bluuebunny/crossref_metadata_2025 huggingface dataset:
Bioemulsifying potential of exopolysaccharide produced by an indigenous species of Aureobasidium pullulans RYLF10
Authors: Yadav Kanchanlata Lata , Rahi Deepak Kumar , Soni Sanjeev Kumar
Published: January 2018

In this study, the bioemulsifying potential of exopolysaccharide produced by an indigenous species of Aureobasidium pullulans RYLF10 has been determined and various factors affecting the emulsification activity has been evaluated. The emulsification activity was determined with 8 different vegetable oils (olive, soybean, sesame, sunflower, coconut, mustard, groundnut and almond oil) which are mainly used for various food purposes. The result obtained revealed the emulsification activity (%EA) of the test EPS was quite fair with all the vegetable oils used in the study. However, it was found maximum (56%) with olive oil at the concentration of 1.5% and was very much comparable with the emulsification activity of gum Arabic, the standard emulsifier. Therefore, the olive oil was used for studies related to various factors affecting the emulsification activity of the test emulsifier. The emulsion formed was found to be oil in water (o/w) type which possessed remarkable temperature, pH and salt for 24 hours. Droplet size analysis of the test emulsifier revealed to possess monomodal type of size distribution with droplet size of 105 µm which was responsible for stabilizing the emulsion. The result obtained suggest that the emulsion of the test EPS with olive oil can potentially be used in various food applications where olive oil is used.
Sequence composition diversity in Alaskan glacier and other metagenomes
Authors: Choudhari Sulbha , Dial Roman J , Kumar Dibyendu , Shain Daniel H , Grigoriev Andrey
Published: January 2018

Metagenomics by next generation sequencing has become an important tool for interrogating complex microbial communities. In this study we analyzed several pairs of metagenomic samples obtained by different methods and observed biases, resulting in different nucleotide composition of the sequenced reads. The pairwise sample comparison was based on the principal component analysis of dinucleotide word frequencies in sequences obtained from different platforms. We found bias in the sequences obtained from the different platforms for the amplified hypervariable regions in 16S rRNA but not in shotgun metagenome reads aligned to such hypervariable regions. The differences and consistency of the distributions of the nucleotides suggest that the biases are likely due to a combination of biases introduced by PCR and different sequencing protocols, and they are related to the GC content of the reads produced. For this reason, caution should be exercised when interpreting the results of comparative metagenomics studies, as they may vary depending on the sequencing technology.
Proteomic responses to hypoxia at different temperatures in the Great Scallop (Pecten maximus)
Authors: Artigaud Sébastien SA , Lacroix Camille CL , Richard Joëlle JR , Flye-Sainte-Marie Jonathan , Bargelloni Luca LB , Pichereau Vianney
Published: January 2018

Hypoxia and hyperthermia are two connected consequences of the ongoing global change that constitute major threats for coastal marine organisms. In the present study, we used a proteomic approach to characterize the changes induced by hypoxia in individuals of the great scallop, Pecten maximus, subjected to three different temperatures, i.e. 10°C, 18°C and 25°C. We did not observe any significant change induced by hypoxia in animals acclimated at 10°C. Contrastingly at 18°C and 25°C, 16 and 11 protein spots were differentially accumulated between normoxia and hypoxia, respectively. Moreover, biochemical data, i.e. octopine dehydrogenase activity and arginine assays suggests that animals grown at 25°C switched their metabolism towards anaerobic metabolism when exposed to either normoxia or hypoxia, suggesting that this temperature is out of the scallops’ optimal thermal window. In all, 11 proteins could be unambiguously identified by mass spectrometry, involved in protein modifications and signaling (e.g. CK2, TBK1), metabolism (e.g. ENO3) or cytoskeleton (GSN). The potential roles of these proteins in the thermal-dependent response of scallops to hypoxia are discussed.
Low cost audiovisual playback and recording triggered by radio frequency identification using Raspberry Pi
Authors: Lendvai Adam Z , Akçay Çağlar , Weiss Talia , Haussmann Mark F. , Moore Ignacio T , Bonier Frances
Published: January 2018

Carrying out playbacks of visual or audio stimuli to wild animals is a widely used experimental tool in behavioral ecology. In many cases, however, playback experiments are constrained by observer limitations such as the time observers can be present, or the accuracy of observation. These problems are particularly apparent when playbacks are triggered by specific events or are targeted to specific individuals. We developed a low-cost automated playback/recording system, using two field-deployable devices: radio-frequency identification (RFID) readers and Raspberry Pi micro-computers. This system detects a specific passive integrated transponder (PIT) tag attached to an individual, and subsequently plays back the stimuli, or records audio or visual information. To demonstrate the utility of this system, we tagged female and male tree swallows from two box-nesting populations with PIT tags and carried out playbacks of nestling begging calls every time females entered the nestbox over a six-hour period. We show that the RFID-Raspberry Pi system presents a versatile, low-cost, field-deployable system that can be adapted for many audio and visual playback purposes. The low cost and the small learning curve make this set-up a feasible system for use by field biologists.
HaloTag is an effective expression and solubilisation fusion partner for a range of fibroblast growth factors
Authors: Sun Changye , Li Yong , Taylor Sarah E , Mao Xianqing , Wilkinson Mark C , Fernig David G
Published: January 2018

The production of recombinant proteins such as the fibroblast growth factors (FGFs) is the key to establishing their function in cell communication. The production of recombinant FGFs in E. coli is limited, however, due to expression and solubility problems. HaloTag has been used as a fusion protein to introduce a genetically-encoded means for chemical conjugation of probes. We have expressed 11 FGF proteins with an N-terminal HaloTag, followed by a tobacco etch virus (TEV) protease cleavage site to allow release of the FGF protein. These were purified by heparin-affinity chromatography, and in some instances by further ion-exchange chromatography. It was found that HaloTag did not adversely affect the expression of FGF1 and FGF10, both of which expressed well as soluble proteins. The N-terminal HaloTag fusion was found to enhance the expression and yield of FGF2, FGF3 and FGF7. Moreover, whereas FGF6, FGF8, FGF16, FGF17, FGF20 and FGF22 were only expressed as insoluble proteins, their N-terminal HaloTag fusion counterparts (Halo-FGFs) were soluble, and could be successfully purified. However, cleavage of Halo-FGF6, -FGF8 and -FGF22 with TEV resulted in aggregation of the FGF protein. Thus, HaloTag provides a means to enhance the expression of soluble recombinant proteins, in addition to providing a chemical genetics route for covalent tagging of proteins.
Preliminary needs assessment of mobile technology use for healthcare among homeless veterans
Authors: McInnes D Keith , Fix Gemmae M , Solomon Jeffrey L , Petrakis Beth Ann , Sawh Leon , Smelson David A
Published: January 2018

BACKGROUND: Homeless veterans have complex healthcare needs, but experience many barriers to treatment engagement. While information technologies (IT), especially mobile phones, are used to engage patients in care, little is known about homeless veterans’ IT use. This study examines homeless veterans’ access to and use of IT, attitudes toward health-related IT use, and barriers to IT in the context of homelessness.

METHODS: Qualitative interviews were conducted with 30 homeless veterans in different housing programs in Boston, MA. Inductive thematic analysis was used.

RESULTS: Most participants (90%) had a mobile phone and were receptive to IT use for health-related communications. A common difficulty communicating with providers was the lack of a stable mailing address. Some participants were using mobile phones to stay in touch with providers. Participants felt mobile-phone calls or text messages could be used to remind patients of appointments, prescription refills, medication taking, and returning for laboratory results. Mobile phone text messaging was seen as convenient, helped participants stay organized because necessary information was saved in text messages. Some reported concerns about the costs associated with mobile phone use (calls and texting), the potential to be annoyed by too many text messages, and not knowing how to use text messaging.

CONCLUSION: Homeless veterans use IT and welcome its use for health-related purposes. Technology-assisted outreach among this population may lead to improved engagement in care.
Morphological evidence supports Dryolestoid affinities for the living Australian marsupial mole Notoryctes
Authors: Agnolin Federico , Chimento Nicolás
Published: January 2018

Recent discoveries demonstrated that the southern continents were a cradle for the evolutionary radiation of dryolestoid mammals at the end of the Cretaceous. Moreover, it becomes evident that some of these early mammals surpassed the K/T boundary in South America, at least. Notoryctes is a poorly known living mammal, currently distributed in the deserts of central Australia. Due to its extreme modifications to fossoriality and peculiar anatomy, the phylogenetic relationships of this genus were debated in the past, but most recent authors agree in its marsupial affinities. A comparative survey of the anatomy of Notoryctes reveals the poorly sustained marsupial affinities for the genus and striking plesiomorphies for a living mammal. Surprisingly, Notoryctes exhibits similarities with dryolestoids. Dryolestoids were a diverse and mainly mesozoic mammalian group phylogenetically nested between the egg-lying monotremes and derived therians. In particular, Notoryctes share a number of shared features with the extinct dryolestoid Necrolestes, from the Miocene of Patagonia. Both taxa conform a clade of burrowing and animalivorous dryolestoids that survived other members of their lineage probably due to their peculiar habits. Accordingly, Notoryctes constitutes a “living-fossil” from the supposedly extinct dryolestoid radiation, extending the biochron of the group more than 20 million years to the present day. The intermediate phylogenetic position of Notoryctes has the pivotal potential to shed light on crucial anatomical, physiological, ecological, and evolutionary topics in the deep transformation from egg-lying to placental mammals. This finding, together with the Australian monotremes, constitutes the second example of early mammals that survived in Gondwana well after the KT boundary.
A white-box model of population growth
Authors: Kalmykov Lev V. , Kalmykov Vyacheslav L.
Published: January 2018

Background. Integration of reductionist and holistic approaches is one of the great challenges for mathematical modeling. Mathematical models of complex systems are divided into black-box, white-box and grey-box types. A black-box model is completely nonmechanistic as internal mechanisms of a modeled complex system are hidden. A white-box model demonstrates direct mechanisms of functioning of a complex system. It holistically shows all events at microlevel, mesolevel and macrolevel of a modeled system at all stages of its dynamics. Earlier we have used the white-box modeling for verification and reformulation of the competitive exlusion principle. Here we investigate our white-box model of single-species population dynamics. This is fundamentally important because most basic ecological models are of black-box type, including Malthusian, Verhulst, Lotka-Volterra models. Methods. Our white-box model of single-species population growth is a purely logical deterministic individual-based cellular automata model. A biological prototype of the model is a vegetative propagation of rhizomatous lawn grasses. Using the Monte Carlo method, we investigate a role of different initial positioning of an individual in the habitat. We also investigate different size and structure of the habitat and two types of fecundity. Results. We have created and investigated a logical white-box model of an ecosystem with one species. This model demonstrates mechanisms of the S-shaped and double S-shaped population growth. We have investigated population growth limited by different factors, in particular by resources, habitat structure, intraspecific competition, lifetime of individuals, regeneration time and fecundity of individuals. We have compared the S-shaped curves with J-shaped curves of population growth. Conclusion. We present a basic white-box model of population dynamics which combines reductionist and holistic approaches. Integration of reductionist and holistic approaches is provided by the simultaneous modeling of both part-whole and cause-effect relations in complex system. We consider this holystic multi-level white-box modeling approach as a method of artificial intelligence which works as hyper-logical automatic deductive inference that provides direct mechanistic insights into complex systems. The white-box modeling by logical deterministic cellular automata is a perspective way for investigation not only of population dynamics but also of any complex systems.
A field based study of swimbladder adjustment in a physostomous teleost fish
Authors: Ganias Kostas , Nunes Cristina
Published: January 2018

The present study assesses swimbladder dynamics in natural occurring sardine, Sardina pilchardus, populations with the aim to examine whether this is affected by bathymetric positioning and the physiological state of the individuals. To do so swimbladder size and shape were modeled in relation to catch depth and the size of various visceral compartments such as gonad, liver, fat and stomach. Swimbladder size was shown to be related to depth in a way that individuals with smaller swimbladders occurred at larger depths. Moreover, evidence is provided that swimbladder in sardine might have a functional relationship both with the reproductive and the feeding state of individuals since none of the fish with hydrated gonads and/or large stomachs displayed distended swimbladders.
Impact of wolf hunting policy on moose populations in northern Minnesota
Authors: Kelly Thomas B , Mackey Thomas J
Published: January 2018

An ongoing and politically sensitive aspect of proper ecological stewardship revolves around improving the conditions and health of all of the species in the area of concern including both predator and prey species. Human industrial activities have dramatically reduced the land area available to the native species which has placed stresses and fragility into the ecological web. Maintaining proper ecological dynamics has become a critical aspect of policy initiatives designed to safeguard our natural reserves including the establishment of ecological forests and sanctuaries. Herein we outline our proposal to tackle a central issue in wildlife management: improving our knowledge of predator-prey dynamics that vary both temporally and specially in non-linear ways. By leveraging techniques pioneered in other disciplines in addition to the traditional methods, we aim to drastically improve our understanding of the Moose-Grey Wolf interaction and to develop a system with applicability in other regions and other species.
Effects of simulated nitrogen deposition and a stable isotopic assessment for the neotropical epiphytic orchid Laelia speciosa
Authors: Díaz-Álvarez Edison A. , Lindig-Cisneros Roberto , Reyes-García Casandra , de la Barrera Erick
Published: January 2018

The accelerated increase of nitrogen deposition is the third cause of biodiversity loss, as a result of saturation of ecosystems worldwide. The effects of nitrogen deposition on the endemic and endangered neotropical epiphytic orchid, Laelia speciosa, were evaluated via a dose-response experiment and a stable isotopic field assessment for individuals from a city and from an oak forest, in order to evaluate the potential risk facing this orchid, and record the history of the nitrogen deposition of series of consecutive annually produced pseudobulbs. Lower doses of nitrogen of up to 20 kg N ha yr–1 the dose that led to optimal performance of plants, acted as fertilizer. For instance, chlorophyll content and chlorophyll fluorescence (Fv/Fm) peaked at 0.66 ± 0.03 g m-2 and 0.85 ± 0.01, respectively. In contrast, toxic effects were observed at the higher doses of 40 and 80 kg N ha yr–1, leading a decrease of 38% of the chlorophyll content and 23% of the chlorophyll fluorescence. For the field assessment, a tissue nitrogen content of 1.2 ± 0.1% (dry mass basis) for the orchids suggested non-toxic deposition rates both at the city and the oak forest. However, their respective isotopic signatures revealed different sources of N at each site. Indeed, in the oak forest δ15N amounted –3.1 ± 0.3‰, typical of places with low industrial activities, while in the city the δ15N reached 5.6 ± 0.2‰, typical of sites with some degree of industrial and automobile activity. Laelia speciosa would be an adequate bioindicator of nitrogen deposition because its ability to take up nitrogen from the atmosphere while preserving its isotopic signature and showing a clear physiological response to increasing inputs of nitrogen. However, its limited geographical distribution precludes the orchid as an ideal candidate for biomonitoring. Thus other vascular epiphytes should be considered for this purpose.
Dark Research: information content in many modern research papers is not easily discoverable online
Authors: Mounce Ross
Published: January 2018

Background: Research is published in indexed, online scholarly journals so that published knowledge can be easily found and built upon by others. Most scholars rely on relatively few online indexing service providers to search for relevant scholarly content. It is under-appreciated that the quality of indexing can vary across different journals and that this can have an adverse effect on the quality of research. Objective: In this short paper I compare the recall of commonly used online indexers; Google Scholar, Web of Knowledge, Scopus, Microsoft Academic Search and Mendeley Search against a selection of over 20,000 papers published in two different high-volume journals: PLOS ONE and Zootaxa. Results: When using Google Scholar, content in Zootaxa has low recall for search terms that are known to occur in it, significantly lower than the near-perfect recall of the same terms in PLOS ONE. All other indexers tend to have lower recall than Google Scholar except Scopus which outperformed Google Scholar for recall on Zootaxa searches. I also elaborate why Dark Research is undesirable for optimal scientific progress with some recommendations for change. Conclusion: This research is a basic proof-of-concept which demonstrates that when searching for published scholarly content, relevant studies can remain hidden as ’Dark Research’ in poorly-indexed journals, even despite expertise-informed efforts to find the content. The technological capability to do full text indexing on all modern scholarly journal content certainly exists, it is perhaps just publisher-imposed access-restrictions on content that prevents this from happening.
Observations of Blossfeldia liliputana (Cactaceae) populations in Jujuy province (Argentina)
Authors: Panassiti Bernd , Ahumada Osvaldo , Porembski Stefan
Published: January 2018

Introduction. Blossfeldia liliputana Werdermann (Cactaceae) is known as the tiniest cactus with a distribution from southern Bolivia and to mid-west Argentina. Due to the inconspicuous habitus, little was known about the environmental effects on its distribution. The main objectives of this study were to describe the distribution of B. liliputana in Jujuy province, north-western Argentina, and to identify abiotic and biotic environmental parameters affecting the numerical abundance of B. liliputana populations.

Material and methods. Using existing information about ecology and previously described growth sites, we localized populations of B. liliputana and counted the number of above ground stems (hereinafter referred as “heads”) within plots of 10cm2. A set of environmental data was derived from direct measurements, laboratory analysis and literature. Descriptive and multivariate statistics were used to infer habitat requirements.

Results. We found seven locations with B. liliputana populations at Jujuy. Average populations size per plot ranged from four to 22 heads. B. liliputana prefers shaded rock crevices made of shale and slates and a annual mean temperature below 14°C and a annual precipitation lower than 200 mm. Seed dispersal by ants was not observed.

Discussion. Although even after extensive field survey as much as seven locations were found, the cactus is not scarcely distributed rather the habitat is located in hardly accessible areas. Our findings suggest that B. liliputana is a habitat specialist adapted to extreme environments.
Predictors of exercise participation are different depending on ambulatory status among older people with multiple sclerosis
Authors: Ploughman Michelle , Harris Chelsea , Wallack Elizabeth M , Drodge Olivia , Beaulieu Serge , Hogan Stephen ,   Health Lifestyle and Aging with MS Canadian Consortium
Published: January 2018

Background: Exercise at moderate intensity may confer neuroprotective benefits in multiple sclerosis (MS), however it has been reported that people with MS (PwMS) exercise less than national guideline recommendations. We aimed to determine predictors of moderate to vigorous exercise among a sample of older Canadians with MS who were divided into ambulatory (less disabled) and non-ambulatory (more disabled) groups. Methods: We analysed data collected as part of a national survey of health, lifestyle and aging with MS. Participants (n=743) were Canadians over 55 years of age with MS for 20 or more years. We identified ‘a priori’ variables (demographic, personal, socioeconomic, physical health, exercise history and health care support) that may predict exercise at moderate to vigorous intensity (>6.75 metabolic equivalent hours/week). Predictive variables were entered into stepwise logistic regression, adding and deleting correlated variables until best fit was achieved for each of the two groups (ambulatory and non-ambulatory). Results: Seventy-seven percent (77%) of participants in the ambulatory group (n=351) and 35% of the non-ambulatory group (n=392) were classified as exercisers. In the ambulatory group, exercise predictors included degree of disability (OR 1.95, 95%CI 1.18-3.25), depressive symptoms (OR 0.51, 95%CI 0.29-0.89) and perseverance (OR 1.8, 95%CI 1.04-3.10). In the non-ambulatory group, exercise predictors included degree of disability (OR 5.3, 95%CI 3.22-8.71) and perseverance (OR 2.1, 95%CI 1.27-3.54). It was also notable that the factors, age, gender, years with MS, co-morbid conditions, social support, health care support and financial status were not predictive of exercise. Conclusions: This is the first examination of exercise and exercise predictors among older, more disabled PwMS. Disability and perseverance are major predictors of exercise participation (at moderate to vigorous levels) in both ambulatory and non-ambulatory groups. Presence of depressive symptoms was only predictive in the ambulatory group. Our results suggest that more exercise options must be developed for people with greater disability. Perseverance and depression are both characteristics that are modifiable and are potential targets for exercise adherence interventions.
Genetic approaches to understanding the population-level impact of wind energy development on migratory bats: a case study of the eastern red bat (Lasiurus borealis)
Authors: Vonhof Maarten , Russell Amy L.
Published: January 2018

Documented fatalities of bats at wind turbines have raised serious concerns about the future impacts of increased wind power development on populations of migratory bat species. However, for most bat species we have no knowledge of the size of populations and their demographic trends, the degree of structuring into discrete subpopulations, and whether different subpopulations use spatially segregated migratory routes. Here, we utilize genetic data from eastern red bats (Lasiurus borealis), one of the species most highly affected by wind power development in North America, to (1) evaluate patterns of population structure across the landscape, (2) estimate effective population size (Ne), and (3) assess signals of growth or decline in population size. Using a large dataset of both nuclear and mitochondrial DNA variation, we demonstrate that this species forms a single, panmictic population across their range with no evidence for the historical use of divergent migratory pathways by any portion of the population. Further, using coalescent estimates we estimate that the effective size of this population is in the hundreds of thousands to millions of individuals. Our results showing high population connectivity and gene flow among populations of eastern red bats provides valuable context for understanding levels and patterns of mortality, and indicate that monitoring and management of eastern red bats must integrate information across the range of this species.
Development of soil microbial communities for promoting sustainability in agriculture and a global carbon fix
Authors: Johnson David , Ellington Joe , Eaton Wesley
Published: January 2018

The goals of this research were to explore alternative agriculture management practices in both greenhouse and field trials that do not require the use of synthetic and/or inorganic nutrient amendments but instead would emulate mechanisms operating in natural ecosystems, between plant and Soil Microbial Communities (SMC), for plant nutrient acquisition and growth.

Greenhouse plant-growth trials, implementing a progression of soil conditions with increasing soil carbon (C) (C= 0.14% to 5.3%) and associated SMC population with increasing Fungal to Bacterial ratios (F:B) ( from 0.04 to 3.68), promoted a) increased C partitioning into plant shoot and plant fruit partitions (m=4.41, r2=0.99), b) significant quantities of plant photosynthate, 49%-97% of Total System New C (CTSN), partitioned towards increasing soil C c) four times reduction in soil C respiration (CR) as F:B ratios increased, starting with 44% of initial treatment soil C content respired in bacterial-dominant soils (low F:B), to 11% of soil C content respired in higher fertility fungal-dominant soils (Power Regression, r2=0.90; p=0.003).

Plant growth trials in fields managed for increased soil C content and enhanced SMC population and structure (increased F:B) demonstrated: a) dry aboveground biomass production rates (g m-2) of ~1,980 g in soils initiating SMC enhancement (soil C=0.87, F:B= 0.80) with observed potentials of 8,450 g in advanced soils (soil C=7.6%, F:B=4.3) b) a 25-times increase in active soil fungal biomass and a ~7.5 times increase in F:B over a 19 month application period to enhance SMC and c) reduced soil C respiration rates, from 1.25 g C m-2 day-1 in low fertility soils (soil C= 0.6%, F:B= 0.25) with only a doubling of respiration rates to 2.5 g C m-2 day-1 in a high-fertility soil with an enhanced SMC (F:B= 4.3) and >7 times more soil C content (soil C= 7.6%).

Enhancing SMC population and F:B structure in a 4.5 year agricultural field study promoted annual average capture and storage of 10.27 metric tons soil C ha-1 year -1 while increasing soil macro-, meso- and micro-nutrient availability offering a robust, cost-effective carbon sequestration mechanism within a more productive and long-term sustainable agriculture management approach.
Epidemiological evaluation of rubella virus infection among pregnant women in Ibadan, Nigeria
Authors: Adewumi Olubusuyi M , Olayinka Adebowale O. , Olusola Adebiyi B. , Faleye Temitope O.C. , Sule Folorunso W. , Adesina Olubukola
Published: January 2018

Abstract: Rubella is a vaccine-preventable, mild rash-inducing viral disease with complications that include a spectrum of birth defects in the developing foetus, especially if the infection is acquired in the early months of pregnancy. Consequently, the primary objective of global rubella control programmes is prevention of congenital rubella infection and associated birth defects often collectively referred to as congenital rubella syndrome.Despite the availability of safe and effective vaccines, and elimination of rubella virus in many developed countries substantial commitment to rubella control has not been demonstrated in the developing countries. This study appraises immunity to rubella, and consequently makes appropriate recommendations aimed at facilitating effective control. A cross-sectional sero-surveillance study was carried out among 272 consenting ante-natal clinic attendees in south-western, Nigeria. Prevalence rates of 91.54% and 1.84% were recorded for anti-rubella virus (anti-RV) IgG and IgM respectively. Also, 90.7% and 92.3% of the women aged ≤30 years and ›30 years respectively had detectable anti-RV IgG. No significant association (p=0.94) was recorded between anti-RV IgG detection and age of the women. Previous exposure and susceptibility of significant fraction of the population to rubella infection were confirmed. Considerable political commitment and promotion of free rubella immunization specifically for women with childbearing potential were recommended.
Non-coding RNAs and the deregulation of ubiquitin-proteasome network in neurodegeneration: a familia tria?
Authors: Persengiev Stephan S
Published: January 2018

Small non-coding RNAs (ncRNAs) represent a diverse group of gene regulatory factors that can posttranscriptionally regulate gene expression in response to various stimuli during brain development and differentiation. Subsets of ncRNAs and miRNAs in particular, are very specifically expressed within the central nervous system and participate in the regulation of important brain functions. miRNAs are essential for the postmitotic survival of neurons, and therefore might play a role in neuroprotection. A number of miRNAs have been reported to be dysregulated in several neurodegenerative diseases implying that they can contribute to pathogenesis. Furthermore, in light of the neuroprotective properties of some miRNAs, these small RNA species may themselves be the focus for drug development. Here, we review recent studies that imply a link between miRNA role in the regulation of ubiquitine-proteasome pathways and neurodegeneration and discuss how increased knowledge of miRNAs might serve the diagnosis and treatment of neurodegenerative diseases.
Nine simple ways to make it easier to (re)use your data
Authors: White Ethan P. , Baldridge Elita , Brym Zachary T. , Locey Kenneth J. , McGlinn Daniel J. , Supp Sarah R.
Published: January 2018

Sharing data is increasingly considered to be an important part of the scientific process. Making your data publicly available allows original results to be reproduced and new analyses to be conducted. While sharing your data is the first step in allowing reuse, it is also important that the data be easy to understand and use. We describe nine simple ways to make it easy to reuse the data that you share and also make it easier to work with it yourself. Our recommendations focus on making your data understandable, easy to analyze, and readily available to the wider community of scientists.
Improvement of enzymatic saccharification in Arabidopsis thaliana by ectopic expression of the rice SUB1A-1 transcription factor
Authors: Núñez-López Lizeth , Aguirre-Cruz Andrés , Barrera-Figueroa Blanca Estela , Peña-Castro Julian Mario
Published: January 2018

Saccharification of polysaccharides releases monosaccharides that can be used by ethanol-producing microorganisms in biofuel production. To improve plant biomass as a raw material for saccharification, factors controlling the accumulation and structure of carbohydrates must be identified. Rice SUB1A-1 is a transcription factor that represses the turnover of starch and postpones energy-consuming growth processes under submergence stress. Arabidopsis was employed to test if heterologous expression of SUB1A-1 or SUB1C-1 (a related gene) can be used to improve saccharification. Cellulolytic and amylolytic enzymatic treatments confirmed that SUB1A-1 transgenics had better saccharification yield than wild-type (Col-0), mainly from accumulated starch. This high saccharification yield was developmentally controlled since juvenile transgenic plants yielded 200-300% more glucose than Col-0. We measured photosynthetic parameters, starch granule microstructure, and transcript abundance of genes involved in starch degradation (SEX4, GWD1), juvenile transition (SPL3-5) and meristematic identity (FUL, SOC1) but found no differences to Col-0, indicating that starch accumulation may be controlled by down-regulation of CONSTANS and FLOWERING LOCUS T by SUB1A-1 as previously reported. SUB1A-1 transgenics also offered less resistance to deformation than wild-type concomitant to up-regulation of AtEXP2 expansin and BGL2 glucan-1,3,-beta-glucosidase. We conclude that heterologous SUB1A-1 expression can improve saccharification yield and softness, two traits needed in bioethanol production.
Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies
Authors: Dececchi T. Alexander , Balhoff James P , Lapp Hilmar , Mabee Paula M
Published: January 2018

The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in non-computer readable text, and requires enormous investments of time and resources to integrate across large numbers of taxa and studies. Here we present a new methodology, using ontology-based reasoning systems working with the Phenoscape Knowledgebase (KB), to automatically integrate large amounts of evolutionary character state descriptions into a synthetic character matrix of neomorphic (presence/absence) data. Using the KB, which includes more than 55 studies of sarcopterygian taxa, we generated a synthetic supermatrix of 1051 variable characters scored for 639 taxa resulting in over 145,000 populated cells. Of these characters, over 76% were made variable through the addition of inferred presence/absence states derived by machine reasoning over the formal semantics of the source ontologies. Inferred data reduced the missing data in the variable character-subset from 98.5% to 78.2%. Machine reasoning also enables the isolation of conflicts in the data, i.e., cells where both presence and absence are indicated; reports regarding conflicting data provenance can be generated automatically. Further, reasoning enables quantification and new visualizations of the data, here for example, allowing identification of character space that has been undersampled across the fin to limb transition. The approach and methods demonstrated here to compute synthetic presence/absence supermatrices are applicable to any taxonomic and phenotypic slice across the tree of life, providing the data are semantically annotated. Because such data can also be linked to model organism genetics through computational scoring of phenotypic similarity, they open a rich set of future research questions into phenotype to genome relationships.
spliceR: An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data
Authors: Vitting-Seerup Kristoffer , Porse Bo T , Sandelin Albin , Waage Johannes E
Published: January 2018

Background: With the increasing depth and decreasing costs of RNA-sequencing researchers are now able to profile the transcriptome with unprecedented detail. These advances not only allow for precise approximation of gene expression levels, but also for the characterization of alternative transcript usage/switching between conditions. Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential.

Results: spliceR uses the full-length transcripts output from RNA-seq assemblers, to detect single- and multiple exon skipping, alternative donor and acceptor sites, intron retention, alternative first or last exon usage, and mutually exclusive exon events. For each of these events spliceR also annotates the genomic coordinates of the differentially spliced elements facilitating downstream sequence analysis. Furthermore, isoform fraction values are calculated for effective post-filtering, i.e. identification of transcript switching between conditions. Lastly spliceR predicts the coding potential, as well as the potential nonsense mediated decay (NMD) sensitivity of each transcript.

Conclusions: spliceR is a easy-to-use tool that allows detection of alternative splicing, transcript switching and NMD sensitivity from RNA-seq data, extending the usability of RNA-seq and assembly technologies. spliceR is implemented as an R package and is freely available from the Bioconductor repository (http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html).
Experimental reintroduction revealed novel reproductive variation in Crested Ibis Nipponia nippon
Authors: Liu Dongping , Wang Chao , Qing Baoping , Lu Jun
Published: January 2018

The Crested Ibis Nipponia Nippon formerly occurred throughout East Asia, but since 1981 its unique population has been confined to a narrow area in Central China. During 2004-2005, 23 Crested Ibises were experimentally reintroduced to an isolated basin in Qinling Mountains, where they and their offspring exhibited variation in reproduction never observed in wild population. Crested Ibis has been considered to be a monogamous species, and breeding pair is solitary and territorial in breeding season. However, 3.4% of breeding females exhibited polyandry and 43.1% of nests were observed in colony in the reintroduced population during 2006-2014. The mating system flexibility is likely related to male-biased sex ratio in the small isolated reintroduced population, due to greater dispersal capacity by female. The colonial nesting is attributed to the availability of large nest trees and abundant food supply. First nest failure in reintroduced population occurred much earlier than that in wild, which resulted in significantly higher probability of renesting. The phenotypic plasticity in Crested Ibis may play important role in the restoration of this critical endangered species under a changing environment, and future reintroductions provide opportunity to further understand the degree and cost of adaptive phenotypic plasticity in Crested Ibis.
CRISPR-Cas9 in gene therapy: much control on breaking, little control on repairing
Authors: Daneshvar Kaveh
Published: January 2018

Recent advances in CRISPR-Cas9 genome editing tool have made great promises to basic and biomedical research as well as gene therapy. Efforts to make the CRISPR-Cas9 system applicable in gene therapy are largely focused on two aspects: 1) increasing the specificity of this system by eliminating off-target effects, and 2) optimizing in vivo delivery of the CRISPR-Cas9 DNA constructs to target cells and limiting the expression of Cas9 and gRNA to prevent toxicity immune responses. However, there is an unnoted but crucial consideration about the mode of DNA repair at the lesion caused by CRISPR-Cas9. In this commentary, I briefly highlight recent publications on in vivo use of the CRISPR-Cas9 system in gene therapy. I then discuss the undesired on-target DNA repair events that can occur as a result of the activity of CRISPR-Cas9. Overall, this commentary underscores the need for more study on controlled DNA repair in systems targeted with CRISPR-Cas9 genome editing tools.
UTBiome: citizen science and campus community engagement
Authors: Maestre Juan , Sangireddy Harish , Passalacqua Paola , Kinney Kerry A.
Published: January 2018

The University of Texas main campus is located at the heart of the city of Austin. The university campus can be used as “living” laboratory to engage students, faculty, and the public in general, in science. The UTBiome (aka “Mapping the UTBiome”) project, is a cross-disciplinary educational, research and outreach effort to (1) engage the community in the collection and analysis of environmental samples from campus environment, and (2) to create an open access web-based mapping platform to disseminate the environmental and microbiological data obtained. In this project, both indoor and outdoor environments are being interrogated to answer diverse scientific questions. Over 250 citizens from the university community have been involved to date in the collection of biological samples and environment metadata associated with key water quality metrics including temperature, nitrate, phosphate, dissolved oxygen, alkalinity, pH, turbidity and fecal indicator bacteria. A data management system was designed and implemented for both, ‘online’ data input through student’s mobile phones and to facilitate sample tracking. In order to fully engage the students and the UT community, we envisioned an interactive and innovative workflow, involving technology, automation, and social media. The interactive mapping platform we have created allow users within and outside the university to access and download the results and associated environmental data by simply clicking on the interactive map. The comprehensive UTBiome map created in ArcGIS can be found in this website http://crwr-utbiome.austin.utexas.edu/utb_webapp/utbiome.html (or just http://tinyurl.com/UTBiomeMap). The online platform design offers access to the environmental information, providing resources for students, faculty and the general public to learn more about the environment that surrounds us.
Melting barriers to faunal exchange across ocean basins
Authors: McKeon C. Seabird , Weber Michele X. , Alter S. Elizabeth , Seavy Nathaniel E. , Crandall Eric D. , Barshis Daniel J. , Fechter-Leggett Ethan , Oleson Kirsten L.L.
Published: January 2018

Accelerated loss of sea ice in the Arctic is opening routes connecting the Atlantic and Pacific oceans for longer periods each year. These changes will increase the ease and frequency with which marine birds and mammals are able to move between the Pacific and Atlantic ocean basins. Indeed, recent observations of birds and mammals suggest these movements are already occurring. Reconnection of the Pacific and Atlantic Ocean basins will present both challenges to marine ecosystem conservation and an unprecedented opportunity to examine the ecological and evolutionary consequences of faunal exchange in real time. To understand these changes and implement effective conservation of marine ecosystems, we need to further develop modeling efforts to predict the rate of dispersal and consequences of faunal exchange. These predictions can be tested by closely monitoring wildlife dispersal through the Arctic Ocean and using modern methods to explore the ecological and evolutionary consequences of these movements.
GPT: a web-server to map phylogenetic trees on a virtual globe
Authors: Puigbo Pere , Major Jacqueline M
Published: January 2018

GPT (Global Positioning Trees) is a web-server that maps phylogenetic trees on a virtual globe. The minimum requirements are a phylogenetic tree and geographical coordinates of leaves to generate a Keyhole Markup Language (KML) file that can be viewed on Google Earth. An advantage of GPT is the results may be pre-visualized directly on the web. This web-server also implements several tools to display geolocation and geotrack data. GPT has been designed to be an easy-to-use tool to track evolutionary processes and will be useful for phylogeographical and spatial epidemiological studies. It covers a wide-range of visualizations divided in three components increasingly complex: geolocation, geotrack and GPT. This web-server is freely available at http://ppuigbo.me/programs/GPT and only requires Internet access, a web browser, and an earth browser able to read KML files. Several examples and a tutorial are accessible from the web-server’s home page.
Order and metric geometry compatible stochastic processing
Authors: Greenhoe Daniel J
Published: January 2018

A traditional random variable X is a function that maps from a stochastic process to the real line. Here, "real line" refers to the structure (R,<=,|x-y|), where R is the set of real numbers, <= is the standard linear order relation on R, and d(x,y)=|x-y| is the usual metric on R. The traditional expectation value E(X) of X is then often a poor choice of a statistic when the stochastic process that X maps from is a structure other than the real line or some substructure of the real line. If the stochastic process is a structure that is not linearly ordered (including structures totally unordered) and/or has a metric space geometry very different from that induced by the usual metric, then statistics such as E(X) are often of poor quality with regards to qualitative intuition and quantitative variance (expected error) measurements. For example, the traditional expected value of a fair die is E(X)=(1/6)(1+2+...+6)=3.5. But this result has no relationship with reality or with intuition because the result implies that we expect the value of [ooo] (die face value "3") or [oooo] (dice face value "4") more than we expect the outcome of say [o] or [oo]. The fact is, that for a fair die, we would expect any pair of values equally. The reason for this is that the values of the face of a fair die are merely symbols with no order, and with no metric geometry other than the discrete metric geometry. On a fair die, [oo] is not greater or less than [o]; rather [oo] and [o] are simply symbols without order. Moreover, [o] is not "closer" to [oo] than it is to [ooo]; rather, [o], [oo], and [ooo] are simply symbols without any inherit order or metric geometry. This paper proposes an alternative statistical system, based somewhat on graph theory, that takes into account the order structure and metric geometry of the underlying stochastic process.