ALBERT

Description: The issue of uncertainty is the basis for any application of knowledge (“Uncertainty is an attribute of information.” From L. Zadeh, 2005) and has to be one of the main tasks in Earth’s systems study. Knowledge about natural systems may be only obtained by the analysis of the empirical (instrumental) data. Uncertainty starts from unveiling of the research task by the researcher. The main source of uncertainty comes from the natural system “extraction” (unit’s boundaries) for modeling and limitations of data representing both time and space variability. The consideration of uncertainty is placed in context of time and space with use of the U.S. part of the Great Lakes watershed as an example. All possible empirical (instrumental) data were used for this research. Data analysis was completed for river discharge, precipitation and air temperatures. Results of data analysis provide a base for regionalization, a multi-scaled description of the structure of river watersheds and their interaction with climate characteristics, and uncertainty of the obtained knowledge. The consideration of uncertainty in research helps practical applications like water balance estimations for conservation and/or management of water resources of different scales, and educating the public/communities about environmental issues.

Description: Management strategies aimed at rehabilitating degraded and cleared forests often rely on temporary or permanent exclusion of herbivores (wild animals, livestock or both). But in many cases, this simple management technique is not sufficient to induce ecosystem restoration: many negative effects keep the ecosystem in a suboptimal, low biomass state. The presence of such stable states requires restoration measures to act on multiple stress factors simultaneously.Compensating for all limiting factors is neither practically nor economically feasible. But detailed knowledge about the autoecology of tree species – i.e. their site requirements, regeneration strategies and recruitment dynamics – may be used to tailor management to the most pertinent problems. Here we illustrate this approach with results from forest restoration experiments in grazing exclosures in northern Ethiopia using African wild olive (Olea europaea ssp. cuspidata) as a representative Afromontane climax species.The recruitment of African wild olive is affected by seed limitation, restricted seed dispersal and germination and survival limitation. The exclusion of grazing animals as a single measure to restore forest is not enough. Degraded grazing land moves into a state dominated by persistent shrubs, arresting forest succession and discouraging local stakeholders. Direct sowing or planting of seedlings in fertile patches under selected pioneer shrubs, however, may help to overcome this form of bush encroachment, in particular during years with an above-average rainfall.

Description: The oceans’ carbon uptake substantially reduces the rate of anthropogenic carbon accumulation in the atmosphere1, and thus slows global climate change. Some diagnoses of trends in ocean carbon uptake have suggested a significant weakening in recent years2-8, while others conclude that decadal variability confounds detection of long-term trends9-11. Here, we study trends in observed surface ocean partial pressure of CO2 (pCO2) in three gyre-scale biomes of the North Atlantic, considering decadal to multidecadal timescales between 1981 and 2009. Trends on decadal timescales are of variable magnitudes and depend sensitively on the precise choice of years. As more years are considered, oceanic pCO2 trends begin to converge to the trend in atmospheric pCO2. North of 30oN, it takes 25 years for the influence of decadal-timescale climate variability to be overcome by a long-term trend that is consistent with the accumulation of anthropogenic carbon. In the permanently stratified subtropical gyre, warming has recently become a significant contributor to the observed increase in oceanic pCO2. This warming, previously attributed to both a multidecadal climate oscillation and anthropogenic climate forcing12,13, is beginning to reduce ocean carbon uptake.

Description: The issue of uncertainty is the basis for any application of knowledge (“Uncertainty is an attribute of information.” From L. Zadeh, 2005) and has to be one of the main tasks in Earth’s systems study. Knowledge about natural systems may be only obtained by the analysis of the empirical (instrumental) data. Uncertainty starts from unveiling of the research task by the researcher. The main source of uncertainty comes from the natural system “extraction” (unit’s boundaries) for modeling and limitations of data representing both time and space variability. The consideration of uncertainty is placed in context of time and space with use of the U.S. part of the Great Lakes watershed as an example. All possible empirical (instrumental) data were used for this research. Data analysis was completed for river discharge, precipitation and air temperatures. Results of data analysis provide a base for regionalization, a multi-scaled description of the structure of river watersheds and their interaction with climate characteristics, and uncertainty of the obtained knowledge. The consideration of uncertainty in research helps practical applications like water balance estimations for conservation and/or management of water resources of different scales, and educating the public/communities about environmental issues.

Description: Approximately 70% of the tropical crop species depend on pollinators for optimum yields (Roubik, 1995, Klein 2007). The economic value of such pollinated crops to India is $726 million and India is the world’s second largest vegetable producer (Sidhu, 2005). This status has been underpinned by large-scale changes in land-use and pesticide dependency (Fazal, 2000; Shaw & Satish, 2007). A method (c.f. Aizen et al. 2008) that partitions crops into categories depending on their relative pollinator dependence (Index of pollinator dependence, DI) was applied to analysis of vegetable yields for India over 45 years (1963-2008) using FAO data. This has revealed that since 1993, relative yields of crop production has either flattened or declined, while pollinator non dependent crops show no similar decline. This pattern of yield limitation may be due to several factors, among which pollinator limitation would be a major factor (Kearns et al. 1998) and this risk is discussed. Pollinator decline will have serious socio-economic consequences for countries like India, which host a large population of small and marginal farms for whom falling yield level would be critical for subsistence (Kearns et al. 1998; Kremen et al., 2002; Klein et al., 2007; Potts et al., 2010). We show here for the first time any indication of pollination limitation in India, an emerging economy that is still predominantly agrarian. Detailed land use and ecological surveys are urgently required to assess the ecology of pollinating insects within and around agricultural systems in India.

Description: During the summer of 2010, three student interns from Sisseton Wahpeton Tribal College along with researchers from South Dakota State University engaged in a pilot project to assess the feasibility of using Landsat imagery to determine water transparency in reservation lakes in northeastern South Dakota. The students were trained to assist with data collection, image processing, and spatial and statistical analyses. Secchi depth measurements and lake algae bloom observations were made on cloud-free Landsat overpass days. Measurement locations were geo-referenced using GPS. Field observations and satellite image classification and interpretation techniques were used to create a land use map for the watershed and explore possible land-use-related causes of the variation in water transparency. The results of this project included a better understanding of the relationship between Landsat images and on site observations of water transparency at first and then land use and water quality in reservation lakes.

Description: Patterns of biodiversity predicted by the neutral theory rely on a simple phenomenological model of speciation. To further investigate the effect of speciation on neutral biodiversity, we define the metacommunity as a system of populations exchanging migrants and use this framework to study allopatric & parapatric speciation. We find that with realistic mutation rates, our metacommunity model driven by neutral processes cannot support more than a few species. Adding natural selection in the population genetics of speciation increases the number of species in the metacommunity but the level of diversity found in Barro Colorado Island is difficult to reach.

Description: During the summer of 2010, three student interns from Sisseton Wahpeton Tribal College along with researchers from South Dakota State University engaged in a pilot project to assess the feasibility of using Landsat imagery to determine water transparency in reservation lakes in northeastern South Dakota. The students were trained to assist with data collection, image processing, and spatial and statistical analyses. Secchi depth measurements and lake algae bloom observations were made on cloud-free Landsat overpass days. Measurement locations were geo-referenced using GPS. Field observations and satellite image classification and interpretation techniques were used to create a land use map for the watershed and explore possible land-use-related causes of the variation in water transparency. The results of this project included a better understanding of the relationship between Landsat images and on site observations of water transparency at first and then land use and water quality in reservation lakes.

Description: Animals living in groups make movement decisions that depend, among other factors, on social interactions with other group members. Our present understanding of social rules in animal collectives is based on empirical fits to observations and we lack first-principles approaches that allow their derivation. Here we show that patterns of collective decisions can be derived from the basic ability of animals to make probabilistic estimations in the presence of uncertainty. We build a decision-making model with two stages: Bayesian estimation and probabilistic matching.In the first stage, each animal makes a Bayesian estimation of which behavior is best to perform taking into account personal information about the environment and social information collected by observing the behaviors of other animals. In the probability matching stage, each animal chooses a behavior with a probability given by the Bayesian estimation that this behavior is the most appropriate one. This model derives very simple rules of interaction in animal collectives that depend only on two types of reliability parameters, one that each animal assigns to the other animals and another given by the quality of the non-social information. We test our model by obtaining theoretically a rich set of observed collective patterns of decisions in three-spined sticklebacks, Gasterosteus aculeatus, a shoaling fish species. The quantitative link shown between probabilistic estimation and collective rules of behavior allows a better contact with other fields such as foraging, mate selection, neurobiology and psychology, and gives predictions for experiments directly testing the relationship between estimation and collective behavior.

Description: In this paper the realized niche of the Snowy Plover (Charadrius alexandrinus), a primarily resident Florida shorebird, is described as a function of the scenopoetic and bionomic variables at the nest-, landscape-, and regional-scale. We identified some possible geomorphological controls that influence nest-site selection and survival using data collected along the Florida Gulf coast. In particular we focused on the effects of beach replenishment interventions on the Snowy Plover (SP), and on the migratory Piping Plover (PP) (Charadrius melodus ) and Red Knot (RK) (Calidris canutus ). Additionally, we investigated the potential differences between the SP breeding and wintering distributions using only regional-scale physiognomic variables and the recorded occur- rences. To quantify the relationship between past renourishment projects and shorebird species we used a Monte Carlo procedure to sample from the posterior distribution of the binomial probabilities that a region is not a nesting or a wintering ground conditional on the occurrence of a beach replenishment intervention in the same and the previous year. The results indicate that it was 2.3, 3.1, and 0.8 times more likely that a region was not a wintering ground following a year with a renourishment intervention for the SP, PP and RK respectively. For the SP it was 2.5. times more likely that a region was not a breeding ground after a renourishment event. Through a maximum entropy principle model we observed small differences in the habitat use of the SP during the breeding and the wintering season. However the habitats where RK was observed appeared quite different. While ecological niche models at the macro-scale are useful for determining habitat suitability ranges, the characterization of the species’ local niche is fundamentally important for adopting concrete multi-species management scenarios. Maintaining and creating optimal suitable habitats for SP characterized by sparse low vegetation in the foredunes areas, and uneven/low-slope beach surfaces, is the proposed conservation scenario to convert anthropic beach restorations and SP populations into a positive feedback without impacting other threatened shorebird species.

Description: How biotic and abiotic factors interact to shape the overall pattern of dispersal of propagules is critical in understanding the evolution of dispersal mechanisms as well as predicting dispersal rates between patchily-distributed habitats. But which plant traits, demographic and/or habitat factors best predict the capacity for dispersal? We introduce the concept of migration potential (v), a readily interpretable parameter that combines recruitment efficiency (recruits per adult / seeds per adult per dispersal cycle) with level of habitat occupancy for predicting effective long-distance dispersal (LDD) of seeds. Using our empirical (genotype assignment) estimates of LDD and statistics on life-history traits and demographic features for contrasting co-occurring shrub species as a test case, and comparing alternative plant traits, we demonstrate that rate of LDD is best described as a simple function of v. As the direct consequence of life-history and demographic traits in a specific environmental context, v has the potential to predict LDD rates in both stable and changing ecosystems

Description: The behavior and pattern of NPs of minerals in the evolutionary history of the earth vis – a –vis the environmental context are inquired into, with a riverine system as a model. The study of fractal dimensions of NPs of interest serves as an aid to obtain a comprehensive view of natural NPs in the model system. The present study combines inputs from work done on nanoparticles, derived from the Subanarekha River System and products of base metal mine effluents that are rich in NPs of minerals. The authors believe this study would help to establish certain universalities about NPs and provide an updated framework for understanding the current state of nanomineral science.

Description: A plasmodium of acellular slime mould Physarum polycephalum is a large single cell with many nuclei. Presented to a configuration of attracting and repelling stimuli a plasmodium optimizes its growth pattern and spans the attractants, while avoiding repellents, with efficient network of protoplasmic tubes. Such behaviour is interpreted as computation and the plasmodium as an amorphous growing biological computer. Till recently laboratory prototypes of slime mould computing devices (Physarum machines) employed rolled oats and oat powder to represent input data. We explore alternative sources of chemo-attractants, which do not require a sophisticated laboratory synthesis. We show that plasmodium of P. polycephalum prefers sedative herbal tablets and dried plants to oat flakes and honey. In laboratory experiments we develop a hierarchy of slime-mould’s chemo-tactic preferences. We show that Valerian root (Valeriana officinalis) is the strongest chemo-attractant of P. polycephalum outperforming not only most common plants with sedative activities but also some herbal tablets.

Description: The Baltimore Ecosystem Study (BES) is one of two urban Long-Term Ecological Research (LTER) projects in the United States. It began its third funding cycle in 2011. Although the project continues key measurements that were started in 1997 at the inception of the research, the third phase is characterized by a new conceptual framework. Phase III of BES focuses on metropolitan Baltimore, Maryland, as a system poised for transition from a “sanitary city”—characterized by engineered environmental solutions, management via discrete disciplines, and government control to a “sustainable city”—which would be characterized by additional biological solutions, collaborative management, and polycentric and multi-level governance. In such a situation, the guiding research question becomes, “What are the effects of adaptive processes aimed at sustainability in the Baltimore socio-ecological system?” Adaptive processes are those social and biophysical features and actions which allow a complex system to adjust to changing internal and external drivers. The full proposal and other details of BES can be discovered on the project website: www.beslter.org

Description: The Baltimore Ecosystem Study (BES) is one of two urban Long-Term Ecological Research (LTER) projects in the United States. It began its third funding cycle in 2011. Although the project continues key measurements that were started in 1997 at the inception of the research, the third phase is characterized by a new conceptual framework. Phase III of BES focuses on metropolitan Baltimore, Maryland, as a system poised for transition from a “sanitary city”—characterized by engineered environmental solutions, management via discrete disciplines, and government control to a “sustainable city”—which would be characterized by additional biological solutions, collaborative management, and polycentric and multi-level governance. In such a situation, the guiding research question becomes, “What are the effects of adaptive processes aimed at sustainability in the Baltimore socio-ecological system?” Adaptive processes are those social and biophysical features and actions which allow a complex system to adjust to changing internal and external drivers. The full proposal and other details of BES can be discovered on the project website: www.beslter.org

Description: Shade coffee cultivation in the Peruvian Andes assists in reducing emissions from deforestation because it avoids conversion to non-forest land uses such as coca and sun grown coffee farming. REDD+ is a potential finance mechanism which may provide incentives for local coffee cooperatives to maintain high shade tree cover. REDD+ has potential multiple benefits other than carbon sequestration, including the conservation of biodiversity. When monitoring for REDD+, surveys of bird biodiversity may prove to be particularly valuable: apart from their high intrinsic value and their value as essential ecosystem service providers, birds inhabiting forest habitats are extremely sensitive to forest loss and forest degradation and are therefore potential useful indicators for the impact of habitat and climate disturbances on biodiversity and environmental health.We analyzed the impact of coffee cultivation on the conservation of birds and assessed what can be learned from bird surveys when monitoring the Peruvian mountain forests for REDD+. Using twelve day-long transect walks, bird species were recorded in two sites in the buffer zone of the Bahuaja-Sonene National Park in SE Peru. The two sites had contrasting human pressure: one site an intimate mixture of shade coffee plantations, orchards, secondary forest patches and coca plantations and the other site secondary forest with patchily distributed shade coffee, fruit and coca plantations. An indirect gradient approach (non-metric multidimensional scaling and multi-response permutation procedure tests) was used to detect differences in forest degradation between sites.In a two-dimensional ordination space, individual counts of the less disturbed site were separated from the other counts, but sites did not differ significantly at the community-level. Observed birds were indicative for one habitat type. The bird assemblage was dominated by species of forest edges and second growth habitat (78%). The majority of species (68%) had a wide range covering Amazonia and the east slopes of the Andes; only 25 species (29%) were more or less restricted to Andes and the outlying ridges.The current state of the forest, in both sites with contrasting human influence, can be described as disturbed secondary montane evergreen forest of the transition zone between the Andes and the Amazon. Despite severe human impact, several forest specialists (22%) of both Andean montane and Amazonian forest persisted –including the enigmatic Andean cock-of-the-rock and Military macaw. For such species, REDD+ projects should not only focus on the sustainable management of the shade coffee stands but also aim to conserve the remaining old-growth secondary forest patches.

Description: Shade coffee cultivation in the Peruvian Andes assists in reducing emissions from deforestation because it avoids conversion to non-forest land uses such as coca and sun grown coffee farming. REDD+ is a potential finance mechanism which may provide incentives for local coffee cooperatives to maintain high shade tree cover. REDD+ has potential multiple benefits other than carbon sequestration, including the conservation of biodiversity. When monitoring for REDD+, surveys of bird biodiversity may prove to be particularly valuable: apart from their high intrinsic value and their value as essential ecosystem service providers, birds inhabiting forest habitats are extremely sensitive to forest loss and forest degradation and are therefore potential useful indicators for the impact of habitat and climate disturbances on biodiversity and environmental health.We analyzed the impact of coffee cultivation on the conservation of birds and assessed what can be learned from bird surveys when monitoring the Peruvian mountain forests for REDD+. Using twelve day-long transect walks, bird species were recorded in two sites in the buffer zone of the Bahuaja-Sonene National Park in SE Peru. The two sites had contrasting human pressure: one site an intimate mixture of shade coffee plantations, orchards, secondary forest patches and coca plantations and the other site secondary forest with patchily distributed shade coffee, fruit and coca plantations. An indirect gradient approach (non-metric multidimensional scaling and multi-response permutation procedure tests) was used to detect differences in forest degradation between sites.In a two-dimensional ordination space, individual counts of the less disturbed site were separated from the other counts, but sites did not differ significantly at the community-level. Observed birds were indicative for one habitat type. The bird assemblage was dominated by species of forest edges and second growth habitat (78%). The majority of species (68%) had a wide range covering Amazonia and the east slopes of the Andes; only 25 species (29%) were more or less restricted to Andes and the outlying ridges.The current state of the forest, in both sites with contrasting human influence, can be described as disturbed secondary montane evergreen forest of the transition zone between the Andes and the Amazon. Despite severe human impact, several forest specialists (22%) of both Andean montane and Amazonian forest persisted –including the enigmatic Andean cock-of-the-rock and Military macaw. For such species, REDD+ projects should not only focus on the sustainable management of the shade coffee stands but also aim to conserve the remaining old-growth secondary forest patches.

Description: A major element of variability of olivine melt inclusions in Mauna Loa lavas is here proved to be strictly related to olivine crystallization at inclusion walls, at low pressure and decreasing temperature. In so doing it is probably worth it to interpret trace elements and isotope variability in these olivine trapped liquids as the effect of disequilibrium (isotope) fractionation. In this respect, the accurate analytical work performed by Sobolev et al. (2011) does not document the presence of a heterogeneous source, rather representing a tool to explore poorly documented aspects of magmatic crystallization that are controlled by the kinetics of liquid-solid phase transition.

Description: Historical trends in monthly, seasonal, and annual mean streamflows, as well as minimum and maximum monthly streamflows, were investigated at nine hydrometric stations in the Okanagan River watershed from south-central British Columbia, Canada. Overall, mean annual streamflows in the Okanagan River watershed are not exhibiting any significant time trends. No consistent declines in monthly minimum streamflows are evident at any point during the hydrologic year. Mean monthly and monthly maximum streamflows in tributary streams to the mainstem system appear to be significantly increasing over time during the spring snowmelt period of March and April. Any temporal changes in flow patterns at the mainstem Okanagan River stations likely reflect alterations in water management strategies over time at the respective upstream dams.

Description: Bacteria and plants are able to form population waves as a result of their consumer behaviour and propagation. A soliton-like interpenetration of colliding population waves was assumed but not proved earlier. Here we show how and why colliding population waves of trophically identical but fitness different species can interpenetrate through each other without delay. We have hypothesized and revealed here that the last mechanism provides a stable coexistence of two, three and four species, competing for the same limiting resource in the small homogeneous habitat under constant conditions and without any fitness trade-offs. We have explained the mystery of biodiversity mechanistically because (i) our models are bottom-up mechanistic, (ii) the revealed interpenetration mechanism provides strong violation of the competitive exclusion principle and (iii) we have shown that the increase in the number of competing species increases the number of cases of coexistence. Thus the principled assumptions of fitness neutrality (equivalence), competitive trade-offs and competitive niches are redundant for fundamental explanation of species richness.

Description: ObjectivesPrevious studies reported inherited BRCA1/2 deficits can cause cancer by impairing normal protective responses. Opportunistic carcinogens can exploit these deficits by causing chronic inflammation, constant cell death and replacement in a mutagenic environment, DNA crosslinking or double strand breaks. Some of the resulting cancers may be prevented if opportunistic carcinogens are identified.MethodsThe literature was systematically searched for carcinogens capable of exploiting deficits in BRCA1/2 pathways. Search criteria were common exposure, available information, required BRCA1/2 pathway repairs, increased risks for any cancer, and effects on stem cells.ResultsFormaldehyde and acetaldehyde are closely related carcinogens and common pollutants that seem everywhere. Alcohol metabolism also produces acetaldehyde. High levels of either carcinogen overwhelm normal detoxification systems, cause inflammation, inhibit DNA repair and produce DNA cross links as critical carcinogenic lesions. Searching model system studies revealed both carcinogens activate stem cells, BRCA1/2 pathways and connected BRCA1/2 pathways to myeloid leukemia. For example, the BRCA1-BARD1 complex is required for proper nucleophosmin functions. Nucleophosmin prevents a major subset of acute myeloid leukemia (AML). Next, these concepts were independently tested against risks for myeloid leukemia. Epidemiologic results showed that BRCA2 gene defects inherited on both chromosomes increased risks so dramatically that AML occurs in most children. Using data from 14 studies, known/potential heterozygous BRCA1/BRCA2 mutations increased risks for myeloid leukemias by at least 3 fold in 7 studies and by at least 50% in 12. Acetaldehyde occurs in breast milk. In model studies, excessive acetaldehyde/alcohol exposure affects estrogen metabolism and stimulates alternate alcohol detoxification pathways. These pathways can also cause DNA cross linking by releasing oxygen species and activating procarcinogens. Acetaldehyde in rats’ drinking water increased incidence of leukemias, lymphomas, pancreatic tumors and fibroadenomas. Six human epidemiologic studies support an association between alcohol related genotype or alcohol consumption and early onset breast cancers, including those in BRCA1/2 mutation carriers. Conclusions Although it is difficult to prove direct causation, BRCA1/2 mutation carriers may reduce cancer risks by avoiding excessive formaldehyde and acetaldehyde. Broader genetic testing and pharmacologic/nutritional detoxification are possible.

Description: Schizophrenia is a very common psychiatric disorder. However, its etiology and pathogenesis is still unknown. Current theory saying that neurotransmitter imbalance such as serotonin or dopamine only provides limited effectiveness in schizophrenia treatment by drugs changing serotonin and dopamine concentration. Despite of such treatment, majority of schizophrenia patients still have very poor prognosis. Thus, the neurotransmitter imbalance theory is not correct. Here, I propose that schizophrenia is actually a TH2 dominant autoimmune disorder. The candidate of autoantigen could be acetylcholine receptors of CNS. My theory can explain the positive as well as negative symptoms of schizophrenia. By microarray analysis of PBMCS, one-tenth of the total 519 significantly expressed genes are immune-related genes. Among them, TH2 related genes are significantly up-regulated including IL-4, histidine decarboxylase, aldehyde dehydrogenase, CCR9, IgE Fc receptor, GATA2, serotonin receptor, phospholipase A2, and prostaglandin D2 synthase. Besides, TH1 and TH17 related genes are down-regulated including CXCL5, cathepsin C, and neutrophil related S100 binding proteins. The new theory sheds a light to better control this detrimental illness. Anti-inflammatory agents could be used to manage schizophrenia in the near future.

Description: Animal models are often used to obtain a better understanding of psychiatric, neurodegenerative, and neurodevelopmental disorders. Despite many years of research, these models have not led to many novel therapies or treatments. Translating results between species will always be difficult, and it is argued that inappropriate statistical analyses, failure to identify the experimental unit, lack of random assignment to treatment conditions, and unblinded assessment of outcomes contribute to the low rate of translating preclinical in vivo studies into successful therapies. It is known that these shortcomings can generate biased estimates, too many false positives and false negatives, and unreproducible results. These issues have been raised repeatedly, but have largely gone unheeded by scientists. Two recommendations are made to improve the situation.

Description: Mobile Platform Informatics (MPI) and Smartphone Informatics (SPI) methods like Mobile Image Ratiometry (MIR) are potentially transformative point-of-use instantaneous analysis tools that are useful across a variety of industries. In agriculture, MIR-compatible immuno test strips allow early detection of a number of biotic stressors before devastating crop losses occur. Here we describe a low-cost and easy-to-use Smartphone and/or tablet-based protocol (Mobile Assay Inc., www.mobileassay.com) for the detection and on-sight instantaneous analysis of B. cinerea, a fungus that causes significant damage to a variety of plants and flowers. Early detection and tracking of the B. cinerea fungus before the visible gray mold appears has the potential to increase agricultural productivity especially in the developing world.

Description: Here we show a new interaction mechanism of colliding population waves. It provides a stable coexistence of two similar but different species competing for the same limiting resource during their asexual propagation in a limited homogeneous environment under constant conditions. The revealed mechanism opens new opportunities in conservation biology.

Description: Two erectoid hominids from Sarstedt prompted a detailed examination of the course of the impressions of the Arteria meningea media and their characteristics within the line of hominidae.

Description: Genomic Replikin CountsTM of Infectious Salmon Anemia Virus (ISAV) in Canada Exceed the Counts in Lethal Outbreaks in Norway, Chile, and Scotland. Real-Time Tracking of the Evolution of the ISAV Genome and the Resultant Replikins Solid Phase ISAV Vaccine Make ISAV Pandemic Prevention Possible.

Description: Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).Description: The HTRIdb is an open-access database of experimentally validated interactions among human TFs and their TGs. HTRIdb can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network using the Cytoscape Web software. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 283 TFs that regulate 11886 genes, totaling 18160 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.Conclusions: HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes.

Description: Genome-wide association studies (GWAS) have become a standard method for finding genetic variations that contribute to common, complex diseases. Recently, it is suggested that these diseases may be caused by epistatic interactions of multiple genetic variations. Although tens of software tools have been developed for epistasis detection, few are able to infer pathway importance from the identified epistatic interactions. AntEpiSeeker is originally an algorithm for detecting epistatic interactions in case-control studies, using a two-stage ant colony optimization (ACO) algorithm. We have developed AntEpiSeeker2.0, which extends the AntEpiSeeker algorithm to inference of epistasis-associated pathways, based on a natural use of the ACO pheromones. By looking at pheromone distribution across pathways, epistasis-associated pathways can be easily identified. The effectiveness of AntEpiSeeker2.0 in inferring epistasis-associated pathways is demonstrated through a simulation study and a real data application. AntEpiSeeker 2.0 was designed to provide efficient inference of epistasis-associated pathways based on ant colony optimization and is freely available at http://lambchop.ads.uga.edu/antepiseeker2/.

Description: Natural agricultural production functions in open system, where energy and matter are exchanged freely between geosphere (especially pedosphere), biosphere, and atmosphere. The self regulation of biophysical processes in these spheres is crucial for global sustainability. However, modern farming practices have stressed the system to the extent that damaged C, N, and P cycles are threatening catastrophic consequences. High food-wastage coupled with high food price, high soil fertility zones but low crop productivity, and highly productive irrigated farming marred with ecological disasters are examples of global paradoxes associated with modern farming. High incidence of pesticide residues in soil and water bodies, low use efficiency of agricultural inputs, vulnerability to climate, and low conversion of energy by crops leaving high amount of residues and their subsequent burden on environment, and hunger and malnutrition in many parts of the world are threatening civilizations to crumble. Nanotechnology promises to break these vicious cycles, because technology is based on applying exact amounts of inputs for use by the crops, and only when they are required. Some of the examples are: nanofabricating nutrient ions to improve nutrient use efficiency, targeted use of nano-pesticides, holding of water and then releasing it at the time of crop need by nps, forecasting and elimination of diseases, packaging of food to improve shelf-life, protecting food during storage, DNA nanotechnology, smart treatment delivery systems, bioanalytical nanosensors, bioselective surfaces, nanobioprocessing, protection of the environment by the reduction and conversion of agricultural materials into valuable products, design and development of new nanocatalysts to convert vegetable oils into biobased fuels and biodegradable industrial solvents, and controlled ecological life support system.

Description: “A disruptive innovation is an innovation that helps create a new market and value network, and eventually goes on to disrupt an existing market and value network (over a few years or decades), displacing an earlier technology. The term is used in business and technology literature to describe innovations that improve a product or service in ways that the market does not expect.” -WikipediaOn April 3rd, 2012 Nature Precedings, Nature Publishing Group’s experiment in free pre-print publishing was shut down and no longer accepts submissions. According to the Nature Precedings website it was created in 2007 as “a place for researchers to share documents, including presentations, posters, white papers, technical papers, supplementary findings, and non-peer-reviewed manuscripts.” It was designed to “provide a rapid means for scientists to share preliminary findings, disseminate emerging results, solicit community feedback, and claim priority over discoveries.” It was designed in a way to “make such material easy to archive, share and cite.” Now that Nature Precedings is no more, a new disruptive open data-sharing platform (ODSP) for the life sciences is needed. Based, in part, by the model Nature Precedings established. Here I propose 5 qualities of an ideal ODSP and outline 10 benefits (see Table 1) to scientists for embracing such a potentially disruptive model.

Description: Innovative molecular tools allow neuroscientists to study neural circuitry associated with specific behaviors. Consequently, behavioral methods must be developed to interface with these new molecular tools in order for neuroscientists to identify the causal elements underlying behavior and decision-making processes. Here we present an apparatus and protocol for a novel Go/No-Go behavioral paradigm to study the brain attention and motivation/reward circuitry in awake, head-restrained rodents. This experimental setup allows: (1) Painless and stable restraint of the head and body; (2) Rapid acquisition to simple or complex operant tasks; (3) Repeated electrophysiological single and multiple unit recordings during ongoing behavior; (4) Pharmacological and viral manipulation of various brain regions via targeted guide cannula, and; (5) Optogenetic cell-type specific activation and silencing with simultaneous electrophysiological recording. In addition to the experimental advantages, the head-restraint system is relatively inexpensive and training parameters can be easily modulated to the specifications of the experimenter. The system runs on custom LabView software. In summary, our novel apparatus and protocol allows researchers to study and manipulate components of behavior, such as motivation, impulsivity, and reward-related working memory during an ongoing operant behavioral task without interference from non task-related behaviors. For more information on the custom apparatus, software or to collaborate please visit www.neuro-cloud.net/nature-precedings/dolzani.

Description: The genomes of all groups of viruses whose sequences are listed on Pubmed, specimens since 1918, analyzed by a software from Bioradar UK Ltd., contain Replikins which range in concentration from a Replikin Count (number of Replikins per 100 amino acids) of less than 1 to 30 (see accompanying communications for higher Counts in tuberculosis, malaria, and cancer, associated with higher lethality). Counts of less than 4.0 were found in ‘resting’ virus states; Counts greater than 4.0, found to be associated with rapid replication, were found invariably to accompany or to predict virus outbreaks, by as much as two years, in viral hosts examined from salmon, to birds, to livestock, to humans. X-ray diffraction showed Replikins to be on the surface of the hemagglutinin gene of influenza and to spread as the Count increased from 3.2 to 10.1, prior to, then during, the 2009 H1N1 influenza pandemic. The degree of lethality of these outbreaks was found to be a function of the statistically significant increase in Replikin Count, particularly in the influenza polymerase gene p B1 or its equivalent in other viruses. Prediction up to two years in advance of the outbreak, and the geographic location of the outbreak, now done in 7/7 trials (see Bogoch, Nature Precedings), has permitted the solid phase synthesis of Replikin vaccines in 7 days, with time to permit manufacture, adequate testing for safety and efficacy, and distribution freeze-dried to all populations. These completely synthetic Replikins vaccines so far have been shown to be effective against Taura Syndrome virus in shrimp, and H5N1 in chickens. Thus for the first time this new technology provides the practical possibility to prevent pandemics rather than just to react to them.

Description: We provide the first formalization true to the best of our knowledge to the problem of finding bicliques in a directed graph. The problem is addressed employing a two-stage approach based on an existing biclustering algorithm. This novel problem is useful in several biological applications of which we focus only on analyzing the viral-host protein interaction graphs. Strong and significant bicliques of HIV-1 and human proteins are derived using the proposed methodology, which provides insights into some novel regulatory functionalities in case of the acute immunodeficiency syndrome in human.

Description: Analysis of the electron salvation process data indicates that the electron transfer between the electron donor and acceptor is hindered by the electron salvation process. It is proposed that the electron transfer in the cell environment must be assisted by intermediate messenger called the “transport protein”.

Description: TRPC   channels   have   been   implicated   in   social   behaviors   (TRPC4)   and   anxiety   (TRPC5).   TRPC1   channels   are   widely  expressed  in  the  mammalian  brain.  TRPC1  subunits  form  heteromultimeric  channels  with  TRPC3,  4,  and   5  subunits  that  are  activated  following  Gq-­coupled  signaling  cascades.  Robust  expression  of  TRPC1  was  found   in  the  corticolimbic  areas  of  the  brain  including  the  prefrontal  cortex  (PFC),  striatum,  hippocampus  (HIP),  and  lateral septum (LS). Knock-out of TRPC1 in the brain was confirmed via immunoblots. Real-time  PCR  experiments  show  no  compensation  in  the  PFC  by  other  TRPC  channels  following  loss  of  TRPC1.  The   dense  expression  of  the  TRPC1  channels  in  the  PFC,  LS  and  HIP  led  us  to  examine  behaviors  associated  with   those  regions.  Here  we  show  no  differences  in  cocaine  mediated  behaviors  in  TRPC1-­/-­  compared  to  +/+  mice.

Description: Genomic Replikin Counts predict both the increase and the decrease of lethality of malaria

Description: The genomic Replikin Count of all the sequences on Pubmed of different strains of tuberculosis were analyzed. The lowest Counts occurred with species within the lowest drug resistance, the highest Counts with sequences of the highest drug resistance and lethality.

Description: Potential historical temporal trends in the overwinter and spring snowpack were investigated for the Canadian portions of the Okanagan and Similkameen Valleys in south-central British Columbia. Significant evidence is available that the Okanagan and Similkameen River watersheds are exhibiting both spatially and temporally heterogeneous declines in snowpacks over the past several decades, but whether the causes are part of a natural cycle or result from longer term climatic changes is not clear. The variability in the magnitude, timing, and location of any significant time trends in snowpack decline also precludes efforts towards developing reliable hydrologic models that reflect a response to potential future changes in snowpack patterns for these regions of British Columbia.

Description: Grassland management experiment (GrassMan) was set up in 2008 on a permanent semi-natural grassland in the Solling uplands, Germany. The main research focus is on the ecosystem functioning of the phytodiverse grassland (e.g. productivity and forage quality, water and nutrient fluxes). The aim of our study was to analyse the effects of vegetation composition and functional diversity on productivity and forage quality of the semi-natural permanent grassland. Variation in sward composition was achieved by herbicide application and resulted in three sward types: control sward type (without herbicide application), monocot-reduced and dicot-reduced. Further management factors included different nutrient input levels (without fertilizer and 180-30-100 kg/ha of N-P-K per year) and use intensity (cut once or three times a year). Functional diversity was determined by estimation of the yield shares for each species in the species composition and their specific functional characteristics. Forage quality was analysed by near infrared spectroscopy (NIRS). While sward type influenced the forage quality, yield variation was explained mainly by the management regime.

Description: The mechanism whereby biodiversity varies between habitats differing in productivity is a missing link between ecological and evolutionary theory with vital implications for biodiversity conservation, management and the assessment of ecosystem services. A unimodal, humped-back relationship, with biodiversity greatest at intermediate productivities, is evident when plant, animal and microbial communities are compared across productivities in nature. However, the mechanistic, evolutionary basis of this observation remains enigmatic. We show, for natural and semi-natural plant communities across a range of bioclimatic zones, that biodiversity is greatest where communities include species with widely divergent values for phenotypic traits involved in resource economics and reproductive timing, coinciding with intermediate biomass production, whilst each productivity extreme is associated with small numbers of specialised species with similar trait values. Our data demonstrate that evolution can generate a greater range of phenotypes where large, fast-growing species are prevented from attaining dominance and extreme adaptation to a harsh abiotic environment is not a prerequisite for survival.

Description: Dr. Nil Ratan Dhar Memorial LectureSoil could be perceived as a four dimensional system where a broad three dimensional structural fabric is filled by dynamic and reactive colloidal constituents. There are interconnected relationships between authegenic, neogenic and stable-phase crystallite constituents, most of which are in nano-phase, and the system seldom reaches equilibrium. Also, variations in composition, pH, and other properties make soil unique at each place. Therefore, understanding of soil system helps to develop insight into mobility and reactivity of nano-materials. The origin of nanoscience can be traced to the discovery that clay minerals were crystalline and of micrometer size. The unit cell dimensions of clay minerals are in nanometer scale in all three axes (x, y, and z). Nanoclays played a catalytic role in the synthesis of ribosome in RNA, a process that led to genesis of life on Earth. This fact makes clays the most life-compatible material in nanotechnology. Methods followed in industry (like melting materials at a high temperature) cannot be copied for agricultural nanotechnology. Yet this is no hindrance, because nanoclays obey the laws of ion exchange, adsorption-desorption, aggregation-dispersion and solubility-precipitation, to name a few. The most vital yardstick is that the nanosystem has to be capable of releasing nutrient ions in plant-available forms. Clays have both covalent and ionic bonds; a feature unique for developing passive control systems for nutrient supply mechanisms. There are numerous examples in soils, where bonds are changed from one type to another through isomorphous substitution or insertion of small ions, or by the use of organic compounds. Nanotechnology in clay system does not promise a control system such as we experience in electrical machines, or in satellites, or in chemical reactors. But, it has to be a knowledge based passive system, and for sure, it is going to create millions of rhizospheres in an acre of land to support the growth of millions of plants of a crop; a breakthrough to take agriculture into the new millennium.

Description: Grassland management experiment (GrassMan) was set up in 2008 on a permanent semi-natural grassland in the Solling uplands, Germany. The main research focus is on the ecosystem functioning of the phytodiverse grassland (e.g. productivity and forage quality, water and nutrient fluxes). The aim of our study was to analyse the effects of vegetation composition and functional diversity on productivity and forage quality of the semi-natural permanent grassland. Variation in sward composition was achieved by herbicide application and resulted in three sward types: control sward type (without herbicide application), monocot-reduced and dicot-reduced. Further management factors included different nutrient input levels (without fertilizer and 180-30-100 kg/ha of N-P-K per year) and use intensity (cut once or three times a year). Functional diversity was determined by estimation of the yield shares for each species in the species composition and their specific functional characteristics. Forage quality was analysed by near infrared spectroscopy (NIRS). While sward type influenced the forage quality, yield variation was explained mainly by the management regime.

Description: Demography and population growth are the most important subjects of population ecology and economics. Finite and intrinsic growth rates have been used as standard parameters for describing and comparing growth potentials of populations. The predation potentials of predator populations or consumption potentials of consumer populations cannot be properly described using these growth rates alone. A standard parameter is needed for the description of the predation or consumption potential, as well as for the quantitative evaluation of a predator population in an ecosystem or biological control program. We show that the finite predation rate can be the standard parameter by linking the finite rate, the stable age-stage distribution, and the age-stage specific predation rate. The finite predation rate can be used to describe and compare the predation potentials of natural enemies used in biological control and in predicting the damage potential of different pest populations to crops.

Description: Dr. Nil Ratan Dhar Memorial LectureSoil could be perceived as a four dimensional system where a broad three dimensional structural fabric is filled by dynamic and reactive colloidal constituents. There are interconnected relationships between authegenic, neogenic and stable-phase crystallite constituents, most of which are in nano-phase, and the system seldom reaches equilibrium. Also, variations in composition, pH, and other properties make soil unique at each place. Therefore, understanding of soil system helps to develop insight into mobility and reactivity of nano-materials. The origin of nanoscience can be traced to the discovery that clay minerals were crystalline and of micrometer size. The unit cell dimensions of clay minerals are in nanometer scale in all three axes (x, y, and z). Nanoclays played a catalytic role in the synthesis of ribosome in RNA, a process that led to genesis of life on Earth. This fact makes clays the most life-compatible material in nanotechnology. Methods followed in industry (like melting materials at a high temperature) cannot be copied for agricultural nanotechnology. Yet this is no hindrance, because nanoclays obey the laws of ion exchange, adsorption-desorption, aggregation-dispersion and solubility-precipitation, to name a few. The most vital yardstick is that the nanosystem has to be capable of releasing nutrient ions in plant-available forms. Clays have both covalent and ionic bonds; a feature unique for developing passive control systems for nutrient supply mechanisms. There are numerous examples in soils, where bonds are changed from one type to another through isomorphous substitution or insertion of small ions, or by the use of organic compounds. Nanotechnology in clay system does not promise a control system such as we experience in electrical machines, or in satellites, or in chemical reactors. But, it has to be a knowledge based passive system, and for sure, it is going to create millions of rhizospheres in an acre of land to support the growth of millions of plants of a crop; a breakthrough to take agriculture into the new millennium.

Description: For the broad spectrum of cognitive biological phenomena having ‘dual’ information sources, isolation from crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts at multiple scales, similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems. Entropy gradient models adapted from nonequilibrium thermodynamics lead to an index theorem in which analytic solutions of empirical equations describe different possible topological modes. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative broadcasts that link selected subsets of those structures to address problems. As for animal consciousness, the ‘stream’ of cognitive physiological broadcast is constrained by the riverbanks of embedding context, expressed in terms of systematic regularities of an enveloping environmental information source and the limitations imposed by developmental trajectory.

Description: Earlier studies have shown that the increased concentration of a new class of virus genomic peptides, Replikins, precedes and predicts virus outbreaks. We now find that the area in the genome of the highest concentration of Replikins, and the country in which this peak exists in scout viruses, have permitted in the past five years seven consecutive accurate predictions of the geographic localization of coming outbreaks, including those now realized in Mexico for H1N1, and in Cambodia for H5N1. Real-time Replikin analysis of the evolution of the virus genome identified both mutations and structural reorganization of the hemagglutinin and p B1 genes over several years before each outbreak. This information, together with the specific Replikin sequences so obtained, permitted solid-phase synthesis of Replikin vaccines in seven days, which blocked H5N1 in chickens. The information also now provides up to two years of time to thoroughly test and distribute vaccines to high risk individuals in the countries identified; thus for the first time, a quantitative genomic Replikins method to both predict initial outbreaks and to prevent the development of a pandemic.

Description: We developed an efficient “Combinatorial Strategy” for cloning different vectors with various clone sites. 1) Using originally existed clone sites from circular vectors to prepare the inserts, and if no appropriate sites are available, performing SDM to create compatible sites, to achieve maximal correct digestion of the inserts. 2) Different vectors were digested with various restriction endonucleases, and then dephosphorylated with CIP. 3) Top10 competent cells were used for transformation to increase the transformant colonies. Our results showed that, when blunt sites, or a Xba I site was adopted for ligation, the percentages of positive clones were about 50%. Whereas, when different sites, including one blunt and another Pst I sites, Not I and Xho I sites, the percentages of positive clones were nearly 100%. Using this strategy, most vectors could be successfully cloned through “one ligation, one transformation, three to five minipreps.”

Description: Alzheimer’s disease (AD) is one of the most prominent neurodegenerative disorders, particularly in elder persons over 65 age. It is characterized by progressive cognitive deterioration together with declining activities. Amyloid precursor protein (APP) cleaves at A-beta (Aβ) peptide by rate limiting factor of Beta-site APP cleaving enzyme (BACE-1) in amyloidogenic pathway. Elevated level of BACE-1 leads to the accumulation of an insoluble form of Aβ peptides (Senile Plaques), an important hallmark in the pathogenesis of Alzheimer disease. Five published inhibitors of BACE-1, thiazolidinediones, rosiglitazone, pioglitazone, Sc7 and tartaric acid are available with poor pharmacological properties and intolerable side effects. Therefore, a computational approach was undertaken to design novel inhibitors against human BACE-1. The crystal structure of human BACE-1 was retrieved from the protein data bank and optimized by applying OPLS force field in Maestro v9.2. An ASINEX database (115,000 ligands) was downloaded and compounds were prepared using LigPrep. The optimized ligand dataset was docked into the BACE-1 through sequential application of Glide HTVS, SP and XP methods that penalizes more stringently for minor steric classes subsequently. Finally, seven leads were reported and ranked based on XPGscore with better binding affinity and good pharmacological properties compared with existing inhibitors. Six leads were proposed for human BACE-1. Among the six, lead 1, with XPGscore -8.051Kcal/mol, would be intriguing for rational drug design against Alzheimer’s disease and would be highly encouraging for future Alzheimer’s therapy if tested in animal models.

Description: In this work I attempt to justify the claim that the discovery of statistically relevant brain correlates of consciousness supports Non-Reductive Physicalism. First I distinguish the main varieties of Reductive and Non-Reductive Physicalism, selecting the right one that is benefited by progress in brain sciences. Second, I discuss epistemological problems in the search of brain correlates of consciousness, focusing on the simultaneous occurrence of conscious activity, known by means of subjective report, and the corresponding brain activity, registered with the help of technology. Finally, I argue – using Salmon´s concept of Statistical Explanation – that statistics affords a distinction of causal (physical) from casual (illusory) correlations.

Description: Despite predictive success, population dynamics and evolutionary game theory still pose fundamental problems. Violation of the competitive exclusion principle in plankton communities provides an example. A promising solution of this ‘paradox of the plankton’ comes from theories involving cyclic competition, an evolutionary analogue of the classical rock-paper-scissors (RPS) game. However, modeling probabilistic RPS structures, one encounters a fundamental difficulty: the pairs rock-scissors, scissors-paper, and paper-rock possess representations in separate Kolmogorovian probability spaces, but a single global probability space for entire triplets does not exist. Populations that take part in cyclic competition should therefore involve probabilistic incompatibilities, analogous to those occurring in quantum mechanics. Here, using experimental data collected from 1990 to 2011 on the RPS cycles of lizards, we show that the incompatibilities are indeed unavoidable, and the data cannot be reconstructed from a single Kolmogorovian probability space. We then prove that the effect is genuinely quantum probabilistic, i.e. all the probabilities can be formulated in terms of a single density matrix and a set of non-commuting projectors. This formal quantum structure is dormant in games where probabilities of strategies do not entangle with probabilities of payoffs, and thus could be overlooked. In more realistic scenarios, involving games ‘with ace in a sleeve’, the non-Kolmogorovian structure can be activated. Surprisingly, lizards occasionally do play such games. In consequence, the formalism of evolutionary games, similarly to quantum mechanics, should begin with density matrix equations. Implications of our finding extend beyond lizard communities, given that RPS games are common in nature and higher dimensional RPS games may be even more common in ecosystems.

Description: A wide variety of chemicals having distinct odors are smelled by humans. Odor perception initiates in the nose, where it is detected by a large family of olfactory receptors (ORs). Based on divergence of evolutionary model a sequence of human ORs database has been proposed by D. Lancet et al (2000, 2006). It is quite impossible to infer whether a given sequence of nucleotides is a human OR or not, without any biological experimental validation. In our perspective, a proper quantitative understanding of these ORs is required to justify or nullify whether a given sequence is a human OR or not. In this paper, all human OR sequences have been quantified, and a set of clusters have been made using the quantitative results based on two different metrics. Using this proposed quantitative model, one can easily make probable justification or deterministic nullification whether a given sequence of nucleotides is a probable human OR homologue or not, without seeking any biological experiment. Of course a further biological experiment is essential to validate the probable human OR homologue.

Description: Drug Discovery is shifting focus from the industry to outside partners and in the process creating new bottlenecks, suggesting the need for a more disruptive overhaul. Technologies like high throughput screening (HTS) have moved to a larger number of academic and institutional laboratories in the US, with little apparent coordination or consideration of the outputs and creating a translational gap. While there have been collaborative public private partnerships in Europe to share pharmaceutical data, the USA has lagged behind. Sharing precompetitive computational models may be the next frontier to provide more confidence in the quality of the leads produced and attract investment. We suggest there needs to be an awareness of what research is going on in the screening centers, more collaboration and coordination. These efforts will shift the focus to finding the best researchers to fund and require a rethink of how to reward their collaborative efforts.

Description: Climate change has manifested differential impacts on various components of the earth system. The impact of climate change is not merely limited to the climatic variable. Climate change has resulted in complex, unforeseen consequences in the biosphere of earth. The silent but gradual changes arise out of varied responses of disease-causing organism to the combination of the disease-conducive environmental variables. The change is the same for both the target hosts plant as well as the animal kingdom. There is an urgent need to look into the changing disease dynamics and the disease pathogen genome sensitivity to the changes in climatic variables. The long memory of genetic makeup of disease pathogen to capture, inherit and evolve or mutate the changed or impacted gene due to climate change in generation after generation may invite a cascading effect on the next generation of biosphere. These silent but gradual changes in the genome of disease organism are rarely investigated or included in simulation models. This also enhances the risk of quantification of uncertainties of various disease simulation models. Thus, chances and lists of black swan events in life and food insecurity are on the rise.

Description: Climate change has manifested differential impacts on various components of the earth system. The impact of climate change is not merely limited to the climatic variable. Climate change has resulted in complex, unforeseen consequences in the biosphere of earth. The silent but gradual changes arise out of varied responses of disease-causing organism to the combination of the disease-conducive environmental variables. The change is the same for both the target hosts plant as well as the animal kingdom. There is an urgent need to look into the changing disease dynamics and the disease pathogen genome sensitivity to the changes in climatic variables. The long memory of genetic makeup of disease pathogen to capture, inherit and evolve or mutate the changed or impacted gene due to climate change in generation after generation may invite a cascading effect on the next generation of biosphere. These silent but gradual changes in the genome of disease organism are rarely investigated or included in simulation models. This also enhances the risk of quantification of uncertainties of various disease simulation models. Thus, chances and lists of black swan events in life and food insecurity are on the rise.

Description: Protein chemistry uses protein description and classification based on molecular mass and isoelectric point as general features. Enzymes are also compared by enzymatic reaction constants, namely Km and kcat values. Proteins are also studied by binding to different oligonucleotides. Here we suggest a simple experimental method for such a comparison of DNA binding proteins, which we call "nucleic acid-protein fingerprints". The experimental design of the method is based on an use of short oligonucleotides immobilized inside microarray of hydrogel cells – biochip. As a first stage, we solved a simple experimental task: what is the shortest single strand oligonucleotide to be recognized by protein? We tested binding of oligonucleotides from 2 to 12 bases, and we have obtained unexpected result that tetranucleotide one is long enough for specific protein binding. This 4-mer can contain two universal bases – 5-nitroindole nucleoside analogue (Ni) and only two meaningful bases, like A, G, T and C. The result obtained opens a way for constructing the simplest protein binding microarray. This microarray consists of 16 meaningful dinucleotides, like AA, AG, CT, GG etc. Physical sequences of all the nucleotides were NiNiAA, etc, where Ni is bound to gel through the amino linker. We prepared such an array and tested it for specific binding of several DNA/RNA binding proteins, labeled with fluorescent dyes like Texas Red of Bodipy. We tested RNase A and Binase for binding on the simplest microarray. It contains only 16 units, and there is a significant difference in the binding patterns. The microarray based on 3-mers must contains 64 units and must have much more specificity. The new principle of protein classification based on nucleic acid-protein recognition has been proposed and experimentally proved. Such an experimental approach must lead to a universal classification of specific DNA/RNA binding proteins.

Description: This paper presents a novel method to segment/decode DNA sequences based on n-gram statistical language model. Firstly, we find the length of most DNA “words” is 12 to 15 bps by analyzing the genomes of 12 model species. The bound of language entropy of DNA sequence is about 1.5674 bits. After building an n-gram biology languages model, we design an unsupervised ‘probability approach to word segmentation’ method to segment the DNA sequences. The benchmark of segmenting method is also proposed. In cross segmenting test, we find different genomes may use the similar language, but belong to different branches, just like the English and French/Latin. We present some possible applications of this method at last.

Description: For a broad spectrum of low level cognitive regulatory and other biological phenomena, isolation from signal crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts of interacting physiological processes at multiple scales. The argument is similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological subsystems. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative larger scale broadcasts that link selected subsets of functional modules to address problems. This multilevel dynamical viewpoint has implications for initiatives in translational medicine that have followed the implosive collapse of pharmaceutical industry ‘magic bullet’ research. In short, failure to respond to the inherently multilevel, multiscale nature of human pathophysiology will doom translational medicine to a similar implosion.

Description: For a long time ecologists have questioned the variations of biodiversity across the latitudinal gradient. Recently it has emerged that the changes in β-diversity are caused simply by changes in the sizes of species pools. I combined the species pool size and the fractal nature of ecosystems to clarify some general patterns of this gradient. Considering temperature, humidity and NPP as the main variables of an ecosystem niche and as the axis of the polygon in the Cartesian plane, it is possible to build fractal hypervolumes, whose the fractal dimension rises up to three, moving towards the equator. It follows that the best figure that graphically synthesizes the evolutionary forces that fit this ecosystem hypervolume is the fractal cauliflower.

Description: We studied the dispersion of Aedes aegypti during egg laying in natural conditions. Two independent experiments involving mosquitoes dispersing from urbanization towards adjacent un-urbanized areas were carried out and analyzed in statistical terms. We find relations between stochastic variables related to the egg laying mosquito activity (ELMA), useful to assess dispersion probabilities, despite the lack of knowledge of the total number of ovipositions in the zone. We propose to evaluate the activity as minus the logarithm of the fraction of negative ovitraps at different distances from buildings. We also estimate the average number of eggs laid per oviposition using a regression between the ELMA and the number of eggs found. Three zones with different oviposition activity were determined: a corridor surrounding the urbanized area, a second region between 10m and 25m and the third region extending from 30m to 45m from the urbanization. The landscape (plant cover) and the human activity in the area appear to have an influence in the dispersal of Aedes aegypti.

Description: Human CK2α2 is an enzyme that belongs to the Serine/Threonine protein kinase family which is involved in signal transduction. Over expression of CK2α2 causes kidney cancer therefore, human CK2α2 has been identified as a drug target for the development of potential antagonists against cancer therapy. The existing human CK2α2 inhibitors in clinical practice are having side effects like fatigue, diarrhea, nausea, anorexia and vomiting. High-throughput virtual screening is one of the most common method used to identify lead compounds was implemented in the present study to identify potential inhibitors of human CK2α2. The co-crystal structure of human CK2α2 was retrieved from the protein data bank. A 2D similarity search was performed for available five human CK2α2 inhibitors (Apigenin, VX680, Sunitinib, SUI4813 and CCK) taken from PDB and PubMed to acquire 1942 structural analogs. The 3D structural conversion and multiple confirmations for 1942 compounds were generated using LigPrep. The docking and scoring calculations were performed using Glide v5.7 which includes high throughput virtual screening (HTVS), Standard precision (SP) docking and extra precision (XP) docking. Obtained 39 leads were compared with docking scores of the existing inhibitors and proposed six leads having good binding affinity. The binding orientation of CK2α2-lead 1complex was correlating with native co-crystal structure. Hence, lead ‘1’ can be suggested as potent inhibitor against human CK2α2 involved in kidney cancer.

Description: Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and ``ancient” Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com.

Description: Peroxisome proliferator-activated receptor (PPAR γ) acts as a key regulator on adipocyte differentiation and glucose homeostasis. PPAR γ has been implicated in the pathology of type 2 diabetes. As human PPAR γ activity is considered important in improving insulin sensitivity, in silico screening was carried out to find potent agonists for human PPAR γ protein. The co-crystal structure of PPAR γ, solved through X-Ray diffraction method was retrieved from the protein data bank. Four PPAR γ agonists selected from literature were submitted to subsequent 2D searching protocol using Ligand.Info, which yielded 1699 structural analogs. The PPAR γ co-crystal structure and ligand dataset were preprocessed using protein preparation wizard and LigPrep, respectively. Further, docking was performed by using three phased docking protocol of Maestro v9.2 that implements Glide v5.7. The obtained thirteen leads through docking were compared with the existing inhibitors and seven leads with good binding affinity with PPAR γ were proposed. The binding orientations of the seven leads were coinciding well with the native co-crystal structure of human PPAR γ. Thus, the proposed seven leads can be suggested as potential agonists for improving insulin sensitivity in the treatment of type 2 diabetes mellitus if synthesized and validated in animal models

Description: Background: The consumption of diets high in calories and low in nutrient value is becoming increasingly common in modern society, which can lead to metabolic disorders like diabetes and obesity, and potentially to psychiatric disorders. We have performed studies to assess how the shift from a healthy diet rich in omega-3 fatty acids to a diet rich in saturated fatty acid affects the substrates for brain plasticity and function, and anxiety and depression-like behavior. Methods: Pregnant rats were fed with omega-3 supplemented diet from their 2nd day of gestation period as well as their male pups for 12 weeks. Afterwards, the animals were randomly assigned to either a group fed on the same diet or a group fed on a high-fat diet (HFD) rich in saturated fats for 3 weeks. Anxiety and depression-like behaviors were assessed by using open field (OF) and elevated plus maze (EPM). Molecular assessments were performed in the frontal cortex and hippocampus as dysfunctions in these brain regions are main contributors towards depression, anxiety-like behavior and stress. Results: We found that the HFD increased vulnerability for anxiety and depression-like behavior, and that these modifications harmonized with changes in the anxiety-related neuropeptide Y (NPY)-1 receptor. The HFD reduced levels of brain-derived neurotrophic factor (BDNF), and the BDNF signaling receptor pTrkB, as well as the cyclic AMP response element binding protein (CREB), in these brain regions. Brain DHA contents were significantly associated with the levels of anxiety and depression-like behavior in these rats. Conclusions: These results suggest that the change in dietary lifestyle leading to alteration of dietary n3/n-6 fatty acids levels imposes a risk factor for anxiety-like behaviors. Dietary DHA might help for building cognitive reserve that can resist psychiatric disorders.