in a similar manner to the motion of a side-winding snake. The producer of S. robledoensis is more distinctive than in B. delicatulus , and is suggestive of the lysorophian Brachydectes . This is the first locomotory trace to be assigned to this 'amphibian' group.     

The local phospholipid environment modulates the activation of blood clotting

Examples abound of membrane-bound enzymes for which the local membrane environment plays an important role, including the ectoenzyme that triggers blood clotting, the plasma serine protease, factor VIIa, bound to the integral membrane protein, tissue factor. The activity of this enzyme complex is markedly influenced by lipid bilayer composition and further by tissue factor partitioning into membrane microdomains on some cell surfaces. Unfortunately, little is known about how membrane microdomain composition controls factor VIIa-tissue factor activity, as reactions catalyzed by membrane-tethered enzymes are typically studied under conditions in which the experimenter cannot control the composition of the membrane in the immediate vicinity of the enzyme. To overcome this problem, we used a nanoscale approach that afforded complete control over the membrane environment surrounding tissue factor by assembling the factor VIIa.tissue factor complex on stable bilayers containing 67 +/- 1 phospholipid molecules/leaflet (Nanodiscs). We investigated how local changes in phospholipid bilayer composition modulate the activity of the factor VIIa.tissue factor complex. We also addressed whether this enzyme requires a pool of membrane-bound protein substrate (factor X) for efficient catalysis, or alternatively if it could efficiently activate factor X, which binds directly to the membrane nanodomain adjacent to tissue factor. We have shown that full proteolytic activity of the factor VIIa.tissue factor complex requires extremely high local concentrations of anionic phospholipids and further that a large pool of membrane-bound factor X is not required to support sustained catalysis.     

The role of tumor microenvironment in prostate cancer bone metastasis

Prostate cancer (PCa) epithelial cells require a number of factors to facilitate their establishment and growth at a distant site of metastasis. Their ability to adapt to their microenvironment, proliferate and recruit an underlying stroma is integral to the survival and growth of the metastasis. PCa predominantly metastasizes to the bone, and bone metastases are the main cause of morbidity. The bone marrow provides a permissive environment for the formation of a metastasis. In some cases, the cells may remain dormant for some time, eventually proliferating in response to an unknown "trigger." The marrow is rich in progenitor cells that differentiate into numerous cell types, producing new blood vessels, supporting fibroblasts, and an underlying extracellular matrix (ECM) that form the reactive stroma. By secreting a number of cytokines, growth factors and proteases they recruit auxiliary cells required to produce a functional stroma. These components are involved in a reciprocal interaction between the stroma and the PCa cells, allowing for the growth and survival of the tumor. Left unchecked, once a PCa tumor has established itself in the bone marrow it will eventually replace the marrow, interrupting bone homeostasis and typically promoting an osteoblastic response in the bone including osteoclastic events. The abundant deposition of new woven bone results in nerve compression, bone pain and an increase in fractures in patients with PCa bone metastases. This review will examine the tumor microenvironment, its role in facilitating tumor dissemination, growth and the resultant pathologies associated with PCa bone metastasis.     

Substituted thiophene-anthranilamides as potent inhibitors of human factor Xa

A series of thiophene-containing non-amidine factor Xa inhibitors is described. Simple methyl-substituted thiophene analogs were relatively weak inhibitors. However, introduction of hydrophilic substituents at C-4 or C-5 of the thiophene afforded inhibitors with low nanomolar potency. Optimization of the thiophene substituent at C-4 afforded subnanomolar inhibitors with improved in vitro anticoagulant activity. Incorporating basic amine substituents on the thiophene increased hydrophilicity and improved anticoagulant activity. The pharmacokinetic profile of one inhibitor was evaluated in dogs, and the X-ray crystal structure of this compound bound to factor Xa provides insight into the observed SAR for binding to factor Xa.