bluuebunny/crossref_metadata_2025 huggingface dataset:
The draft genome of Ruditapes philippinarum (the Manila clam), a promising model system for mitochondrial biology
Authors: Ghiselli Fabrizio , Komissarov Aleksey , Milani Liliana , Dunham Joseph P , Breton Sophie , Nuzhdin Sergey V , Passamonti Marco
Published: January 2018

The Class Bivalvia is a highly successful and ancient group including 20,000+ known species. They represent a good model for studying adaptation (anoxia/hypoxia, salinity, temperature, ...), and they are useful bioindicators for monitoring the concentration of pollutants in the water. They also make up an important source of food all over the world, with a production corresponding to ~20% of the global aquaculture yield. A striking feature of bivalves is the presence of an unusual mitochondrial inheritance system: the Doubly Uniparental Inheritance (DUI), so far detected in ~100 bivalve species. In DUI species, two mitochondrial genomes (mtDNAs) are present: one is transmitted through eggs (F-type), the other through sperm (M-type); the amino acid p-distance between conspecific M and F genomes ranges from 10% to over 50%. DUI provides a unique point of view for studying mitochondrial biology. In DUI systems: i) males are naturally heteroplasmic, with very divergent mtDNAs; ii) it is possible to study mitochondrial inheritance and bottleneck by following germ line mitochondria during development; iii) mitochondria are under selection for male functions. Here we present the draft genome of the DUI species Ruditapes philippinarum (the Manila clam). DNA from a male individual was sequenced with 40x Illumina HiSeq and 30x PacBio RSII. The best de novo assembly was obtained with Canu assembler, with contig N50=76kb (86% complete, 5% fragmented, and 9% missing metazoan orthologs according to BUSCO). Here we report the results of the first analyses and the technical challenges we faced, especially with the de novo assembly.
A Tyrannosauroid Metatarsus from the Merchantville Formation of New Jersey increases the diversity of non-Tyrannosaurid Tyrannosauroids on Appalachia
Authors: Brownstein Chase D
Published: January 2018

For almost the entirely of the latter half of the Cretaceous, the continent of North America was divided into two sections, Laramidia in the west and Appalachia in the east. Unfortunately, this latter landmass recorded only a sparse fossil record of dinosaurs, obscuring those forms which must have occupied the eastern portion of North America during this time. Appalachian dinosaur faunas, though obscure, do seem to be different in composition from Laramidian ones. One particular element of Appalachian faunas that has attracted significant attention are the non-tyrannosaurid tyrannosauroids of the continent. Tyrannosauroids on Appalachia, though represented by at least two taxa (Appalachiosaurus montgomeriensis and Dryptosaurus aquilunguis), as well as many partial and fragmentary skeletons and elements, are nevertheless poorly know when compared to their western contemporaries. Here, one specimen, the partial metatarsus of a tyrannosauroid from the Campanian Merchantville Formation of New Jersey, is described in detail. The specimen may be differentiated from Appalachiosaurus montgomeriensis, Dryptosaurus aquilunguis, and an unnamed specimen from the Maastrichtian of New Jersey by several notable morphological features outside the spectrum of individual variation, as well as by factoring in biogeographical considerations. The new specimen thus has significance for representing a new morphotype of tyrannosauroid from Appalachia, suggesting greater diversity of the clade on the landmass. Because of this, tyrannosaur diversity in the Campanian of Appalachia was compared to the diversity of tyrannosaurs in Laramidia during the same period to analyze the similarities and differences between the biogeography of tyrannosaurs on each landmass. The results suggest that Appalachian non-tyrannosaurid tyrannosauroids experienced a similar amount of diversity to tyrannosaurids in Laramidia during the Campanian.
UTR and non-coding RNA: reconnecting terms to function
Authors: brandao adeilton
Published: January 2018

Scientific terms should be as accurate and meaningful as possible for both researchers and the general science readership. Currently, some scientific terms do not properly describe the activity or function to which they are associated to, being frequently characterized by negative reference to a prior feature or finding. UTR (Untranslated Region) and non-coding RNA fall within this class. In this article, I argue for a revision of these terms to account for the growing lines of evidence about their known function and activity in the cell.
Theropod specimens from the Navesink Formation and their implications for the Diversity and Biogeography of Ornithomimosaurs and Tyrannosauroids on Appalachia
Authors: Brownstein Chase D
Published: January 2018

The sparse dinosaur record of eastern North America has rendered the dinosaurs of the Late Cretaceous landmass of Appalachia obscure. This landmass, isolated from the western landmass Laramidia by a great inland sea known as the Western Interior Seaway, may have been a safe haven for dinosaur species which would be replaced on Appalachia’s western contemporary. An excellent example of these isolated forms are the tyrannosaurs of Appalachia, which have not only been grouped outside Tyrannosauridae proper in phylogenetic analyses, but also bare distinct morphologies, including a gigantic manus in one form, from these ‘western tyrants’. However, Appalachian tyrannosaurs are only represented currently by the two valid taxa Dryptosaurus aquilunguis and Appalachiosaurus montgomeriensis, both which are only known from partial skeletons with few overlapping elements. Recently, the generic name Teihivenator was given to another tyrannosaur named “Laelaps” macropus by Cope (1868) by Yun (2017). However, examination of the specimens by the author show morphologies at odds with the morphological descriptions given by Yun (2017). The tyrannosaur named by Yun (2017), known from partial lower hindlimb elements including the portions of two metatarsals and a partial tibia, is shown herein to be a chimaera of ornithomimosaur and tyrannosauroid hindlimb elements. The several different dinosaur specimens which compose the syntypes of “Teihivenator” include three ornithomimosaur pedal phalanges with affinities to derived ornithomimid taxa, a proximal end of the right metatarsal II and a distal end of the right metatarsal II from either ornithomimosaurs or tyrannosauroids, and a partial tibia of a tyrannosauroid distinct from Dryptosaurus or Appalachiosaurus but nevertheless considered here to be from an indeterminate taxon based on the lack of observable autopomorphies and issues with the comparability of the specimen to other taxa. The specimens are nevertheless important for revealing further the theropod fauna of the Maastrichtian Navesink Formation of New Jersey, as well as for possibly increasing the diversity of tyrannosauroids and further illuminating the presence of ornithomimosaurs on Appalachia.
Experimental moose reduction lowers wolf density and stops decline of endangered caribou
Authors: Serrouya Robert , McLellan Bruce N , van Oort Harry , Mowat Garth , Boutin Stan
Published: January 2018

The expansion of moose into southern British Columbia caused the decline and extirpation of woodland caribou due to their shared predators, a process commonly referred to as apparent competition. Using an adaptive management experiment, we tested the hypothesis that reducing moose to historic levels would reduce apparent competition and therefor recover caribou populations. Nested within this broad hypothesis were three specific hypotheses: 1) sport hunting could be used to substantially reduce moose numbers to an ecological target; 2) wolves in this ecosystem were primarily limited by moose abundance; and 3) caribou were limited by wolf predation. These hypotheses were evaluated with a before-after control-impact (BACI) design that included response metrics such as population trends and vital rates of caribou, moose, and wolves. Three caribou subpopulations were subject to the moose reduction treatment and two were in a reference area where moose were not reduced. When the moose harvest was increased, the moose population declined substantially in the treatment area (by 70%) but not the reference area, suggesting that the policy had the desired effect and was not caused by a broader climatic process. Wolf numbers subsequently declined in the treatment area, with wolf dispersal rates 2.5 × greater, meaning that dispersal was the likely mechanism behind the wolf numerical response, though reduced recruitment and starvation was also documented in the treatment area. Caribou adult survival increased from 0.78 to 0.88 in the treatment area, but declined in the reference. Caribou recruitment was unaffected by the treatment. The largest caribou subpopulation stabilized in the treatment area, but declined in the reference area. The observed population stability is comparable to other studies that used intensive wolf control, but is insufficient to achieve recovery, suggesting that multiple limiting factors and corresponding management tools must be addressed simultaneously to achieve population growth.
LuxS quorum sensing system, its protein modeling and active-binding sites and phylogenetic analysis from Aeromonas hydrophila
Authors: Ali Farman , Yao Zujie , Li Wanxin , Lina Sun , Lin Wenxiong , Lin Xiangmin
Published: January 2018

LuxS is commonly found in various bacterial species, like A. hydrophila which causes infection in fish, shrimps, and prawns and is a great threat to aquaculture industry as well as public health. It is an essential enzyme and highly conserved in various bacterial species, and has a wide range of functions such as involved in quorum sensing (QS), sporulation, virulence and synthesis of biofilm. This study focused on the prediction of 3D-sturcture of LuxS by template similarity and its ligand binding sites analysis to define its structure-function relationship. Primary structure analysis of LuxS examined that about 42% of residues content are alpha-helix, which makes it stable for three-dimensional structure homology. For the con struction of homology modeling of LuxS, crystal structure (5e68.1.A) has been used as a template and Swiss model as a work space. The validation of model by ProSA, SAVES, PROCHECK, PROSAII and RMSD. All results analysis shows that refined model is reliable and it has78.11% amino acids sequence similarity with the template,0.4Åas RMSD, and Z-score is -6.21 and Ramachandran plot analysis shows that 83.4% of residues found in the most favored regions where only 0.4% falls into the disallowed regions. Zinc ion ligand was predicted with highest MAMMOTH score and its binding residues His-54, His-58 and Cys-128 were analyzed by COACH-Meta server. LuxS phylogeny was constructed by sequences and structures of the most similar sequences were analyzed. In silico, the information has been generated in this work expects to be the first step towards the structure determination of LuxS in A. hydrophila.
Finding biologically significant biclusters: a new function for co-expression evaluation
Authors: Luna-Taylor Jorge E. , Brizuela Carlos A. , Alvarado Ivan N.
Published: January 2018

Analysis of DNA microarray data has been very useful for experimental molecular biology, as it provides unprecedented opportunities to study a wide variety of biological processes. As a part of this analysis, biclustering has been consolidated as one of the first steps in the discovery of new knowledge. Biclustering consists in identifying clusters of genes that present coherent behavior patterns for a subset of experimental conditions. The measure to assess this consistency is a key factor in the quality of discovered biclusters. In this paper, we propose a new function (VF) to evaluate the coherence of biclusters. This function recognizes shifting, and positive and negative scaling patterns, more efficiently than well-known reported functions with a similar purpose. Also, the VF function identifies positive and negative scaling subpatterns, which may be of biological interest and have not previously been discussed in the literature. To assess the performance of the VF function, a biclustering genetic algorithm (BGA VF) was also designed, and tested on both synthetic and real data. The results show that the BGA VF algorithm obtains high percentages of significant biclusters and recognizes all the analyzed combinations of coherence patterns.
Finding biologically significant biclusters: a new function for co-expression evaluation
Authors: Luna-Taylor Jorge E. , Brizuela Carlos A. , Alvarado Ivan N.
Published: January 2018

Analysis of DNA microarray data has been very useful for experimental molecular biology, as it provides unprecedented opportunities to study a wide variety of biological processes. As a part of this analysis, biclustering has been consolidated as one of the first steps in the discovery of new knowledge. Biclustering consists in identifying clusters of genes that present coherent behavior patterns for a subset of experimental conditions. The measure to assess this consistency is a key factor in the quality of discovered biclusters. In this paper, we propose a new function (VF) to evaluate the coherence of biclusters. This function recognizes shifting, and positive and negative scaling patterns, more efficiently than well-known reported functions with a similar purpose. Also, the VF function identifies positive and negative scaling subpatterns, which may be of biological interest and have not previously been discussed in the literature. To assess the performance of the VF function, a biclustering genetic algorithm (BGA_VF) was also designed, and tested on both synthetic and real data. The results show that the BGA_VF algorithm obtains high percentages of significant biclusters and recognizes all the analyzed combinations of coherence patterns.
The role of biomaterials in the treatment of meniscal tears
Authors: Kean Crystal O , Brown Robert J , Chapman James
Published: January 2018

Extensive investigations over the recent decades have established the anatomical, biomechanical and functional importance of the meniscus in the knee joint. As a functioning part of the joint, it serves to prevent the deterioration of articular cartilage and subsequent osteoarthritis. To this end, meniscus repair and regeneration is of particular interest from the biomaterial, bioengineering and orthopaedic research community. Even though meniscal research is previously of a considerable volume, the research community with evolving material science, biology and medical advances are all pushing toward emerging novel solutions and approaches to the successful treatment of meniscal difficulties.
PIsCO: A Performance indicators framework for collection of bioinformatics resource metrics
Authors: Artaza Haydee , Hancock John M. , Jimenez Rafael C. , Corpas Manuel
Published: January 2018

We present PIsCO, a server-side JavaScript framework for the collection, registration and sharing of metrics that can be used to evaluate the impact of bioinformatics-related resources such as software, repositories, training or databases. The metrics framework can be used to capture standard definitions of metrics, facilitate the collection of data, monitor resources and share data to be reused by other teams, laboratories or academic institutions. In addition, PIsCO is able to collect those metrics and present them in a visual way to allow their easy interpretation.
Best practice in mixed effects modelling and multi-model inference in ecology
Authors: Harrison Xavier A , Donaldson Lynda , Correa-Cano Maria Eugenia , Evans Julian , Fisher David N , Goodwin Cecily , Robinson Beth , Hodgson David J , Inger Richard
Published: January 2018

The use of linear mixed effects models (LMMs) is increasingly common in the analysis of biological data. Whilst LMMs offer a flexible approach to modelling a broad range of data types, ecological data are often complex and require complex model structures, and the fitting and interpretation of such models is not always straightforward. The ability to achieve robust biological inference requires that practitioners know how and when to apply these tools. Here, we provide a general overview of current methods for the application of LMMs to biological data, and highlight the typical pitfalls that can be encountered in the statistical modelling process. We tackle several issues relating to the use of information theory and multi-model inference in ecology, and demonstrate the tendency for data dredging to lead to greatly inflated Type I error rate (false positives) and impaired inference. We offer practical solutions and direct the reader to key references that provide further technical detail for those seeking a deeper understanding. This overview should serve as a widely accessible code of best practice for applying LMMs to complex biological problems and model structures, and in doing so improve the robustness of conclusions drawn from studies investigating ecological and evolutionary questions.
Stem-loop structure preference for site-specific RNA editing by APOBEC3A and APOBEC3G
Authors: Sharma Shraddha , Baysal Bora E
Published: January 2018

APOBEC3A and APOBEC3G cytidine deaminases inhibit viruses and endogenous retrotransposons. We recently demonstrated the novel cellular C-to-U RNA editing function of APOBEC3A and APOBEC3G. Both enzymes deaminate single-stranded DNAs at multiple TC or CC nucleotide sequences, but edit only a select set of RNAs, often at a single TC or CC nucleotide sequence. To examine the specific site preference for APOBEC3A and -3G-mediated RNA editing, we performed mutagenesis studies of the endogenous cellular RNA substrates of both proteins. We demonstrate that both enzymes prefer RNA substrates that have a predicted stem-loop with the reactive C at the 3ʹ-end of the loop. The size of the loop, the nucleotides immediately 5ʹ to the target cytosine and stability of the stem have a major impact on the level of RNA editing. Our findings show that both sequence and secondary structure are preferred for RNA editing by APOBEC3A and -3G, and suggest an explanation for substrate and site-specificity of RNA editing by APOBEC3A and -3G enzymes.
Greedy motif-based approach to parsing large and diverge coiled-coil proteins into domains
Authors: Khakzad Hamed , Malmström Johan , Malmström Lars
Published: January 2018

Bacterial surfaces are complex, built of from membranes, peptide-glycans and, importantly, proteins. The proteins play crucial roles as the key regulator of how the bacterium interacts with its environment. A full catalog of the motifs in coiled-coil proteins and their relative conservation grade is a pre-requisite to target the protein-protein interaction that bacterial surface protein makes to host proteins. Here, we present a greedy approach to iteratively identify conserved motifs in large sequence collections, identify all occurrences of these motifs and mask them. Remaining unmasked sequences are subjected to the second round of motif detection until no more significant motifs can be found or all protein segments have been assigned to a motif. We present the results for the S. pyogenes M protein. Given the speed and flexibility of our approach, we believe it will be useful in breaking analyzing surface protein of pathogens as these proteins are under high selective pressure and therefore cannot be analyzed using more traditional approaches such as multiple-sequence alignments. Preliminary data indicates that many of the newly discovered motifs are not always present together with adjacent motifs, indicating that they might have different and independent functions.
The State of OA: A large-scale analysis of the prevalence and impact of Open Access articles
Authors: Piwowar Heather , Priem Jason , Larivière Vincent , Alperin Juan Pablo , Matthias Lisa , Norlander Bree , Farley Ashley , West Jevin , Haustein Stefanie
Published: January 2018

Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles.

We use three samples, each of 100,000 articles, to investigate OA in three populations: 1) all journal articles assigned a Crossref DOI, 2) recent journal articles indexed in Web of Science, and 3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI.

We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made free-to-read on the publisher website, without an explicit Open license.

We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice.
Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region
Authors: Hanna Zachary R , Henderson James B , Sellas Anna B , Fuchs Jérôme , Bowie Rauri C. K. , Dumbacher John P
Published: January 2018

We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100-375 nt and Sanger sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts).
De novo species delimitation in metabarcoding datasets using ecology and phylogeny
Authors: Potter Caitlin , Tang Cuong Q , Fonseca Vera , Lallias Delphine , Gaspar John M , Thomas Kelley , Creer Simon
Published: January 2018

Background: Metabarcoding studies allow a wide variety of taxa to be analysed simultaneously in a fraction of the time taken by morphological identification, but currently metabarcoding studies must rely on sequence similarity-based methodologies to delimit operational taxonomic units (OTUs). Similarity-based OTU clustering methodologies can lead to inaccurate estimates of diversity, species’ distributions or responses to change, meaning that there is a critical need for methods to delimit species in metabarcoding datasets.

Methods: We introduce SNAPhy (Species delimitation using Niche And PHYlogeny), a novel approach which utilises ecological and phylogenetic information to delimit de novo OTUs in metabarcoding datasets and avoids the problems associated with current OTU clustering methods. Sequencing reads are first divided into ecological groups based on co-occurrence, thereby reducing data complexity and facilitating the use of evolutionary and phylogenetic models (e.g. BEAST and GMYC) to delimit species-level groupings within discrete ecologically informed phylogenies. The utility of SNAPhy is demonstrated using an 18S rDNA nuclear small subunit (nSSU) dataset representing replicated samples taken along the entire length of an estuarine salinity gradient, and SNAPhy is then compared to existing OTU clustering methods.

Results: All of the OTU clustering methods compared yielded different numbers of OTUs and a different taxonomic distribution of OTUs, which we suggest is due to the taxon differences that are known to exist in the degree of intraspecific divergence. SNAPhy and UCLUST (with a 98% similarity threshold) gave the most plausible numbers of OTUs, especially within the Nematoda. Additionally, the degree of variation within nematode OTUs delimited by SNAPhy lies within the range of variation in deeply metabarcoded individuals.

Discussion: SNAPhy avoids the static clustering threshold problems associated with current OTU clustering methods and instead focuses on genuine biological diversity delimited according to a general lineage species concept. We suggest that the SNAPhy approach should play a crucial role in future sequencing-based biodiversity assessment by providing more accurate estimates of species diversity and distributions than current methods, thereby enabling more accurate impact assessments and better informing managerial decisions.
The inheritance of viable mitochondria
Authors: Milani Liliana , Ghiselli Fabrizio
Published: January 2018

Mitochondria cannot be produced de novo by the cell, but are inherited across generations. Their peculiar genetics (multiple genomes per cell, no meiosis, replication independent from cell cycle, high mutation rate) and the possible exposition to Reactive Oxygen Species (ROS) are predicted to produce a fast accumulation of deleterious mutations, a phenomenon known as Müller’s ratchet. Nonetheless, mitochondrial genomes persist accurately over million years. How is a viable mitochondrial genetic information preserved? To answer this question we review the following relevant topics: 1) the sources of mtDNA mutation (replication and ROS); 2) the origin of mitochondrial membrane potential; 3) the activity of germ line mitochondria; 4) the mitochondrial bottleneck; 5) mtDNA drift and selection. Finally we discuss such topics in the light of an unusual biological system (Doubly Uniparental Inheritance of mitochondria, DUI), in which also sperm mtDNA is regularly transmitted to the progeny.
Project Airless: addressing the problem of pyrite oxidation in a large fossil collection
Authors: Miles Kieran
Published: January 2018

The Natural History Museum in London holds around 7 million fossils, a diverse collection of huge scientific and historical importance. The Conservation Centre is responsible for a wide range of specimen care issues, including those affecting the palaeontology collections. One of the most serious of these problems is pyrite oxidation. Pyrite, a form of iron sulphide, can often be found in fossils or their surrounding matrix. Oxidation occurs when unstable pyrite, often in its microcrystalline form, reacts with atmospheric oxygen and water. This reaction is accelerated at relative humidity above 60%, and produces a variety of harmful by-products, usually comprising ferrous sulphate, hydrogen sulphide and sulphuric acid.

Airless, a three-year project that started in August 2015, aims to address this problem. The goal is to identify, treat and prevent pyrite oxidation in the Earth Science collections. A small team of conservation technicians are surveying the collections looking for signs of pyrite decay. Affected specimens are taken to a dedicated lab space where remedial treatments, such as dry brushing or ammonia vapour treatment, are carried out, before re-storage of specimens in anoxic microenvironments. These are individually hand-made using barrier film, with oxygen scavenging sachets added to remove oxygen from the sealed bag. In addition, the project has a digitisation aspect, with the use of web-based applications, improving the museum’s database with high-quality photographs that partly compensate for the reduced physical access to the specimens. To date, the team has completed work on nearly 3000 specimens, including ichthyosaurs, plesiosaurs and pterosaurs.
Facilitative and competitive interaction components among New England salt marsh plants
Authors: Bruno John F , Rand Tatyana A , Emery Nancy C , Bertness Mark D
Published: January 2018

Intra- and interspecific interactions can be broken down into facilitative and competitive components. The net interaction between two organisms is simply the sum of these counteracting elements. Disentangling the positive and negative components of species interactions is a critical step in advancing our understanding of how the interaction between organisms shift along physical and biotic gradients, and whether component interactions are unique or redundant across species in natural communities. We performed a manipulative field experiment to quantify the positive and negative components of the interactions between a perennial forb, Aster tenuifolius, and three dominant, matrix-forming grasses and rushes in a New England salt marsh. Specifically, we asked whether positive and negative interaction components: (1) are unique or redundant across three matrix-forming grass and rush species (Juncus gerardi, Distichlis spicata, and Spartina patens), and (2) change across Aster life stages (seedling, juvenile, and adult). For adult forbs, the strength of the facilitative component of the matrix-forb interaction was stronger than the competitive component for two of the three matrix species, leading to net positive interactions. There was no statistically significant variation among matrix species in their net or component effects, however, the competitive effect of J. gerardi was negligible, especially compared to that of D. spicata. We found little difference in the effects of J. gerardi on Aster at later life-history stages; interaction component strengths did not differ between juveniles and adults. However, mortality of seedlings in neighbor removal plots was 100%, indicating a particularly strong and critical facilitative effect of matrix species on this forb during the earliest life stages. Overall, our results indicate that matrix forming grasses and rushes have important, yet largely redundant, positive net effects on Aster performance across its life cycle. Studies that untangle various components of interactions and their contingencies are critical to both expanding our basic understanding of community organization, and predicting how natural communities and their component parts will respond to environmental change.
The remedial conservation and support jacketing of the neotype specimen of the dinosaur Massospondylus carinatus
Authors: Graham Mark R
Published: January 2018

In March 2017 the neotype specimen of the Early Jurassic South African prosauropod dinosaur Massospondylus carinatus was appraised and condition reported at the Evolutionary Studies Institute, University of the Witwatersrand (WITS), Johannesburg, in readiness for remedial conservation and re-storage. The work was necessitated by deterioration of the specimen, which was caused by handling over a number of years and an inadequate and failing support mount.

Formally numbered BP/1/4934, but more affectionately known to staff as ‘Big Momma’, the specimen was contained within several individual blocks on flimsy support bases and presented various conservation challenges.These included treatment of fractures and cracking across several surfaces of the fossil and the production of clam shell supports to allow for articulated display within the constraints of an existing display cabinet. Part of the brief was to facilitate safer handling and access for researchers.

This project was led by the author who also trained the curatorial and preparation staff at WITS in the methods and techniques employed. The visit was funded by the Palaeontological Scientific Trust (PAST), the DST/NRF Centre of Excellence in Palaeosciences and The University of the Witwatersrand (WITS).
Monitoring microbial communities using light sheet fluorescence microscopy
Authors: Parthasarathy Raghuveer
Published: January 2018

Microbes often live in dense, dynamic, multi-species communities whose architecture and function are intimately intertwined. Imaging these complex, three-dimensional ensembles presents considerable technical challenges, however. In this review, I describe light sheet fluorescence microscopy, a technique that enables rapid acquisition of three-dimensional images over large fields of view and over long durations, and I highlight recent applications of this method to microbial systems that include artificial closed ecosystems, bacterial biofilms, and gut microbiota. I comment also on the history of light sheet imaging and the many variants of the method. Light sheet techniques have tremendous potential for illuminating the workings of microbial communities, a potential that is just beginning to be realized.
Habitat suitability – density relationship in an endangered woodland species: the case of the Blue Chaffinch (Fringilla polatzeki)
Authors: Carrascal Luis M. , Moreno Angel C. , Delgado Alejandro , Suárez Víctor , Trujillo Domingo
Published: January 2018

Background. Understanding constraints to the distribution of threatened species may help to ascertain whether there are other suitable sectors for reducing the risks associated with species that are recorded in only one protected locality, and to inform about the suitability of other areas for reintroduction or translocation programs.

Methods. We studied the Gran Canaria blue chaffinch (Fringilla polatzeki), a habitat specialist endemic of the Canary Islands restricted to the pine forest of Inagua, the only area where the species has been naturally present as a regular breeder in the last 25 years. A suitability distribution model using occurrences with demographic relevance (i.e., nest locations of successful breeding attempts analysed using boosted classification trees) was built considering orographic, climatic and habitat structure predictors. By means of a standardized survey program we monitored the yearly abundance of the species in 100 sectors since the declaration of Inagua as a Strict Nature Reserve in 1994.

Results. The variables with the highest relative importance in blue chaffinch habitat preferences were pine height, tree cover, altitude, and rainfall during the driest trimester (July-September). The observed local abundance of the blue chaffinch in Inagua (survey data) was significantly correlated with habitat suitability derived from modelling the location of successful nesting attempts (using linear and quantile regressions). The outcomes of the habitat suitability model were used to quantify the suitability of other natural, historic, pine forests of Gran Canaria. Tamadaba is the forest with most suitable woodland patches for the species. We estimated a population size of 195-430 blue chaffinches in Inagua since 2011 (95% CI), the smallest population size of a woodland passerine in the Western Palearctic.

Discussion. Habitat suitability obtained from modelling the location of successful breeding attempts is a good surrogate of the observed local abundance during the reproductive season. The outcomes of these models can be used for the identification of potential areas for the reintroduction of the species in other suitable pine forests and to inform forest management practices.
The science behind Smarter Lunchrooms
Authors: Robinson Eric
Published: January 2018

The Smarter Lunchrooms intervention approach aims to tackle childhood obesity by promoting healthier nutrition through the use of choice architecture or ‘nudge’ tactics in school lunchrooms. I reviewed research papers that were described by Cornell University as forming the evidence base for the Smarter Lunchrooms approach. Here I discuss concerns about the way that research informing the Smarter Lunchrooms approach has been conducted and disseminated. The widespread implementation of the Smarter Lunchrooms approach is discussed and the likely efficacy of this public health intervention is also considered.
How to share data for collaboration
Authors: Ellis Shannon E , Leek Jeffrey T
Published: January 2018

Within the statistics community, a number of guiding principles for sharing data have emerged; however, these principles are not always made clear to collaborators generating the data. To bridge this divide, we have established a set of guidelines for sharing data. In these, we highlight the need to provide raw data to the statistician, the importance of consistent formatting, and the necessity of including all essential experimental information and pre-processing steps carried out to the statistician. With these guidelines we hope to avoid errors and delays in data analysis.
Involving undergraduates in genomics research to narrow the education-research gap
Authors: Mangul Serghei , Martin Lana , Eskin Eleazar
Published: January 2018

While the benefits of undergraduate research experiences (UREs) are recognized for undergraduates, the advantages of UREs for graduate students, post-doctoral scholars, and faculty are not clearly outlined. The analysis of genomic data is particularly well-suited for successful involvement of undergraduates. We offer a framework for engaging undergraduates in genomics research while simultaneously improving lab productivity. The proposed strategy can be easily reproduced at other institutions, is pedagogically flexible, and is scalable from smaller to larger laboratory sizes. We hope that genomics researchers will involve undergraduates in more computational tasks that benefit both students and senior laboratory members.
An algorithm for calculating top-dimensional bounding chains
Authors: Carvalho J. Frederico , Vejdemo-Johansson Mikael , Kragic Danica , Pokorny Florian T.
Published: January 2018

We describe the \textsc{Coefficient-Flow} algorithm for calculating the bounding chain of an $(n-1)$--boundary on an $n$--manifold-like simplicial complex $S$. We prove its correctness and show that it has a computational time complexity of $O(|S^{(n-1)}|)$ (where $S^{(n-1)}$ is the set of $(n-1)$--faces of $S$). We estimate the big-$O$ coefficient which depends on the dimension of $S$ and the implementation. We present an implementation, experimentally evaluate the complexity of our algorithm, and compare its performance with that of solving the underlying linear system.
Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C
Authors: Prostova Maria A , Deviatkin Andrei A , Tcelykh Irina O , Lukashev Alexander N , Gmyl Anatoly P
Published: January 2018

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features low fidelity, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein.

Methods.To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C.

Results.A total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y=U/C, N=any nucleotide, H=A/C/U). The putative RNA-binding tripeptide 154-156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific.

Discussion. Despite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition.
Particle bombardment and subcellular protein localization analysis in the aquatic plant Egeria densa
Authors: Osaki Yasuhide , Kodama Yutaka
Published: January 2018

Particle bombardment is a powerful and relatively easy method for transient expression of genes of interest in plant cells, especially those that are recalcitrant to other transformation methods. This method has facilitated numerous analyses of subcellular localization of fluorescent fusion protein constructs. Particle bombardment delivers genes to the first layer of plant tissue. In leaves of higher plants, epidermal cells are the first cell layer. Many studies have used the epidermal cell layer of onion bulb (Allium cepa) as the experimental tissue, because these cells are relatively large. However, onion epidermal cells lack developed plastids (i.e., chloroplasts), thereby precluding subcellular localization analysis of chloroplastic proteins. In this study, we developed a protocol for particle bombardment of the aquatic plant Egeria densa, and showed that it is a useful system for subcellular localization analysis of higher plant proteins. E. densa leaflets contain only two cell layers, and cells in the adaxial layer are sufficiently large for observation. The cells in both layers contain well-developed chloroplasts. We fused fluorescent proteins to conventional plant localization signals for the nucleus, cytosol, mitochondria, peroxisome, and chloroplast, and used particle bombardment to transiently express these fusion constructs in E. densa leaves. The plant subcellular localization signals functioned normally and displayed the expected distributions in transiently transformed E. densa cells, and even chloroplastic structures could be clearly visualized.
The prehistory of biology preprints: a forgotten experiment from the 1960s
Authors: Cobb Matthew
Published: January 2018

In 1961, the NIH began to circulate biological preprints in a forgotten experiment called the Information Exchange Groups (IEGs). This system eventually attracted over 3600 participants and saw the production of over 2,500 different documents, but by 1967 it was effectively shut down by journal publishers’ refusal to accept articles that had been circulated as preprints. This article charts the rise and fall of the IEGs and explores the parallels with the 1990s and the biomedical preprint movement of today.
Comparative skull biomechanics in Varanus and Salvator ‘Tupinambis’
Authors: Dutel Hugo , Sharp Alana C , Jones Marc E H , Evans Susan E , Fagan Micheal J , Gröning Flora
Published: January 2018

The lizard species Salvator ‘Tupinambis’ merianae and Varanus ornatus evolved independently in South America and Africa but share similar ecology and feeding behaviour, despite having notable differences in their skull structure. Tupinambis has a compact, relatively short and wide snout, whereas that of Varanus is more slender and narrow. In addition, a postorbital bar (POB) is present in Tupinambis but absent in Varanus, and the former lacks the mid-frontal suture that is present in the latter. Here, we explore the biomechanical significance of these differences using 3D computer-based mechanical simulations based on micro-computed tomography, detailed muscle dissections, and in vivo data. First, we simulated muscle activity and joint-reaction forces during biting using Multibody Dynamics Analysis. Then, the forces calculated from these models were used as an input for Finite Element Analysis, to investigate and compare the strains of the skull in these two species. The effects of the presence/absence of structures, such as the POB, were investigated by constructing artificial models which geometry was altered. Our results indicate that strains in the skull bones are lower in Tupinambis than in Varanus, in particular at the back of the skull. The presence of a POB clearly reduces the strains in the bones during posterior biting in Tupinambis, but not in Varanus. Our results hence highlight how the morphological differences between these two taxa affect the mechanical behaviour of their respective skulls during feeding.
Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A
Authors: Calkins Shelby S , Elledge Nicole C , Marek Stephen M. , Couger M B. , Elshahed Mostafa S , Youssef Noha H
Published: January 2018

Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.