bluuebunny/crossref_metadata_2025 huggingface dataset:
An attempt to understand Barstar, Barnase and Olfactory receptor protein folding problems using mathematical biological approach
Authors: Goswami Arunava , Hassan Sk Sarif , Pal Choudhury Pabitra
Published: October 2010

Protein folding problem as attracted structural biologists immensely (1). Till date, correlation between X-ray crystallographic and NMR data are considered to be the best methods for determining structure of intra-cellular proteins. Generating crystals and finding correct experimental conditions for NMR are largly a gamble and resultant data processing highly time consuming. Even if, a large number of laboratories around the world and India make crystals of protein but majority of them fail to generate crystallographic data less than or equal to 10A resolution with currently available instruments. This means that X-ray crystallographic data have been generated from protein crystals with non-uniform lattices. We believe that a large portion of (chain of amino acids) all proteins, be it an intra-cellular, transmembrane or extra-cellular proteins form uniform lattices following precise deterministic mathematical rules in natural condition inside cells or membranes or in extra-cellular conditions. This hypothesis has several advantages. First, stacking of protein chains like lattices (lattices of helix or beta-sheet etc.) allows a particular protein to resist forces of compression and relaxation. Secondly, it will be easier to expose hydrophobic and hydrophilic domains following a mathematical rule described in this paper. Barstar, Barnase and olfactory receptors (ORs) have 90, 110 and ~312 amino acids respectively. Using Young-Fibonacci graph area model, here we show that all naturally available protein folding problems can be solved or a preliminary idea about their secondary and tertiary structures can be predicted. This is absolutely necessary considering the fact that there are zillions of proteins present in the animal and plant world. The process of X-ray crystallography and NMR followed by computer modeling for elucidating the secondary and tertiary structures of these vast numbers of proteins might take hundreds of years.
Identification of Potent Leads for Human cAMP Dependent Protein Kinase Catalytic Subunit Alpha: A Strategic Application of Virtual Screening for Cancer Therapeutics
Authors: Swargam Sandeep , Pradhan Dibyabhaba , Umamaheswari Amineni
Published: October 2010

The advancement in therapeutic applications focused on specific macromolecular compounds of deregulated cell signaling pathways bestowed novel approach to design the ligands as drug molecules against several life threatening diseases such as Cancer. In humans, protein kinase A is one of the important kinases those were involved in cell signaling mechanism. cAMP, G-proteins and ATP molecules were required for activation of protein kinase A (PKA), upon activation, PKA catalytic subunits (PRKACA,PRKACB and PRKACG) undergoes many cellular functions like cell proliferations, cell cycle regulation, and survival of cells through acting on many substrates. Overexpression of extracellular cAMP dependent protein kinase A catalytic subunits (PRKACA) causes severe tumorgenesis in different organs (prostate gland, breast, lungs and pancreas) leading to cancer. High throughput virtual screening was implemented herein to identify the potent leads for human PRKACA that stimulates chronic form of cancers. In silico functional and phylogenetic analysis of PRKACA protein provided enough evidences towards its cancer stimulating nature. The human PRKACA crystal structure in complex with inhibitor ‘796’ (PDB ID: 2GU8) was optimized in Maestro v9.0 and the amino acid residues constituting inhibitor interaction site were determined. Fifteen published inhibitors were selected including HA1077, Flavopiridol, Roscovitine, MLN-518, PP2 and Gleevec which were already in clinical trials for high throughput screening at Ligand.Info database. An in house library of 5388 compounds was designing from the above screening procedure were prepared in LigPrep for molecular docking with human PRKACA. Maestro Glide docking from lesser to higher stringency towards minor steric classes were applied subsequently to the prepared ligand dataset against a grid around centroid of the identified inhibitor interaction site of human PRKACA and 21 lead molecules with good docking scores were obtained. Lead ‘1’ (Leptosidin) with relatively least docking score (-11.02 Kcal/mol) compared to other 20 lead molecules and 15 published inhibitors delineates it as potentially the best competitive inhibitor among all. The promising inhibitory activity of Leptosidin is further supported from analysis of binding orientations of human PRKACA- Leptosidin complex deciphering the Lead 1 blocks the active site residues Thr51, Glu121, Val123, Glu127 and Thr183 by forming hydrogen bond. Thus, Leptosidin could be futuristic perspective chemical compound to design drug molecule against human PRKACA in numerous cancers, however, further in vitro and in vivo studies were required to verify the computational strategic prediction of PKA holoenzyme against cancer therapeutics.
The Thrifty Microbiome: The Role of the Gut Microbiota in Obesity in the Amish
Authors: Fraser-Liggett Claire , Shuldiner Alan
Published: October 2010

Emerging evidence that the gut microbiota may contribute in important ways to human health and disease has led us and others to hypothesize that both symbiotic and pathological relationships between gut microbes and their host may by key contributors to obesity and the metabolic complications of obesity. Our “Thrifty Microbiome Hypothesis” posits that gut microbiota play a key role in human energy homeostasis. Specifically, constituents of the gut microbial community may introduce a survival advantage to its host in times of nutrient scarcity, promoting positive energy balance by increasing efficiency of nutrient absorption and improving metabolic efficiency and energy storage. However, in the presence of excess nutrients, fat accretion and obesity may result, and in genetically predisposed individuals, increased fat mass may result in preferential abdominal obesity, ectopic fat deposition (liver, muscle), and metabolic complications of obesity (insulin resistance, hypertension, hyperlipidemia). Furthermore, in the presence of excess nutrients, a pathological transition of the gut microbial community may occur, causing leakage of bacterial products into the intestinal lymphatics and portal circulation, thereby inducing an inflammatory state, further aggravating metabolic syndrome traits and accelerating atherosclerosis. This pathological transition and the extent to which antimicrobial leakage occurs and causes inflammatory and other maladaptive sequelae of obesity may also be influenced by host factors, including genetics. In the proposed study, we will directly test the Thrifty Mirobiome Hypothesis by performing detailed genomic and functional assessment of gut microbial communities in intensively phenotyped and genotyped human subjects before and after intentional manipulation of the gut microbiome. To address this hypothesis, we will enroll three age- and sex-matched groups from the Old Order Amish: (i) 50 obese subjects (BMI > 30 kg/m2) with one or more dysmetabolic manifestations (malignant obesity), (ii) 50 obese subjects (BMI > 30 kg/m2) without any dysmetabolic manifestations (benign obesity), and (iii) 50 nonobese subjects (BMI < 25 kg/m2) without any features of the metabolic syndrome and characterize the architecture of the gut microbiota from the subjects enrolled in this study by high-throughput sequencing of 16S rRNA genes. These studies will provide a deeper understanding of the role of gut microbes in terms of ‘who’s there?’, ‘what are they doing?’, and ‘how are they influencing host energy homeostasis, obesity and its metabolic complications?’
Report on the status of SBGN ER and proposed extensions
Authors: Le Novere Nicolas
Published: October 2010

The Systems Biology Graphical Notation (SBGN) is an effort to standardize the graphical notation used in maps of biochemical and cellular processes studied in systems biology. SBGN is made up of three orthogonal languages, representing different visions of biological systems. Each language defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules how maps are to be interpreted. In this presentation I recapitulated why SBGN was developed, and discuss the current state of the Entity Relationships language. I then describe the coming evolutions and the pending issues.
Composition of Biochemical Networks using Domain Knowledge
Authors: Goodfellow Martin , Wilson John , Hunt Ela
Published: October 2010

Graph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand possible drug interactions, one has to merge known networks and examine topological variants arising from such composition. Similarly, the design of sensor nets may use existing network infrastructures, and the superposition of one network on another can help with network design and optimisation. The problem of network composition has not received much attention in algorithm and database research. Here, we work with biological networks encoded in Systems Biology Markup Language (SBML), based on XML syntax. We focus on XML merging and examine the algorithmic and performance challenges we encountered in our work and the possible solutions to the graph merge problem. We show that our XML graph merge solution performs well in practice and improves on the existing toolsets. This leads us into future work directions and the plan of research which will aim to implement graph merging primitives using domain knowledge to perform composition and decomposition on specific graphs in the biological domain.
LibSBGN: Electronic Processing of SBGN maps
Authors: Demir Emek , Dogrusoz Ugur , Le Novère Nicolas , Matsuoka Yukiko , Sorokin Anatoly , Funahashi Akira , Mi Huaiyu , Kitano Hiroaki , Aladjem Mirit , van Iersel Martijn , Blinov Michael , Boyd Sarah , Villéger Alice , Bergmann Frank , Moodie Stuart , Schreiber Falk , Luna Augustin , Czauderna Tobias
Published: October 2010

Introduction Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that enables diagram exchange while preserving biological meaning and relations.

Results

To meet this need, we are developing an Extensible Markup Language (XML) schema definition. In addition we are developing a software library called LibSBGN. Besides reading and writing files, this library will also be used to validate SBGN maps against the specifications, and convert to and from related systems biology standards, such as SBML and BioPAX.LibSBGN is still under development, but is already being adopted by several tools (See the LibSBGN project page for an up-to-date list of client software). The early adoption of LibSBGN by those tools helps to ensure that LibSBGN is independent of a specific software application, and does not contain artifacts for specific tools. LibSBGN is currently implemented in Java, a parallel C++ version is planned for the future.A test-suite of dozens of LibSBGN documents, covering every possible feature of SBGN maps, was created. This test-suite can be used by developers to check for compliance with the standard, and compare rendering capabilities with other tools.LibSBGN is a community effort, involving people from institutes all around the world, representing a wide selection of pathway tools. The community is organized around a sourceforge project site (http://libsbgn.sourceforge.net), a mailing list and monthly online meetings.A first release of LibSBGN, covering only the Process Description (PD) language, is planned in October 2010. Support for all three languages of SBGN is planned for a later release.
Searching BioModels Database
Authors: Henkel Ron , Waltemath Dagmar , Peters Andre , Endler Lukas , le Novère Nicolas
Published: October 2010

*Aim*The increasing number of computational models of biological systems demands a better support for search facilities. One possible improvement is to enable ranked retrieval of models based on existing model annotation. Applying existing Information Retrieval (IR) techniques to computational models, we have implemented a new search strategy in BioModels Database. In this search strategy the index of search terms contains not only the model descriptions in the database, but is expanded by including ontological and textual information about a model and its constituents retrieved from external sources. To add more background knowledge, we additionally index the abstracts of the reference publications. 

Results

 The new search system was integrated into BioModels Database and is based on a Lucene implementation. The model index includes 454 models and 154854 terms, the semantic index 2353 constituents and 437244 terms. Different sources are incorporated in the retrieval and ranking process, the most important of them via MIRIAM annotations to models and model constituents.The search results are sorted with regard to different aspects, i.e. model authors, dates, constituents, or SBML elements. Several state-of-the-art information retrieval features are supported, such as fuzzy, proximity or range search. As a result the user is enabled to specify the criteria relevant for a search, and is provided with a ranked result set of relevant models. The search was implemented in the demo version of BioModels Database and is available at http://www.ebi.ac.uk/biomodels-demo/.A detailed description of the technical realisation is given in:[Henkel et al., 2010]: Henkel, R., Endler, L., Peters, A., Novere, N., and Waltemath, D. (2010). Ranked retrieval of computational biology models. BMC Bioinformatics, 11(1):423+..
CellML 1.1 modularity
Authors: Nielsen Poul
Published: October 2010

CellML 1.1 is an open XML-based language designed to store and exchange computer-based mathematical models. It has a simple facility to import existing models in order to create new models. The import facility encourages the development of hierarchical models and model reuse through the creation of well-curated model components in public model repositories. This presentation describes some of the features of CellML 1.1 and best practices for taking advantage of these features.
Inferring a Transcriptional Regulatory Network from Gene Expression Data Using Nonlinear Manifold Embedding
Authors: Zare Hossein , Kaveh Mostafa , Khodursky Arkady
Published: October 2010

Transcriptional networks consist of multiple regulatory layers corresponding to the activity of global regulators, specialized repressors and activators of transcription as well as proteins and enzymes shaping the DNA template. Such intrinsic multi-dimensionality makes uncovering connectivity patterns difficult and unreliable and it calls for adoption of methodologies commensurate with the underlying organization of the data source. Here we present a new computational method that predicts interactions between transcription factors and target genes using a compendium of microarray gene expression data and the knowledge of known interactions between genes and transcription factors. The proposed method called Kernel Embedding of REgulatory Networks (KEREN) is based on the concept of gene-regulon association and it captures hidden geometric patterns of the network via manifold embedding. We applied KEREN to reconstruct gene regulatory interactions in the model bacteria E.coli on a genome-wide scale. Our method not only yields accurate prediction of verifiable interactions, which outperforms on certain metrics comparable methodologies, but also demonstrates the utility of a geometric approach to the analysis of high-dimensional biological data. We also describe the general application of kernel embedding techniques to some other function and network discovery algorithms.
Optimization of antioxidant potential of Aspergillus terreus through different statistical approaches
Authors: Arora Daljit Singh , Chandra Priyanka
Published: October 2010

A three‐step optimization strategy, which includes a one‐factor‐at‐a‐time classical method and different statistical approaches [Plackett–Burman design and RSM (response surface methodology)], were applied to optimize the antioxidant potential of Aspergillus terreus. Antioxidant activity was assayed by different procedures and compared with TPC (total phenolic content). Primarily, different carbon and nitrogen sources were screened by classical methods, which revealed sucrose and NaNO3 to be the most suitable. The significance of the components of Czapek Dox's medium with respect to antioxidant activity was evaluated with the Plackett–Burman design, which supported sucrose and NaNO3 to be the most significant. In a second step, sucrose and NaNO3 along with temperature were further taken as three variables for RSM to study their interaction. Response surface analysis showed 4% sucrose, 0.1% NaNO3 and an incubation temperature of 30 °C to be the optimal conditions. Under these conditions, the antioxidant potential assayed through the different procedures was 88.1, 74.9 and 70.2% scavenging effect for DPPH (1,1‐diphenyl‐2‐picryl hydrazyl) radical, ferrous ion and nitric oxide ion respectively. The reducing power showed an absorbance of 2.0 with 71.5% activity for the FRAP (ferric reducing antioxidant power) assay. TPC under different physio‐chemical conditions and antioxidant potential under various assay procedures correlated positively.
Molecular determinants involved in activation of caspase 7
Authors: Boucher Dave , Blais Véronique , Drag Marcin , Denault Jean-Bernard
Published: October 2010

During apoptosis, initiator caspases (8, 9 and 10) activate downstream executioner caspases (3, 6 and 7) by cleaving the IDC (interdomain connector) at two sites. Here, we demonstrate that both activation sites, site 1 and site 2, of caspase 7 are suboptimal for activation by initiator caspases 8 and 9 in cellulo, and in vitro using recombinant proteins and activation kinetics. Indeed, when both sites are replaced with the preferred motifs recognized by either caspase 8 or 9, we found an up to 36-fold improvement in activation. Moreover, cleavage at site 1 is preferred to site 2 because of its location within the IDC, since swapping sites does not lead to a more efficient activation. We also demonstrate the important role of Ile195 of site 1 involved in maintaining a network of contacts that preserves the proper conformation of the active enzyme. Finally, we show that the length of the IDC plays a crucial role in maintaining the necessity of proteolysis for activation. In fact, although we were unable to generate a caspase 7 that does not require proteolysis for activity, shortening the IDC of the initiator caspase 8 by four residues was sufficient to confer a requirement for proteolysis, a key feature of executioner caspases. Altogether, the results demonstrate the critical role of the primary structure of caspase 7's IDC for its activation and proteolytic activity.
Validating the use of woodrat (Neotoma) middens for documenting natural invasions
Authors: Lyford Mark E. , Jackson Stephen T. , Gray Stephen T. , Eddy Robert G.
Published: October 2010

Aim  Plant macrofossils in fossil woodrat (Neotoma) middens are the primary source of information on late Quaternary biogeographical history of plants in arid and semi‐arid regions of North America. Macrofossil records from middens are playing particularly important roles in documenting spatial and temporal patterns of plant migrations and invasions since the last glacial maximum 21,000 years ago. However, relatively few actualistic studies comparing contents of modern middens with surrounding flora and vegetation have been carried out. The primary aim of this study is to assess the reliability of midden assemblages in detecting the presence of tree, shrub and several other plant species growing on the surrounding landscape. The secondary aims are to determine whether probability of occurrence of species in middens is related to abundance in vegetation, and whether representation of individual species in middens is contingent on presence/absence or abundance of other species.

Location  Our five study sites were bedrock escarpments or canyons in the central Rocky Mountains (north‐eastern Utah, central Wyoming and south‐central Montana). All sites were in conifer woodland or forest/woodland variously dominated by Juniperus osteosperma, J. scopulorum, Pinus edulis, P. flexilis and Pseudotsuga menziesii. Neotoma cinerea is the only woodrat species in the region.

Methods  Macrofossil assemblages from 59 modern middens (all showing clear signs of recent or ongoing woodrat activity) were compared with floristic composition of vegetation within 50 m of the middens, and with percent cover of vegetation within 30 m of the middens.

Results  Coniferous trees and shrubs were well‐represented in middens, occurring consistently even when abundance in the local vegetation was very low. Juniperus osteosperma and J. scopulorum were particularly well‐represented, occurring in middens regardless of local abundance. Other conifers (P. edulis, P. flexilis, P. ponderosa, Pseudotsuga menziesii) were occasionally absent from middens when abundance in vegetation was low (< 20% canopy cover). Occurrence of dicot shrubs and graminoids was less consistent.

Main conclusions  Middens constructed by N. cinerea are highly reliable sensors of presence/absence of J. osteosperma and J. scopulorum, and hence can be used to infer invasions and past biogeographical distributions of these species. The middens are also reliable in registering populations of other conifers, although presence in middens may be contingent on local abundance. Additional comparative studies are needed to develop a sound empirical basis for using middens of N. cinerea and other species to infer past presence/absence of plant species on the landscape, and to explore the vegetation‐sensing properties of midden assemblages.
Do we need land‐cover data to model species distributions in Europe?
Authors: Thuiller Wilfried , Araújo Miguel B , Lavorel Sandra
Published: October 2010

Aim  To assess the influence of land cover and climate on species distributions across Europe. To quantify the importance of land cover to describe and predict species distributions after using climate as the main driver.

Location  The study area is Europe.

Methods  (1) A multivariate analysis was applied to describe land‐cover distribution across Europe and assess if the land cover is determined by climate at large spatial scales. (2) To evaluate the importance of land cover to predict species distributions, we implemented a spatially explicit iterative procedure to predict species distributions of plants (2603 species), mammals (186 species), breeding birds (440 species), amphibian and reptiles (143 species). First, we ran bioclimatic models using stepwise generalized additive models using bioclimatic variables. Secondly, we carried out a regression of land cover (LC) variables against residuals from the bioclimatic models to select the most relevant LC variables. Finally, we produced mixed models including climatic variables and those LC variables selected as decreasing the residual of bioclimatic models. Then we compared the explanatory and predictive power of the pure bioclimatic against the mixed model.

Results  (1) At the European coarse resolution, land cover is mainly driven by climate. Two bioclimatic axes representing a gradient of temperature and a gradient of precipitation explained most variation of land‐cover distribution. (2) The inclusion of land cover improved significantly the explanatory power of bioclimatic models and the most relevant variables across groups were those not explained or poorly explained by climate. However, the predictive power of bioclimatic model was not improved by the inclusion of LC variables in the iterative model selection process.

Main conclusion  Climate is the major driver of both species and land‐cover distributions over Europe. Yet, LC variables that are not explained or weakly associated with climate (inland water, sea or arable land) are interesting to describe particular mammal, bird and tree distributions. However, the addition of LC variables to pure bioclimatic models does not improve their predictive accuracy.
Effects of climate and local aridity on the latitudinal and habitat distribution of Arvicanthis niloticus and Arvicanthis ansorgei (Rodentia, Murinae) in Mali
Authors: Sicard B. , Catalan J. , Ag'Atteynine S. , Abdoulaye D. , Britton‐Davidian J.
Published: October 2010

Introduction  The genus Arvicanthis (Lesson 1842) (Rodentia: Murinae), usually referred to as the unstriped grass rat, is mainly distributed in savanna and grassland habitats of Sub‐Saharan Africa. Among the four chromosomal forms of Arvicanthis recently differentiated in Western and Central Africa, the one with a diploid chromosomal number (2n) of 62 and an autosomal fundamental number (NFa) of 62 or 64 is ascribed to Arvicanthis niloticus (Demarest 1822), while the one with 2n = 62 and a NFa between 74 and 76 is referred to A. ansorgei (Thomas 1910). Despite the broad area of sympatry recently uncovered along the inner delta of the Niger river in Mali [details in Volobouev et al. (2002) Cytogenetics and Genome Research, 96, 250–260], the distribution of the two species is largely parapatric and follows the latitudinal patterns of the West‐African biogeographical domains, which are related to the latitudinal patterns of annual rainfall in this region. Here, we analyse the suggestion that the two species show specific adaptations to differences in climate aridity.

Methods  Karyologically screened animals were sampled in 19 localities in seasonally flooded regions located along the ‘Niger’ river in Mali and extending from 1100 to 200 mm of mean annual rainfall. The analysis of trapping success (TS) data allowed us to investigate the respective effects of climate (i.e. annual rainfall) and local (i.e. duration of the green herbaceous vegetation) aridity on the latitudinal and habitat distribution of the two species.

Conclusions  The broad zone of sympatry was found to correspond to a northward expansion of the recognized distribution area of A. ansorgei. TS values indicated that the two species responded very differently to climatic and local conditions of aridity. Arvicanthis ansorgei decreased in TS as regional conditions became more arid; a similar trend was also observed within regions where habitat occupancy decreased with local aridity. The higher TS observed in the most humid habitat relative to the others persisted throughout the latitudinal rainfall gradient. In contrast, TS of A. niloticus increased with latitudinal aridity. This species was present in more arid habitats than A. ansorgei from 1000 mm down to 400 mm of mean annual rainfall where a shift to the most humid habitat occurred. These opposite trends in TS distribution between species suggest that A. ansorgei is less adapted than A. niloticus to arid environments at both a regional and habitat level; thus, A. ansorgei would be able to invade dry regions only along the extensive floodplains bordering the inner delta of the ‘Niger’ river. Several biological traits that may be involved in limiting the southward distribution of A. niloticus are discussed.
The distribution of South American galaxiid fishes: the role of biological traits and post‐glacial history
Authors: Cussac Víctor , Ortubay Silvia , Iglesias Gustavo , Milano Daniela , Lattuca María E. , Barriga Juan P. , Battini Miguel , Gross Miguel
Published: October 2010

Aim  The aim of this work is to update the distribution data of Galaxiidae in South America, relating extant distribution to physiological and reproductive characteristics of the species, latitude, temperature, and post‐glacial opportunities for colonization.

Location  Lakes and rivers of Patagonia.

Methods  We compared, and eventually reconsidered, general data about distribution based on the original literature about capture sites, incorporating several published and unpublished data to the analysis of the biological traits and distribution of Galaxiidae.

Results  The more consistent issue in the comprehension of galaxiid biogeography in South America is the ability to establish landlocked populations. Different founding events in landlocked populations of Galaxias maculatus suggest the possible existence of older and younger landlocked populations. This difference in the time since the establishment of lacustrine populations could have been expressed in their ability for colonization of post‐glacial areas. Galaxias maculatus, Aplochiton and Brachygalaxias are more clearly excluded from the post‐glacial area than G. platei. For all the species we could note a more abundant record of lake populations at the area of glacial refuges. It could be noted that the most successful species, Galaxias platei, is a specialized deep bottom dweller. Deep bottom dwelling helps to endure winter constraints and it appears to be an alternative to the colonization of the littoral and limnetic zones of post‐glacial lakes, the prefered habitat of the other Patagonian fish species.

Main conclusions  At the end of this process of post‐glacial colonization, in the beginning of twentieth century, man introduced several salmonid species in Patagonia. In addition, antropogenic actions had its more recent consequences in global warming. Nowadays we were able to observe new localities for Brazilian fishes into the Austral Subregion and expect some changes in the distribution of Galaxiidae. Northern limits for all species and southern limits for landlocked G. maculatus, Brachigalaxias bullocki and Aplochiton zebra, could be displaced southward. Probably, the species less affected by the changes will be G. platei. These predictions could be accurately formulated using the model of B.J. Shuter & J.R. Post (1990) Transactions of the American Fisheries Society119, 314–336, when biological database on these species are completed.
Low diversity but high differentiation: the population genetics of Aglaope infausta (Zygaenidae: Lepidoptera)
Authors: Schmitt Thomas , Seitz Alfred
Published: October 2010

Aim  Aglaope infausta is a thermophilous Zygaenid of Atlanto‐Mediterranean origin, distributed in Portugal, Spain, France and north‐western Italy reaching its north‐eastern distribution limit in western Germany. The local, regional and inter‐regional genetic structure of this species is studied in this analysis.

Location and methods  The allozymes of 456 individuals from 12 populations (11 from western Germany and one from southern Portugal) were studied by electrophoresis.

Results  Six of the 19 loci analysed were monomorphic. Genetic differentiation between populations was high (FST: 0.404), while the mean genetic diversity was low (He: 3.4%). Most (96.5%) of the genetic variance between populations was between the Portuguese and the German samples, but also the differentiation within Germany was considerable (FSR: 0.101).

In Germany, A. infausta occurs in two major regions (middle Rhine and Nahe) that are geographically separated, and 55.5% of the genetic variance was found between these two regions. The populations of both areas do not differ in their genetic diversity, but those of the middle Rhine have significantly higher genetic distances among them than the Nahe populations (0.020 and 0.015, respectively). FST was also higher in the middle Rhine region than in the Nahe region (0.089 and 0.045, respectively).

Main conclusions  Aglaope infausta shows a very low level of genetic heterogeneity for a lepidopteran species. However, this genetic poverty is not affecting the species’ viability. During the ice ages, differentiation into two genetic lineages occurred, most probably in a south‐western and a south‐eastern differentiation centre in Iberia. The gap in the distribution range in Germany is clearly reflected in the genetic structure. This differentiation must have developed relatively quickly because western Germany most probably was colonized during the climatic optimum 6000 years ago.
Fern species richness along a central Himalayan elevational gradient, Nepal
Authors: Bhattarai Khem R. , Vetaas Ole R. , Grytnes John A.
Published: October 2010

Aim  The study explores fern species richness patterns along a central Himalayan elevational gradient (100–4800 m a.s.l.) and evaluates factors influencing the spatial increase and decrease of fern richness.

Location  The Himalayas stretch from west to east by 20°, i.e. 75–95° east, and Nepal is located from 80 to 88° east in this range.

Methods  We used published data of the distribution of ferns and fern allies to interpolate species elevational ranges. Defining species presence between upper and lower elevation limit is the basis for richness estimates. The richness pattern was regressed against the total number of rainy days, and gradients that are linearly related to elevation, such as length of the growing season, potential evapotranspiration (PET, energy), and a moisture index (MI = PET/mean annual rainfall). The regressions were performed by generalized linear models.

Results  A unimodal relationship between species richness and elevation was observed, with maximum species richness at 2000 m. Fern richness has a unimodal response along the energy gradients, and a linear response with moisture gradients.

Main conclusions  The study confirms the importance of moisture on fern distributions as the peak coincides spatially with climatic factors that enhance moisture levels; the maximum number of rainy days and the cloud zone. Energy‐related variables probably control species richness directly at higher elevations but at the lower end the effect is more probably related to moisture.
Climate and satellite‐derived land cover for predicting breeding bird distribution in the Great Lakes Basin
Authors: Venier L. A. , Pearce J. , McKee J. E. , McKenney D. W. , Niemi G. J.
Published: October 2010

Aim  We examined relationships between breeding bird distribution of 10 forest songbirds in the Great Lakes Basin, large‐scale climate and the distribution of land cover types as estimated by advanced very high resolution radiometer (AVHRR) and multi‐spectral scanner (MSS) land cover classifications. Our objective was to examine the ability of regional climate, AVHRR (1 km resolution) land cover and MSS (200 m resolution) land cover to predict the distribution of breeding forest birds at the scale of the Great Lakes Basin and at the resolution of Breeding Bird Atlas data (5–10 km2). Specifically we addressed the following questions. (1) How well do AVHRR or MSS classifications capture the variation in distribution of bird species? (2) Is one land cover classification more useful than the other for predicting distribution? (3) How do models based on climate compare with models based on land cover? (4) Can the combination of both climate and land cover improve the predictive ability of these models.

Location  Modelling was conducted over the area of the Great Lakes Basin including parts of Ontario, Canada and parts of Illinois, Indiana, Michigan, New York, Ohio, Pennsylvania Wisconsin, and Minnesota, USA.

Methods  We conducted single variable logistic regression with the forest classes of AVHRR and MSS land cover using evidence of breeding as the response variable. We conducted multiple logistic regression with stepwise selection to select models from five sets of explanatory variables (AVHRR, MSS, climate, AVHRR + climate, MSS + climate).

Results  Generally, species were related to both AVHRR and MSS land cover types in the direction expected based on the known local habitat use of the species. Neither land cover classification appeared to produce consistently more intuitive results. Good models were generated using each of the explanatory data sets examined here. And at least one but usually all five variable sets produced acceptable or excellent models for each species.

Main conclusions  Both climate and large scale land cover were effective predictors of the distribution of the 10 forest bird species examined here. Models generated from these data had good classification accuracy of independent validation data. Good models were produced from all explanatory data sets or combinations suggesting that the distribution of climate, AVHRR land cover, and MSS land cover all captured similar variance in the distribution of the birds. It is difficult to separate the effects of climate and vegetation on the species’ distributions at this scale.
Comparative phylogeography of Amphicarpaea legumes and their root‐nodule symbionts in Japan and North America
Authors: Parker Matthew A. , Doyle Jane L. , Doyle Jeff J.
Published: October 2010

Aim  Relationships of eastern Asian and eastern North American populations of legumes in the genus Amphicarpaea Elliot ex. Nuttall (Phaseoleae–Glycininae) and their root nodule bacteria (Bradyrhizobium Jordan) were analysed to test whether both organisms share an identical biogeographic history.

Location  Japan and eastern North America (New York and Illinois).

Methods  Sequences of three plant genes (chloroplast trnL region, nuclear ribosomal ITS, and histone H3‐D) and a segment of the bacterial ribosomal region (partial 16S rRNA and 23S rRNA genes, and the 16S rRNA–23S rRNA ITS) were used to analyse phylogenetic relationships.

Results  For plants, Japanese populations formed a sister group to a well‐supported clade of all North American genotypes. For nodule bacteria associated with Amphicarpaea, isolates from North America did not form a single clade relative to Asian genotypes. Japanese Bradyrhizobium isolates were closely related to particular sub‐groups of North American bacteria (lineages ‘B’ and ‘C’), with other American bacteria branching earlier.

Main conclusions  Plants and bacteria showed clear deviations from a pattern of parallel cladogenesis. The most basal Amphicarpaea lineage was associated with a recently‐diverged bacterial group, while one recently‐diverged plant lineage had symbionts that branched in a basal position relative to the other Amphicarpaea bacteria. When analysed with data on symbiotic compatibility from inoculation experiments, the molecular phylogenies suggested that for plants, at least one transition has occurred toward more promiscuous nodulation behaviour. Among bacteria, strains with narrow host range on Amphicarpaea appear to be ancestral to symbiotic generalists.
Bioclimatic perspectives in the distribution of Quercus ithaburensis Decne. subspecies in Turkey and in the Levant
Authors: Dufour‐Dror Jean‐Marc , Ertas Aytekin
Published: October 2010

Aim  To define the bioclimatic tolerance ranges of the two Tabor oak subspecies. Prior to this definition, and considering the confusion in the literature regarding the Tabor oak subspecies geography, a reassessment of their present distribution is proposed.

Location  Turkey and the Levant.

Methods  The bioclimatic tolerance range of each subspecies was characterized by four parameters: (1) the humidity category (Q2), (2) the winter variant (m) – the two basic variables used in Emberger's method for the definition of Mediterranean bioclimates, (3) the length of the dry season (LDS) and (4) its severity, expressed by the dry season water deficit (DSWD). The reference to the last two variables in the definition of bioclimatic tolerance ranges of Mediterranean species has so far never been considered. The concept of bioclimatic niche, based on the reference to these four parameters, is proposed and discussed.

Results  The reassessment of the Tabor oak subspecies distribution shows that their extents of occurrence do not overlap and are significantly distant. The comparison between the characteristics of each subspecies bioclimatic niche has highlighted three major differences: (1) The bioclimatic niche of the subspecies macrolepis is characterized by a great heterogeneity as it includes up to 10 distinct bioclimate types, whereas only four types have been found in the bioclimatic niche of the subspecies ithaburensis. (2) A 10 °C gap has been found between the winter variants of both bioclimatic niches. (3) The third major difference relates to the dry season characteristics: the bioclimatic niche of the subspecies ithaburensis is characterized by an LDS 40–75% longer than it is in the bioclimatic niche of the subspecies macrolepis. Moreover, and surprisingly, although the most arid humidity categories are found in the bioclimatic niche of the subspecies macrolepis, the bioclimatic niche of the subspecies ithaburensis is characterized by a significantly more severe dry season as the DSWD is 36–180% greater than in the bioclimatic niche of the subspecies macrolepis. It is suggested that the duration and the severity of the dry season is a major limiting factor in the spatial distribution of the subspecies macrolepis.

Main conclusions  The reference to the duration (LDS) and severity (DSWS) of the dry season is essential when defining the bioclimatic niche of Mediterranean species.
Phytogeography of the Kaieteur Falls, Potaro Plateau, Guyana: floral distributions and affinities
Authors: Kelloff Carol L. , Funk V. A.
Published: October 2010

Aim  The plant diversity of one location on the Guiana Shield, Kaieteur National Park in Guyana, is used to examine the various hypothesized origins of the flora and to evaluate which may best explain the current plant distributions.

Location  Kaieteur National Park is located on eastern edge of the Potaro Plateau in central Guyana, South America. The species examined have distributions that vary from local to global.

Methods  The distribution patterns of the families, genera and species known from Kaieteur are examined using generalized distribution patterns.

Results  Data on distribution patterns, elevation and habitat were gathered from 131 flowering plant families, 517 genera and 1227 species. These plants represent all taxa that are currently known to occur in the area of the original Kaieteur National Park. Families tend to have cosmopolitan or pantropical distribution, genera are mostly neotropical and at the species level, most species are restricted to the Guiana Shield (c. 40%), northern South America (69%) or neotropical (96%) in distribution, each level inclusive of the previous.

Conclusions  The flora at the study site in Kaieteur National Park has its strongest affinity with the Guiana Shield; 42.1% of the species have a distribution that corresponds with the Shield or is more restricted within the Shield. There is a distinct flora on the Guiana Shield and its affinities lie with the flora of northern South American and beyond that, the neotropics. The flora is not closely affiliated with the floras of the Brazilian Shield, the Amazon, the Andes, the eastern coastal forests of Brazil, southern South America, or Africa as has been previous suggested.
Tropical and north Pacific teleconnections influence fire regimes in pine‐dominated forests of north‐eastern California, USA
Authors: Norman S. P. , Taylor A. H.
Published: October 2010

Aim  To assess the importance of drought and teleconnections from the tropical and north Pacific Ocean on historical fire regimes and vegetation dynamics in north‐eastern California.

Location  The 700 km2 study area was on the leeward slope of the southern Cascade Mountains in north‐eastern California. Open forests of ponderosa pine (Pinus ponderosa var. ponderosa Laws.) and Jeffrey pine (P. jeffreyi Grev. & Balf) surround a network of grass and shrub‐dominated meadows that range in elevation from 1650 to 1750 m.

Methods  Fire regime characteristics (return interval, season and extent) were determined from crossdated fire scars and were compared with tree‐ring based reconstructions of precipitation and temperature and teleconnections for the period 1700–1849. The effect of drought on fire regimes was determined using a tree‐ring based proxy of climate from five published chronologies. The number of forest‐meadow units that burned was compared with published reconstructions of the El Niño/Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO).

Results  Landscape scale fires burned every 7–49 years in meadow‐edge forests and were influenced by variation in drought, the PDO and ENSO. These widespread fires burned during years that were dryer and warmer than normal that followed wetter and cooler years. Less widespread fires were not associated with this wet, then dry climate pattern. Widespread fires occurred during El Niño years, but fire extent was mediated by the phase of the PDO. Fires were most widespread when the PDO was in a warm or normal phase. Fire return intervals, season and extent varied at decadal to multi‐decadal time scales. In particular, an anomalously cool, wet period during the early 1800s resulted in widespread fires that occurred earlier in the year than fires before or after.

Main conclusions  Fire regimes in north‐eastern California were strongly influenced by regional and hemispheric‐scale climate variation. Fire regimes responded to variation that occurred in both the north and tropical Pacific. Near normal modes of the PDO may influence fire regimes more than extreme conditions. The prevalence of widespread teleconnection‐driven fires in the historic record suggests that variation in the Pacific Ocean was a key regulator of fire regimes through its influence on local fuel production and successional dynamics in north‐eastern California.