Differences in spatial predictions among species distribution modeling methods vary with species traits and environmental predictors

Prediction maps produced by species distribution models (SDMs) influence decision‐making in resource management or designation of land in conservation planning. Many studies have compared the prediction accuracy of different SDM modeling methods, but few have quantified the similarity among prediction maps. There has also been little systematic exploration of how the relative importance of different predictor variables varies among model types and affects map similarity. Our objective was to expand the evaluation of SDM performance for 45 plant species in southern California to better understand how map predictions vary among model types, and to explain what factors may affect spatial correspondence, including the selection and relative importance of different environmental variables. Four types of models were tested. Correlation among maps was highest between generalized linear models (GLMs) and generalized additive models (GAMs) and lowest between classification trees and GAMs or GLMs. Correlation between Random Forests (RFs) and GAMs was the same as between RFs and classification trees. Spatial correspondence among maps was influenced the most by model prediction accuracy (AUC) and species prevalence; map correspondence was highest when accuracy was high and prevalence was intermediate (average prevalence for all species was 0.124). Species functional type and the selection of climate variables also influenced map correspondence. For most (but not all) species, climate variables were more important than terrain or soil in predicting their distributions. Environmental variable selection varied according to modeling method, but the largest differences were between RFs and GLMs or GAMs. Although prediction accuracy was equal for GLMs, GAMs, and RFs, the differences in spatial predictions suggest that it may be important to evaluate the results of more than one model to estimate the range of spatial uncertainty before making planning decisions based on map outputs. This may be particularly important if models have low accuracy or if species prevalence is not intermediate.     

Does begging call convergence increase feeding rates to nestling tree swallows Tachycineta bicolor?

Some studies suggest that offspring might coordinate their begging displays to send a more effective brood signal, which in turn, could increase parental feeding rates. In tree swallows Tachycineta bicolor , when nestlings call together, their calls are more similar in structure than when they call alone. Here, we tested the hypothesis that call convergence enhances the overall brood signal, thus increasing parental provisioning rates. We played back similar and dissimilar calls (as measured by cross-correlation) to parents during a one-h playback period, and filmed the response of parents and nestlings. Contrary to our hypothesis, parental feeding rates did not differ in relation to call similarity. Based on these results, call similarity does not appear to function as a coordinated brood signal in tree swallows.     

Origin and seasonality of subfossil caprine dung from the discovery site of the Iceman (Eastern Alps)

The discovery of a Neolithic glacier mummy (dated to 3300–3100 cal b.c.) on a remote site of an Alpine pass at 3,200 m in the Ötztal Mountains is still puzzling. In the initial phase of the Iceman research, four hypotheses were suggested to explain the find in its entirety. The speculations vary from a hunter or warrior to a shaman, a miner or a shepherd. None of these proposals is accepted or corroborated by archaeological findings, but on the basis of palynological investigations conducted in the vicinity of the discovery site the assumption that the Iceman was involved in an early form of transhumance has now gained general acceptance. Concerning this assumption we present in this paper a recent study conducted on about a hundred caprine (sheep/goat or ibex/chamois) dung pellets recovered from the find spot of the Iceman and which were dated from 5400 to 2000 cal b.c. The approach was to determine through plant remains from these faeces whether they were droppings derived from animals grazing in anthropogenic habitats at low altitudes or in alpine grasslands. The former case would suggest they were livestock, the latter game. The results showed that all droppings derive from animals grazing at high altitudes.     

Calcium homeostasis is required for contact-dependent helical and sinusoidal tip growth in Candida albicans hyphae

Hyphae of the dimorphic fungus, Candida albicans , exhibit directional tip responses when grown in contact with surfaces. On hard surfaces or in liquid media, the trajectory of hyphal growth is typically linear, with tip re-orientation events limited to encounters with topographical features (thigmotropism). In contrast, when grown on semisolid surfaces, the tips of C. albicans hyphae grow in an oscillatory manner to form regular two-dimensional sinusoidal curves and three-dimensional helices. We show that, like thigmotropism, initiation of directional tip oscillation in C. albicans hyphae is severely attenuated when Ca²⁺ homeostasis is perturbed. Chelation of extracellular Ca²⁺ or deletion of the Ca²⁺ transporters that modulate cytosolic [Ca²⁺] (Mid1, Cch1 or Pmr1) did not affect hyphal length but curve formation was severely reduced in mid1 Δ and cch1 Δ and abolished in pmr1 Δ. Sinusoidal hypha morphology was altered in the mid1 Δ, chs3 Δ and heterozygous pmr1 Δ/ PMR1 strains. Treatments that affect cell wall integrity, changes in surface mannosylation or the provision of additional carbon sources had significant but less pronounced effects on oscillatory growth. The induction of two- and three-dimensional sinusoidal growth in wild-type C. albicans hyphae is therefore the consequence of mechanisms that involve Ca²⁺ influx and signalling rather than gross changes in the cell wall architecture.     

The genome and variation of Bacillus anthracis

The Bacillus anthracis genome reflects its close genetic ties to Bacillus cereus and Bacillus thuringiensis but has been shaped by its own unique biology and evolutionary forces. The genome is comprised of a chromosome and two large virulence plasmids, pXO1 and pXO2. The chromosome is mostly co-linear among B. anthracis strains and even with the closest near neighbor strains. An exception to this pattern has been observed in a large inversion in an attenuated strain suggesting that chromosome co-linearity is important to the natural biology of this pathogen. In general, there are few polymorphic nucleotides among B. anthracis strains reflecting the short evolutionary time since its derivation from a B. cereus-like ancestor. The exceptions to this lack of diversity are the variable number tandem repeat (VNTR) loci that exist in genic and non genic regions of the chromosome and both plasmids. Their variation is associated with high mutability that is driven by rapid insertion and deletion of the repeats within an array. A notable example is found in the vrrC locus which is homologous to known DNA translocase genes from other bacteria.     

Bio-sintering processes in hexactinellid sponges: Fusion of bio-silica in giant basal spicules from Monorhaphis chuni

The two sponge classes, Hexactinellida and Demospongiae, comprise a skeleton that is composed of siliceous skeletal elements (spicules). Spicule growth proceeds by appositional layering of lamellae that consist of silica nanoparticles, which are synthesized via the sponge-specific enzyme silicatein. While in demosponges during maturation the lamellae consolidate to a solid rod, the lamellar organization of hexactinellid spicules largely persists. However, the innermost lamellae, near the spicule core, can also fuse to a solid axial cylinder. Similar to the fusion of siliceous nanoparticles and lamella, in several hexactinellid species individual spicules unify during sintering-like processes. Here, we study the different stages of a process that we termed bio-sintering, within the giant basal spicule (GBS) of Monorhaphis chuni. During this study, a major GBS protein component (27 kDa) was isolated and analyzed by MALDI-TOF-MS. The sequences were used to isolate and clone the encoding cDNA via degenerate primer PCR. Bioinformatic analyses revealed a significant sequence homology to silicatein. In addition, the native GBS protein was able to mediate bio-silica synthesis in vitro. We conclude that the syntheses of bio-silica in M. chuni, and the subsequent fusion of nanoparticles to lamellae, and finally to spicules, are enzymatically-driven by a silicatein-like protein. In addition, evidence is now presented that in hexactinellids those fusions involve sintering-like processes.     

Induction of Therapeutic Antibodies by Vaccination against External Loops of Tumor-Associated Viral Latent Membrane Protein

Some human herpesviruses (HHV) are etiological contributors to a wide range of malignant diseases. These HHV express latent membrane proteins (LMPs), which are type III membrane proteins consistently exposed at the cell surface in these malignancies. These LMPs have relatively large cytoplasmic domains but only short extracellular loops connecting transmembrane segments that are accessible at the surface of infected cells, but they do not elicit antibodies in the course of natural infection and tumorigenesis. We report here that conformational peptides mimicking two adjacent loops of the Epstein-Barr virus (EBV) LMP1 (2LS peptides) induce high-affinity antibodies with remarkable antitumor activities in mice. In active immunization experiments, LMP1-targeting 2LS vaccine conferred tumor protection in BALB/c mice. Moreover, this tumor protection is dependent upon a humoral anti-2LS immune response as demonstrated in DO11.10 (TCR-OVA) mice challenged with LMP1-expressing tumor and in SCID mice xenografted with human EBV-positive lymphoma cells. These data provide a proof of concept for 2LS immunization against short external loops of viral LMPs. This approach might possibly be extended to other infectious agents expressing type III membrane proteins.After the primary infection, some viruses, especially human herpesviruses (HHV) such as Epstein-Barr virus (EBV), cytomegalovirus, Kaposi''s sarcoma herpesvirus (HHV8), varicella-zoster virus, and herpes simplex virus, persist lifelong in all infected individuals, most often in an asymptomatic latent form. However, in the long term, some HHV can be involved in the emergence of malignant diseases in a small subset of infected individuals. EBV-associated lymphomas and carcinomas (22, 37), HHV8-associated Kaposi''s sarcomas (30), and human cytomegalovirus-associated glioblastomas (24) are examples of beta- and gammaherpesvirus-related human malignancies. All these malignancy-associated viruses encode type III membrane proteins which are expressed during the latent state of infection and thus can be called latent membrane proteins (LMPs). These viral LMPs (vLMPs), or “multipass” membrane proteins, appeared to be necessary for virus-driven host cell survival and/or transforming activity (1, 3, 28, 31). They are regarded by some authors as evolutionary mimics of cellular chemokine/cytokine receptors, and, like cellular receptors, they recruit numerous cytoplasmic adaptors. The several transmembrane domains of these vLMPs seem to mimic activated cellular chemokine/cytokine receptor structures and to function with versatile signaling devices, reprogramming cellular signaling networks to modulate cellular function after infection. They contribute prominently to virus survival in latently infected individuals and to virus-related human pathologies, including cancer (8, 14, 19, 34, 36). Despite expressing vLMP antigens at their membrane surface, these latently infected cells are very poor in initiating effective immune responses in infected individuals, thus facilitating viral persistence in humans (2, 17, 38). One reason for this poor immunogenicity may be the constitutive cell signaling property reported for these vLMPs in latently infected cells (3, 16, 35, 38). Consequently, unnecessary overexpression and large extracellular domains for ligand binding may facilitate vLMP immune escape (3, 35, 38). Thus, a major therapeutic approach involved the discovery of naturally active compounds or pharmacological agents that specifically block viral receptor functioning (12, 35). Compounds emerged from high-throughput screening of synthetic chemical libraries, but we still lack specific agents for vLMPs, as they cross-react with cellular chemokine/cytokine receptors and cellular signaling pathways (35). Functional antibodies (Abs) recognizing membrane proteins for anticancer therapies have recently emerged, but there are very few of these and they resulted mostly from serendipity rather than from a systematic design strategy (5). To date, LMPs as a target for a virus-specific immunotherapeutic Ab strategy have not been explored extensively. Some studies have been conducted with purified full-length LMPs from EBV, a gammaherpesvirus, but these studies failed to produce or detect Abs recognizing LMP extracellular domains (10, 20, 29). One reason for this poor immunogenicity could be the too-short extracellular structure of these LMPs, which could explain the failure of latently infected individuals to produce cytolytic Abs (21). To test this hypothesis, we used as an LMP model the EBV-encoded oncoprotein LMP1 which mimics a constitutively active tumor necrosis factor receptor-like molecule and is expressed during EBV latent infection (16). This LMP1 expression was observed in most EBV-carrying malignancies (16, 22, 37), therefore causing EBV to be classified as a class I human carcinogenic agent (11). Here, we report an original humoral approach, because Abs have unlimited diversity and are often exquisitely specific and readily produced. Indeed, to overcome the too-short extracellular size of LMP, we hypothesized that synthesis of a peptide mimicking several extracellular loops of LMP would be a successful general strategy for the development of Abs with the high-pressure liquid chromatography affinity necessary for neutralizing and cytolytic effectiveness, as described previously (4, 33a). We argue here that this new process (D. Tranchand Bunel, 28 January 2003, French patent application FR0300943; D. Tranchand Bunel, 28 July 2005, U.S. Patent Office, US069140) was rewarding, as by vaccinating mice with peptides that covered two adjacent extracellular loops of LMP1 (2LS peptides), we obtained the production of neutralizing and cytolytic high-affinity Abs. Moreover, these Abs induced by 2LS peptide vaccination appeared to confer protection of mice against the development of tumors expressing LMP1.     

The Pentapeptide Repeat Proteins MfpAMt and QnrB4 Exhibit Opposite Effects on DNA Gyrase Catalytic Reactions and on the Ternary Gyrase-DNA-Quinolone Complex

MfpA_Mt and QnrB4 are two newly characterized pentapeptide repeat proteins (PRPs) that interact with DNA gyrase. The mfpA_Mt gene is chromosome borne in Mycobacterium tuberculosis, while qnrB4 is plasmid borne in enterobacteria. We expressed and purified the two PRPs and compared their effects on DNA gyrase, taking into account host specificity, i.e., the effect of MfpA_Mt on M. tuberculosis gyrase and the effect of QnrB4 on Escherichia coli gyrase. Whereas QnrB4 inhibited E. coli gyrase activity only at concentrations higher than 30 μM, MfpA_Mt inhibited all catalytic reactions of the M. tuberculosis gyrase described for this enzyme (supercoiling, cleavage, relaxation, and decatenation) with a 50% inhibitory concentration of 2 μM. We showed that the D87 residue in GyrA has a major role in the MfpA_Mt-gyrase interaction, as D87H and D87G substitutions abolished MfpA_Mt inhibition of M. tuberculosis gyrase catalytic reactions, while A83S modification did not. Since MfpA_Mt and QnrB4 have been involved in resistance to fluoroquinolones, we measured the inhibition of the quinolone effect in the presence of each PRP. QnrB4 reversed quinolone inhibition of E. coli gyrase at 0.1 μM as described for other Qnr proteins, but MfpA_Mt did not modify M. tuberculosis gyrase inhibition by fluoroquinolones. Crossover experiments showed that MfpA_Mt also inhibited E. coli gyrase function, while QnrB4 did not reverse quinolone inhibition of M. tuberculosis gyrase. In conclusion, our in vitro experiments showed that MfpA_Mt and QnrB4 exhibit opposite effects on DNA gyrase and that these effects are protein and species specific.The pentapeptide repeat protein (PRP) family includes more than 500 proteins in the prokaryotic and eukaryotic kingdoms (45). PRPs are characterized by the repetition of the pentapeptide repeat motif [S,T,A,V][D,N][L,F][S,T,R][G] (6), which results in a right-handed β-helical structure (8, 17). The functions of the majority of the members of this large and heterogeneous family remain unknown, but three PRPs, McbG (from Escherichia coli), MfpA_Mt (from Mycobacterium tuberculosis), and Qnr (from Klebsiella pneumoniae and other enterobacteria) were reported to interact with DNA gyrase, at least with the E. coli enzyme (17, 33, 35, 44). McbG was shown to protect E. coli DNA gyrase from the toxic action of microcin B17 (33). Qnr and MfpA_Mt were involved in resistance to fluoroquinolones, which are synthetic antibacterial agents prescribed worldwide for the treatment of various infectious diseases, including tuberculosis (7).DNA gyrase is an essential ATP-dependent enzyme that transiently cleaves a segment of double-stranded DNA, passes another piece of DNA through the break, and reseals it (12). DNA gyrase is unique in catalyzing the negative supercoiling of DNA in order to facilitate the progression of RNA polymerase. Most eubacteria, such as E. coli, have two type II DNA topoisomerases, i.e., DNA gyrase and topoisomerase IV, but a few, such as M. tuberculosis, harbor only DNA gyrase (11).Quinolones target type II topoisomerases, and their activity is measured by the inhibition of supercoiling by gyrase or decatenation by topoisomerase IV and stabilization of complexes composed of topoisomerase covalently linked to cleaved DNA (16). The DNA gyrase active enzyme is a GyrA₂GyrB₂ heterotetramer. The quinolone-gyrase interaction site in gyrase is thought to be located at the so-called quinolone resistance-determining regions (QRDR) in the A subunit (amino acids 57 to 196 in GyrA) and the B subunit (amino acids 426 to 466 in GyrB), which contain the majority of mutations conferring quinolone resistance (19). The GyrB QRDR is thought to interact with the GyrA QRDR to form a drug-binding pocket (18). Resistance to quinolones is usually due to chromosomal mutations either in the structural genes encoding type II topoisomerases (QRDR) (19, 22) or in regulatory genes producing decreased cell wall permeability or enhancement of efflux pumps (36). The recent emergence of plasmid-borne resistance genes, such as qnr (9, 13, 31, 38, 46), aac(6′)-Ib-cr (32, 39) and qepA (34, 47), renewed interest in quinolone resistance, and especially interest in the new Qnr-based mechanism. Three qnr determinants have been identified so far: qnrA (variants A1 to A6), qnrB (variants B1 to B19), and qnrS (variants S1 and S2) (15, 21, 23, 27). Qnr confers a new mechanism of quinolone resistance by mediating DNA gyrase protection (42): in vitro, QnrA1 and QnrB1 protect E. coli DNA gyrase and topoisomerase IV from the inhibitory effect of fluoroquinolones in a concentration-dependent manner (23, 42-44). Although Qnr was shown to bind GyrA and GyrB and compete with DNA binding, the consequences of Qnr binding for enzyme performance are not yet clear.mfpA, a chromosomal gene that encodes a 192-amino-acid PRP, is an intrinsic quinolone resistance determinant of Mycobacterium smegmatis (29). A similar gene, mfpA_Mt, was found in the M. tuberculosis genome, and MfpA_Mt shows 67% identity with MfpA. Recent crystallography analysis of MfpA_Mt showed that its atomic structure displays size, shape, and electrostatic similarity to B-form DNA, and MfpA_Mt has been suggested to interact with DNA gyrase via DNA mimicry (17). The effect of MfpA_Mt was studied by testing E. coli DNA gyrase, and MfpA_Mt showed catalytic inhibition (17, 37), but whether it protects gyrase from quinolones was not assessed. Because the structure and functions of the M. tuberculosis gyrase, as well as its interaction with quinolones, differ from those of the E. coli gyrase (2, 3, 20, 26, 28), we suspected that the PRP-topoisomerase interaction exhibits species specificity, i.e., depends on the proteins issued from the same host.Our objective was to compare the effects of MfpA_Mt and Qnr on their respective targets, i.e., the effect of MfpA_Mt on the M. tuberculosis gyrase and the effect of Qnr on the E. coli gyrase, by assessing (i) the catalytic reactions of the enzyme and (ii) the interaction with the DNA gyrase-DNA-fluoroquinolone ternary complex. Among the Qnr proteins, we selected the QnrB4 protein, which is a frequent variant of QnrB and has not yet been purified and studied. We cloned, expressed, and purified the two PRPs, MfpA_Mt and QnrB4, as recombinant His tag fusion proteins and assessed their functions under the same experimental conditions.