bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copyright and the Use of Images as Biodiversity Data
Authors: Egloff Willi , Agosti Donat , Kishor Puneet , Patterson David , Miller Jeremy A. 
Published: November 2016

1.AbstractTaxonomy is the discipline responsible for charting the world’s organismic diversity, understanding ancestor/descendant relationships, and organizing all species according to a unified taxonomic classification system. Taxonomists document the attributes (characters) of organisms, with emphasis on those can be used to distinguish species from each other. Character information is compiled in the scientific literature as text, tables, and images. The information is presented according to conventions that vary among taxonomic domains; such conventions facilitate comparison among similar species, even when descriptions are published by different authors.There is considerable uncertainty within the taxonomic community as to how to re-use images that were included in taxonomic publications, especially in regard to whether copyright applies. This article deals with the principles and application of copyright law, database protection, and protection against unfair competition, as applied to images. We conclude that copyright does not apply to most images in taxonomic literature because they are presented in a standardized way and lack the creativity that is required to qualify as 'copyrightable works'. There are exceptions, such as wildlife photographs, drawings and artwork produced in a distinctive individual form and intended for other than comparative purposes (such as visual art). Further exceptions may apply to collections of images that qualify as a database in the sense of European database protection law. In a few European countries, there is legal protection for photographs that do not qualify as works in the usual sense of copyright. It follows that most images found in taxonomic literature can be re-used for research or many other purposes without seeking permission, regardless of any copyright declaration. In observance of ethical and scholarly standards, re-users are expected to cite the author and original source of any image that they use.
Giardiaalters commensal microbial diversity throughout the murine gut
Authors: Barash NR , Maloney JG , Singer SM , Dawson SC 
Published: November 2016

ABSTRACTGiardia lambliais the most frequently identified protozoan cause of intestinal infection. Over one billion people are estimated to have acute or chronic giardiasis, with infection rates approaching 90% in endemic areas. Despite its significance in global health, the mechanisms of pathogenesis associated with giardiasis remain unclear as the parasite neither produces a known toxin nor induces a robust inflammatory response.Giardiacolonization and proliferation in the small intestine of the host may, however, disrupt the ecological homeostasis of gastrointestinal commensal microbes and contribute to diarrheal disease associated with giardiasis. To evaluate the impact ofGiardiainfection on the host microbiota, we use culture-independent methods to quantify shifts in the diversity of commensal microbes throughout the entire gastrointestinal tract in mice infected withGiardia. We discovered thatGiardia’scolonization of the small intestine causes a systemic dysbiosis of aerobic and anaerobic bacterial taxa. Specifically, giardiasis is typified by both expansions in aerobicProteobacteriaand decreases in anaerobicFirmicutesandMelainabacteriain the murine foregut and hindgut. Based on these shifts, we created a quantitative index of murineGiardia-induced microbial dysbiosis. This index increased at all gut regions during the duration of infection, including both the proximal small intestine and the colon. Thus giardiasis could be an ecological disease, and the observed dysbiosis may be mediated directly via the parasite’s unique anaerobic fermentative metabolism or indirectly via parasite induction of gut inflammation. This systemic alteration of murine gut commensal diversity may be the cause or the consequence of inflammatory and metabolic changes throughout the gut. Shifts in the commensal microbiota may explain observed variation in giardiasis between hosts with respect to host pathology, degree of parasite colonization, infection initiation, and eventual clearance.
Combining Inferred Regulatory and Reconstructed Metabolic Networks Enhances Phenotype Prediction in Yeast
Authors: Wang Zhuo , Danziger Samuel A. , Heavner Benjamin D. , Ma Shuyi , Smith Jennifer J. , Li Song , Herricks Thurston , Simeonidis Evangelos , Baliga Nitin S. , Aitchison John D. , Price Nathan D. 
Published: November 2016

AbstractGene regulatory and metabolic network models have been used successfully in many organisms, but inherent differences between them make networks difficult to integrate. Probabilistic Regulation Of Metabolism (PROM) provides a partial solution, but it does not incorporate network inference and underperforms in eukaryotes. We present an Integrated Deduced REgulation And Metabolism (IDREAM) method that combines statistically inferred Environment and Gene Regulatory Influence Network (EGRIN) models with the PROM framework to create enhanced metabolic-regulatory network models. We used IDREAM to predict phenotypes and genetic interactions between transcription factors and genes encoding metabolic activities in the eukaryote,Saccharomyces cerevisiae.IDREAM models contain many fewer interactions than PROM and yet produce significantly more accurate growth predictions. IDREAM consistently outperformed PROM using any of three popular yeast metabolic models and across three experimental growth conditions. Importantly, IDREAM’s enhanced accuracy makes it possible to identify subtle synthetic growth defects. With experimental validation, these novel genetic interactions involving the pyruvate dehydrogenase complex suggested a new role for fatty acid-responsive factor Oaf1 in regulating acetyl-CoA production in glucose grown cells.Author SummaryThe integration of gene regulatory and metabolic network models is an important goal in computational biology, in order to develop methods that can identify the underlying mechanistic links in biological networks and advance metabolic engineering techniques. In this paper, we develop a framework called Integrated Deduced REgulation And Metabolism (IDREAM) that can improve our ability to predict phenotypes of microorganisms, and particularly it can address the challenges in evaluating phenotypic consequence of perturbing transcriptional regulation of metabolism in a eukaryotic cell. We compare the predictive performance of an IDREAMS. cerevisiaemodel with a PROM model using a TRN available from the YEASTRACT database. IDREAM outperforms PROM using any of three popular yeast metabolic models and across three experimental growth conditions, making it possible to identify subtle synthetic growth defects, and a new role for Oaf1 in the regulation of acetyl-CoA biosynthesis.
Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation
Authors: Ruffier Magali , Kähäri Andreas , Komorowska Monika , Keenan Stephen , Laird Matthew R. , Longden Ian , Proctor Glenn , Steve Searle , Staines Daniel , Taylor Kieron , Vullo Alessandro , Yates Andrew , Zerbino Daniel , Flicek Paul 
Published: November 2016

AbstractThe Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl “Core” database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. Our databases and APIs are publicly available and all of our source code is released with a permissive Apache v2.0 licence athttp://github.com/Ensembl.
Eavesdropping and crosstalk between secreted quorum sensing peptide signals that regulate bacteriocin production inStreptococcus pneumoniae
Authors: Miller Eric L. , Kjos Morten , Abrudan Monica I. , Roberts Ian S. , Veening Jan-Willem , Rozen Daniel E. 
Published: November 2016

AbstractQuorum sensing (QS), where bacteria secrete and respond to chemical signals to coordinate population-wide behaviors, has revealed that bacteria are highly social. Here, we investigate how diversity in QS signals and receptors can modify social interactions controlled by the QS system regulating bacteriocin secretion inStreptococcus pneumoniae, encoded by theblpoperon (bacteriocin-likepeptide). Analysis of 4 096 pneumococcal genomes detected nineblpQS signals (BlpC) and five QS receptor groups (BlpH). Imperfect concordance between signals and receptors suggested widespread social interactions between cells, specifically eavesdropping (where cells respond to signals that they do not produce) and crosstalk (where cells produce signals that non-clones detect). This was confirmedin vitroby measuring the response of reporter strains containing each of six differentblpQS receptors to cognate and non-cognate peptides. Assays between pneumococcal colonies grown adjacent to one another provided further evidence that crosstalk and eavesdropping occur at endogenous levels of signal secretion. Finally, simulations of QS strains producing bacteriocins revealed that eavesdropping can be evolutionarily beneficial even when the affinity for non-cognate signals is very weak. Our results highlight that social interactions can mediate intraspecific competition among bacteria and reveal that competitive interactions can be modified by polymorphic QS systems.
An annotated draft genome for Radix auricularia (Gastropoda, Mollusca)
Authors: Schell Tilman , Feldmeyer Barbara , Schmidt Hanno , Greshake Bastian , Tills Oliver , Truebano Manuela , Rundle Simon D. , Paule Juraj , Ebersberger Ingo , Pfenninger Markus 
Published: November 2016

AbstractMolluscs are the second most species-rich phylum in the animal kingdom, yet only eleven genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72x. The assembly contains 94.6 % of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ~690 Mb compared to the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70 % mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly-available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum.
Problem‐based learning in internal medicine: virtual patients or paper‐based problems?
Authors: Sobocan Monika , Turk Neja , Dinevski Dejan , Hojs Radovan , Pecovnik Balon Breda 
Published: November 2016

BackgroundTeaching using paper problem‐based learning (p‐PBL) sessions has left some students fatigued with the learning process. Therefore, attempts have been made to replace p‐PBL with digitally enhanced, decision‐making PBL in the form of virtual patients (VP). Student enthusiasm for substituting p‐PBL with VP has not been quantitatively evaluated on the intended educational effects.AimTo determine the educational effects of substituting p‐PBL sessions with VP on undergraduate medical students in their internal medicine course.MethodsWe conducted a randomised controlled study on 34 third‐year undergraduate medical students in the academic year 2015–2016. Student performance after an intervention substituting p‐PBL sessions with VP was analysed. The educational outcomes were measured with knowledge exams and the Diagnostic Thinking Inventory.ResultsThere was no difference in exam performance between groups (P > 0.833) immediately after the intervention, or in long term. Nor was there a significant difference in improvement of diagnostic thinking between groups (P > 0.935 and P > 0.320).ConclusionsOur study showed no significant improvement in diagnostic thinking abilities or knowledge exam results with the use of VP. Educators can add VP to sessions to motivate students, but a significant improvement to educational outcome should not be expected.
Human Oral Buccal Microbiomes Are Associated with Farmworker Status and Azinphos-Methyl Agricultural Pesticide Exposure
Authors: Stanaway Ian B. , Wallace James C. , Shojaie Ali , Griffith William C. , Hong Sungwoo , Wilder Carly S. , Green Foad H. , Tsai Jesse , Knight Misty , Workman Tomomi , Vigoren Eric M. , McLean Jeffrey S. , Thompson Beti , Faustman Elaine M. 
Published: November 2016

ABSTRACT

In a longitudinal agricultural community cohort sampling of 65 adult farmworkers and 52 adult nonfarmworkers, we investigated agricultural pesticide exposure-associated changes in the oral buccal microbiota. We found a seasonally persistent association between the detected blood concentration of the insecticide azinphos-methyl and the taxonomic composition of the buccal swab oral microbiome. Blood and buccal samples were collected concurrently from individual subjects in two seasons, spring/summer 2005 and winter 2006. Mass spectrometry quantified blood concentrations of the organophosphate insecticide azinphos-methyl. Buccal oral microbiome samples were 16S rRNA gene DNA sequenced, assigned to the bacterial taxonomy, and analyzed after “centered-log-ratio” transformation to handle the compositional nature of the proportional abundances of bacteria per sample. Nonparametric analysis of the transformed microbiome data for individuals with and without azinphos-methyl blood detection showed significant perturbations in seven common bacterial taxa (>0.5% of sample mean read depth), including significant reductions in members of the common oral bacterial genus
Streptococcus
. Diversity in centered-log-ratio composition between individuals' microbiomes was also investigated using principal-component analysis (PCA) to reveal two primary PCA clusters of microbiome types. The spring/summer “exposed” microbiome cluster with significantly less bacterial diversity was enriched for farmworkers and contained 27 of the 30 individuals who also had azinphos-methyl agricultural pesticide exposure detected in the blood.

IMPORTANCE
In this study, we show in human subjects that organophosphate pesticide exposure is associated with large-scale significant alterations of the oral buccal microbiota composition, with extinctions of whole taxa suggested in some individuals. The persistence of this association from the spring/summer to the winter also suggests that long-lasting effects on the commensal microbiota have occurred. The important health-related outcomes of these agricultural community individuals' pesticide-associated microbiome perturbations are not understood at this time. Future investigations should index medical and dental records for common and chronic diseases that may be interactively caused by this association between pesticide exposure and microbiome alteration.
Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool
Authors: Hoetzinger Matthias , Schmidt Johanna , Jezberová Jitka , Koll Ulrike , Hahn Martin W. 
Published: November 2016

ABSTRACT

Microdiversification of a planktonic freshwater bacterium was studied by comparing 37
Polynucleobacter asymbioticus
strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome is clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located. These positions are occupied strain specifically from a set of 28 GI variants, classified according to similarities in their gene content. One variant, present in 62% of the isolates, encodes a pathway for the degradation of aromatic compounds, and another, found in 78% of the strains, contains an operon for nitrate assimilation. Both variants were shown in ecophysiological tests to be functional, thus providing the potential for microniche partitioning. In addition, detected interspecific horizontal exchange of GIs indicates a large gene pool accessible to
Polynucleobacter
species. In contrast to core genes, GIs are spread more successfully across spatially separated freshwater habitats. The mobility and functional diversity of GIs allow for rapid evolution, which may be a key aspect for the ubiquitous occurrence of
Polynucleobacter
bacteria.

IMPORTANCE
Assessing the ecological relevance of bacterial diversity is a key challenge for current microbial ecology. The polyphasic approach which was applied in this study, including targeted isolation of strains, genome analysis, and ecophysiological tests, is crucial for the linkage of genetic and ecological knowledge. Particularly great importance is attached to the high number of closely related strains which were investigated, represented by genome-wide average nucleotide identities (ANI) larger than 97%. The extent of functional diversification found on this narrow phylogenetic scale is compelling. Moreover, the transfer of metabolically relevant genomic islands between more distant members of the
Polynucleobacter
community provides important insights toward a better understanding of the evolution of these globally abundant freshwater bacteria.
Identification of a New Phosphatase Enzyme Potentially Involved in the Sugar Phosphate Stress Response in Pseudomonas fluorescens
Authors: Maleki Susan , Hrudikova Radka , Zotchev Sergey B. , Ertesvåg Helga 
Published: November 2016

ABSTRACT

The alginate-producing bacterium
Pseudomonas fluorescens
utilizes the Entner-Doudoroff (ED) and pentose phosphate (PP) pathways to metabolize fructose, since the upper part of its Embden-Meyerhof-Parnas pathway is defective. Our previous study indicated that perturbation of the central carbon metabolism by diminishing glucose-6-phosphate dehydrogenase activity could lead to sugar phosphate stress when
P. fluorescens
was cultivated on fructose. In the present study, we demonstrate that PFLU2693, annotated as a haloacid dehalogenase-like enzyme, is a new sugar phosphate phosphatase, now designated Spp, which is able to dephosphorylate a range of phosphate substrates, including glucose 6-phosphate and fructose 6-phosphate,
in vitro
. The effect of
spp
overexpression on growth and alginate production was investigated using both the wild type and several mutant strains. The results obtained suggested that sugar phosphate accumulation caused diminished growth in some of the mutant strains, since this was partially relieved by
spp
overexpression. On the other hand, overexpression of
spp
in fructose-grown alginate-producing strains negatively affected both growth and alginate production. The latter implies that Spp dephosphorylates the sugar phosphates, thus depleting the pool of these important metabolites. Deletion of the
spp
gene did not affect growth of the wild-type strain on fructose, but the gene could not be deleted in the alginate-producing strain. This indicates that Spp is essential for relieving the cells of sugar phosphate stress in
P. fluorescen
s actively producing alginate.

IMPORTANCE
In enteric bacteria, the sugar phosphate phosphatase YigL is known to play an important role in combating stress caused by sugar phosphate accumulation. In this study, we identified a sugar phosphate phosphatase, designated Spp, in
Pseudomonas fluorescens
. Spp utilizes glucose 6-phosphate, fructose 6-phosphate, and ribose 5-phosphate as substrates, and overexpression of the gene had a positive effect on growth in
P. fluorescens
mutants experiencing sugar phosphate stress. The gene was localized downstream of
gnd
and
zwf-2
, which encode enzymes involved in the pentose phosphate and Entner-Doudoroff pathways. Genes encoding Spp homologues were identified in similar genetic contexts in some bacteria belonging to several phylogenetically diverse families, suggesting similar functions.
Zn
2+
-Inducible Expression Platform for Synechococcus sp. Strain PCC 7002 Based on the
smtA
Promoter/Operator and
smtB
Repressor
Authors: Pérez Adam A. , Gajewski John P. , Ferlez Bryan H. , Ludwig Marcus , Baker Carol S. , Golbeck John H. , Bryant Donald A. 
Published: November 2016

ABSTRACT

Synechococcus
sp. strain PCC 7002 has been gaining significance as both a model system for photosynthesis research and for industrial applications. Until recently, the genetic toolbox for this model cyanobacterium was rather limited and relied primarily on tools that only allowed constitutive gene expression. This work describes a two-plasmid, Zn
2+
-inducible expression platform that is coupled with a
zurA
mutation, providing enhanced Zn
2+
uptake. The control elements are based on the metal homeostasis system of a class II metallothionein gene (
smtA
7942
) and its cognate SmtB
7942
repressor from
Synechococcus elongatus
strain PCC 7942. Under optimal induction conditions, yellow fluorescent protein (YFP) levels were about half of those obtained with the strong, constitutive phycocyanin (
cpcBA
6803
) promoter of
Synechocystis
sp. strain PCC 6803. This metal-inducible expression system in
Synechococcus
sp. strain PCC 7002 allowed the titratable gene expression of YFP that was up to 19-fold greater than the background level. This system was utilized successfully to control the expression of the
Drosophila melanogaster
β-carotene 15,15′-dioxygenase, NinaB, which is toxic when constitutively expressed from a strong promoter in
Synechococcus
sp. strain PCC 7002. Together, these properties establish this metal-inducible system as an additional useful tool that is capable of controlling gene expression for applications ranging from basic research to synthetic biology in
Synechococcus
sp. strain PCC 7002.

IMPORTANCE
This is the first metal-responsive expression system in cyanobacteria, to our knowledge, that does not exhibit low sensitivity for induction, which is one of the major hurdles for utilizing this class of genetic tools. In addition, high levels of expression can be generated that approximate those of established constitutive systems, with the added advantage of titratable control. Together, these properties establish this Zn
2+
-inducible system, which is based on the
smtA
7942
operator/promoter and
smtB
7942
repressor, as a versatile gene expression platform that expands the genetic toolbox of
Synechococcus
sp. strain PCC 7002.