Spatial clumping of food and social dominance affect interference competition among ruddy turnstones

In studying the success of foraging animals, studies of interferencecompetition have put emphasis on effects of competitor density,whereas studies of resource defense have focused on the effectsof the spatial distribution of food within patches. Very fewstudies have looked at both factors simultaneously, that is,determined whether the effects of competitor density on foragingsuccess depend on the spatial distribution of food. We studiedthe behavior and the foraging success of ruddy turnstones (Arenariainterpres) using an experiment in which we varied both the presenceof a competitor and the food distribution. Because turnstonesmay differ strongly in their relative dominance status, we alsoexperimentally varied the foragers' relative dominance status.We found that the presence of a competitor only reduced theforaging success of subordinate birds foraging at the clumpedfood distribution. At this condition, dominant and subordinatebirds differed markedly in their foraging success. Contraryto our expectations, we did not observe more agonistic behaviorat the clumped food distribution. This indicates that the amountof agonistic behavior observed may be a bad indicator of interferenceeffects. These findings have specific implications for modelsof interference competition. Most notably they show that theeffects of competitor density on agonistic behavior and foragingsuccess may well depend on the spatial distribution of foodand the foragers' relative dominance status. Additionally, ourresults suggest that social dominance will not be fully understoodwithout considering long-term processes such as the formationand maintenance of social dominance hierarchies.     

Tight junction proteins expression and modulation in immune cells and multiple sclerosis

The tight junction proteins (TJPs) are major determinants of endothelial cells comprising physiological vascular barriers such as the blood–brain barrier, but little is known about their expression and role in immune cells. In this study we assessed TJP expression in human leukocyte subsets, their induction by immune activation and modulation associated with autoimmune disease states and therapies. A consistent expression of TJP complexes was detected in peripheral blood leukocytes (PBLs), predominantly in B and T lymphocytes and monocytes, whereas the in vitro application of various immune cell activators led to an increase of claudin 1 levels, yet not of claudin 5. Claudins 1 and 5 levels were elevated in PBLs of multiple sclerosis (MS) patients in relapse, relative to patients in remission, healthy controls and patients with other neurological disorders. Interestingly, claudin 1 protein levels were elevated also in PBLs of patients with type 1 diabetes (T1D). Following glucocorticoid treatment of MS patients in relapse, RNA levels of JAM3 and CLDN5 and claudin 5 protein levels in PBLs decreased. Furthermore, a correlation between CLDN5 pre‐treatment levels and clinical response phenotype to interferon‐β therapy was detected. Our findings indicate that higher levels of leukocyte claudins are associated with immune activation and specifically, increased levels of claudin 5 are associated with MS disease activity. This study highlights a potential role of leukocyte TJPs in physiological states, and autoimmunity and suggests they should be further evaluated as biomarkers for aberrant immune activity and response to therapy in immune‐mediated diseases such as MS.     

Systematics and phylogeography of Acanthodactylus schreiberi and its relationships with Acanthodactylus boskianus (Reptilia: Squamata: Lacertidae)

Acanthodactylus is a widespread lacertid genus occurring from the Iberian Peninsula and western North Africa to western India including the Middle East, Cyprus, and the Arabian Peninsula. The genus is in dire need of a taxonomic revision, and the phylogenetic relationships amongst and within its species remain unclear. In particular, the taxonomy and relationship of the allopatric, narrow‐ranged Acanthodactylus schreiberi and its close relative, the widespread Acanthodactylus boskianus asper, are poorly understood. We estimated the phylogenetic and phylogeographical structure of A. schreiberi across its distribution range, and evaluated its relationships to A. b. asper, using mitochondrial and nuclear data. The phylogenetic results indicate that both species are paraphyletic, with A. schreiberi nested within A. b. asper, and the subspecies A. schreiberi syriacus nested within a distinct lineage of A. b. asper. We suggest that the group is in need of a taxonomic revision because the identified lineages and genetic diversity are incongruent with the currently recognized taxonomy. We tentatively conclude that A. schreiberi is restricted to Cyprus and Turkey, reduced to a single form, and that the populations in Lebanon and Israel belong to A. b. asper. © 2014 The Linnean Society of London     

Location and Color Learning in Bumblebees in a Two-Phase Conditioning Experiment

Bees use spatial and visual cues that characterize flowers to make dietary choices. If two such cues always appear together nonambiguously, they provide identical information. In such cases, do bees base dietary choices on one cue and ignore the other, or do they consider both cues? We allowed bumblebees to forage on two patches of artificial flowers that differed in location, color, and reward presence in a two-phase experiment. We switched either the display color, the location, or both the color and the location associated with the rewarding patch between phases. We tested for the effects of the switch on the bees' choices. Immediately following a switch in the location or both the location and the color of the rewarding patch, the bees' performance decreased, as they continued to visit the patch that was previously rewarding. This decrease did not occur when only the color of the rewarding patch was changed or in no-change controls. We suggest that the bees' foraging choices were guided mostly by a location cue when both the location and the color conveyed the same information.     

Phosphoproteomics reveals novel modes of function and inter‐relationships among PIKKs in response to genotoxic stress

The DNA damage response (DDR) is a complex signaling network that relies on cascades of protein phosphorylation, which are initiated by three protein kinases of the family of PI3‐kinase‐related protein kinases (PIKKs): ATM, ATR, and DNA‐PK. ATM is missing or inactivated in the genome instability syndrome, ataxia‐telangiectasia (A‐T). The relative shares of these PIKKs in the response to genotoxic stress and the functional relationships among them are central questions in the genome stability field. We conducted a comprehensive phosphoproteomic analysis in human wild‐type and A‐T cells treated with the double‐strand break‐inducing chemical, neocarzinostatin, and validated the results with the targeted proteomic technique, selected reaction monitoring. We also matched our results with 34 published screens for DDR factors, creating a valuable resource for identifying strong candidates for novel DDR players. We uncovered fine‐tuned dynamics between the PIKKs following genotoxic stress, such as DNA‐PK‐dependent attenuation of ATM. In A‐T cells, partial compensation for ATM absence was provided by ATR and DNA‐PK, with distinct roles and kinetics. The results highlight intricate relationships between these PIKKs in the DDR.     

Stimulus Deprivation Increases Pineal Gsα and Gβ

Denervation and other forms of stimulus deprivation cause an increase in the magnitude of subsequent responses, a phenomenon commonly referred to as denervation supersensitivity. This has been well demonstrated with the cyclic AMP response to norepinephrine in the pineal gland. In the present report, we address the question of whether stimulus deprivation alters alpha and beta subunits of the GTP binding regulatory protein that stimulates adenylyl cyclase activity (Gs). Stimulus deprivation of the pineal gland was produced by denervation (superior cervical ganglionectomy), decentralization of the superior cervical ganglia, or by exposure of the animal to continuous lighting. All increased both the alpha and beta subunits of Gs (Gs alpha and G beta) by up to fourfold, as estimated using semiquantitative western blot technology. These effects were detectable after 1 day of stimulus deprivation and were sustained for 2 weeks. The stimulatory effects of constant light-induced stimulus deprivation were also apparent by measuring cholera toxin-dependent ADP-ribosylation of Gs alpha, which revealed a four-fold increase in the amount of labeled substrate. The results of in vivo studies were confirmed with in vitro studies, which demonstrated a spontaneous increase in both Gs alpha and G beta during 72 h of organ culture. The constant light-induced increases in both Gs alpha and G beta were prevented by continuous administration of isoproterenol (0.3 mg/kg/day), supporting the suggestion that adrenergic stimulation controls the levels of Gs alpha and G beta. These studies indicate that stimulus deprivation increases both Gs alpha and G beta.(ABSTRACT TRUNCATED AT 250 WORDS)     

Dinoflagellate bloom development and collapse in Lake Kinneret: a sediment trap study

Warm monomictic Lake Kinneret, Israel, is characterized by awinter–spring water bloom of the large (~50 µm diameter)dinoflagellate Peridinium gatunense Nygaard. Usually the P.gatunense bloom declines in May–June and a less prominentbloom of smaller dinoflagellates (mostly Peridiniopsis spp.of ~20–30 µm diameter) develops. Water column abundancesand sedimentation losses to those dinoflagellates were followedthroughout 1994 and 1995. The objective was to quantify thevariables that describe population dynamics, that in turn willshed more light on the seasonal patterns of bloom dynamics.Sedimentation losses were measured by means of sediment trapswith and without a preservative (formaldehyde) that were exposedfor 24 h once every 2–3 weeks. Annual sedimentation lossesof Peridinium (hypolimnetic trap catches) were 209 g wet wtm^-2 year^-1 in 1994 and 187 g wet wt m^-2 year^-1 in 1995, whichconstituted 16 and 23% of Peridinium production in those years,respectively. This study revealed that increased death ratespreceded a mass sedimentation flux of Peridinium and causedthe decline of the bloom in Lake Kinneret. Annual sedimentationlosses of Peridiniopsis were 55 g wet wt m^-2 year^-1 in 1994and 34 g wet wt m^-2 year^-1 in 1995. In contrast to live Peridiniumcells, Peridiniopsis cells continued to swim to the lower trapafter the onset of thermal stratification, possibly taking advantageof the higher nutrient concentrations below the thermocline,at a time when the lake is already stratified and the epilimnionis nutrient depleted. This could be an important factor allowingPeridiniopsis spp. to peak after the decline of Peridinium.     

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper

Across the life sciences, processing next generation sequencing data commonly relies upon a computationally expensive process where reads are mapped onto a reference sequence. Prior to such processing, however, there is a vast amount of information that can be ascertained from the reads, potentially obviating the need for processing, or allowing optimized mapping approaches to be deployed. Here, we present a method termed FlexTyper which facilitates a “reverse mapping” approach in which high throughput sequence queries, in the form of k-mer searches, are run against indexed short-read datasets in order to extract useful information. This reverse mapping approach enables the rapid counting of target sequences of interest. We demonstrate FlexTyper’s utility for recovering depth of coverage, and accurate genotyping of SNP sites across the human genome. We show that genotyping unmapped reads can correctly inform a sample’s population, sex, and relatedness in a family setting. Detection of pathogen sequences within RNA-seq data was sensitive and accurate, performing comparably to existing methods, but with increased flexibility. We present two examples of ways in which this flexibility allows the analysis of genome features not well-represented in a linear reference. First, we analyze contigs from African genome sequencing studies, showing how they distribute across families from three distinct populations. Second, we show how gene-marking k-mers for the killer immune receptor locus allow allele detection in a region that is challenging for standard read mapping pipelines. The future adoption of the reverse mapping approach represented by FlexTyper will be enabled by more efficient methods for FM-index generation and biology-informed collections of reference queries. In the long-term, selection of population-specific references or weighting of edges in pan-population reference genome graphs will be possible using the FlexTyper approach. FlexTyper is available at https://github.com/wassermanlab/OpenFlexTyper.     

Suppression of the in vivo malignancy and in vitro cell multiplication of myeloid leukemic cells by hybridization with normal macrophages.

Mouse myeloid leukemic cells that multiplied in vitro and were malignant in vivo were hybridized with non-malignant non-multiplying normal mouse or human macrophages. Both the hybrids with mouse and with human macrophages were non-malignant and non-multiplying. The suppression of malignancy and cell multiplication in these hybrids was associated with the expression of eight other properties expressed in normal macrophages but not in the myeloid leukemic cells. These properties were C3 and Fc rosettes and immune phagocytosis, rosettes and phagocytosis of uncoated erythrocytes, synthesis and secretion of lysozyme and a high frequency of cap formation by concanavalin A (ConA). The hybrids also expressed two properties of the myeloid leukemic cells, a lack of cell attachment to the surface of a Petri dish and staining for myeloperoxidase. The use of specific antibodies has shown that the lysozyme produced by hybrids between human macrophages and mouse myeloid leukemic cells was human lysozyme. The results indicate that the in vivo malignancy and in vitro cell multiplication of myeloid leukemic cells was suppressed in hybrids with normal macrophages, and that his suppression can be dissociated from the normal macrophage property of cell attachment.