bluuebunny/crossref_metadata_2025 huggingface dataset:
Developmental effects of environmental light on male nuptial coloration in Lake Victoria cichlid fish
Authors: Wright Daniel S. , Rietveld Emma , Maan Martine E.
Published: January 2018

Background. Efficient communication requires that signals are well transmitted and perceived in a given environment. Natural selection therefore drives the evolution of different signals in different environments. In addition, environmental heterogeneity at small spatial or temporal scales may favour phenotypic plasticity in signaling traits, as plasticity may allow rapid adjustment of signal expression to optimize transmission. In this study, we explore signal plasticity in the nuptial coloration of Lake Victoria cichlids, Pundamilia pundamilia and Pundamilia nyererei. These two species differ in male coloration, which mediates species-assortative mating. They occur in adjacent depth ranges with different light environments. Given the close proximity of their habitats, overlapping at some locations, plasticity in male coloration could contribute to male reproductive success but interfere with reproductive isolation.

Methods. We reared P. pundamilia, P. nyererei, and their hybrids under light conditions mimicking the two depth ranges in Lake Victoria. From photographs, we quantified the nuptial coloration of males, spanning the entire visible spectrum. In experiment 1, we examined developmental colour plasticity by comparing sibling males reared in each light condition. In experiment 2, we assessed colour plasticity in adulthood, by switching adult males between conditions and tracking coloration for 100 days.

Results. We found that nuptial colour in Pundamilia did respond plastically to our light manipulations, but only in a limited hue range. Fish that were reared in light conditions mimicking the deeper habitat were significantly greener than those in conditions mimicking shallow waters. The species-specific nuptial colours (blue and red) did not change. When moved to the opposing light condition as adults, males did not change colour.

Discussion. Our results show that species-specific nuptial colours, which are subject to strong divergent selection by female choice, are not plastic. We do find plasticity in green coloration, a response that may contribute to visual conspicuousness in darker, red-shifted light environments. These results suggest that light-environment-induced plasticity in male nuptial coloration in P. pundamilia and P. nyererei is limited and does not interfere with reproductive isolation.
Controlled NOT function can provoke biased interpretation from Bell’s test experiments
Authors: de Castro Alexandre
Published: January 2018

Recently, we showed that the controlled NOT function is a permutation that cannot be inverted in subexponential time in the worst case [Quantum Information Processing. 16:149 (2017)]. Here, we show that such a condition can provoke biased interpretations from Bell’s test experiments.
Vertical motion triggers bouncing perception in retinotopic and body-centered spaces
Authors: Gobara Akihiko , Yamada Yuki
Published: January 2018

When two identical objects travel toward each other, overlap completely, and continue on toward opposite ends of a space, observers perceive them as streaming through or bouncing off each other (stream/bounce perception). In this phenomenon, proportion of perceiving bouncing increases as motion path becomes more vertical (Gobara & Yamada, submitted). However, it remains unclear whether this effect is based on the motion path defined by retinotopic or body-centered coordinates. In this study, we investigated this issue by observers tilting their head. In the experiment, the motion path of two black discs were manipulated from horizontal to vertical. Observers tilted their head 30° left or right using a head rest while they viewed display, and were asked to judge whether the two moving objects streamed through or bounced off each other. The results indicated that the peak of a psychometric function fitted to the rate of bouncing perception significantly shifted toward the direction of the head tilt. These results suggest that the effect of verticality of the motion path on stream/bounce perception is based on retinotopic coordinate.
Querying and analyzing biological data with BioGraph
Authors: Messina Antonio , Fiannaca Antonino , La Paglia Laura , La Rosa Massimo , Urso Alfonso
Published: January 2018

Nowadays, a huge amount of biomedical data of different biological entities is provided by many online databases and services, each with its own data model, user interface and query language. However, typical bioinformatics scenarios require the use of more than one resource. Therefore, the availability of a single bioinformatics platform that integrates many biological resources and services is a fundamental issue.

Some attempts to go beyond the drawbacks of a handcrafted combination of different resources have already been made. Regardless of focus and considered biological data sources, existing tools lack one or more high-level functional features, such as web interface availability, dynamic data visualization, custom queries support, analytics, and expandability.

Here, we present BioGraph, a web application that allows to query, visualize and analyze biological data belonging to several online available resources.

BioGraph is built on top of our previously developed graph database called BioGraphDB, which collects and integrates heterogeneous biological data and makes them available through a common structure and Gremlin as unique query language.

BioGraph makes use of state-of-the-art technologies and provides some pre-compiled bioinformatics scenarios, as well as the possibility to perform custom queries and obtaining an interactive and dynamic visualization of results.
Profiling waitlisted incoming students for future delinquency with an ensemble of statistical machine learning algorithms
Authors: Lauron Maureen Lyndel C , Pabico Jaderick P
Published: January 2018

Given a dataset \(\mathcal{R}=\{R_1, R_2, \dots, R_r\}\) of \(r\)~records of waitlisted incoming freshman students (WIFS), where for any \(i=1, 2, \dots, r\), \(R_i\) is a \((m+1)\)--tuple \((O_i, P_i^{(1)}, P_i^{(2)}, \dots, P_i^{(m)})\), \(O_i\) is any one in a set \(\mathcal{O}=\{O_1, O_2, \dots, O_o\}\) of \(o\)~classes, and \(P_i^{(1)}, P_i^{(2)}, \dots, P_i^{(m)}\) are \(m\)~potential predictors for~\(O_i\). Our purpose is to find a statistical machine learning algorithm (SMLA) \(\mathbb{A}\) such that \(V_i=\mathbb{A}(P_i^{(1)}, P_i^{(2)}, \dots, P_i^{(m)})\), where \(V_i\) is a predicted class by~\(\mathbb{A}\) that was developed using \(n\le m\) correct number of predictors for \(O\in\mathcal{O}\), and \(\mathbb{A}\)~is the best algorithm such that the metric \(v^{-1}\sum_{i=1}^v |O_i - V_i|\) is minimum across \(v<r\)~records in the validation set \(\mathcal{V}\subset\mathcal{R}\). Our problem is to find the subset \(\{P_i^{(1)}, P_i^{(2)}, \dots, P_i^{(n)}\}\) and to train \(\mathbb{A}\)~using \(t<r\) records from the training set \(\mathcal{T}\subset\mathcal{R}\), such that \(\mathcal{T}\cap\mathcal{V}=\emptyset\), so that \(\mathbb{A}\)~can predict whether a WIFS trying to enter an undergraduate program at UPLB will incur at least a ``delinquency'' once the student is accepted into the program. The \(\mathbb{A}\)~can be a useful decision-support tool for UPLB deans and college secretaries in deciding whether a WIFS will be accepted into the program or not.
Taphonomy and palaeoecology of the White Hunter Local Fauna
Authors: Myers Troy
Published: January 2018

The White Hunter (WH) Local Fauna (LF) is one of the oldest assemblages from the Riversleigh World Heritage Area, belonging to Faunal Zone A and tentatively dated at approximately 24 Ma. The mammalian fauna has many plesiomorphic taxa and a wide range of body sizes are represented, although it is depauperate in medium to large arboreal mammals and over-represented by small to medium-sized macropodoids, vombatomorphians and carnivores. The non-mammalian vertebrate fauna also covers a wide body size range.

The palaeoenvironmental conditions at the time of deposition have been contentious, ranging from hypotheses of cold and dry woodland to warm, wet rainforest, and many climatic and vegetation combinations in between. The autecologies of various species provide only equivocal support for palaeoenvironmental conclusions.

Taphonomic and palaeoecologic data were tested herein to further illuminate palaeoenvironmental understanding. Mammalian post-cranial elements were examined for degree of weathering, abrasion, fragmentation, taxonomic bias and susceptibility to transport. No obvious bias against small vertebrates was observed. The fauna does not appear to represent a mixed-assemblage. Animals most likely died within close proximity to the site of deposition, although the absence of scavenger/carnivore damage militates against predation as the main source of accumulation. Trampling of elements may have been significant.

Results suggest that WH may have been a moderately large ephemeral water body, subject to periodic drying and fed by a slow-moving creek. The climate was cooler than the early Miocene, with a distinct wet and dry season. Surrounding vegetation may have been a type without modern analogue combining structural, but not floristic, equivalents of open dry forest and closed rainforest. There is no evidence for gradational wet open forest types, but this may represent a rapid move to closed forest. These results are reinforced by palaeocommunity analysis of Riversleigh LFs which unite WH LF with a suite of early Miocene Lfs as a similar palaeocommunity type, perhaps antecedent to them.
A Quality Management System for scientific research activities and its related management software
Authors: Caruana Luca , Pensato Alessandro , Riccobono Loredana , Liguori Giovanna , Lanati Antonella , Kisslinger Annamaria , Di Carlo Marta , Bongiovanni Antonella
Published: January 2018

Quality disciplines have been widely used for decades in industrial and business fields. It is only in recent times, however, that Quality management and approaches have received proper attention in life science. The development, optimization, validation and dissemination of an innovative way of planning and organizing research activity, inspired by Quality and Project Management principles, is the aim of the present work. Hence, we have generated a Quality Management System for a pilot life science research laboratory that deals with the housing and handling of marine organisms. Based on our Quality system, we have also created the modular software prototype Help4Lab. We could demonstrate that a proper and accurate transfer of Quality culture and methodologies to intellectual and scientific production can facilitate and strengthen scientific research.
Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs
Authors: Guðbrandsson Jóhannes , Franzdóttir Sigríður Rut , Kristjánsson Bjarni Kristófer , Ahi Ehsan Pashay , Maier Valerie Helene , Snorrason Sigurður Sveinn , Jónsson Zophonías Oddur , Pálsson Arnar
Published: January 2018

Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, in both cases leading to altered transcription of genes during the structural and functional development of the body. Comparative developmental studies of closely related species or variable populations of the same species can help to elucidate the molecular mechanisms related to population divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ~10.000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during a timeframe in early development.

Expectedly, developmental time was the predominant explanatory variable. As the data were affected by RNA-degradation, an estimate of 3’-bias was the second most common explanatory variable. Morph, both as a independent variable and as interaction with developmental time, affected the expression of numerous transcripts. The majority of transcripts with significant morph effects separated the limnetic and the benthic morphs. However, gene ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as Arid4a and Tsn. The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.
Additional conjugation systems for inter-domain plasmid transfer to the diatom Phaeodactylum tricornutum
Authors: Kang Anthony K. , Bielinski Vincent A , Bolt Tayah M. , Dupont Christopher L , Weyman Philip D
Published: January 2018

Bacterial conjugation utilizes a type IV secretion system and a DNA transfer mechanism to deliver DNA from one cell to another. Conjugative partners are conventionally confined to the prokaryotic domain. In a prominent exception, Agrobacterium tumefaciens type IV secretion-mediated transfer of DNA to plant cells can result in subsequent chromosomal integration. Recently, we demonstrated interdomain conjugation from Escherichia coli to the diatom Phaeodactylum tricornutum with the subsequent maintenance of an episome at chromosomal copy numbers if it contains diatom centromeres or centromere-like elements. The genes involved in the conjugation process can be separated into those encoding the type IV secretion system, also called the mating pair formation (MPF) genes, and genes involved in DNA processing called the mobilization (MOB) genes. Various protein families compose each class of conjugation genes, including common MOB types F, P, and Q and MPF types F, P, and T. The conjugative transfer from E. coli to P. tricornutum was demonstrated with a vector expressing MOBP and MTFP. Here we show that the MOBPsystem can be deleted and complemented with a MOBQ system in E.coli-diatom conjugations with subsequent episomal maintenaince. Utilization of both MOBP and MOBQ systems results in substantially higher efficiencies in E. coli-diatom conjugation. Finally, we demonstrate conjugative gene transfer between P. tricornutum and A. tumefaciens expressing a MPFT, the first demonstration of this system in diatoms,resulting in episomal maintainance or chromosomal integration, depending on the ex-conjugant. The promiscuity of MOB and MTF systems permitting prokaryote to diatom conjugative DNA transfer suggest major environmental and evolutionary importance of this process. The increased efficiency of dual MOB systems immediately improves genetic engineering in diatoms and has interesting basic cellular biology implications.
Exploiting transcriptomic data in genome-scale metabolic networks: new insights into obesity
Authors: Granata Ilaria , Troiano Enrico , Sangiovanni Mara , Guarracino Mario R
Published: January 2018

Systems Biology is a holistic approach, based on the integration of multiscale models and different kinds of data, aimed at studying the underlying mechanisms of complex biological systems. A GEnome-scale metabolic Model (GEM) is the representation of the metabolic structure of a cell in terms of chemical reactions, involved metabolites, and associated genes. GEMs provide a functional scaffold for constraint-based mathematical methods aimed at simulating and predicting metabolic fluxes in living organisms. The most widely used constraint-based method is the Flux Balance Analysis (FBA), that exploits the stoichiometric matrix, a mathematical representation of the relations between substrates and products of all the reactions in the GEM. Recently, the increasing availability of large amounts of high-throughput sequencing data has fostered the research of new approaches in which the structural information described by GEMs is integrated with the knowledge coming from omics data, with the aim to build more accurate descriptions of metabolic states. Here we propose to use a recently published method, in which transcriptomic data are integrated into genome-scale metabolic models through the maximization of the correlation between the steady-state pattern of the predicted fluxes and the corresponding absolute gene expression data generated under the condition of interest. This approach has the interesting property that no cell growth function must be minimized to execute the model. We used this methodology to simulate a novel GEM of the human adipocyte (iAdipocytes1809), with the aim of getting new insights into the metabolic mechanisms underlying obesity and its relationships with cancer. Obesity is a complex disorder associated with an increased risk of developing several comorbid chronic diseases, ranging from cardiovascular alterations to diabetes, hypertension and cancer. In particular, weight increase and obesity have been identified as the most important risk and prognostic factors for breast cancer, especially in postmenopausal women. We discuss some preliminary results obtained with this approach, hilighting the importance of data integration, and the need for developing new methods that could help in improving our interpretation of biological phenomena.
Distributed stream processing for genomics pipelines
Authors: Versaci Francesco , Pireddu Luca , Zanetti Gianluigi
Published: January 2018

Personalized medicine is in great part enabled by the progress in data acquisition technologies for modern biology, such as next-generation sequencing (NGS). Conventional NGS processing workflows are composed by independent tools implementing shared-memory parallelism which communicate by means of intermediate files. With increasing data sizes this approach is showing its limited scalability and robustness characteristics – problems that make it unsuitable for large-scale, population-wide personalized medicine applications. In this work we propose the adoption of the stream computing architecture to make the genomics pipeline more scalable, and fault-tolerant. We implemented the first processing phases for Illumina sequencing data – from raw data to alignment – using the Apache Flink distributed stream processing framework and Apache Kafka. The new pipeline has been tested processing the raw output of an Illumina HiSeq3000 sequencer and producing aligned reads in CRAM format. The results show near optimal scalability characteristics on experiments from 1 to 12 computing nodes, with a speed-up of 9.5x over the conventional solution (which cannot automatically run on multiple nodes). This result is particularly positive considering that the very short runtime of the experiment – less than 15 minutes – makes significant the constant time costs imposed by the overheads of the frameworks.
Insights into viral community composition of the cnidarian model metaorganism Aiptasia using RNA-Seq data
Authors: Brüwer Jan D , Voolstra Christian R
Published: January 2018

Current research posits that all multicellular organisms live in symbioses with associated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems and their well-being strongly relies on forming mutualistic relationships with endosymbiotic algae of the genus Symbiodinium. So far, only few studies characterized viral diversity and the potential underlying functional importance to coral holobionts. Here we analyzed an existing RNA-Seq dataset of the coral model metaorganism Aiptasia CC7 (sensu Exaiptasia pallida) associated with aposymbiotic, partially populated, and fully symbiotic anemones with Symbiodinium to gain further insight into viral community composition and the relation to the algal endosymbiosis. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (~ 3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences (paired-end read pairs) could be assigned as of viral origin. Taxonomic annotation shows that Aiptasia is associated with a diverse viral community consisting of 116 viral taxa covering 40 families. The viral community was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral community, we found that some viral taxa significantly changed in relative abundance when Aiptasia engage in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present in all samples revealed an Aiptasia core virome of 15 viral taxa from 11 viral families that was comprised of many viruses previously reported in coral viromes. Our study provides a first insight into the viral community of Aiptasia. Aiptasia seem to harbor a diverse and overall stable viral community, although certain members change in abundance when the anemone host associates with its algal endosymbiont. However, the functional significance of this remains to be determined.
Distinguishing polemic from commentary in science: Some guidelines illustrated with the case of Sage and Burgio, 2017
Authors: Grimes David Robert , Bishop Dorothy V
Published: January 2018

Exposure to non-ionizing radiation used in wireless communication remains a contentious topic in the public mind - while the overwhelming scientific evidence to date suggests that microwave and radio frequencies used in modern communications are safe, public apprehension remains considerable. A recent paper in Child Development has caused concern by alleging a causative connection between non-ionizing radiation and a host of conditions, including autism and cancer. In this work, we outline why these claims are devoid of merit, and why they should not have been given a scientific veneer of legitimacy. We also outline some hallmarks of potentially dubious science, with the hope that authors, reviews and editors might be better able to avoid suspect scientific claims.
Good Practice for Conference Abstracts and Presentations: GP-CAP
Authors: Foster Cate , Wager Elizabeth , Marchington Jackie , Patel Mina , Banner Steve , Kennard Nina C , Panayi Antonia , Stacey Rianne
Published: January 2018

This preprint document has been developed following discussions among the authors, all of whom work within the medical communications field. These discussions have indicated a clear need for guidance and consistency around conference abstracts and presentations, so we propose various recommendations and welcome input from any interested individuals. Any guidelines must be based on the principles of transparency, consistency and practicality, but we note that specific congress requirements should always be followed.
Automatic simulation of RNA editing in plants for the identification of novel putative Open Reading Frames
Authors: Fassetti Fabio , Giallombardo Claudia , Leone Ofelia , Palopoli Luigi , Rombo Simona E , Ruffolo Pierluigi , Saiardi Adolfo
Published: January 2018

In plant mitochondria an essential mechanism for gene expression is RNA editing, often influencing the synthesis of functional proteins. RNA editing alters the linearity of genetic information transfer, intro- ducing differences between RNAs and their coding DNA sequences that hind both experimental and computational research of genes. Thus common software tools for gene search, successfully exploited to find canonic genes, often can fail in discovering genes encrypted in the genome of plants. In this work we propose a novel strategy useful to intercept candidate coding sequences resulting from some possible editing substitutions on the start and stop codons of a given input organism DNA. Our method is based on the simulation of the RNA editing mechanism, in order to generate candidate Open Reading Frame (ORF) sequences that could code for some, yet unknown, proteins. Results obtained on the mtDNA of Oryza sativa are promising, since we identified ORF sequences trascripted in Oriza, that do not cor- respond to already known proteins in this organism. Part of the corresponding amino acid sequences present high homologies with proteins already discovered in other organisms, the remaining ones could represent novel proteins not yet discovered in Oryza.
Seqs-Extractor: Automated sequences extraction to reduce tedious manual corrections of large datasets
Authors: Pereira Patrick D C , Dias Cleyssian , Melo Mauro A D , Magalhães Nara G M , Diniz Cristovam G , Diniz Cristovam W P
Published: January 2018

The analysis of large numbers of sequences requires the reduction of ambiguities during the analytical work to ensure that the effort will focus only on confirmed sequences. Performing this work automatically may help to minimize potential errors associated with tedious manual correction, allowing more effective results. Basic local alignment search tool (BLAST) seems to be the most widely used sequence analysis program. It is free, but commercial parties enhanced BLAST applications and charge a fee for their uses. There are some tools of public domain that can perform the search of microsatellites in the next generation sequencing (NGS) data, as the microsatellite identification tool (MISA), which has some features to discover microsatellites in large datasets. Here, we developed a basic shell script (BASH script) to be ran under Linux environment that can be used to extract from a sequence dataset only confirmed (BLASTed) sequences from both nucleotide (BLASTN) and protein (BLASTX) databases and extract sequences that contains microsatellites using MISA tool, using a friendly interface and no fees charged. Seqs-Extractor is a helpful tool that may enhance the analysis of large datasets in BLAST+ and MISA by minimizing the time of management, reducing potential errors caused by manipulating data and no fees charged. Seqs-Extractor is available at https://github.com/patrick-douglas/Seqs-Extractor/wiki .
Ten years of progress and promise of induced pluripotent stem cells: historical origins, characteristics, mechanisms, limitations, and potential applications
Authors: Omole Adekunle Ebenezer , Fakoya Adegbenro Omotuyi John
Published: January 2018

The discovery of induced pluripotent stem cells (iPSCs) by Shinya Yamanaka in 2006 was heralded as a major breakthrough of the decade in stem cell research. The ability to reprogrammed human somatic cells to a pluripotent embryonic stem cell-like state through the ectopic expression of a combination of embryonic transcription factors was greeted with great excitement by scientists and bioethicists. The reprogramming technology offers the opportunity to generate patient-specific stem cells for modeling human diseases, drug development and screening, and individualized regenerative cell therapy. However, fundamental questions have been raised regarding the molecular mechanism of iPSCs generation, a process still poorly understood by scientists. The efficiency of reprogramming of iPSCs remains low due to the effect of various barriers of reprogramming. There is also the risk of chromosomal instability and oncogenic transformation associated with the use of viral vectors, such as retrovirus and lentivirus, which deliver the reprogramming transcription factors by integration in the host cell genome. These challenges can hinder the therapeutic prospects and promise of iPSCs and their clinical applications. Consequently, extensive studies have been done to elucidate the molecular mechanism of reprogramming and novel strategies have been identified which help to improve the efficiency of reprogramming methods and overcome the safety concerns linked with iPSCs generation. Distinct barriers and enhancers of reprogramming have been elucidated and non-integrating reprogramming methods have been reported. Here, we summarize the progress and the recent advances that have been made over the last 10 years in the iPSCs field, with emphasis on the molecular mechanism of reprogramming, strategies to improve the efficiency of reprogramming, characteristics and limitations of iPSCs, and the progress made in the applications of iPSCs in the field of disease modelling, drug discovery and regenerative medicine. Additionally, this study appraised the role of genomic editing technology in the generation of healthy iPSCs.
Microsatellite markers developed in the stingless bee Melipona fasciculata by next-generation sequencing and an exploratory analysis of geographic genetic variation
Authors: Silva Geice R , Souza Isis G B , Souza Bruno A , Pereira Fábia M , Lopes Maria Teresa R , Bentzen Paul , Diniz Fabio Mendonça
Published: January 2018

Background. Native meliponines are currently threatened by increased human impacts. The assessment of their genetic variation by microsatellite DNA markers can assist in the conservation of populations and help in the planning and establishment of efficient management strategies. Next generation sequencing has proven to be useful for identifying microsatellite loci from the large amounts of sequence data generated.

Methods. The purpose of this study was to develop the first set of microsatellite markers for Melipona fasciculata, selected from partial genome assembly of Illumina paired-end reads. Contigs were created from the resulting paired-end sequence data and these were analyzed with specialized software to extract those reads that contained microsatellite loci. Primer pairs were designed for each detected locus at their flanking regions. Bee samples were genotyped from two different locations for markers characterization and validation.

Results. A total of 17 microsatellite loci displayed polymorphism from two different populations of Northeastern Brazil. Mean HE and HO heterozygosities were 0.453 and 0.536, respectively. PIC across all loci ranged from 0.108 to 0.714. A genetic diversity analysis revealed high values for population differentiation estimates (FST = 0.194, RST = 0.230, and Dest = 0.162). PCoA and Bayesian clustering showed a separation of the species into two distinct clusters.

Discussion. The Illumina paired-end sequencing system provided a large number of microsatellite loci from the M. fasciculata genome. From the genotyped data this study was able to reveal high FST and RST estimates and suggest the existence of genetic structure. These microsatellite markers have demonstrated strong potential for population-level genetic studies and can be used effectively as a molecular tool. Moreover, the exploratory analysis of the genetic diversity in M. fasciculata provides provisional evidence of significant population differentiation between the two studied populations.
Protective effect of Rhus coriaria fruit extracts against hydrogen peroxide-induced oxidative stress in muscle progenitors and zebrafish embryos
Authors: Najjar Fadia , Rizk Francine , Carnac Gilles , Nassar Rim , Jabak Sara , Sobolev Anatoly Petrovich , Bou Saada Yara , El Sabban Marwan , Hamade Aline
Published: January 2018

Background and purpose Oxidative stress is involved in normal and pathological functioning of skeletal muscle. Protection of myoblasts from oxidative stress may improve muscle contraction and delay aging. Here we studied the effect of R. coriaria sumac fruit extract on human myoblasts and zebrafish embryos in conditions of hydrogen peroxide-induced oxidative stress.

Study design and Methods Crude ethanolic 70 % extract (CE) and its fractions was obtained from sumac fruits. The composition of sumac ethyl acetate EtOAc fraction was studied by 1H NMR. The viability of human myoblasts treated with CE and the EtOAc fraction was determined by trypan blue exclusion test. Oxidative stress, cell cycle and adhesion were analyzed by flow cytometry and microscopy. Gene expression was analyzed by qPCR.

Results The EtOAc fraction (IC50 2.57 μg/mL) had the highest antioxidant activity and exhibited the best protective effect against hydrogen peroxide-induced oxidative stress. It also restored cell adhesion. This effect was mediated by superoxide dismutase 2 and catalase. Pre-treatment of zebrafish embryos with low concentrations of the EtOAc fraction protected them from hydrogen peroxide-induced death in vivo. 1H NMR analysis revealed the presence of gallic acid in this fraction.

Conclusion Rhus coriaria extracts inhibited or slowed down the progress of skeletal muscle atrophy by decreasing oxidative stress via superoxide dismutase 2 and catalase-dependent mechanisms.
The coast of giants: An anthropometric survey of high schoolers on the Adriatic coast of Croatia
Authors: Grasgruber Pavel , Prce Stipe , Stračárová Nikola , Hrazdíra Eduard , Cacek Jan , Popović Stevo , Hřebíčková Sylva , Potpara Predrag , Davidovič Ivan
Published: January 2018

The aim of this anthropometric survey was to map regional differences in height and body proportions in eight counties adjacent to the Adriatic coast of Croatia. Body height was measured in 1803 males and 782 females aged 17-20 years at 66 schools in 23 towns. When corrected for population size, average male height in the eight counties is 182.6 cm (182.8 cm in seven counties of Adriatic Croatia and 183.7 cm in four counties of Dalmatia proper). Regional variation is considerable (3.5 cm): from 180.6 cm in the county of Karlovac to 184.1 cm in the county of Split-Dalmacija. The height of females in the eight counties is 168.2 cm (168.3 cm in Adriatic Croatia and 168.5 cm in Dalmatia proper), but it is based on more limited data. The results show that young men from Dalmatia are currently the tallest in the world in the age category of 18 years, and the north-to-south gradient of increasing stature on the Adriatic coast largely mirrors that in Bosnia and Herzegovina (BiH). These parallel changes of height in Croatia and BiH can most likely be explained by unique genetic predispositions that are shared by the local populations of the Dinaric Alps.
Investigation of the seasonal microbiome of Anopheles coluzzii in Mali
Authors: Krajacich Benjamin J , Huestis Diana L , Dao Adama , Yaro Alpha S , Diallo Moussa , Krishna Asha , Xu Jiannong , Lehmann Tovi
Published: January 2018

The poorly understood mechanisms of the seasonal maintenance of Anopheles spp. mosquitoes through the dry season in Africa remain a critical gap in our knowledge of Plasmodium disease transmission. While it is thought that adult mosquitoes remain in a dormant state throughout this seven-month dry season, the nature of this state remains unknown and has largely not been recapitulated in laboratory settings. To elucidate possible life history traits allowing for this phenotype, the spatiotemporal change in the microbiome of mosquitoes in the dry and wet seasons in Mali was analyzed by sequencing the 16S ribosome bacterial region in whole bodies of adult mosquitoes collected from two locations with varying water availability. These locations were a village near the Niger River with year-round water sources (N’Gabakoro, “Riparian”), and an area closer to the Sahara with highly seasonal breeding sites (Thierola Area, “Sahelian”). The 16S bacterial data consisted of 2057 unique sequence variants in 426 genera across 184 families. With these, we found several compositional differences that were seasonally and spatially linked. Counter to our initial hypothesis, there was a more pronounced seasonal difference in the bacterial microbiome in the Riparian than Sahelian area. These major seasonal shifts were in Ralstonia, Sphingorhabdus, and Duganella spp. bacteria that are usually soil and water-associated, indicating that these changes may be from bacteria acquired in the larval environment, rather than during adulthood. In the Sahelian dry season mosquitoes, there was a unique intracellular bacteria, Anaplasma, which likely was acquired through non-human blood feeding. Coupled with this finding, cytochrome B analysis showed a greater heterogeneity in host choice of An. coluzzii independent of season in the Thierola area compared to N’Gabakoro (77.5% vs. 94.6% human-origin blood meal, respectively), which may indicate a relaxation of anthropophily in some locations. This study highlights the diversity present in the bacterial composition of individual mosquitoes, characterizes the spatial and seasonal differences in this composition, and indicates some possible qualitative biomarkers in areas of intense seasonal change.
Versioned data: why it is needed and how it can be achieved (easily and cheaply)
Authors: Falster Daniel , FitzJohn Richard G , Pennell Matthew W. , Cornwell William K.
Published: January 2018

The sharing and re-use of data has become a cornerstone of modern science. Multiple platforms now allow quick and easy data sharing. So far, however, data publishing models have not accommodated on-going scientific improvements in data: for many problems, datasets continue to grow with time -- more records are added, errors fixed, and new data structures are created. In other words, datasets, like scientific knowledge, advance with time. We therefore suggest that many datasets would be usefully published as a series of versions, with a simple naming system to allow users to perceive the type of change between versions. In this article, we argue for adopting the paradigm and processes for versioned data, analogous to software versioning. We also introduce a system called Versioned Data Delivery and present tools for creating, archiving, and distributing versioned data easily, quickly, and cheaply. These new tools allow for individual research groups to shift from a static model of data curation to a dynamic and versioned model that more naturally matches the scientific process.
The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics
Authors: Bahram Mohammad , Vanderpool Dan , Pent Mari , Hiltunen Markus , Ryberg Martin
Published: January 2018

Although recent advances in molecular methods have facilitated understanding the evolution of fungal symbiosis, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Basidiomycota), a largely uncultured ectomycorrhizal clade that form symbiotic associations with a wide variety of plant species. Using metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, followed by classifying contigs into fungi and bacteria based on BLAST alignments as well as their differential coverage and GC content, we obtained a highly complete fungal genome, containing 93% of core eukaryotic genes. I. terrigena genome was more related to previously published ectmycorrhizal and brown rot than white rot genomes; however, it showed a significant reduction in lignin degradation capacity compared to closely related ectomycorrhizal clades, supporting independent evolution of ectomycorrhizal symbiosis in Inocybe. The microbiome of I. terrigena harboured bacteria with relatively high-coverage assemblies as well as with known symbiotic functions in hypogeous fungal tissues, suggesting the symbiotic functions of these bacteria in fungal tissues independent of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.
Xenoposeidon is the earliest known rebbachisaurid sauropod dinosaur
Authors: Taylor Michael P
Published: January 2018

Xenoposeidon proneneukos is a sauropod dinosaur represented by a single partial dorsal vertebra, NHMUK R2095, which consists of the centrum and the base of a tall neural arch. Despite its fragmentary nature, it is recognisably distinct from all other sauropods, and is here diagnosed with five unique characters. One character previously considered unique is here recognised as shared with Rebbachisaurus garasbae: an “M”-shaped arrangement of laminae on the lateral face of the neural arch. Following the more complete Rebbachisaurus garasbae, these laminae are now interpreted as ACPL and lateral CPRL, which intersect anteriorly; and PCDL and CPOL, which intersect posteriorly. Similar arrangements are also seen in some other rebbachisaurid specimens (though not all, possibly due to serial variation), but never in non-rebbachisaurid sauropods. Xenoposeidon is therefore referred to Rebbachisauridae. Due to its elevated parapophysis, the holotype vertebra is considered a posterior dorsal despite its elongate centrum. Since Xenoposeidon is from the from the Berriasian–Valanginian (earliest Cretaceous) Ashdown Beds Formation of the Wealden Supergroup of southern England, it is the earliest known rebbachisaurid by some 10 million years. Electronic 3D models were invaluable in determining Xenoposeidon's true affinities: descriptions of complex bones such as sauropod vertebrae should always provide them where possible.
Empirical model predictions and field measurements manifested divergent changes of SOC and SIC in calcareous soils in China
Authors: Wang Huimei , Wang Wenjie
Published: January 2018

Background. Considerable amounts of calcareous soils exist in China and various management practices are used for improving their productivity; however, no holistic view is currently available of their effects on soil organic carbon (SOC) and soil inorganic carbon (SIC) pools. Our study aims to define co-current changes of SOC and SIC by using empirical model predictions and reviewing analysis of actual field data.

Methods. Three datasets were compiled for the present study; the first was obtained from 9 soil survey reports from China and included data for SOC and SIC concentrations and various soil fertility parameters of soil N and available N; soil P and available P; soil K and available K; and soil pH and cation exchange capacity (CEC). These data were used for empirical prediction of SIC and SOC changes with changes in other soil properties via regression analysis. The second dataset comprised 111 data points from concurrent measurements of SOC and SIC from long-term fixed sites and paired sampling sites (long-term fertilization, tillage treatment, paired land-uses, degraded farmland afforestation etc), which were used to confirm the empirical predication. The third dataset comprised separated measurements of rates of changes in SIC (36 data points) and SOC (74 data points), and frequent distribution and averages were analyzed for finding changing rate differences. These datasets were used to determine the relative magnitude of rates of changes in SIC and SOC to identify the importance of co-inclusion of the two components for soil carbon budget estimation.

Results. Empirical relationships between soil fertility parameters (total N and available N; total P and available P; total K and available K; and pH and CEC) and SOC were generally opposite to relationships between soil fertility parameters and SIC (p < 0.001), indicating that soil physicochemical changes as a result of management strategies may affect SOC and SIC in a divergent direction. A total of 111 concurrent measurements of SIC and SOC revealed that soil fertilization and tillage practices could increase SOC andlower SIC by 18% and 11%, respectively, compared to control practices. Similarly, the dataset comprising separated measurements showed that SOC changing rate averaged at 37.3 g m-2 yr-1(SOC accrual), and SIC changing rate averaged at -17.1 g m-2 yr-1(SIC loss), counteracting the SOC accumulation.

Discussion. Changes in SIC are more complicated than those of SOC. In a semiarid region with abundant CO 2 and Ca 2+ , pedogenic formation of SIC was observed, while in a moist region (such as a karst land region) with sufficient water supply, dissolution-induced SIC loss in surface soils was frequently observed. Our findings highlight that SOC and SIC should be simultaneously included in the computation of soil carbon budgets to avoid false estimation of carbon changes as a result of using either SOC or SIC alone.
Coccolith arrangement follows Eulerian mathematics in the coccolithophore Emiliania huxleyi
Authors: Xu Kai , Hutchins David , Gao Kunshan
Published: January 2018

Background. The globally abundant coccolithophore, Emiliania huxleyi, plays an important ecological role in oceanic carbon biogeochemistry by forming a cellular covering of plate-like CaCO3 crystals (coccoliths) and fixing CO2. It is unknown how the cells arrange different sizes of coccoliths to maintain full coverage as the cell surface area changes due to growth and cell division.

Methods. We used Euler’s polyhedron formula and simulation software CaGe, validated with the geometries of coccoliths, to analyses the coccolith topology of coccosphere and the arrange mechanism.

Results. The cells arrange each of the coccoliths to interlock with 4–6 others to keep pace with cell growth and cell division.

Conclusions. This study represents an example of how natural selection has arrived at a solution based on Euler’s polyhedral formula in response to the challenge of maintaining a CaCO3 covering on coccolithophore cells as cell size changes.