bluuebunny/crossref_metadata_2025 huggingface dataset:
Metatranscriptomics of the prokaryotic community in response to atmospheric deposition in the Western North Pacific Ocean
Authors: Tan Shangjin , Shun Yan Shun Yan , Ho Tung-Yuan , Liu Hongbin
Published: January 2018

Atmospheric deposition represents a major vector of both macro- and micro-nutrients to the oligotrophic open oceans, potentially imposing a profound impact on the functioning of the microbial community. Whereas responses of the prokaryotes to atmospheric deposition are being studied at the community level, corresponding functional changes are essentially unknown. Here we used metatranscriptomic approaches to elucidate taxonomic and functional profiles of the prokaryotic community in response to Asian aerosols in the Western North Pacific Ocean. While Bacteria were downrepresented, Virus and Archaea were overrepresented in the aerosol treatment compared to the control. Within Bacteria, transcripts related to Cyanobacteria, including Prochlorococcus, Trichodesmium and Synechococcus, decreased dramatically, whereas transcripts related to Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes showed differential increases in the aerosol treatment. Nutrients and organic matters were enriched as evidenced by an overexpression of transporters for amino acids and utilization of various carbohydrates and a down-expression of transcripts related with phosphorus metabolism. Increased expression included transcripts involved in tricarboxylic acid cycle, pentose phosphate pathway, glycolysis and gluconeogenesis. Unexpectedly, the expression of transcripts associated with Fe metabolism suggested that Fe limitation was intensified. Transcripts associated with N fixation declined, corresponding to the decline of diazotroph-related transcripts. This result is against the paradigm of Fe fertilization from atmospheric deposition but may represent an extreme case that Fe was scavenged after aerosol addition. Negative effects included impaired sugar utilization and the stimulation of oxidative stress and heavy metal toxicity. All these changes lead the community to an energy-conserving lifestyle and promoted motility, chemotaxis and interspecies competition and interaction. The results provide new insights into the biogeochemical impacts of atmospheric deposition in the Western North Pacific Ocean.
Diversification patterns in the North Andean Block: a perspective from biogeographical hypotheses
Authors: Ayus Ortiz Viviana L , Miranda-Esquivel Daniel R
Published: January 2018

We used 637 species from six taxonomic classes to identify the pattern(s) of diversification, occurring in the North Andean Block estimating phylogenetic relationships, divergence times, dispersal-vicariance events, and ancestral distributions. We assessed four hypotheses that explain the diversification in the NAB. For each hypothesis, we specified: three sets of unequal rates of dispersal between areas and a temporal stratification, containing four-time intervals for the Miocene. The North Andean taxa showed three ancestral distributions such as the Amazonian region, Central America, and Central Andes where we recovered the major dispersal events. The pattern from North Andean Cordilleras to lowlands fit better the diversification inside the NAB. However, according to the smaller log-likelihood deltas obtained between hypotheses, the taxa followed two patterns, from lowlands to highlands and vice-versa. We found seven out of 15 groups that diversified at the rhythm of the North Andean uplift showing different times to reach each Cordillera. The south-to-north pattern was supported by 80% of the groups. Furthermore, exchanges between South and Central America were identified occurring between 15 to 10 Ma. The two altitudinal patterns from lowlands to North Andean Cordilleras and vice-versa are plausible regardless the ancestral area estimated, and these patterns occurred multiple times in the same temporal frame (Miocene). However, the pattern from North Andean Cordilleras to lowlands fit better which might support a highlands origin inside or outside the NAB. Finally, the North Andean taxa followed the mountain building scenario, where the Central Cordillera raised first, later the Western Cordillera, and last the Eastern Cordillera.
Activation of Rho-kinase and focal adhesion kinase regulates the organization of stress fibers and focal adhesions in the central part of fibroblasts
Authors: Katoh Kazuo
Published: January 2018

Specific regulation and activation of focal adhesion kinase (FAK) are thought to be important for focal adhesion formation, and activation of Rho-kinase has been suggested to play a role in determining the effects of FAK on the formation of stress fibers and focal adhesions. To clarify the role of FAK in stress fiber formation and focal adhesion organization, we examined the formation of new stress fibers and focal adhesions by activation of Rho-kinase in FAK knockout (FAK–/–) fibroblasts. FAK–/– cells were elliptical in shape, and showed reduced numbers of stress fibers and focal adhesions in the central part of the cells along with large focal adhesions in the peripheral regions. Activation of Rho-kinase in FAK–/– cells transiently increased the actin filaments in the cell center, but these did not form typical thick stress fibers. Moreover, only plaque-like structures as the origins of newly formed focal adhesions were observed in the center of the cell. Furthermore, introduction of an exogenous GFP-labeled FAK gene into FAK–/– cells resulted in increased numbers of stress fibers and focal adhesions in the center of the cells, which showed typical fibroblast morphology. These results indicated that FAK plays an important role in the formation of stress fibers and focal adhesions as well as in regulation of cell shape and morphology with the activation of Rho-kinase.
Diversity of fish sound types in the Pearl River Estuary, China
Authors: Wang Zhi-Tao , Nowacek Douglas , Akamatsu Tomonari , Wang Kexiong , Liu Jian-Chang , Duan Guo-Qin , Cao Han-Jiang , Wang Ding
Published: January 2018

Background. Repetitive species-specific sound enables the identification of the presence and behavior of soniferous species by acoustic means. Passive acoustic monitoring has been widely applied to monitor the spatial and temporal occurrence and behavior of calling species. Methods. Underwater biological sounds in the Pearl River Estuary, China, were collected using passive acoustic monitoring, with special attention paid to fish sounds. A total of 1408 suspected fish calls comprising 18,942 pulses were qualitatively analyzed using a customized acoustic analysis routine. Results. We identified a diversity of 66 types of fish sounds. In addition to single pulse, the sounds tended to have a pulse train structure. The pulses were characterized by an approximate 8 ms duration, with a peak frequency from 500 to 2600 Hz and a majority of the energy below 4000 Hz. The median inter-pulsepeak interval (IPPI) of most call types was 9 or 10 ms. Most call types with median IPPIs of 9 ms and 10 ms were observed at times that were exclusive from each other, suggesting that they might be produced by different species. According to the literature, the two section signal types of 1+1 and 1+N10 might belong to big-snout croaker (Johnius macrorhynus), and 1+N19 might be produced by Belanger's croaker (J. belangerii). Discussion. Categorization of the baseline ambient biological sound is an important first step in mapping the spatial and temporal patterns of soniferous fishes. The next step is the identification of the species producing each sound. The distribution pattern of soniferous fishes will be helpful for the protection and management of local fishery resources and in marine environmental impact assessment. Since the local vulnerable Indo-Pacific humpback dolphin (Sousa chinensis) mainly preys on soniferous fishes, the fine-scale distribution pattern of soniferous fishes can aid in the conservation of this species. Additionally, prey and predator relationships can be observed when a database of species-identified sounds is completed.
Cannabis chemovar classification: terpenes hyper-classes and targeted genetic markers for accurate discrimination of flavours and effects
Authors: Henry Philippe
Published: January 2018

The classification of Cannabis varieties has been increasingly discussed in the past years, particularly in the wake of emerging legal markets, with implications for intellectual property development, marketing and improvement of the scientific understanding of this contentious plant. While the concept of chemovars has been proposed and has gained popularity of late, the lack of guidance in introducing this concept and the fact that chemovars are based on indirectly assessed traits with a heritable basis has likely impeded the implementation of the concept to a broader audience. Here I propose a simplified version of terpene hyper-classes based on three dominant terpenes that is shown to outperformed the classic indica-sativa-hybrid scheme of classification as well as a recently proposed terpene super-class scheme. This information was used to identify the most informative genetic markers for chemovar classification based on the terpene hyper-classes. I demonstrate the ability of clearly clustering accessions based on their dominant terpene and propose to extent this approach as a benchmark for chemovar classification in lieu of previously proposed models.
Population structure and phenotypic variation of Sclerotinia sclerotiorum from dry bean (Phaseolus vulgaris) in the United States
Authors: Kamvar Zhian N , Amaradasa Bimal S , Jhala Rachana , McCoy Serena , Steadman James R , Everhart Sydney E
Published: January 2018

The ascomycete pathogen Sclerotinia sclerotiorum is a necrotrophic pathogen on over 400 known host plants, and is the causal agent of white mold on dry bean. Currently, there are no known cultivars of dry bean with complete resistance to white mold. For more than 20 years, bean breeders have been using white mold screening nurseries with natural populations of S. sclerotiorum to screen new cultivars for resistance. It is thus important to know if the genetic diversity in populations of S. sclerotiorum within these nurseries a) reflect the genetic diversity of the populations in the surrounding region and b) are stable over time. Furthermore, previous studies have investigated the correlation between mycelial compatibility groups (MCG) and multilocus haplotypes (MLH), but none have formally tested these patterns. We genotyped 366 isolates of S. sclerotiorum from producer fields and white mold screening nurseries surveyed over 10 years in 2003–2012 representing 11 states in the United States of America, Australia, France, and Mexico at 11 microsatellite loci resulting in 165 MLHs. Populations were loosely structured over space and time based on analysis of molecular variance and discriminant analysis of principal components, but not by cultivar, aggressiveness, or field source. Of all the regions tested, only Mexico (n=18) shared no MLHs with any other region. Using a bipartite network-based approach, we found no evidence that the MCGs accurately represent MLHs. Our study suggests that breeders should continue to test dry bean lines in several white mold screening nurseries across the US to account for both the phenotypic and genotypic variation that exists across regions.
A Gene Set Enrichment Analysis of multiomic celiac disease data
Authors: Del Prete Eugenio , Facchiano Angelo , Liò Pietro
Published: January 2018

Celiac disease is a chronic condition, which can be described as inflammatory and autoimmune. The well-known treatment is a lifelong gluten-free diet, but it can be not totally effective for a high percentage of the patients. The aim of this work is to approach the celiac disease complexity from a bioinformatics point of view. The idea is to analyse the state of the art from GEO online repository and revisit the works, by integrating gene expression data and Gene Ontology (GO) terms.

Gene Set Enrichment Analysis (GSEA) is a set of statistical methods to classify genes in groups, which are related to common biological function, chromosomal location or regulation. The work is developed in R environment. The packages are downloaded by the online repository Bioconductor. The studies are not standardized. In these circumstances, the candidate genes subset is chosen with a trade-off among all the scores, thus the creation of a GO graph eludes the Fishers exact test, keeping its biological importance to define process clusters.

A little framework on the biological processes involved in each study on celiac disease is suggested: GSE11501, peptidyl-tyrosine phosphorylation, phosphatidylinositol 3-kinase signaling, and response to endoplasmic reticulum stress; GSE87629, mitosis regulation, microtubule cytoskeleton organisation, and protein destabilization; GSE72625, signaling pathway and cellular response about interferon-gamma; GSE61849a, immune response and immune system development; GSE61849b, protein phosphorylation, apoptotic process, and regulation of cell adhesion; GSE76168, cytokine mediate signaling pathways.
Interaction of antimutagenic 1,4-dihydropyridine AV-153-Na with DNA and DNA-damaging molecules and its impact on DNA repair activity
Authors: Leonova Elina , Rostoka Evita , Sauvaigo Sylvie , Smelovs Edgars , Baumane Larisa , Borisovs Vitalijs , Selga Turs , Sjakste Nikolajs
Published: January 2018

1,4-dihydropyridines (1,4-DHP) possess important biochemical and pharmacological properties, including antioxidant and antimutagenic activities. Interaction of some 1,4-DHP with DNA was recently reported. AV-153-Na, an antimutagenic and DNA-repair-enhancing compound appeared to be able to interact with DNA by intercalation. The aim of the current study was to characterize DNA’s capacity for the binding of AV-153-Na, and using different approaches, to test intracellular distribution of the compound, to test the ability of the compound to scavenge peroxynitrite and hydroxyl radical and to assess the ability of the compound to modify the activity of DNA repair enzymes. The DNA binding activity of AV-153-Na was determined by means of fluorescence assay. Titration of the AV-153-Na solutions with DNA gradually increased fluorescence of the solution, indicating direct interactions of the molecule with DNA. AV-153-Na quenched the fluorescence of ethidium bromide and DNA complex, which points to intercalation binding mode. Binding via intercalation was confirmed by means of cyclic voltammetry and circular dichroism spectroscopy. The compound could interact with the four DNA bases in vitro, manifesting a higher affinity to guanine. Some ability to scavenge hydroxyl radical by AV-153-Na was detected by the EPR method. AV-153-Na turned out to be incapable of reacting chemically with peroxynitrite. However, AV-153-Na effectively decreased DNA damage produced by peroxynitrite in cultured HeLa cells. The effects of AV-153-Na on the activity of DNA repair enzymes were tested using Glyco-SPOT and ExSy-SPOT assays. The Glyco-SPOT test essentially revealed an inhibition by AV-153-Na of the enzymes involved thymine glycol repair. Results with ExSy-SPOT chip indicate that AV-153-Na significantly stimulates excision/synthesis repair of 8-oxoguanine (8-oxoG), abasic sites (AP sites) and alkylated bases. Laser confocal scanning fluorescence microscopy demonstrated that within the cells AV-153-Na was found mostly in the cytoplasm; however, a stain in nucleolus was also detected. Binding to cytoplasmic structures might occur due to high affinity of the compound to protein, revealed by fluorescence spectroscopy titration and circular dichroism. Activation of DNA repair enzymes after binding to DNA appears to be the basis for the antimutagenic effects of AV-153-Na.
Density and population viability of coastal marten: a rare and geographically isolated small carnivore
Authors: Linnell Mark A , Moriarty Katie , Green David S , Levi Taal
Published: January 2018

Pacific martens (Martes caurina) in coastal forests of Oregon and northern California in the United States are rare and geographically isolated, prompting a petition for listing under the Endangered Species Act. If listed, regulations have the potential to substantially influence land-use decisions and forestry on public and private lands, but no estimates of population size, density, and viability of remnant marten populations are available for evaluating their conservation status. We used GPS telemetry, territory mapping, and spatial mark-recapture to estimate population size and density within the current extent of Pacific martens in central Oregon, within coastal forest in the Oregon dunes national recreational area. We then estimated population viability at differing levels of human-caused mortality (e.g. roadkill). We estimated 63 adult martens (95% Credible Interval: 58-73) and 73 (range: 46-91) potential territories across two subpopulations separated by a large barrier (Umpqua River). Marten density was 1.02 per km2, the highest reported in North America. Using population viability analysis, extinction risk for a subpopulation of 30 martens ranged from 34% to 100% with two or more annual human-caused mortalities. Absent broad-scale restoration of forest to conditions which support marten populations, limiting human-caused mortalities would likely have the greatest conservation impact.
Evolutionary relationships of microbial transglutaminases
Authors: Giordano Deborah , Facchiano Angelo
Published: January 2018

Transglutaminases (TGases) are a class of enzyme widely spread in nature, and observed in plants, microorganisms, vertebrates and invertebrates. This enzyme catalyzes post-translational protein modification, by acyl transfer reactions, deamidation and crosslinking (polymerisation). There is a large interest for TGases functions, in particular for human TGases and their involvement in physiopathological processes. In bacteria, TGases appear largely present, although the function of this enzyme is still unknown. Microbial TGases (MTG, or MTGase) are of extreme interest, in particular MTGase from Streptomyces mobaraensis, used in biopolymers industry, in cosmetics production, in wool textiles, and in the food processing. We present the results of bioinformatics analysis on MTGases sequences, based on database searching, sequence comparisons and alignments, phylogenetic tree constructions, with the aim of improving the knowledge of MTGases, in the perspective of investigating by protein modelling and simulations techniques the functional features.
Visualizing mutation occurrence using Big Data
Authors: Albert Silvana Iuliana
Published: January 2018

The volume of collected genetic data has been growing exponentially in the past few years and we need to improve the way we store, analyze and visualize it in order to be able to draw relevant conclusions that could improve the life quality of people. Extracting patterns and predicting future mutations and their impact will rely heavily on the efficient use of Big Data. Often a mutation on its own cannot provide enough information about a disorder or disease. Only if we combine the genetic information with the organism’s environment we can draw some conclusions about penetrance and expressively of the mutation. Because many genes can cause a single disease and at the same time a single gene can cause multiple diseases, we need to analyze the whole context of a person.

In this work, a distributed solution that provides demographics and metrics about diagnostics and mutations is pro posed. Seeing the occurrence of a mutation in a particular geographic region can help medical special ists narrow down the search for a patient’s mutations without sequencing the whole genome.
Behavior and biocompatibility of rabbits bone marrow mesenchymal stem cells with bacterial cellulosic membrane
Authors: Alencar Marcello Silva , Carvalho Yulla Klinger , Carvalho Camila Ernanda , Feitosa Matheus Tajra , Carvalho Fernando Aécio de Amorim , Viana Bartolomeu Cruz , Miglino Maria Angélica , Jozala Ângela Faustino , Carvalho Maria Acelina
Published: January 2018

Introduction: Tissue engineering is being redesigned through promising studies that present great potential to create biomaterials capable of forming functional tissues. The cellular expansion and integration depends very much on the quality and adequacy of the surface of the scaffold being determinant for the success in the biological implants. The objective of this research was to characterize and evaluate in vitro the behavior of rabbits Bone Marrow Mesenchymal Stem Cells (BMMSC) when associated with Bacterial Cellulose Membrane (BCM) verifying the adhesion, expansion, cells integration into the biomaterial and the capacity macrophage activation as well as the evaluation of the bacterial cellulosic membrane cytotoxicity and toxicity. Materials and methods: Samples of rabbit bone marrow and mesenchymal stem cells were collected and mesenchymal stem cells were isolated from the medullary aspirates for fibroblast colony forming unit (CFU-F) assays, osteogenic and chondrogenic cellular differentiation induction, cellular integration study to the bacterial cellulosic membrane by Scanning Electron Microscopy (SEM) in the time interval of 1, 7 and 14 days as well as cytotoxicity (NO induction), BCM toxicity (MTT) and phagocytic activity. Results: The CFC-F assay showed cells with fibroblastoid morphology organized in colonies distributed across the culture area surface. In the growth curve two phases (lag and log) were observed in the course of 15 days. The cells multipotentiality was evident after osteogenic and chondrogenic lineages induction. Regarding the BMMSC bioelectrical integration to BCM, in the first 24 hours, the BMMSC were anchored in the BCM. On the seventh day of culture the cytoplasm was scattered and on fourteenth day the cells were fully integrated into the biomaterial. In the phagocytic activity assay there was a significant macrophages activation and for the nitric oxide concentrations and MTT analysis no cytotoxic biomaterial was observed. Conclusion: The bacterial cellulosic membrane allowed the bone marrow progenitor cells expansion and biointegration with stable cytotoxic profile thus presenting itself as biomaterial with potential for tissue engineering.
Male aggressiveness as intrasexual contest competition in 78 societies.
Authors: Carter Tara-Lyn , Kushnick Geoff
Published: January 2018

Sexual selection favors traits that increase mating and, thus, reproductive success. Some scholars have suggested that intrasexual selection driven by contest competition has shaped human male aggression. If this is the case, one testable hypothesis is that beliefs and behavior related to male aggression should be more prevalent in societies where the intensity and strength of sexual selection is higher, as measured by factors such as: (a) the presence and scope of polygyny; (b) the number of same-sex competitors relative to potential mates; and, (c) the amount of effort males have available to allocate to mating. Using mixed-effect linear regression models with data from 78 societies from the Standard Cross-Cultural Sample, we found mixed support for the hypothesis using individual variables related to male aggression, but strong support when using a composite measure of male ‘aggressiveness’. We ruled out some potential alternative explanations by controlling for spatial autocorrelation, and confounding variables such as political complexity and warfare.
Emulation of surgical fluid interactions in real-time
Authors: Stredney Donald , Hittle Bradley , Medina-Fetterman Hector , Kerwin Thomas , Wiet Gregory
Published: January 2018

The surgical skills required to successfully maintain hemostasis, the control of operative blood, requires considerable deliberate practice. Hemostasis requires the deft orchestration of bi-dexterous tool manipulation. We present our approach to computationally emulate both irrigation and bleeding associated with neurotologic surgical technique. The overall objective is to provide a visually plausible, three dimensional, real-time simulation of bleeding and irrigation in a virtual otologic simulator system. The results present a unique simulation environment for deliberate study and practice.
Comparative transcriptomic analysis of heterophylly of the aquatic plant Potamogeton octandrus (Potamogetonaceae)
Authors: He Dingxuan , Guo Pin , Gugger Paul F , Guo Youhao , Liu Xing , Chen Jinming
Published: January 2018

Many plant species exhibit heterophylly, displaying different leaves upon a single plant. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, were sequenced using a high-throughput sequencing technique (RNA-Seq), which aims to assist with the gene discovery and functional studies of genes involved in heterophyllous leaf development. A total of 81,103 unigenes were identified from the submerged and floating leaves, and a total of 6,822 differentially expressed genes (DEGs) were identified by comparing the samples from each developmental stage. KEGG pathway enrichment analysis categorized these unigenes into 128 pathways (p-value < 10-5). A total of 24,025 differentially expressed genes were involved in the carbon metabolic pathway, biosynthesis of amino acids, ribosomes, and plant-pathogen interaction. KEGG pathway enrichment analysis categorized a total of 70 DEGs into plant hormone signal transduction pathways. This study describes the initial results of the high-throughput transcriptome sequencing of heterophylly. Understanding the transcriptomes of floating and submerged leaves of the aquatic plant P. octandrus will assist with gene cloning and functional studies of genes involved in leaf development. This is especially the case with those involved in heterophyllous leaf development.
Brain network connectivity underlying decisions between the "lesser of two evils"
Authors: Mills-Finnerty Colleen , Hanson Catherine , Hanson Stephen J
Published: January 2018

In daily life we are often forced to choose between the “lesser of two evils,” yet there remains limited understanding of how the brain encodes choices between aversive stimuli, particularly choices involving hypothetical futures. We tested how choice framing affects brain activity and network connectivity by having participants make choices about individualized, aversive, hypothetical stimuli (i.e. illnesses, car accidents, etc.) under approach and avoidance frames (“which would you rather have/avoid”) during fMRI scanning. We tested whether limbic and frontal regions show patterns of signal intensity and network connectivity that differed by frame, and compared this to response to similar appetitive choices involving appetitive preferences (i.e. hobbies, vacation destinations). We predicted that regions such as the insula, amgydala, and striatum would respond differently to approach vs. avoidance choices during aversive hypothetical choices. We identified activations for both choice frames in areas broadly associated with decision making, including the putamen, insula, and anterior cingulate, as well as deactivations in areas shown to be sensitive to valence, including the amygdala, insula, prefrontal cortex, and hippocampus. Connectivity between brain regions differed based on choice frame, with greater connectivity among deactive regions including the amygdala, insula, and ventromedial prefrontal cortex during avoidance frames compared to approach frames. These differences suggest that approach and avoidance frames lead to different behavioral and brain network response when deciding which of two evils are the lesser.
Linear time-varying Luenberger observer applied to diabetes
Authors: Orozco López Onofre , Castañeda Hernández Carlos Eduardo , Rodríguez Herrero Agustín , García Saéz Gema , Hernando María Elena
Published: January 2018

We present a linear time-varying Luenberger observer (LTVLO) using compartmental models to estimate the unmeasurable states in patients with type 1 diabetes. The LTVLO proposed is based on the linearization in an operation point of the virtual patient (VP), where a linear time-varying system is obtained. LTVLO gains are obtained by selection of the asymptotic eigenvalues where the observability matrix is assured. The estimation of the unmeasurable variables is done using Ackermann's methodology. Additionally, it is shown the Lyapunov approach to prove the stability of the time-varying proposal. In order to evaluate the proposed methodology, we designed three experiments: A) VP obtained with the Bergman minimal model; B) VP obtained with the compartmental model presented by Hovorka in 2004; and C) real patients data set. For experiments A) and B), it is applied a meal plan to the VP, where the dynamic response of each state model is compared to the response of each variable of the time-varying observer. Once the observer is evaluated in experiment B), the proposal is applied to experiment C) with data extracted from real patients and the unmeasurable state space variables are obtained with the LTVLO. LTVLO methodology has the feature of being updated each instant of time to estimate the states under a known structure. The results are obtained using simulation with MatlabTM and SimulinkTM. The LTVLO estimates the unmeasurable states from in silico patients with high accuracy by means of the update of Luenberger gains at each iteration. The accuracy of the estimated state space variables is validated through fit parameter.
Shifting from closed-source graphical-interface to open-source programming environment: a brief tutorial on running Maxent in R
Authors: Feng Xiao , Gebresenbet Fikirte , Walker Cassondra
Published: January 2018

Ecological niche modeling (ENM) is increasingly being used in studying the relationship between species distributions and environmental conditions. The development of ENM software/algorithms is heading toward open-source programming, for the advantage of efficiency in handling big data and incorporating new methods. Maxent is one of the commonly used ENM algorithms, but there has been limited information and efforts in implementing Maxent in an open-source programming environment (e.g., R). Therefore, we aim to fill the gap of knowledge for using Maxent in R. More specifically, we demonstrate the general implementation of Maxent in R based on a commonly used ENM procedure, provide a function that bridges the Maxent algorithm and R computing environment for easier use, and demonstrate the manipulation of a few crucial Maxent parameters in R. We expect our efforts will promote a shift of the Maxent user community from a graphical-interface to open-source programming.
Effects of novel bacteriophage on red abalone (Haliotis rufescens) and white abalone (H. sorenseni) exposed to Candidatus Xenohaliotis californiensis – the causative agent of abalone withering syndrome
Authors: Vater Ashley , Byrne Barbara A , Marshman Blythe C , Ashlock Lauren W , Moore James D
Published: January 2018

The Rickettsiales-like prokaryote - Candidatus Xenohaliotis californiensis (Ca. Xc) – has decimated black abalone populations along the Pacific coast of North America. White abalone, – Haliotis sorenseni – are also susceptible and nearly extinct in the wild due to overfishing in the 1970s. Candidatus Xenohaliotis californiensis proliferates in epithelial cells of the abalone gastrointestinal tract and causes clinical signs of starvation. In 2012, evidence of a putative phage associated with Ca. Xc in Haliotis rufescens was described. In this study, we investigated the virulence of Ca. Xc in red and white abalone at different environmental temperatures in the presence of phage. Using a comparative experimental design, we observed differences over time between the two abalone species in mortality, body condition, and bacterial load by quantitative real time PCR (qPCR). By day 251, all white abalone exposed to the Ca. Xc and its phage in the warm water (18.5ºC) treatment died, while red abalone exposed to the same conditions had a mortality rate of 10% despite a relatively heavy bacterial burden as determined by qPCR of posterior esophagus tissue and histological assessment at the termination of the experiment. These data support the phage as a protective and potentially therapeutic agent for withering syndrome in red abalone, while white abalone appear to remain susceptible to this disease even in phage presence. These findings have important implications for implementation of a white abalone recovery program, particularly with respect to the thermal regimes of locations where captively-reared individuals will be outplanted.
The energetic costs of mounting an immune response in Pallas’s long-tongued bat (Glossophaga soricina)
Authors: Cabrera-Martinez Lucia , Herrera M. L. Gerardo , Cruz Neto Ariovaldo
Published: January 2018

Activation of immune response has been long assumed to be an energy-costly process but direct measures of changes in metabolic rate after eliciting immune response disputes the universality of this assertion. The acute phase response (APR) is the first line of defense of the vertebrate immune system against pathogens and is thought to be energetically costly. Measures of APR energetic cost in birds are higher than in rodents suggesting that this response is less expensive and important for mammals. However, large increase in metabolic rate after APR activation measured in a piscivorous bat species (Myotis vivesi) suggests that immune response is unusually costly for bats. Here we quantified the energetic cost and body mass change associated with APR in the nectarivorous Pallas’s long-tongued bat Glossophaga soricina and compared with values previously measured for piscivorous bats and other vertebrates. APR activation implied an energy cost for G. soricina as indicated by a short-term decrease in body mass and an increase in resting metabolic rate (RMR). However, the increase in RMR was far from the large increase detected in piscivorous bats and it was similar to the highest values measured in birds. Caloric cost of APR represented only 2% of the total daily energy expenditure estimated for G. soricina. Overall our results suggest that the costs of APR for bats may vary interespecifically probably in relation to feeding habits. Measurement of the energy cost of vertebrate immune response is limited to a few species and further work is warranted to evaluate its significance for the animal´s energy budget.
A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus
Authors: Kong Hanghui , Liu Wanzhen , Yao Gang , Gong Wei
Published: January 2018

The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψrps19 and Ψycf1 were in the LSC/IR/SSC boundaries, Ψrps16 and ΨinfA in the LSC region, and Ψycf15 in the IRb region. The nucleotide variability (Pi) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58 – 62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species.
A historical legacy of antibiotic utilization on bacterial seed banks in sediments
Authors: Madueño Laura , Paul Christophe , Junier Thomas , Bayrychenko Zhanna , Filippidou Sevasti , Beck Karin , Greub Gilbert , Bürgmann Helmut , Junier Pilar
Published: January 2018

The introduction of antibiotics for both medical and non-medical purposes has had a positive effect in human welfare and agricultural output in the past century. However, there is also an important legacy in the use and disposal of antimicrobial agents in natural ecosystems. This historical legacy was investigated by quantifying two antibiotic resistance genes (ARG) conferring resistance to tetracycline (tet(W)) and sulfonamide (sul1) in bacterial seed bank DNA in sediments. The industrial introduction of antibiotics caused an abrupt increase in the total abundance of tet(W) and a steady increase in sul1. The abrupt change in tet(W) corresponded to an increase in relative abundance from ca. 1960 that peaked around 1976. This pattern of accumulation was highly correlated with the abundance of specific members of the seed bank community belonging to the Phylum Firmicutes. In contrast, the relative abundance of sul1 increased after 1976. This correlated with a taxonomically broad spectrum of bacteria, reflecting sul1 dissemination through horizontal gene transfer. The accumulation patterns of both ARGs correspond to the temporal scale of medical antibiotic use. Our results show that the bacterial seed bank can be used to look back at the historical usage of antibiotics and resistance prevalence.
Which melodic universals emerge from repeated signaling games?
Authors: Ravignani Andrea , Verhoef Tessa
Published: January 2018

Language and music are peculiar human behaviors. We spend a large portion of our lives speaking, reading, processing speech, performing music and listening to tunes. At the same time, we still know very little as to why and how these structured behaviors emerged in our species. For the particular case of music, the mystery is even greater than language. Music is a widespread human behavior which does not seem to confer any evolutionary advantage. A possible approach to study the origins of music is to hypothesize and empirically test the mechanisms behind this structured behavior [1, 2]. For language, potential mechanisms were first tested in-silico [3, 4], showing how random pairs of signal-meanings become more structured and systematic when artificial agents play a ‘game of telephone’ with them. These results were replicated with human participants evolving a language-like system [5], confirming the importance of computer simulations in testing hypotheses on the cultural evolution of human behavior. Finally, recent work applied this approach to musical rhythm [6], showing that musical structures can indeed emerge via cultural transmission. A recent paper in Artificial Life adopted this methodological approach, testing the emergence of a sound system at the boundary between music and language [7]. Similar to communication systems found in humans, other animals and in-silico experiments, a meaning space was paired with a signal space. The meaning space coincided with a set of pictures showing different facial emotional expressions. The signal space was a set of 5-note patterns. Crucially, the experimenters randomly paired meanings to signals, which were in turn randomly structured. These random pairings of emotional expressions and random note sequences were then used in signaling games, where pairs of participants used note sequences to communicate emotional states. The resulting signal-meaning pairs, with all their human-introduced variations, were then used in new signaling games with new participants. Over time, the small biases introduced in each artificial transmission step accumulated, displaying quantitative trends. In particular, the authors found the emergence, over the course of artificial human generations, of features resembling some properties of language and music.
The mathematics of extinction across scales: from populations to the biosphere
Authors: Carlson Colin , Burgio Kevin , Dallas Tad , Getz Wayne
Published: January 2018

The sixth mass extinction poses an unparalleled quantitative challenge to conservation biologists. Mathematicians and ecologists alike face the problem of developing models that can scale predictions of extinction rates from populations to the level of a species, or even to an entire ecosystem. We review some of the most basic stochastic and analytical methods of calculating extinction risk at different scales, including population viability analysis, stochastic metapopulation occupancy models, and the species area relationship. We also consider two major extensions of theory: the possibility of evolutionary rescue from extinction in a changing environment, and the posthumous assignment of an extinction date from sighting records. In the case of the latter, we provide a new example using data on Spix's macaw (Cyanopsitta spixii), the "rarest bird in the world," to demonstrate the challenges associated with extinction date research.
Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing
Authors: O'Connell Lauren , Gao Song , McCorquodale Donald , Fleisher Jay , Lopez Jose V
Published: January 2018

Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution and nutrients to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities (“microbiomes”) in major port inlets is important due to their impacts on surrounding marine environments. We hypothesize annual microbial fluctuations based on seasons (wet vs dry), assessed by high throughput 16S rRNA amplicon library sequencing. Surface water samples were collected weekly for one year, creating a high sampling frequency and fine sampling scale. Over 1.4 million 16S rRNA V4 reads generated a total of 16,384 Operational Taxonomic Units (OTUs) from the PEI habitat. We observed Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria as the most dominant phyla. Analysis of potentially pathogenic genera show the presence of Staphylococcus and Bacillus, albeit at lower relative abundances during peak shipping and tourist months (November –April), thus underscoring their relatively low presence. Statistical analyses indicated significant alpha diversity differences when comparing microbial communities with respect to time. This observation probably stems from the low community richness and abundance in August, which had lower than average rainfall levels for Florida’s wet season. The lower rainfall levels may have contributed to less runoff, and subsequently fewer bacterial groups being introduced into the port surface waters. Bacterioplankton beta diversity differed significantly by month and season. The 2013-2014 dry season (October-April), was warmer and wetter than historical averages, which may have driven the significant differences in beta diversity. Increased nitrogen and phosphorous concentrations were also observed in these months, possibly creating favorable bacterial growth conditions. To our knowledge, this study represents the first to sample a large port at this fine sampling scale. These data can help establish underlying inlet microbial community baselines, and supplement the vital monitoring of local marine and recreational environments, which appears more poignant in the context of local reef disease outbreaks and worldwide coral reef collapses in the wake of a harsh 2015-16 El Nino event.
Generation and characterisation of temperature sensitive mutants of genes encoding the fission yeast spindle pole body
Authors: Tang Ngang Heok , Fong Chii Shyang , Masuda Hirohisa , Jourdain Isabelle , Yukawa Masashi , Toda Takashi
Published: January 2018

The spindle pole body (SPB) in fungi is the equivalent of the animal centrosome. A number of previous studies have identified many, if not all, components of the SPB. The SPB is the structural platform for microtubule nucleation and plays important roles, both in mitosis and meiosis. The SPB is absolutely essential for cell survival and its abnormalities give rise to aberrant cell division and morphogenesis. Therefore, it is crucial to understand how the SPB organises itself and how the functions of individual SPB components are regulated. We report here a procedure to generate temperature sensitive mutants in the fission yeast, Schizosaccharomyces pombe. The approach has proved useful to characterise functions of individual SPB components. This original genetic manipulation is however not restricted to analysis of SPB functions, and can be suited to investigate other cellular processes in S. pombe.
Quantifying geographic range measures and their utility as extinction risk proxies
Authors: Boyle James
Published: January 2018

Geographic range is used as a correlate of extinction risk for extant and extinct organisms across the fields of conservation and paleobiology. However, the exact method used to measure geographic range, the biases, and the limitations of each are rarely discussed explicitly despite their potential to impact conclusions. Here I examine and quantify properties of five commonly used measures of geographic range (convex hull area, maximum pairwise great circle distance, latitudinal range, longitudinal range, and cell count) along with a rarely used measure (minimum spanning tree distance) in the context of three datasets. A simulated dataset of two shapes with known areal limits, a paleontological occurrence dataset of pre-Cenozoic brachiopod genera from the Paleobiology Database (PBDB), and 50000 occurrence records of birds species in the western hemisphere from the eBird database.

Simulated distributions indicate that when a distribution is simple (i.e. a rectangle) all measures are similarly accurate and precise at varying sample sizes and all measures converge toward the true value with increasing sample size. However, given a more complex distribution (i.e. horseshoe shape) the convex hull area becomes increasingly inaccurate as sample size increases even as it becomes more precise. Within the PBDB dataset the minimum spanning tree was heavily favored by Akaike Information Criterion as the most effective predictor of extinction risk. Analysis of the eBird data set indicated differences between IUCN Red List Categories were significant for all geographic range measures. Overall, these results suggest that for the purpose of categorical comparisons, such as those between victims and survivors of an extinction event, all six geographic range measures are interchangeable. However, the magnitude of the relationship between geographic range and extinction risk is strongly dependent on the choice of measure. Simple linear measures, such as latitudinal range, were relatively poor predictors while minimum spanning tree and cell count measures were strong predictors, especially after sampling was accounted for. The minimum spanning tree measure was found to perform at the same level or better than most other measures with the main drawback being that it is computationally expensive.