bluuebunny/crossref_metadata_2025 huggingface dataset:
The mortality, recovery, and community shifts of scleractinian corals in Puerto Rico one decade after the 2005 regional bleaching event
Authors: García-Sais Jorge R , Williams Stacey M , Amirrezvani Ali
Published: January 2018

This work analyzes the mortality, recovery, and shifts in the composition of scleractinian corals in Puerto Rico one decade after the 2005 regional coral bleaching event. Temporal and spatial patterns of coral community structure were examined using a stratified, non-random sampling approach based on five permanent transects per reef at 16 reef stations. A negative correlation between percent coral cover loss and light attenuation coefficient (Kd490) was observed, suggesting that water turbidity played a major role in coral protection during the bleaching event (“sunblock effect”). Loss of coral cover after the bleaching event was lower at nearshore reefs, and with increasing depth at oceanic and shelf-edge reefs. By 2015, coral recovery was observed at all reefs surveyed, but coastal reefs exhibited a higher rate of recovery. The responses of coral assemblages varied after the bleaching event, including shifts in cover from massive corals (Orbicella spp.) to turf algae and/or by opportunistic (Porites astreoides) and branching corals (Madracis auretenra, P. porites); partial recovery by O. annularis complex; and no measurable change in coral assemblages before and after the event.
Differentiation of Bifidobacterium longum subspecies longum and infantis by quantitative PCR using functional gene targets
Authors: Lawley Blair , Munro Karen , Hughes Alan , Hodgkinson Alison J , Prosser Colin G , Lowry Dianne , Zhou Shao J , Makrides Maria , Gibson Robert A , Lay Christophe , Chew Charmaine , Lee Pheng Soon , Wong Khai Hong , Tannock Gerald W
Published: January 2018

Background. Members of the genus Bifidobacterium are abundant in the feces of babies during the exclusively-milk-diet period of life. Bifidobacterium longum is reported to be a common member of the infant fecal microbiota. However, B. longum is composed of three subspecies, two of which are represented in the bowel microbiota (B. longum subsp. longum; B. longum subsp. infantis). B. longum subspecies are not differentiated in many studies, so that their prevalence and relative abundances are not accurately known. This may largely be due to difficulty in assigning subspecies identity using DNA sequences of 16S rRNA or tuf genes that are commonly used in bacterial taxonomy.

Methods. We developed a qPCR method targeting the sialidase gene (subsp. infantis) and sugar kinase gene (subsp. longum) to differentiate the subspecies using specific primers and probes. Specificity of the primers/probes was tested by in silico, pangenomic search, and using DNA from standard cultures of bifidobacterial species. The utility of the method was further examined using DNA from feces that had been collected from infants inhabiting various geographical regions.

Results. A pangenomic search of the NCBI genomic database showed that the PCR primers/probes targeted only the respective genes of the two subspecies. The primers/probes showed total specificity when tested against DNA extracted from the gold standard strains (type cultures) of bifidobacterial species detected in infant feces. Use of the qPCR method with DNA extracted from the feces of infants of different ages, delivery method and nutrition, showed that subsp. infantis was detectable (0-32.4% prevalence) in the feces of Australian (n = 90), South-East Asian (n = 24), and Chinese babies (n = 91), but in all cases at low abundance (<0.01-4.6%) compared to subsp. longum (0.1-33.7% abundance; 21.4-100% prevalence).

Discussion. Our qPCR method differentiates B. longum subspecies longum and infantis using characteristic functional genes. It can be used as an identification aid for isolates of bifidobacteria, as well as in determining prevalence and abundance of the subspecies in feces. The method should thus be useful in ecological studies of the infant gut microbiota during early life where an understanding of the ecology of bifidobacterial species may be important in developing interventions to promote infant health.
How to make a domesticate
Authors: Stetter Markus G , Gates Daniel J , Mei Wenbin , Ross-Ibarra Jeffrey
Published: January 2018

Crop domestication is an adaptive process that transforms a wild plant into a domesticated species that can reared and maintained for human use. Though there are hundreds of thousands of flowering plant species, only a small fraction has ever been domesticated. Successful domestication is likely influenced by a number of key plant characteristics, including its life history, the usefulness of a crop for early societies, and the maintenance of a large effective population size. Although many studies have sought to identify individual loci with large effects on domestication traits, we argue that relevant phenotypes are likely controlled by a large number of loci, most of relatively small effect. Most of these alleles were probably selected from standing genetic variation present in the wild ancestor rather than new mutations. Both archaeological evidence and quantitative genetics suggest that the process of domestication was in most cases gradual, likely lasting several millennia. We end by discussing how these findings from the past may inform future efforts to domesticate new species.
Early-branching euteleost relationships: Areas of congruence between concatenation and coalescent model inferences
Authors: Campbell Matthew A , Alfaro Michael E , Belasco Max , Lopez J. Andres
Published: January 2018

Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted both in concatenated and joint gene trees and species tree estimation frameworks. Both analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the two analysis types receiving high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are apparent within the Ostarioclupeomorpha and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.
Episomal tools for RNAi in the diatom Phaeodactylum tricornutum
Authors: Bielinski Vincent A , Bolt Tayah M , Dupont Christopher L , Weyman Philip D
Published: January 2018

Background. The diatom Phaeodactylum tricornutum is a model photosynthetic organism. Functional genomic work in this organism has established a variety of genetic tools including RNA interference (RNAi). RNAi is a post-transcriptional regulatory process that can be utilized to knockdown expression of genes of interest in eukaryotes. RNAi has been previously demonstrated in P. tricornutum, but in practice the efficiency of inducing RNAi is low. Methods. We developed an efficient method for construction of inverted repeat hairpins based on Golden Gate DNA assembly into a Gateway entry vector. The hairpin constructs were then transferred to a variety of destination vectors through the Gateway recombination system. After recombining the hairpin into the destination vector, the resulting expression vector was mobilized into P. tricornutum using direct conjugation from E. coli. Because the hairpin expression vectors had sequences allowing for episomal maintenance in P. tricornutum, we tested whether a consistent, episomal location for hairpin expression improved RNAi induction efficiency. Results. We successfully demonstrated that RNAi could be induced using hairpin constructs expressed from an episome. After testing two different reporter targets and a variety of hairpin sequences with 3 polymerase II and 2 polymerase III promoters, we achieved a maximal RNAi induction efficiency of 25% of lines displaying knockdown of reporter activity by 50% or more. We created many useful genetic tools through this work including Gateway destination vectors for P. tricornutum expression from a variety of polymerase II and III promoters including the P. tricornutum FCPB, H4, and 49202 polymerase II promoters as well as the U6 and snRNA polymerase III promoters. We also created Gateway destination vectors that allow a cassette cloned in an entry vector to be easily recombined into a transcriptional fusion with either ShBle or, for polymerase III promoters, the green fluorescent Spinach aptamer. Such transcriptional fusions allow for linkage of expression with a marker such as bleomycin resistance or fluorescence from the Spinach aptamer to easily select or screen for lines that maintain transgene expression. Discussion. While RNAi can be used as an effective tool for P. tricornutum genetics, especially where targeted knockouts may be lethal to the cell, induction of this process remains low efficiency. Techniques resulting in higher efficiency establishment of RNAi would be of great use to the diatom genetics community and would enable this technique to be used as a forward genetic tool for discovery of novel gene function.
Behavioral decoding of Drosophila locomotion in a circular arena
Authors: Qiu Shuang , Robertson R Meldrum , Xiao Chengfeng
Published: January 2018

Motion detection and position tracking of animal behavior over a period of time produce massive amount of information, but analysis and interpretation of such huge datasets are challenging. Here we describe statistical methods to extract major movement structures of Drosophila locomotion in a circular arena, and examine the effects of pulsed light stimulation on these identified locomotor structures. Drosophila adults performed exploratory behavior when restrained individually in the circular arenas (1.27 cm diameter 0.3 cm depth). Measures of the distance to the center of the arena followed a gumbel distribution with mixed components. Representation learning of distance to center from 177,000 observations (from 63 controls and 55 flies with pulsed light stimulation) revealed three major movement components, indicating three locomotor structures characterized as: side-wall walk, angle walk and cross of the central region. Pulsed flies showed reduced cross of the central region compared with controls. We also showed that counter-clockwise walk and clockwise walk were the two major rotation behaviors with equal time proportion. There was a peak relative turning angle at 25.6o for counter-clockwise walk, and 334.4o for clockwise walk. Regression analysis of relative turning angle as a function of distance to center indicated that as distance to center increased, flies switched turning from directions for perimeter-returning to directions for major rotation. Pulsed flies reduced trajectories that had irregular circle-shape and increased trajectories with regular circle-shape during rotation. Taken together, we present a feasible approach to extract major locomotor structures of Drosophila locomotion in a circular arena, and demonstrate how pulsed light stimulation increased the regularity of locomotor trajectory.
Walking behavior in a circular arena modified by pulsed light stimulation in Drosophila melanogaster w1118 line
Authors: Qiu Shuang , Xiao Chengfeng
Published: January 2018

The Drosophila melanogaster white-eyed w1118 line serves as a blank control, allowing genetic recombination of any gene of interest along with a readily recognizable marker. w1118 flies display behavioral susceptibility to environmental stimulation such as light. It is of great importance to characterize the behavioral performance of w1118 flies because this would provide a baseline from which the effect of the gene of interest could be differentiated. Little work has been performed to characterize the walking behavior in adult w1118 flies. Here we show that pulsed light stimulation increased the regularity of walking trajectories of w1118 flies in circular arenas. We statistically modeled the distribution of distances to center and extracted the walking structures of w1118 flies. Pulsed light stimulation redistributed the time proportions for individual walking structures. Specifically, pulsed light stimulation reduced the episodes of crossing over the central region of the arena. An addition of four genomic copies of mini-white, a common marker gene for eye color, mimicked the effect of pulsed light stimulation in reducing crossing in a circular arena. The reducing effect of mini-white was copy-number-dependent. These findings highlight the rhythmic light stimulation-evoked modifications of walking behavior in w1118 flies and an unexpected behavioral consequence of mini-white in transgenic flies carrying w1118 isogenic background.
Accelerating the XGBoost algorithm using GPU computing
Authors: Mitchell Rory , Frank Eibe
Published: January 2018

We present a CUDA based implementation of a decision tree construction algorithm within the gradient boosting library XGBoost. The tree construction algorithm is executed entirely on the GPU and shows high performance with a variety of datasets and settings, including sparse input matrices. Individual boosting iterations are parallelized, combining two approaches. An interleaved approach is used for shallow trees, switching to a more conventional radix sort based approach for larger depths. We show speedups of between 3-6x using a Titan X compared to a 4 core i7 CPU, and 1.2x using a Titan X compared to 2x Xeon CPUs (24 cores). We show that it is possible to process the Higgs dataset (10 million instances, 28 features) entirely within GPU memory. The algorithm is made available as a plug-in within the XGBoost library and fully supports all XGBoost features including classification, regression and ranking tasks.
DNA-spiking in viral metagenome sequencing: A new method with low bias
Authors: Cremers Geert , Gambelli Lavinia , van Alen Theo , van Niftrik Laura , Op den Camp Huub
Published: January 2018

With the emergence of Next Generation Sequencing, major advances were made with regard to identifying viruses in natural environments. However, bioinformatical research on viruses is still limited because of the low amounts of viral DNA that can be obtained for analysis. To overcome this limitation, DNA is often amplified with multiple displacement amplification (MDA), which causes an unavoidable bias. Here, we describe a DNA-spiking method to avoid the bias that is created when using amplification of DNA before metagenome sequencing. To obtain sufficient DNA for sequencing, a bacterial 16S rRNA gene was amplified and the obtained DNA was spiked to a DNA sample containing DNA from a bacteriophage population before sequencing using Ion Torrent technology. After sequencing, the 16S rRNA gene reads DNA was removed by mapping to the Silva database. The new DNA-spiking method was compared with the MDA technique. When MDA was applied, the overall GC content of the reads showed a bias towards lower GC%, indicating a change in composition of the DNA sample. Assemblies using all available reads from both MDA and the DNA-spiked samples resulted in six viral genomes. All six genomes could be almost completely retrieved (97.9%-100%) when mapping the reads from the DNA-spiked sample to those six genomes . In contrast, 6.3%-77.7% of three viral genomes were covered by reads obtained using the MDA amplification method and only three were nearly fully covered (97.4%-100%). The new method provides a simple and inexpensive protocol with very low bias in sequencing of metagenomes for which low amounts of DNA are available.
Unimodal relationship between adult and recruit density in barnacle populations
Authors: Scrosati Ricardo A , Ellrich Julius A
Published: January 2018

Recruitment is a key demographic step for population persistence. This paper focuses on understanding barnacle (Semibalanus balanoides) recruitment. In rocky intertidal habitats from the Gulf of St. Lawrence coast of Nova Scotia (Canada), winter ice scour is common. At the onset of intertidal barnacle recruitment in the spring, mostly only adult barnacles and bare substrate are visible at high elevations on the shore. We conducted a multiannual study to investigate if small-scale barnacle recruitment could be predicted from the density of pre-existing adult barnacles. In a year that exhibited a wide adult density range (ca. 0–130 individuals dm-2), the relationship between adult density and recruit density (referred to the available area for recruitment, which excluded adult barnacles) was unimodal. In years that exhibited a lower adult density range (ca. 0–40/50 individuals dm-2), the relationship between adult and recruit density was positive but simply resembling the lower half of the unimodal relationship. Overall, adult barnacle density was able to explain 26–40 % of the observed variation in recruit density. The unimodal adult–recruit relationship is consistent with previously documented intraspecific interactions. Between low and intermediate adult densities, the positive nature of the relationship relates to the ability of adult barnacles to attract settlement-seeking larvae, likely enhancing local population persistence where it is most needed. Between intermediate and high adult densities, where population persistence may be less compromised and the abundant adults may be detrimental to recruit growth, the negative nature of the relationship suggests that larvae are stimulated to settle elsewhere. This unimodal pattern may be particularly common on shores with moderate rates of larval supply to the shore, as high larval supply rates may swamp the coast with settlers, decoupling recruit density from local adult abundance.
Shared differentially expressed genes of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) seedlings under low nitrogen and phosphorus stress
Authors: Li JianHui , Ma GuiFang , Luo DingWei , Tong ZaiKang , Xu Jinliang , Lu YongQuan
Published: January 2018

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an excellent fast-growing timber species and has significant value in the forestry industry. In order to increase the nitrogen and phosphorus absorption and utilization in Chinese fir, shared differentially expressed genes under low nitrogen and phosphorus stress were screened in this study. Seedling of Chinese fir clone X6 was cultivated in aeroponic system with 3 treatments, namely, low nitrogen (LN), low phosphorus (LP) and a control check (with nitrogen and phosphorus sufficient, CK). After 4 months of treatment, the roots from the LN, LP and CK groups were collected and transcriptome sequencing was done by LC Sciences (USA) using an Illumina platform. When comparing the LN stress group with the CK group, 977 SDGEs were detected, 264 of which had KEGG annotations; 931 SDGEs were detected when comparing the LP stress group with the CK group, of which 189 had KEGG annotations; 297 SDGEs were detected in both the LN stress and LP stress groups, 78 of which had KEGG annotations representing 98 metabolic pathways. Among the 78 selected SDEGs that were differentially expressed under both LN and LP stress conditions, Twenty-one SDEGs were selected based on the metabolic pathways that nitrogen and phosphorus are involved in, these genes are PNR, PSBA, EGLC, GLC, END, BGLU, AMY, A1E, PAL, GOGAT, NIR1, NIR2, C4M, PAL, PRDX6, POX, CCR, CCoAOMT, FDH, CHS and ANR. These genes can potentially be used in breeding to improve both nitrogen and phosphorus utilization efficiency in Chinese fir.
Sails at the water: ecological convergence between sphenacodontids and spinosaurids?
Authors: Mazurek Dawid
Published: January 2018

Spinosaurids (Diapsida: Spinosauridae) and sphenacodontids (Synapsida: Sphenacodontidae) share not only a characteristic tall neural spines, but also an atypical – compared to their close respective relatives – ecology, i.e. apparently piscivorous and possibly semiaquatic mode of life. This similarity might hold clue for the role of their sails. It is here suggested that sails of these animals 1) served thermoregulatory function, warming the animals, otherwise submerged in the water, as well as 2) enabled them to hunt for fish in a way similar to the technique of Recent diapsid, black heron (Egretta ardesiaca).
Neonicotinoid insecticide residues in New Zealand maize paddock soil
Authors: Pook Chris , Gritcan Iana
Published: January 2018

Neonicotinoid are the most commonly used class of insecticides. Between 2005 and 2010 neonicotinoid use in the USA and UK more than doubled. Anecdotal evidence suggests similar trends exist in New Zealand, where neonicotinoid seed coatings are now often applied prophylactically in contravention of the principles of Integrated Pest Management. This widespread use of neonicotinoid insecticides is controversial due to a lack of understanding about their persistence in the environment and the long-term consequences of their use. We present a novel, simple, low-cost method for the extraction and quantification of five neonicotinoids from soil with a detection limit <1 ng g-1. We have applied this method to soil collected from maize paddocks in New Zealand and found clothianidin and imidacloprid in 48 out of 50 samples. Neonicotinoid concentrations ranged from 0.5 to 9.4 ng g wet weight-1 imidacloprid and 2.1 to 26.7 ng g wet weight -1 clothianidin. These concentrations are likely to be hazardous to non-target organisms exposed to them. This is the first study to report the prevalence of neonicotinoid residues in New Zealand’s environment.
The earth is flat (p>0.05): Significance thresholds and the crisis of unreplicable research
Authors: Amrhein Valentin , Korner-Nievergelt Fränzi , Roth Tobias
Published: January 2018

The widespread use of 'statistical significance' as a license for making a claim of a scientific finding leads to considerable distortion of the scientific process (American Statistical Association, Wasserstein & Lazar 2016). We review why degrading p-values into 'significant' and 'nonsignificant' contributes to making studies irreproducible, or to making them seem irreproducible. A major problem is that we tend to take small p-values at face value, but mistrust results with larger p-values. In either case, p-values can tell little about reliability of research, because they are hardly replicable even if an alternative hypothesis is true. Also significance (p≤0.05) is hardly replicable: at a realistic statistical power of 40%, given that there is a true effect, only one in six studies will significantly replicate the significant result of another study. Even at a good power of 80%, results from two studies will be conflicting, in terms of significance, in one third of the cases if there is a true effect. This means that a replication cannot be interpreted as having failed only because it is nonsignificant. Many apparent replication failures may thus reflect faulty judgement based on significance thresholds rather than a crisis of unreplicable research. Reliable conclusions on replicability and practical importance of a finding can only be drawn using cumulative evidence from multiple independent studies. However, applying significance thresholds makes cumulative knowledge unreliable. One reason is that with anything but ideal statistical power, significant effect sizes will be biased upwards. Interpreting inflated significant results while ignoring nonsignificant results will thus lead to wrong conclusions. But current incentives to hunt for significance lead to publication bias against nonsignificant findings. Data dredging, p-hacking and publication bias should be addressed by removing fixed significance thresholds. Consistent with the recommendations of the late Ronald Fisher, p-values should be interpreted as graded measures of the strength of evidence against the null hypothesis. Also larger p-values offer some evidence against the null hypothesis, and they cannot be interpreted as supporting the null hypothesis, falsely concluding that 'there is no effect'. Information on possible true effect sizes that are compatible with the data must be obtained from the observed effect size, e.g., from a sample average, and from a measure of uncertainty, such as a confidence interval. We review how confusion about interpretation of larger p-values can be traced back to historical disputes among the founders of modern statistics. We further discuss potential arguments against removing significance thresholds, such as 'we need more stringent decision rules', 'sample sizes will decrease' or 'we need to get rid of p-values'.
Finding a clear signal: a systematic review of desert radio telemetry research
Authors: Noble Taylor , Lortie Christopher
Published: January 2018

Radio telemetry is a common tool to monitor animals in many ecosystems. Radio telemetry, or radio tracking, typically uses a tag or collar with a radio transmitter attached to an animal that is monitored by researchers with a receiver. This technique is used for research in many disciplines such as wildlife ecology or conservation biology. Within desert ecosystems, this approach has been used since the 1960s in many different research capacities. Many desert species exist at low density and can range widely within a region due to scarce resources, which can make radio telemetry a useful method to use in these environments. Here, we examined the peer-reviewed literature to assess how radio telemetry is used in deserts. Using the Web of Science with additional search validation on Google Scholar to formally summarize this research, we found 97 studies that fit our criteria. Most primary studies used radio telemetry to examine individual behavior and/or habitat use. The majority of published studies were done in the United States. The most common classes of animal studied were mammals (29.9 % large mammals and 25.8 % small mammals). Most species studied were classified as ‘least concern’ for risk status. Vhf radio telemetry devices predominated the technology selected (80.4 %) whilst GPS devices were used in 19.6 % of studies. Radio telemetry devices are an effective tool to survey individual animals and animal populations in harsh desert environments. However, future research can be improved using these tools to improve reproducibility encourage data reuse and comparison between studies. We encourage authors using radio telemetry to publish their data and include details of their study area and tracking methods to accomplish these goals.
Beyond the carapace: skull shape variation and morphological systematics of long-nosed armadillos (genus Dasypus)
Authors: Hautier Lionel , Billet Guillaume , De Thoisy Benoit , Delsuc Frédéric
Published: January 2018

Background. The systematics of long-nosed armadillos (genus Dasypus) has been mainly based on a handful of external morphological characters and classical measurements. Here, we studied the pattern of morphological variation in the skull of long-nosed armadillos species, with a focus on the systematics of the widely distributed nine-banded armadillo (D. novemcinctus). Methods. We present the first exhaustive 3D comparison of the skull morphology within the genus Dasypus, based on µCT-scans. We used geometric morphometric approaches to explore the patterns of the intra- and interspecific morphological variation of the skull with regard to several factors such as taxonomy, geography, allometry, and sexual dimorphism. Results. We show that the shape and size of the skull vary greatly between Dasypus species, with D. pilosus representing a clear outlier compared to other long-nosed armadillos. The study of the cranial intraspecific variation in D. novemcinctus evidences clear links to the geographic distribution and argue in favour of a revision of past taxonomic delimitations. Our detailed morphometric comparisons detected previously overlooked morphotypes of nine-banded armadillo, especially a very distinctive unit circumscribed to the Guiana Shield. Discussion. As our results are congruent with recent molecular data and analyses of the structure of paranasal sinuses, we propose that D. novemcinctus should be regarded either as a polytypic species (with three to four subspecies) or as a complex of several distinct species.
Candidate genes for shell colour polymorphism in Cepaea nemoralis
Authors: Kerkvliet Jesse , de Boer Tjalf , Schilthuizen Menno , Kraaijeveld Ken
Published: January 2018

The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the body and the mantle (the shell-producing tissue) of four individuals of two phenotypes and produced a de novo transcriptome of 147,397 contigs. Differential expression analysis identified a set of 1,961 transcripts that were upregulated in mantle tissue. Sequence variant analysis resulted in a set of 2,592 transcripts with single nucleotide polymorphisms (SNPs) that differed consistently between the phenotypes. Combining these results yielded a set of 197 candidate transcripts, of which 38 were annotated. Four of these transcripts are involved in production of the shell’s nacreous layer. Comparison with morph-associated RAD-tags from a published study yielded seven transcripts that were annotated as metallothionein, a protein that is thought to inhibit the production of melanin in melanocytes. These results thus provide an excellent starting point for the elucidation of the genetic regulation of the Cepaea nemoralis shell colour polymorphism.
An updated understanding of Texas bumble bee (Hymenoptera: Apidae) species presence and potential distributions in Texas, USA
Authors: Beckham Jessica L , Atkinson Samuel
Published: January 2018

Texas is the second largest state in the United States of America, and the largest state in the contiguous USA at nearly 700,000 sq. km. Several Texas bumble bee species have shown evidence of declines in portions of their continental ranges, and conservation initiatives targeting these species will be most effective if species distributions are well established. To date, statewide bumble bee distributions for Texas have been inferred primarily from specimen records housed in natural history collections. To improve upon these maps, and help inform conservation decisions, this research aimed to (1) update existing Texas bumble bee presence databases to include recent (2007-2016) data from citizen science repositories and targeted field studies, (2) model statewide species distributions of the most common bumble bee species in Texas using MaxEnt, and (3) identify conservation target areas for the state that are most likely to contain habitat suitable for multiple declining species. The resulting Texas bumble bee database is comprised of 3,581 records, to include previously compiled museum records dating from 1897, recent field survey data, and vetted records from citizen science repositories. These data yielded an updated state species list that includes 12 species, as well as species distribution models (SDMs) for the most common Texas bumble bee species, including two that have shown evidence of range-wide declines: B. fraternus (Smith, 1854) and B. pensylvanicus (DeGeer, 1773). Based on analyses of these models, we have identified conservation priority areas within the Texas Cross Timbers, Texas Blackland Prairies, and East Central Texas Plains ecoregions where suitable habitat for both B. fraternus and B. pensylvanicus are highly likely to co-occur.
TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation
Authors: Ijaz Ali Z , Jeffries Thomas , Quince Christopher , Hamonts Kelly , Singh Brajesh
Published: January 2018

Amplicon based taxonomic analysis, which determines the presence of microbial taxa in different environments on the basis of marker gene annotations, often uses percentage identity as the main metric to determine sequence similarity against databases. These data are then used to study the distribution of biodiversity as well as response of microbial communities to environmental conditions. However the 16S rRNA gene displays varying degrees of sequence conservation along its length and percentage identity does not fully utilize this information. Additionally, the prevalent usage of Operational Taxonomic Unit, or OTUs is not without its own issues and may lead to a reduction in annotation capability of the system. Hence a novel approach to taxonomic annotation is needed. Here we introduce a new taxonomic annotation pipeline, TaxaSE, which utilizes Shannon entropy to quantify evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotations. Furthermore, the system is capable of annotation of individual sequences in order to improve fine grain taxonomic annotations. We present both in-silico comparison of the new similarity metric with percentage identity, as well as comparison with the popular QIIME pipeline. The results demonstrate the new similarity metric achieves better performance especially at lower taxa levels. Furthermore, the pipeline is able to extract more fine grain taxonomic annotations compared to QIIME. These exhibit not only the effectiveness of the new pipeline but also highlight the need to shift away from both percentage identity and OTU based approaches for ecological projects.
Exposure to elevated sea-surface temperatures below the bleaching threshold impairs coral recovery and regeneration following injury
Authors: Bonesso Joshua Louis , Leggat William , Ainsworth Tracy Danielle
Published: January 2018

Elevated sea surface temperatures (SSTs) are linked to an increase in the frequency and severity of bleaching events due to temperatures exceeding corals’ upper thermal limits. The temperatures at which a breakdown of the coral-Symbiodinium endosymbiosis (coral bleaching) occurs are referred to as the upper thermal limits for the coral species. This breakdown of the endosymbiosis results in a reduction of corals’ nutritional uptake, growth, and tissue integrity. Periods of elevated sea surface temperature, thermal stress and coral bleaching are also linked to increased disease susceptibility and an increased frequency of storms which cause injury and physical damage to corals. Herein we aimed to determine the capacity of corals to regenerate and recover from injuries (removal of apical tips) sustained during periods of elevated sea surface temperatures which result in coral stress responses, but which do not result in coral bleaching (i.e. sub-bleaching thermal stress events). In this study, exposure of the species Acropora aspera to an elevated SST of 32°C (2°C below the bleaching threshold, 34°C) was found to result in reduced fluorescence of green fluorescent protein (GFP), reduced skeletal calcification and a lack of branch regrowth at the site of injury, compared to corals maintained under ambient SST conditions (26°C). Corals maintained under normal, ambient, sea surface temperatures expressed high GFP fluorescence at the injury site, underwent a rapid regeneration of the coral branch apical tip within 12 days of sustaining injury, and showed extensive regrowth of the coral skeleton. Taken together, our results have demonstrated that periods of sustained increased sea surface temperatures, below the corals’ bleaching threshold but above long-term summertime averages, impair coral recovery from damage, regardless of the onset or occurrence of coral bleaching .
Evidence based pathways to intervention for children with language disorders
Authors: Ebbels Susan H , McCartney Elspeth , Slonims Vicky , Dockrell Julie E , Norbury Courtenay
Published: January 2018

Background: Paediatric SLT roles often involve planning individualised intervention for specific children (provided directly by SLTs or indirectly through non-SLTs), working collaboratively with families and education staff and providing advice and training. A tiered approach to service delivery is currently recommended, whereby services become increasingly specialised and individualised for children with greater needs.

Aims: To examine 1) evidence of intervention effectiveness for children with language disorders at different tiers and 2) evidence regarding SLT roles; and to propose an evidence-based model of SLT service delivery.

Methods: Controlled, peer-reviewed studies, meta-analyses and systematic reviews of interventions for children with language disorders are reviewed and their outcomes discussed, alongside the differing roles SLTs play in these interventions. We indicate where gaps in the evidence base exist and present a possible model of service delivery consistent with current evidence, and a flowchart to aid clinical decision making.

Main Contribution: The service delivery model presented resembles the tiered model commonly used in education services, but divides individualised (Tier 3) services into Tier3A: indirect intervention delivered by non-SLTs, and Tier 3B: direct intervention by an SLT. We report the evidence for intervention effectiveness and which children might best be served by each tier, the role SLTs could take within each, and the evidence of effectiveness of these roles. Regarding universal interventions provided to all children (Tier 1) and those targeted at children with language weaknesses (Tier 2), there is growing evidence that approaches led by education services can be effective when staff are highly trained and well-supported. There is currently limited evidence regarding additional benefit of SLT-specific roles at Tiers 1 and 2. With regard to individualised intervention (Tier 3): children with complex or pervasive language disorders progress significantly following direct individualised intervention (Tier 3B), whereas children with milder or less pervasive difficulties can make progress when intervention is managed by an SLT, but delivered indirectly by others (Tier 3A), provided they are well-trained, -supported and -monitored.

Conclusions: SLTs have a contribution to make at all tiers, but where prioritisation for clinical services is a necessity, we need to establish the benefits and cost-effectiveness of each contribution. Good evidence exists for SLTs delivering direct individualised intervention, and we should ensure that this is available to those children with pervasive and/or complex language impairments. In cases where service models are being provided which lack evidence, we strongly recommend that SLTs investigate the effectiveness of their approaches.
Microbiome succession during ammonification in eelgrass bed sediments
Authors: Ettinger Cassandra L , Williams Susan L , Abbott Jessica M , Stachowicz John J , Eisen Jonathan A
Published: January 2018

Background. Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, or diagenesis, from plots at a field site in Bodega Bay, CA.

Methods. Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n= 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 oC) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at 7, 13 and 19 days to characterize the relative abundances of microbial taxa and how they changed throughout early diagenesis.

Results. Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in sulfur reducers (Desulfobacterales) and corresponding increases in sulfide oxidizers (Alteromonadales and Thiotrichales). None of these changes in composition or richness were associated with ammonification rates.

Discussion. Overall, our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we surmise to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g. elemental cycling and eelgrass-microbe interactions).
Bioinformatics approach reveals the gene targets of Ebola virus microRNAs involved in the human skin microbiome
Authors: Hsu Pei-Chun , Chiou Bin-Hao , Huang Chun-Ming
Published: January 2018

The Ebola virus, a negative-sense single-stranded RNA virus, causes severe viral hemorrhagic fever and is highly lethal. Histopathology and immunopathologic study of Ebola virus have revealed that histopathologic changes in skin tissue were mainly various degrees of endothelial cell swelling and necrosis. The interactions of microbes within or on a host are a crucial aspect of the skin immune shield. The discovery of microRNAs in Ebola virus implies that immune escape, endothelial cell rupture and tissue dissolution during Ebola virus infection are all results of the action of Ebola virus miRNAs. Keratinocytes obtained from normal skin and subsequently attached and spread on the thrombospondin protein family may play a role in initiating cell-mediated immune responses in the skin. Several miRNAs have been observed to bind the 3' untranslated region of the thrombospondin mRNA, thereby controlling its stability and translational activity. In this study, we first discover short RNA sequences that might act as miRNAs from Propionibacterium acnes by design a practical workflow of bioinformatics methods. Subsequently, we deciphered the common target gene. These RNA sequences tend to binding to the same thrombospondin protein. These RNA sequences tend to bind to the same protein , THSD4, emphasizing the potential importance of the synergistic binding of miRNAs from Ebola virus, Propionibacterium acnes , and humans to the target. By RNA expression validation, we prove the potential synergistic binding of the miRNA from Ebola virus, Propionibacterium acnes and human to the target.
Virtual reality: a railroad for structural bioinformatics towards advanced cancer research
Authors: Prakaash Dheeraj , Kodagahally Ravikumar R , Honnaiah Mallesha
Published: January 2018

Technology has been a part of everyone’s life for decades now, and its impact on our lifestyle only seems to increase with time. Considering applications in the field of scientific research till date, it has made exponential advancements and created a new hallmark. ‘Virtual Reality’ is one of the most applicable, impressive and recently uplifted technologies that has been implemented in numerous approaches already. In the light of structural biological studies, virtual reality technology enables immersive 3D visualization of molecular structures, interactions, mechanisms etc., and molecular modelling at the atomic level facilitating a better understanding of the ‘science behind the scene’. In molecular cancer studies, this helps peruse and diagnose defective root causes and unveil effective therapeutic approaches. Although this technology has primarily interested a huge number of researchers and institutes performing structural bioinformatics studies, many researchers across the globe and a large section of the public are still in the dark about its practicality and benefits, some of the main reasons being lack of exposure and the issue with affordability. Thus, besides shedding light on the various ways in which virtual reality has been lately implied to cancer research and therapy, this article aims to promote and encourage usage of a simple, cost-effective platform for 3D immersive visualization of molecular structures for the insufficiently funded community to begin with experiencing molecular virtual reality. It also intends to propose a new permutation of concepts to contribute to an advanced approach in structural cancer studies where scientists can superlatively immerse into the cellular environments and seek answers by virtually communicating with the entities in the microscopic realm. This versatile technology has thus far inevitably proven to possess an enormous potential and is already underway in revolutionizing education, training, scientific research and medical therapy. This article aims to educate more people about prevailing VR technologies and primarily to help accelerate this futuristic technique in cancer research and therapeutics. Albeit leading to a progress in scientific exploration, it could also spread hope and soon assist in upgrading the quality of living especially for cancer victims.