Biocomplexity in Pacific herring (Clupea pallasii) of Puget Sound, USA

Small-scale genetic and demographic diversity can stabilize populations on a larger scale. However, subpopulations of pelagic fish species can be difficult to distinguish. Here, we examine demographic diversity in 21 stocks of Pacific herring (Clupea pallasii) in Puget Sound, USA using a multivariate auto-regressive state-space (MARSS) model, and data from both acoustic surveys paired with trawls, and subtidal egg surveys to estimate population growth trends. Herring populations associated with individual spawning beaches are asynchronous, but share a common negative growth rate across the Puget Sound estuary. We found that both survey techniques observe the same underlying demographic processes, and that egg surveys are a more accurate estimator of total spawning biomass. We used states obtained from MARSS analysis to measure portfolio effects in Puget Sound herring, and found that the Puget Sound population as a whole is stabilized by the presence of several separate spawning subpopulations. Available environmental data was not sufficient to explain variations in spawning biomass; however, herring may respond to spawning site conditions that aren’t currently measured

Resurgence of an Apex Marine Predator and the Decline in Prey Body Size

In light of recent recoveries of marine mammal populations worldwide and heightened concern about their impacts on marine food webs and global fisheries, it has become increasingly important to understand the potential impacts of large marine mammal predators on prey populations and their life-history traits. In coastal waters of the northeast Pacific Ocean, marine mammals have increased in abundance over the past 40 to 50 y, including fish-eating killer whales that feed primarily on Chinook salmon. Chinook salmon, a species of high cultural and economic value, have exhibited marked declines in average size and age throughout most of their North American range. This raises the question of whether size-selective predation by marine mammals is generating these trends in life-history characteristics. Here we show that increased predation since the 1970s, but not fishery selection alone, can explain the changes in age and size structure observed for Chinook salmon populations along the west coast of North America. Simulations suggest that the decline in mean size results from the selective removal of large fish and an evolutionary shift toward faster growth and earlier maturation caused by selection. Our conclusion that intensifying predation by fish-eating killer whales contributes to the continuing decline in Chinook salmon body size points to conflicting management and conservation objectives for these two iconic species

Relating multi-sequence longitudinal intensity profiles and clinical covariates in new multiple sclerosis lesions

Structural magnetic resonance imaging (MRI) can be used to detect lesions in the brains of multiple sclerosis (MS) patients. The formation of these lesions is a complex process involving inflammation, tissue damage, and tissue repair, all of which are visible on MRI. Here we characterize the lesion formation process on longitudinal, multi-sequence structural MRI from 34 MS patients and relate the longitudinal changes we observe within lesions to therapeutic interventions. In this article, we first outline a pipeline to extract voxel level, multi-sequence longitudinal profiles from four MRI sequences within lesion tissue. We then propose two models to relate clinical covariates to the longitudinal profiles. The first model is a principal component analysis (PCA) regression model, which collapses the information from all four profiles into a scalar value. We find that the score on the first PC identifies areas of slow, long-term intensity changes within the lesion at a voxel level, as validated by two experienced clinicians, a neuroradiologist and a neurologist. On a quality scale of 1 to 4 (4 being the highest) the neuroradiologist gave the score on the first PC a median rating of 4 (95% CI: [4,4]), and the neurologist gave it a median rating of 3 (95% CI: [3,3]). In the PCA regression model, we find that treatment with disease modifying therapies (p-value < 0.01), steroids (p-value < 0.01), and being closer to the boundary of abnormal signal intensity (p-value < 0.01) are associated with a return of a voxel to intensity values closer to that of normal-appearing tissue. The second model is a function-on-scalar regression, which allows for assessment of the individual time points at which the covariates are associated with the profiles. In the function-on-scalar regression both age and distance to the boundary were found to have a statistically significant association with the profiles

Individual Behavior Drives Ecosystem Function and the Impacts of Harvest

Current approaches for biodiversity conservation and management focus on sustaining high levels of diversity among species to maintain ecosystem function. We show that the diversity among individuals within a single population drives function at the ecosystem scale. Specifically, nutrient supply from individual fish differs from the population average \u3e80% of the time, and accounting for this individual variation nearly doubles estimates of nutrients supplied to the ecosystem. We test how management (i.e., selective harvest regimes) can alter ecosystem function and find that strategies targeting more active individuals reduce nutrient supply to the ecosystem up to 69%, a greater effect than body size–selective or nonselective harvest. Findings show that movement behavior at the scale of the individual can have crucial repercussions for the functioning of an entire ecosystem, proving an important challenge to the species-centric definition of biodiversity if the conservation and management of ecosystem function is a primary goal

Experimental investigation of the elasticity of the human diaphragm

<p>Abstract</p> <p>Background</p> <p>Traumatic diaphragmatic ruptures affect mainly the left side. In an experimental study in human corpses we examined the stretch behaviour of the left and right diaphragmatic halves.</p> <p>Methods</p> <p>In a total of 8 male and 8 female corpses each diaphragmatic half was divided into 4 different segments. Each segments stretch behaviour was investigated. In steps of 2 N the stretch was increased up to 24 N.</p> <p>Results</p> <p>In the female the left diaphragm showed a stronger elasticity compared to the right. Additionally the left diaphragm in females showed a higher elasticity in comparison to the left in males. Traumatic diaphragmatic ruptures affect mostly the central tendineous part or the junction between tendineous and muscular part of the diaphragmatic muscle. Accordingly we found a lower elasticity in these parts compared with the other diaphragmatic segments.</p> <p>Conclusion</p> <p>In summary it can be said that albeit some restrictions we were able to determine the elasticity of different diaphragmatic segments quantitatively and reproduceably with our presented method. Thereby a comparison of results of different diaphragmatic segments as well as of both diaphragmatic halves and of both genders was possible</p

Resource waves: phenological diversity enhances foraging opportunities for mobile consumers

Time can be a limiting constraint for consumers, particularly when resource phenology mediates foraging opportunity. Though a large body of research has explored how resource phenology influences trophic interactions, this work has focused on the topics of trophic mismatch or predator swamping, which typically occur over short periods, at small spatial extents or coarse resolutions. In contrast many consumers integrate across landscape heterogeneity in resource phenology, moving to track ephemeral food sources that propagate across space as resource waves. Here we provide a conceptual framework to advance the study of phenological diversity and resource waves. We define resource waves, review evidence of their importance in recent case studies, and demonstrate their broader ecological significance with a simulation model. We found that consumers ranging from fig wasps (Chalcidoidea) to grizzly bears (Ursus arctos) exploit resource waves, integrating across phenological diversity to make resource aggregates available for much longer than their component parts. In model simulations, phenological diversity was often more important to consumer energy gain than resource abundance per se. Current ecosystem-based management assumes that species abundance mediates the strength of trophic interactions. Our results challenge this assumption and highlight new opportunities for conservation and management. Resource waves are an emergent property of consumer– resource interactions and are broadly significant in ecology and conservationThis is the publisher’s final pdf. The article is copyrighted by the Ecological Society of America and published by John Wiley & Sons, Inc. It can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%291939-9170/Keywords: phenological diversity, resource wave, trophic interaction, model, ecosystem-based management, movement, foraging, time-constraint, landscape heterogeneity, phenological trackin

Genetic inactivation of the Fanconi anemia gene FANCC identified in the hepatocellular carcinoma cell line HuH-7 confers sensitivity towards DNA-interstrand crosslinking agents

Background: Inactivation of the Fanconi anemia (FA) pathway through defects in one of 13 FA genes occurs at low frequency in various solid cancer entities among the general population. As FA pathway inactivation confers a distinct hypersensitivity towards DNA interstrand-crosslinking (ICL)-agents, FA defects represent rational targets for individualized therapeutic strategies. Except for pancreatic cancer, however, the prevalence of FA defects in gastrointestinal (GI) tumors has not yet been systematically explored. Results: A panel of GI cancer cell lines was screened for FA pathway inactivation applying FANCD2 monoubiquitination and FANCD2/RAD51 nuclear focus formation and a newly identified FA pathway-deficient cell line was functionally characterized. The hepatocellular carcinoma (HCC) line HuH-7 was defective in FANCD2 monoubiquitination and FANCD2 nuclear focus formation but proficient in RAD51 focus formation. Gene complementation studies revealed that this proximal FA pathway inactivation was attributable to defective FANCC function in HuH-7 cells. Accordingly, a homozygous inactivating FANCC nonsense mutation (c.553C &gt; T, p.R185X) was identified in HuH-7, resulting in partial transcriptional skipping of exon 6 and leading to the classic cellular FA hypersensitivity phenotype; HuH-7 cells exhibited a strongly reduced proliferation rate and a pronounced G2 cell cycle arrest at distinctly lower concentrations of ICL-agents than a panel of non-isogenic, FA pathway-proficient HCC cell lines. Upon retroviral transduction of HuH-7 cells with FANCC cDNA, FA pathway functions were restored and ICL-hypersensitivity abrogated. Analyses of 18 surgical HCC specimens yielded no further examples for genetic or epigenetic inactivation of FANCC, FANCF, or FANCG in HCC, suggesting a low prevalence of proximal FA pathway inactivation in this tumor type. Conclusions: As the majority of HCC are chemoresistant, assessment of FA pathway function in HCC could identify small subpopulations of patients expected to predictably benefit from individualized treatment protocols using ICL-agents

Proteome wide association studies of LRRK2 variants identify novel causal and druggable proteins for Parkinson\u27s disease

Common and rare variants in the LRRK2 locus are associated with Parkinson\u27s disease (PD) risk, but the downstream effects of these variants on protein levels remain unknown. We performed comprehensive proteogenomic analyses using the largest aptamer-based CSF proteomics study to date (7006 aptamers (6138 unique proteins) in 3107 individuals). The dataset comprised six different and independent cohorts (five using the SomaScan7K (ADNI, DIAN, MAP, Barcelona-1 (Pau), and Fundació ACE (Ruiz)) and the PPMI cohort using the SomaScan5K panel). We identified eleven independent SNPs in the LRRK2 locus associated with the levels of 25 proteins as well as PD risk. Of these, only eleven proteins have been previously associated with PD risk (e.g., GRN or GPNMB). Proteome-wide association study (PWAS) analyses suggested that the levels of ten of those proteins were genetically correlated with PD risk, and seven were validated in the PPMI cohort. Mendelian randomization analyses identified GPNMB, LCT, and CD68 causal for PD and nominate one more (ITGB2). These 25 proteins were enriched for microglia-specific proteins and trafficking pathways (both lysosome and intracellular). This study not only demonstrates that protein phenome-wide association studies (PheWAS) and trans-protein quantitative trail loci (pQTL) analyses are powerful for identifying novel protein interactions in an unbiased manner, but also that LRRK2 is linked with the regulation of PD-associated proteins that are enriched in microglial cells and specific lysosomal pathways