A comparative evaluation of presence-only methods for modelling species distribution

In spite of increasing application of presence-only models in ecology and conservation and the growing number of such models, little is known about the relative performance of different modelling methods, and some of the leading models (e.g. GARP and ENFA) have never been compared with one another. Here we compare the performance of six presence-only models that have been selected to represent an increasing level of model complexity [BIOCLIM, HABITAT, Mahalanobis distance (MD), DOMAIN, ENFA, and GARP] using data on the distribution of 42 species of land snails, nesting birds, and insectivorous bats in Israel. The models were calibrated using data from museum collections and observation databases, and their predictions were evaluated using Cohen's Kappa based on field data collected in a standardized sampling design covering most parts of Israel. Predictive accuracy varied between modelling methods with GARP and MD showing the highest accuracy, BIOCLIM and ENFA showing the lowest accuracy, and HABITAT and DOMAIN showing intermediate accuracy levels. Yet, differences between the various models were relatively small except for GARP and MD that were significantly more accurate than BIOCLIM and ENFA. In spite of large differences among species in prevalence and niche width, neither prevalence nor niche width interacted with the modelling method in determining predictive accuracy. However, species with relatively narrow niches were modelled more accurately than species with wider niches. Differences among species in predictive accuracy were highly consistent over all modelling methods, indicating the need for a better understanding of the ecological and geographical factors that influence the performance of species distribution models.     

Functional coordination of alternative splicing in the mammalian central nervous system

Background

Alternative splicing (AS) functions to expand proteomic complexity and plays numerous important roles in gene regulation. However, the extent to which AS coordinates functions in a cell and tissue type specific manner is not known. Moreover, the sequence code that underlies cell and tissue type specific regulation of AS is poorly understood.

Results

Using quantitative AS microarray profiling, we have identified a large number of widely expressed mouse genes that contain single or coordinated pairs of alternative exons that are spliced in a tissue regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS tissues, relative to the other profiled tissues.

Conclusion

Our findings provide new evidence that specific cellular processes in the mammalian CNS are coordinated at the level of AS, and that a complex splicing code underlies CNS specific AS regulation. This code appears to comprise many new motifs, some of which are located in the constitutive exons neighboring regulated alternative exons. These data provide a basis for understanding the molecular mechanisms by which the tissue specific functions of widely expressed genes are coordinated at the level of AS.     

Group Selection and Contribution of Minority Variants during Virus Adaptation Determines Virus Fitness and Phenotype

Understanding how a pathogen colonizes and adapts to a new host environment is a primary aim in studying emerging infectious diseases. Adaptive mutations arise among the thousands of variants generated during RNA virus infection, and identifying these variants will shed light onto how changes in tropism and species jumps can occur. Here, we adapted Coxsackie virus B3 to a highly permissive and less permissive environment. Using deep sequencing and bioinformatics, we identified a multi-step adaptive process to adaptation involving residues in the receptor footprints that correlated with receptor availability and with increase in virus fitness in an environment-specific manner. We show that adaptation occurs by selection of a dominant mutation followed by group selection of minority variants that together, confer the fitness increase observed in the population, rather than selection of a single dominant genotype.     

A common mode of attraction of larvae and adults of insect predators to the sex pheromone of their prey (Hemiptera: Matsucoccidae)

The attraction of several adult predators, genera Elatophilus, Hemerobius and Sympherobius, to the sex pheromones of pine bast scales, Matsucoccus Cockerell, has already been demonstrated. Here, the hypothesis that the larvae of these predators are similarly attracted to the host prey sex pheromone is tested. The response of predators was tested in field trials using pine tree arenas baited with the sex pheromones of M. josephi Bodenheimer & Harpaz, M. feytaudi Ducasse and M. matsumurae Kuwana. Experiments were conducted in Israel in stands of Pinus halepensis infested by M. josephi and in Portugal in stands of P. pinaster infested by M. feytaudi, respectively. The selectivity of larvae for the three sex pheromones was tested in Petri dish arenas in the laboratory. In the field, the larval stages exhibited similar modes of attraction to those of the conspecific adults: Elatophilus hebraicus Pericart in Aleppo pine forest, E. crassicornis Reuter and Hemerobius stigma Stephens in the maritime pine forests. Laboratory choice tests confirmed the kairomonal selectivity of larvae. Both forest and laboratory tests demonstrated the response of a coccinellid of the genus Rhyzobius to the sex pheromones of M. feytaudi and M. matsumurae. A unique chemical communication system among several taxa of predators of Matsucoccus spp. was highlighted that may be attributed to their coevolution on a geological time scale.     

The adenosine system selectively inhibits TLR-mediated TNF-alpha production in the human newborn

Human newborns are susceptible to microbial infection and mount poor vaccine responses, yet the mechanisms underlying their susceptibility are incompletely defined. We have previously reported that despite normal basal expression of TLRs and associated signaling intermediates, human neonatal cord blood monocytes demonstrate severe impairment in TNF-alpha production in response to triacylated (TLR 2/1) and diacylated (TLR 2/6) bacterial lipopeptides (BLPs). We now demonstrate that in marked contrast, BLP-induced synthesis of IL-6, a cytokine with anti-inflammatory and Th2-polarizing properties, is actually greater in neonates than adults. Remarkably, newborn blood plasma confers substantially reduced BLP-induced monocyte synthesis of TNF-alpha, while preserving IL-6 synthesis, reflecting the presence in neonatal blood plasma of a soluble, low molecular mass inhibitory factor (<10 kDa) that we identify as adenosine, an endogenous purine metabolite with immunomodulatory properties. The neonatal adenosine system also inhibits TNF-alpha production in response to whole microbial particles known to express TLR2 agonist activity, including Listeria monocytogenes, Escherichia coli (that express BLPs), and zymosan particles. Selective inhibition of neonatal TNF-alpha production is due to the distinct neonatal adenosine system, including relatively high adenosine concentrations in neonatal blood plasma and heightened sensitivity of neonatal mononuclear cells to adenosine A3 receptor-mediated accumulation of cAMP, a second messenger that inhibits TLR-mediated TNF-alpha synthesis but preserves IL-6 production. We conclude that the distinct adenosine system of newborns polarizes TLR-mediated cytokine production during the perinatal period and may thereby modulate their innate and adaptive immune responses.     

TCR zeta down-regulation under chronic inflammation is mediated by myeloid suppressor cells differentially distributed between various lymphatic organs

T cell AgR zeta chain down-regulation associated with T cell dysfunction has been described in cancer, infectious, and autoimmune diseases. We have previously shown that chronic inflammation is mandatory for the induction of an immunosuppressive environment leading to this phenomenon. To identify the key immunosuppressive components, we used an in vivo mouse model exhibiting chronic inflammation-induced immunosuppression. Herein, we demonstrate that: 1) under chronic inflammation secondary lymphatic organs display various immunological milieus; zeta chain down-regulation and T cell dysfunction are induced in the spleen, peripheral blood, and bone marrow, but not in lymph nodes, correlating with elevated levels of Gr1(+)Mac-1(+) myeloid suppressor cells (MSC); 2) MSC are responsible for the induction of such an immunosuppression under both normal and inflammatory conditions; and 3) normal T cells administered into mice exhibiting an immunosuppressive environment down-regulate their zeta expression. Such an environment is anticipated to limit the success of immunotherapeutic strategies based on vaccination and T cell transfer, which are currently under investigation for immunotherapy of cancer.     

Comparative morphology and cytology of the male sperm-transmission organs in viviparous species of clinid fishes (Clinidae: Teleostei, Perciformes)

This work comprises the first comparative study of the morphology and cytology of the sperm transmission organs in males of 14 species of viviparous clinid fishes (Clinidae, Blennioidei, Teleostei). The form and dimensions of these organs differ among the various species studied. The organs are composed of intra-abdominal ampullae, into which the sperm ducts and urinary bladder anchor, and an external protruding intromittent papilla used for insemination. The form of the ampullae differs among the various species, from pear-shaped to horseshoe-shaped. It increases in dimensions with increasing length of the male. In all the species this organ is covered by a connective-tissue tunic that encompasses both circular and longitudinal striated muscle bundles. The lumina of the ampullae harbor the epididymis, a strongly convoluted and plicated duct, which becomes filled with spermatozeugmata during reproduction. From here, the epididymis continues into the protruding intromittent papillae, where its folds gradually straighten at the apical part of the intromittent organ. The form and dimensions of this copulatory organ also differ in the various species. Papillae bearing taste buds are found on the apical parts of the intromittent organ, and it is probable that these, together with the difference in forms of the organ, help to prevent interspecific copulation.     

Flexible task allocation and the organization of work in ants

Flexibility in task performance is essential for a robust system of division of labour. We investigated what factors determine which social insect workers respond to colony-level changes in task demand. We used radio-frequency identification technology to compare the roles of corpulence, age, spatial location and previous activity (intra-nest/extra-nest) in determining whether worker ants (Temnothorax albipennis) respond to an increase in demand for foraging or brood care. The less corpulent ants took on the extra foraging, irrespective of their age, previous activity or location in the nest, supporting a physiological threshold model. We found no relationship between ants that tended the extra brood and corpulence, age, spatial location or previous activity, but ants that transported the extra brood to the main brood pile were less corpulent and had high previous intra-nest activity. This supports spatial task-encounter and physiological threshold models for brood transport. Our data suggest a flexible task-allocation system allowing the colony to respond rapidly to changing needs, using a simple task-encounter system for generalized tasks, combined with physiologically based response thresholds for more specialized tasks. This could provide a social insect colony with a robust division of labour, flexibly allocating the workforce in response to current needs.     

Identification of the Zn2+ Binding Site and Mode of Operation of a Mammalian Zn2+ Transporter

Vesicular zinc transporters (ZnTs) play a critical role in regulating Zn²⁺ homeostasis in various cellular compartments and are linked to major diseases ranging from Alzheimer disease to diabetes. Despite their importance, the intracellular localization of ZnTs poses a major challenge for establishing the mechanisms by which they function and the identity of their ion binding sites. Here, we combine fluorescence-based functional analysis and structural modeling aimed at elucidating these functional aspects. Expression of ZnT5 was followed by both accelerated removal of Zn²⁺ from the cytoplasm and its increased vesicular sequestration. Further, activity of this zinc transport was coupled to alkalinization of the trans-Golgi network. Finally, structural modeling of ZnT5, based on the x-ray structure of the bacterial metal transporter YiiP, identified four residues that can potentially form the zinc binding site on ZnT5. Consistent with this model, replacement of these residues, Asp⁵⁹⁹ and His⁴⁵¹, with alanine was sufficient to block Zn²⁺ transport. These findings indicate, for the first time, that Zn²⁺ transport mediated by a mammalian ZnT is catalyzed by H⁺/Zn²⁺ exchange and identify the zinc binding site of ZnT proteins essential for zinc transport.