Resolving the genetic basis of invasiveness and predicting invasions

Considerable effort has been invested in determining traits underlying invasiveness. Yet, identifying a set of traits that commonly confers invasiveness in a range of species has proven elusive, and almost nothing is known about genetic loci affecting invasive success. Incorporating genetic model organisms into ecologically relevant studies is one promising avenue to begin dissecting the genetic underpinnings of invasiveness. Molecular biologists are rapidly characterizing genes mediating developmental responses to diverse environmental cues, i.e., genes for plasticity, as well as to environmental factors likely to impose strong selection on invading species, e.g., resistance to herbivores and competitors, coordination of life-history events with seasonal changes, and physiological tolerance of heat, drought, or cold. Here, we give an overview of molecular genetic tools increasingly used to characterize the genetic basis of adaptation and that may be used to begin identifying genetic mechanisms of invasiveness. Given the divergent traits that affect invasiveness, “invasiveness genes” common to many clades are unlikely, but the combination of developmental genetic advances with further evolutionary studies and modeling may provide a framework for identifying genes that account for invasiveness in related species.     

Early Cambrian record of failed durophagy and shell repair in an epibenthic mollusc

Predation is arguably one of the main driving forces of early metazoan evolution, yet the fossil record of predation during the Ediacaran-Early Cambrian transition is relatively poor. Here, we present direct evidence of failed durophagous (shell-breaking) predation and subsequent shell repair in the Early Cambrian (Botoman) epibenthic mollusc Marocella from the Mernmerna Formation and Oraparinna Shale in the Flinders Ranges, South Australia. This record pushes back the first appearance of durophagy on molluscs by approximately 40Myr.     

Main stem and off‐channel habitat use by juvenile Chinook salmon in a sub‐Arctic riverscape

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Quantification of long-term doxorubicin response dynamics in breast cancer cell lines to direct treatment schedules

While acquired chemoresistance is recognized as a key challenge to treating many types of cancer, the dynamics with which drug sensitivity changes after exposure are poorly characterized. Most chemotherapeutic regimens call for repeated dosing at regular intervals, and if drug sensitivity changes on a similar time scale then the treatment interval could be optimized to improve treatment performance. Theoretical work suggests that such optimal schedules exist, but experimental confirmation has been obstructed by the difficulty of deconvolving the simultaneous processes of death, adaptation, and regrowth taking place in cancer cell populations. Here we present a method of optimizing drug schedules in vitro through iterative application of experimentally calibrated models, and demonstrate its ability to characterize dynamic changes in sensitivity to the chemotherapeutic doxorubicin in three breast cancer cell lines subjected to treatment schedules varying in concentration, interval between pulse treatments, and number of sequential pulse treatments. Cell populations are monitored longitudinally through automated imaging for 600–800 hours, and this data is used to calibrate a family of cancer growth models, each consisting of a system of ordinary differential equations, derived from the bi-exponential model which characterizes resistant and sensitive subpopulations. We identify a model incorporating both a period of growth arrest in surviving cells and a delay in the death of chemosensitive cells which outperforms the original bi-exponential growth model in Akaike Information Criterion based model selection, and use the calibrated model to quantify the performance of each drug schedule. We find that the inter-treatment interval is a key variable in determining the performance of sequential dosing schedules and identify an optimal retreatment time for each cell line which extends regrowth time by 40%-239%, demonstrating that the time scale of changes in chemosensitivity following doxorubicin exposure allows optimization of drug scheduling by varying this inter-treatment interval.     

Inhibition of hydrogen peroxide release from activated macrophages by prior ingestion of erythrocytes or haemoglobin

Abstract Production of hydrogen peroxide by mouse peritoneal macrophages activated with Corynebacterium parvum was induced by incubating the cells with opsonised zymosan. H₂O₂ release was reduced by 47% when macrophages were preincubated with opsonised sheep erythrocytes. A significant decrease also occurred when the cells were preincubated with heat-denatured haemoglobin, but not when preincubated with opsonised erythrocyte ghosts, even though the latter were taken up by the macrophages. The ability of macrophages in an infected lesion to destroy microorganisms may therefore be impaired by ingestion of extravasated erythrocytes.     

Combining Physicochemical and Evolutionary Information for Protein Contact Prediction

We introduce a novel contact prediction method that achieves high prediction accuracy by combining evolutionary and physicochemical information about native contacts. We obtain evolutionary information from multiple-sequence alignments and physicochemical information from predicted ab initio protein structures. These structures represent low-energy states in an energy landscape and thus capture the physicochemical information encoded in the energy function. Such low-energy structures are likely to contain native contacts, even if their overall fold is not native. To differentiate native from non-native contacts in those structures, we develop a graph-based representation of the structural context of contacts. We then use this representation to train an support vector machine classifier to identify most likely native contacts in otherwise non-native structures. The resulting contact predictions are highly accurate. As a result of combining two sources of information—evolutionary and physicochemical—we maintain prediction accuracy even when only few sequence homologs are present. We show that the predicted contacts help to improve ab initio structure prediction. A web service is available at http://compbio.robotics.tu-berlin.de/epc-map/.     

RPM-1 Uses Both Ubiquitin Ligase and Phosphatase-Based Mechanisms to Regulate DLK-1 during Neuronal Development

The Pam/Highwire/RPM-1 (PHR) proteins are key regulators of neuronal development that function in axon extension and guidance, termination of axon outgrowth, and synapse formation. Outside of development, the PHR proteins also regulate axon regeneration and Wallerian degeneration. The PHR proteins function in part by acting as ubiquitin ligases that degrade the Dual Leucine zipper-bearing Kinase (DLK). Here, we show that the Caenorhabditis elegans PHR protein, Regulator of Presynaptic Morphology 1 (RPM-1), also utilizes a phosphatase-based mechanism to regulate DLK-1. Using mass spectrometry, we identified Protein Phosphatase Magnesium/Manganese dependent 2 (PPM-2) as a novel RPM-1 binding protein. Genetic, transgenic, and biochemical studies indicated that PPM-2 functions coordinately with the ubiquitin ligase activity of RPM-1 and the F-box protein FSN-1 to negatively regulate DLK-1. PPM-2 acts on S874 of DLK-1, a residue implicated in regulation of DLK-1 binding to a short, inhibitory isoform of DLK-1 (DLK-1S). Our study demonstrates that PHR proteins function through both phosphatase and ubiquitin ligase mechanisms to inhibit DLK. Thus, PHR proteins are potentially more accurate and sensitive regulators of DLK than originally thought. Our results also highlight an important and expanding role for the PP2C phosphatase family in neuronal development.     

Allele Copy Number and Underlying Pathology Are Associated with Subclinical Severity in Equine Type 1 Polysaccharide Storage Myopathy (PSSM1)

Equine type 1 polysaccharide storage myopathy (PSSM1), a common glycogenosis associated with an R309H founder mutation in the glycogen synthase 1 gene (GYS1), shares pathological features with several human myopathies. In common with related human disorders, the pathogenesis remains unclear in particular, the marked phenotypic variability between affected animals. Given that affected animals accumulate glycogen and alpha-crystalline polysaccharide within their muscles, it is possible that physical disruption associated with the presence of this material could exacerbate the phenotype. The aim of this study was to compare the histopathological changes in horses with PSSM1, and specifically, to investigate the hypothesis that the severity of underlying pathology, (e.g. vacuolation and inclusion formation) would (1) be higher in homozygotes than heterozygotes and (2) correlate with clinical severity. Resting and post-exercise plasma creatine kinase (CK) and aspartate aminotransferase (AST) enzyme activity measurements and muscle pathology were assessed in matched cohorts of PSSM1 homozygotes, heterozygotes or control horses. Median (interquartile range (IR)) resting CK activities were 364 (332–764) U/L for homozygotes, 301 (222–377) U/L for heterozygotes and 260 (216–320) U/L for controls, and mean (+/− SD) AST activity for homozygotes were 502 (+/116) U/L, for heterozygotes, 357 (+/−92) U/L and for controls, 311 (+/−64) U/L and were significantly different between groups (P = 0.04 and P = 0.01 respectively). Resting plasma AST activity was significantly associated with the severity of subsarcolemmal vacuolation (rho = 0.816; P = 0.01) and cytoplasmic inclusions (rho = 0.766; P = 0.01). There were fewer type 2× and more type 2a muscle fibres in PSSM1-affected horses. Our results indicate that PSSM1 has incomplete dominance. Furthermore, the association between plasma muscle enzyme activity and severity of underlying pathology suggests that physical disruption of myofibres may contribute to the myopathic phenotype. This work provides insight into PSSM1 pathogenesis and has implications for related human glycogenoses.     

A SNP test to identify Africanized honeybees via proportion of ‘African’ ancestry

The honeybee, Apis mellifera, is the world's most important pollinator and is ubiquitous in most agricultural ecosystems. Four major evolutionary lineages and at least 24 subspecies are recognized. Commercial populations are mainly derived from subspecies originating in Europe (75–95%). The Africanized honeybee is a New World hybrid of A. m. scutellata from Africa and European subspecies, with the African component making up 50–90% of the genome. Africanized honeybees are considered undesirable for bee‐keeping in most countries, due to their extreme defensiveness and poor honey production. The international trade in honeybees is restricted, due in part to bans on the importation of queens (and semen) from countries where Africanized honeybees are extant. Some desirable strains from the United States of America that have been bred for traits such as resistance to the mite Varroa destructor are unfortunately excluded from export to countries such as Australia due to the presence of Africanized honeybees in the USA. This study shows that a panel of 95 single nucleotide polymorphisms, chosen to differentiate between the African, Eastern European and Western European lineages, can detect Africanized honeybees with a high degree of confidence via ancestry assignment. Our panel therefore offers a valuable tool to mitigate the risks of spreading Africanized honeybees across the globe and may enable the resumption of queen and bee semen imports from the Americas.