bluuebunny/crossref_metadata_2025 huggingface dataset:
Beyond the protein-only hypothesis: A novel mineral-lipid hypothesis in prion and protein-misfolding disease
Authors: Reddy Kavitha
Published: January 2018

A scientific theory or hypothesis is presented, in which mineral particles may play a pivotal role in the prion disease transmissible spongiform encephalopathy (TSE), and possibly also in other protein-misfolding diseases. Montmorillonite clay (Mte) and other minerals are known to bind to scrapie prion protein (PrP-Sc) in soil. The hypothesis is explored that, in transmissible spongiform encephalopathy, Mte or other mineral particles, upon contact with lipids, such as in the gut or at the cell plasma membrane, may interact with lipids or with lipid rafts. The minerals may catalyze formation of lipid vesicles, and might also be capable of inducing lipid raft clustering or other lipid raft or plasma membrane changes. Some of these lipid vesicles or rafts might then contain or bind PrP-Sc, and sometimes also contain montmorillonite or the mineral catalyst. Mte-PrP-Sc or the affected lipid vesicles/particles could also promote PrP-C to PrP-Sc conversion by providing conditions for misfolding. These conditions provided for protein misfolding may include the following: multiple unique compartments providing sizes, shapes or aqueous/lipid environments that promote varied folding conformations, presence of an anion (Mte), negative-charge (Mte), lipid membrane mimetic (e.g. associated lipid particle, vesicle or raft), interaction with bound or contained PrP-Sc, presence of bound copper, and/or copper binding affinity. Mte-catalyzed lipid vesicles are proto-cell-like entities, making them potential candidates to be part of the infectious particle in prion disease, which can behave like an infectious organism but does not appear to depend on nucleic acid. Lipid vesicles or rafts may resemble endosomes, which would be consistent with reports of prion being transported and formed along an endosome-like pathway. Additionally, the vesicles or rafts could accumulate intra-cellularly, and might form tubulovesicular structures, which are hallmarks of prion disease. Potential applications of this theory to more common protein misfolding diseases, Alzheimer’s disease, Parkinson’s disease, and Amyotrophic lateral sclerosis, are discussed. This theory, which I term the mineral-lipid prion hypothesis, provides a basis for potential novel interventions in the field of prion and protein-misfolding diseases. In addition, this theory suggests that similar silicate- or mineral-catalyzed lipid vesicles/liposomes might be further explored as useful compartments that could be manipulated in order to deliver molecules or even proteins to or from cells.
Agronomic and physiological responses of tomato plants grown in different soilless systems to saline conditions
Authors: Rodriguez-Ortega Wilbert Michael , Martinez Vicente , Nieves Manuel , Camara-Zapata Jose Maria , Garcia-Sanchez Francisco
Published: January 2018

Background. The tomato is the most important horticultural crop in the world, regarding area of cultivation and yield. The main production areas have arid and semi-arid climates, with scarce rainfall, which forces the use of saline water for irrigation - leading to a decrease in the agronomic yield of the crop. Currently, many soilless cultivation systems are considered for tomato production, although the behavior of the plants when saline water is used for irrigation is not known in detail. Methods. In this work we study the agronomic and physiological responses of the tomato variety ‘Óptima’, using different soilless crop systems (perlite substrate, hydroponics, and the nutrient film technique) and several levels of salinity in the irrigation water. The yield, quality parameters, vegetative growth, mineral composition, water relations, and gas exchange parameters were measured. Results and conclusions. Salinity caused changes in the water status of the plants, toxicity due to Cl- and Na+, and nutritional imbalances that altered the physiology of the plants, thereby reducing yield, although the fruit quality was improved. Regarding the crop system, hydroponics gave a higher marketable yield, both with and without salinity, with a consumption of nutrient solution intermediate between that of the nutrient film and perlite. Salinity reduced yield similarly in all systems. Plants cultivated with the nutrient film technique had the highest concentrations of Cl- and Na+ and the highest Na+/K+ ratio. The concentrations of Cl- and Na+ in the plants were not related directly to the yield loss. Therefore, the combined influence of the toxicity, osmotic effect, and nutritional imbalance seems to have been responsible for the yield loss.
Evaluation of “being healthy, being away from chronic diseases” public service advertisement in Chongqing, China: A cross-sectional study
Authors: Hu Ping , Wu Ting ting , Wu Cheng bin , Huang Hao , Fu Zhirong , Du Lei , Xu Xiang long , Shi Zumin , Zhao Yong
Published: January 2018

Background: Chronic diseases have become a global public health issue, and mass media campaigns are often used to encourage and sustain positive behavior change. Our aim was to evaluate the effect of public service advertising on the awareness of Chongqing citizens.

Methods: The theme of the public service advertisement launched in Chongqing was “being healthy, being away from chronic diseases.” A self-designed questionnaire was used in an outdoor intercept survey to collect information about the perception of citizens toward the effect of the advertisement on cognitive situations.

Results: A total of 985 valid questionnaires were received. Respondents had good understanding of chronic disease (23.6±4.1, total score: 30), but only 58.4% of participants thought cancer is one type of chronic disease. The awareness of cancer as a chronic disease among the group who had seen this advertisement (63.6%) was higher than that of the group who had not seen the advertisement (56.5%) (p=0.046). After watching the advertisement, approximately 77.4% of participants attempted to remind their family and friends to prevent chronic diseases, roughly 78.2% tried to persuade their family and friends to change their unhealthy lifestyle habits, and 73.2% of participants reported that it increased the possibility of their own lifestyle change. Logistic regression analysis indicates that occupation, educational level, watching the advertising through TV, watching the advertising through indoor LED screen, and watching the advertising through mobile TV affected the three post-viewing behavior changes

Conclusion : The public service advertisement achieved a certain knowledge propaganda effect. It may help change awareness and improve health behavior of the public.

Key words: Public service advertisement , Chronic diseases, Health; Awareness, Behavior
Relating form to function in the hummingbird feeding apparatus
Authors: Rico-Guevara Alejandro
Published: January 2018

A complete understanding of the feeding structures is fundamental in order to study how animals survive. Some birds use long and protrusible tongues as the main tool to collect their central caloric source (e.g. woodpeckers and nectarivores). Hummingbirds are the oldest and most diverse clade of nectarivorous vertebrates, being a perfect subject to study tongue specializations. Their tongue functions to intraorally transport arthropods through their long bills and enables them to exploit the nectarivorous niche by collecting small amounts of liquid, therefore it is of vital importance to study its anatomy and structure at various scales. I focused on the portions of the hummingbird tongue that have been shown to be key for understanding their feeding mechanisms. I used histology, transmission and scanning electron microscopy, microCT, and ex-vivo experiments in order to advance the comprehension of the morphology and functioning of the hummingbird feeding apparatus. I found that hummingbird tongues are composed mainly of thin cornified epithelium, lack papillae, and completely fill the internal cast of the rostral oropharyngeal cavity. Understanding this puzzle-piece match between bill and tongue will be essential for the study of intraoral transport of nectar. Likewise, I found that the structural composition and tissue architecture of the tongue groove walls provide the rostral portion of the tongue with elastic properties that are central to the study of tongue-nectar interactions during the feeding process. Detailed studies on hummingbirds set the basis for comparisons with other nectar-feeding birds and contribute to comprehend the natural solutions to collecting liquids in the most efficient way possible.
RNA expression and disease tolerance are associated with a “keystone mutation” in the ochre sea star Pisaster ochraceus
Authors: Wares John , Chandler Virginia K
Published: January 2018

An overdominant mutation in the elongation factor 1-alpha (EF1A) gene in the sea star Pisaster ochraceus has shown itself to mediate tolerance to "sea star wasting disease", a pandemic that has significantly reduced sea star populations on the Pacific coast of North America. Here we use RNA sequencing of healthy individuals to identify differences in constitutive expression of gene regions that may help explain this tolerance phenotype. Our results show that individuals carrying this single mutation have lower expression at a large contingent of gene regions, and it appears likely that the EF1A locus itself is similarly affected, with a 2-fold reduction in expression of some EF1A transcripts. Individuals without this mutation also appear to have a greater cellular response to temperature stress, which has been implicated in the outbreak of sea star wasting disease. Given the ecological significance of P. ochraceus and the key role of EF1A in cellular composition and maintenance, these results may be useful in predicting the evolutionary and demographic future for Pacific intertidal communities.
In silico analysis of cysteine content, in six genes, across three marine Altererythrobacter strains sampled at varying barometric pressures
Authors: Barrie Conor
Published: January 2018

Marine microbes experience varying degrees of barometric pressure depending on the depth at which they reside. High barometric pressure can create an extreme environment which favors the survival of barophilic and barotolerant bacteria. This paper aims to quantify the cysteine content in six genes across three marine Altererythrobacter strains that were sampled from varying depth, thus living under corresponding degrees of barometric pressure. The purpose of this study is to test whether marine Altererythrobacter strains, living at greater depths, have proportionally more cysteine content, which could improve protein stability under high pressures. It was hypothesized that organisms sampled at greater depths would exhibit higher amounts of cysteine in their proteins as a mechanism to cope with the increased barometric pressure. This hypothesis was tested by selecting three open source genomes, from three marine Altererythrobacter species, which were sampled at different depths. Strains sampled from different depths were found to have similar proportions of cysteine. This study was only intended as a preliminary investigation and in order for the hypothesis to be thoroughly supported or rejected a more comprehensive study would be needed.
Microbial diversity in freshwater samples and their contaminating human and bovine hosts
Authors: Stoppe Nancy C , Torres Tatiana T , Leotti Fabricio C , Sato Maria Inês Z , Ottoboni Laura MM
Published: January 2018

DNA extracted from feces (human and bovine) and water samples was used for the massive pyrosequencing of the hypervariable V3 region of the 16S rRNA gene, revealing 4296 operational taxonomic units (OTUs). The greatest diversity was observed in samples of cattle feces, and the smallest diversity was found in a pristine water sample. Firmicutes was the predominant group in samples of human feces, while in bovine feces the dominant groups were Firmicutes and Bacteroidetes. The interaction network showed that the stool samples had the greatest diversity and, among the water samples, the one with human pollution source had the highest diversity. The LEfSe method was used to identify host biomarkers. Actinobacteria, Betaproteobacteria, and Firmicutes were identified as human biomarkers, while for cattle, the potential markers were Bacteroidetes, Tenericutes, and Spirochaetes. Host-specific markers were identified, but were not found in the water samples, suggesting either that the tools used did not have the resolution to identify markers in environmental samples, or that the contamination in the water bodies was mixed. Additionally, as the host-specific markers were isolated from non-autochthonous microorganisms, they could be affected by adverse environmental effects including physical-chemical factors and competition with native organisms.
Practice guidelines for development and validation of software, with particular focus on bioinformatics pipelines for processing NGS data in clinical diagnostic laboratories
Authors: Whiffin Nicola , Brugger Kim , Ahn Joo Wook
Published: January 2018

Clinical bioinformatics is an emerging field in diagnostic genetics laboratories that are harnessing next-generation sequencing technologies to improve patient care. This document provides guidance for the development and validation of software used for delivery of clinical genetics, focusing on bioinformatics pipelines for next-generation sequencing (NGS) applications. It builds on the literature and guidelines that already exist around software development and validation of clinical genetics diagnostic tests, to detail best practice specific to a clinical bioinformatician’s role.
Diversity, abundance, and host relationships of avian malaria and related haemosporidians in New Mexico pine forests
Authors: Marroquin-Flores Rosario A. , Williamson Jessie L. , Chavez Andrea N. , Bauernfeind Selina M. , Baumann Matthew J. , Gadek Chauncey R. , Johnson Andrew B. , McCullough Jenna M. , Witt Christopher C. , Barrow Lisa N.
Published: January 2018

Avian malaria and related haemosporidian parasites (genera Haemoproteus, Plasmodium, and Leucocytozoon) affect bird demography, species range limits, and community structure, yet they remain unsurveyed in most bird communities and populations. We conducted a community-level survey of these vector-transmitted parasites in New Mexico, USA, to describe their diversity, abundance, and host associations. We focused on the breeding-bird community in the transition zone between piñon-juniper woodland and ponderosa pine forests (elevational range: 2150–2460 meters). We screened 186 birds representing 49 species using both standard PCR and microscopy techniques to detect infections of all three avian haemosporidian genera. We detected infections in 68 out of 186 birds (36.6%), the highest proportion of which were infected with Haemoproteus (20.9%), followed by Leucocytozoon (13.4%), then Plasmodium (8.0%). We sequenced mtDNA for 77 infections representing 43 haplotypes (25 Haemoproteus, 12 Leucocytozoon, 6 Plasmodium). When compared to all previously known haplotypes in the MalAvi and GenBank databases, 63% (27) of the haplotypes we recovered were novel. We found evidence for host specificity at the avian clade and species level, but this specificity was variable among parasite genera, in that Haemoproteus and Leucocytozoon were each restricted to three avian groups (out of six), while Plasmodium occurred in all groups except non-passerines. We found striking variation in infection rate among host species, with nearly universal infection among vireos and no infection among nuthatches. Using rarefaction and extrapolation, we estimated the total avian haemosporidian diversity to be 70 haplotypes (95% CI: 43–98); thus, we may have already sampled ~60% of the diversity of avian haemosporidians in New Mexico pine forests. It is possible that future studies will find higher diversity in microhabitats or host species that are under-sampled or unsampled in the present study. Fortunately, this study is fully extendable via voucher specimens, frozen tissues, blood smears, parasite images, and documentation provided in open-access databases (MalAvi, GenBank, and ARCTOS).
Influenza A virus avian-derived PB1 gene has evolved to match its codon usage to interferon-altered human tRNA pools
Authors: Smith Bartram L , Chen Guifang , Wilke Claus O , Krug Robert M
Published: January 2018

Influenza A viruses cause an annual highly contagious respiratory disease in humans, and are responsible for periodic human pandemics that have high mortality rates. Pandemic influenza A viruses can result from reassortment of one or more gene segments between a human and an avian virus. These avian virus gene segments need to adapt to humans post introduction. The role of synonymous mutations in this adaptation is not known. Here we focus on the human adaptation of the synonymous codons of the avian virus PB1 gene of the 1968 H3N2 pandemic virus. We generate recombinant H3N2 viruses differing only in codon usage of PB1 mRNA, and demonstrate that the codon usage of recent virus isolates enhances replication in interferon-treated human cells rather than in untreated cells, thereby partially alleviating the interferon-induced antiviral state. High-throughput sequencing of tRNA pools explains this virus phenotype: the levels of some tRNAs differ between interferon-treated and untreated human cells; and the codon usage of H3N2 PB1 mRNA has been evolving over time to match the tRNA pools in interferon-treated human cells. Consequently, our results identify a previously unknown mechanism by which influenza A virus counteracts the host interferon-induced antiviral response and highlight the important role of tRNA pools in the regulation of gene expression.
Investigating viral attenuation by promoter knockout: a systems approach
Authors: Paff Matthew L , Jack Benjamin R. , Boutz Daniel R , Smith Bartram L , Wilke Claus O , Bull James J
Published: January 2018

Live attenuated viral vaccines provide the most robust and longest lasting immune response. Yet designing them a priori to have reduced growth capacity and also to be robust to evolutionary reversion can be challenging. On the one hand, genome editing methods now enable us to create almost any conceivable viral genome composition. Yet understanding and predicting how engineered genomes will behave and evolve is a challenge. Here we adopt a systems approach in studying a simple attenuation design in bacteriophage T7: promoter knockout. Either or both promoters for the two most highly expressed genes were abolished. Overall fitnesses, major phenotypes and gene expression levels were measured for all initial genomes and for genomes evolved toward for fitness recovery. Initial genomes behaved broadly as expected, but the genomes showed an unexpected ability to evolve back to high fitness. Genome sequences, RNA Seq and proteomics reveal the molecular foundations of the attenuations and recoveries. Overall, the work suggests that a systems approach is ultimately yielding to understanding, if not predicting the consequences of genome editing and evolutionary recoveries of simple genomes.
Theory of measurement for site-specific evolutionary rates in amino-acid sequences
Authors: Sydykova Dariya K , Wilke Claus O
Published: January 2018

Many applications require the calculation of site-specific evolutionary rates from alignments of amino-acid sequences. For example, catalytic residues in enzymes and interface regions in protein complexes can be inferred from observed relative rates. While numerous approaches exist to calculate amino-acid rates, however, it is not entirely clear what physical quantities the inferred rates represent and how these rates relate to the underlying fitness landscape of the evolving protein. Further, amino-acid rates can be calculated in the context of different amino-acid exchangeability matrices, such as JTT, LG, or WAG, and again it is not known how the choice of the matrix influences the physical interpretation of the inferred rates. Here, we develop a theory of measurement for site-specific evolutionary rates, but analytically solving the maximum-likelihood equations for rate inference performed on sequences evolved under a mutation–selection model. We demonstrate that the measurement process can only recover the true expected rates of the mutation–selection model if rates are measured relative to a naïve exchangeability matrix, in which all exchangeabilities are equal to one. Rate measurements using other matrices are quantitatively close but not mathematically correct. Our results demonstrate that insights obtained from phylogenetic-tree inference do not necessarily apply to rate inference, and best practices for the former may be deleterious for the latter.
Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops
Authors: Saqib Hafiz Sohaib , You Minsheng , Gurr Geoff M
Published: January 2018

Conservation biological control emphasizes the importance of vegetation other than the focal crop for providing natural enemies with refuge and shelter against disturbance. There is an unmet need for better methods to identify types of vegetation that are optimal to support specific natural enemies that may colonize into crops. Here we explore the commonality of the spider fauna of brassica crops with that of adjacent crops of other species and non-crop vegetation, employing spatial-based multivariate ordination approaches, hierarchical clustering and spatial eigenvector analysis. The small-scale mixed cropping and high disturbance frequency of southern Chinese vegetation farming offered a setting to test the role of alternate vegetation for spider conservation. Our findings indicate that spider families differ markedly in occurrence with respect to vegetation type. Grassy field margins, non-crop vegetation, taro and sweetpotato offer the best opportunity for promoting spider taxa that are also brassica-active species. In contrast, pumpkin and litchi contain species not found in brassicas, and so may have little benefit for conservation biological control services for brassicas. Our findings also illustrate the potential utility of advanced statistical approaches for identifying spatial relationships of species and identify the land uses most likely to offer alternative habitats for spider conservation biological control efforts and generates testable hypotheses for future studies.
Can editors protect peer review from bad reviewers?
Authors: D'Andrea Rafael , O'Dwyer James P
Published: January 2018

Peer review is the gold standard for scientific communication, but its ability to guarantee the quality of published research remains difficult to verify. Recent modeling studies suggest that peer review is sensitive to reviewer misbehavior, and it has been claimed that referees who sabotage work they perceive as competition may severely undermine the quality of publications. Here we examine which aspects of suboptimal reviewing practices most strongly impact quality, and test different mitigating strategies that editors may employ to counter them. We find that the biggest hazard to the quality of published literature is not selfish rejection of high-quality manuscripts but indifferent acceptance of low-quality ones. Blacklisting bad reviewers and consulting additional reviewers to settle disagreements can reduce but not eliminate the impact. The other editorial strategies we tested do not significantly improve quality, but pairing manuscripts to reviewers unlikely to selfishly reject them and allowing revision of rejected manuscripts minimize rejection of above-average manuscripts. In its current form, peer review offers few incentives for disinterested reviewing efforts. Editors can help, but structural changes are more likely to have a stronger impact.
Can editors protect peer review from bad reviewers?
Authors: D'Andrea Rafael , O'Dwyer James P
Published: January 2018

Peer review is the gold standard for scientific communication, but its ability to guarantee the quality of published research remains difficult to verify. Recent modeling studies suggest that peer review is sensitive to reviewer misbehavior, and it has been claimed that referees who sabotage work they perceive as competition may severely undermine the quality of publications. Here we examine which aspects of suboptimal reviewing practices most strongly impact quality, and test different mitigating strategies that editors may employ to counter them. We find that the biggest hazard to the quality of published literature is not selfish rejection of high-quality manuscripts but indifferent acceptance of low-quality ones. Blacklisting bad reviewers and consulting additional reviewers to settle disagreements can reduce but not eliminate the impact. The other editorial strategies we tested do not significantly improve quality, but pairing manuscripts to reviewers unlikely to selfishly reject them and allowing revision of rejected manuscripts minimize rejection of above-average manuscripts. In its current form, peer review offers few incentives for impartial reviewing efforts. Editors can help, but structural changes are more likely to have a stronger impact.
Sylvatic host associations of Triatominae and implications for Chagas disease reservoirs: a comprehensive review and new host records based on archival specimens
Authors: Georgieva Anna Y , Gordon Eric R L , Weirauch Christiane
Published: January 2018

Background: The 148 species of kissing bug include important vectors of the debilitating, chronic, and often fatal Chagas disease, which affects several million people in Central and South America. An understanding of the natural hosts of this speciose group of blood-feeding insects has and will continue to aid ongoing efforts to impede the spread of Chagas disease. However, information on kissing bug biology is piecemeal and scattered, developed using methods with varying levels of accuracy over more than 100 years. Existing host records are heavily biased towards well-studied primary vector species and are derived from primarily three different types of observations, associational, immunological or DNA-based, with varying reliability.

Methods: We here gather a comprehensive and unparalleled number of sources reporting host associations via rigorous targeted searches of publication databases to review all known natural, or sylvatic, host records including information on how that record was collected. We integrate this information with novel host records obtained via attempted amplification and sequencing of a ~160 base pair (bp) region of the vertebrate 12S mitochondrial gene from the gastrointestinal tract of 64 archival specimens of Triatominae representing 19 species collected primarily in sylvatic habitats throughout the southern U.S. and Central and South America during the past 10 years. We show the utility of this method for uncovering novel and under-studied groups of Triatominae hosts, as well as detecting the presence of the Chagas disease pathogen via Polymerase Chain Reaction (PCR) of a ~400 bp sequence of the trypanosome 18S gene.

Results: New host associations for several groups of arboreal mammals were determined including sloths, New World monkeys, coatis, arboreal porcupines and, for the first time as a host of any Triatominae, tayras. A thorough review of previously documented sylvatic hosts, organized by triatomine species and the type of observation (associational, antibody-based, or DNA-based), is presented in a phylogenetic context and highlights large gaps in our knowledge of Triatominae biology.

Conclusion: The application of DNA-based methods of host identification towards additional species of Triatominae, including rarely collected species that may require use of archival specimens, is the most efficient and promising way to resolve recognized shortfalls.
Evaluation of the maxillary anterior teeth color distribution according to age and gender with Spectrophotometer
Authors: Karaman Tahir , Altintas Eyyüp , Eser Bekir , Talo Yildirim Tuba , Oztekin Faruk , Bozoglan Alihan
Published: January 2018

Background: This study intended to determine the colour distribution of the maxillary, central, lateral and canine teeth and to investigate the effect of age and gender on this colour distribution.

Materials and methods : The colour measurements of the maxillary right central, lateral and canine teeth were carried out by the Vita Easyshade V (Vita Zahnfabrik, Bad Sackingen, Germany) spectrophotometer on a total of 202 voluntarily patients including 89 (men) and 113 (women). The age distribution in the study was between 15 and 70 (the average was 31). Grey background colour was used in order to prevent the reflection of the background while performing the colour measurement with the Vita EasyShade V (Vita Zahnfabrik, Bad Sackingen, Germay).

Results: When comparing the L*, a* and b* values of the teeth with the gender; statistically significant difference was not fount between the gender and the L* and b* values (P>0,05) while statistically significant difference was observed between the gender and the a* value (P<0,05).

Conclusions: The tooth colour distribution according to the Vitapan Classical; in the central and lateral teeth it was maximum A2, while it was found to be B3 in the canine teeth. The tooth colour distribution according to the VITA Toothguide 3D-MASTER colour scale; in the central teeth the 2M2 colour was measured most often, in the lateral teeth the 3M2 colour was detected the most often while in the canine teeth the 2M3 colour was measured the most often.
Advances in studying brain morphology: The benefits of open-access data
Authors: Madan Christopher R
Published: January 2018

Until recently, neuroimaging data for a research study needed to be collected within one’s own lab. However, when studying inter-individual differences in brain structure, a large sample of participants is necessary. Given the financial costs involved in collecting neuroimaging data from hundreds or thousands of participants, large-scale studies of brain morphology could previously only be conducted by well-funded laboratories with access to MRI facilities and to large samples of participants. With the advent of broad open-access data-sharing initiatives, this has recently changed–here the primary goal of the study is to collect large datasets to be shared, rather than sharing of the data as an afterthought. This paradigm shift is evident as increase in the pace of discovery, leading to a rapid rate of advances in our characterization of brain structure. The utility of open-access brain morphology data is numerous, ranging from observing novel patterns of age-related differences in subcortical structures to the development of more robust cortical parcellation atlases, with these advances being translatable to improved methods for characterizing clinical disorders (see Figure 1 for an illustration). Moreover, structural MRIs are generally more robust than functional MRIs, relative to potential artifacts and in being not task-dependent, resulting in large potential yields. While the benefits of open-access data have been discussed more broadly within the field of cognitive neuroscience elsewhere (Gilmore et al., in press; Poldrack and Gorgolewski, 2014; Van Horn and Gazzaniga, 2013; Van Horn and Toga, 2014; Vogelstein et al., 2016; Voytek, 2016), as well as in other fields (Ascoli et al., 2017; Choudhury et al., 2014; Davies et al., 2017), this opinion paper is focused specifically on the implications of open data to brain morphology research.
Selection on translation rate impacts genic base composition
Authors: Quandt Erik M , Traverse Charles , Ochman Howard
Published: January 2018

The maintenance of a G+C content that is higher than the mutational input to a genome supports the view that selection serves to increase G+C contents in many bacteria. Recent experimental evidence from Escherichia coli has demonstrated that selection for increasing G+C content operates at the level of translation, but the precise mechanism by which this occurs is unknown. To determine the substrate of selection, we asked whether selection on G+C content acts across all sites within a gene or was confined to particular nucleotide positions or genic regions. We systematically altered the G+C contents of the GFP gene and assayed the effects of each variant on cellular fitness. The fitness differences were attributable to the base compositional variation in the terminal portion of the gene: increasing G+C content produced more stable mRNA secondary structures, which, in turn, slowed translation rate and allowed proper protein folding. We show that purifying selection against A and T mutations results from their tendency to increase the rate of translation and perturb the dynamics of protein folding.
DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region
Authors: Yusseff-Vanegas Sohath Z , Agnarsson Ingi
Published: January 2018

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identify immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean; we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.
Life histories predict genetic diversity and population structure within three species of Octopus targeted by small-scale fisheries in Northwest Mexico
Authors: Domínguez-Contreras José F , Munguia-Vega Adrian , Ceballos-Vázquez Bertha P , Arellano-Martínez Marcial , García-Rodríguez Francisco J , Culver Melanie , Reyes-Bonilla Héctor
Published: January 2018

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species with varying life histories targeted by artisanal fisheries in the region, lack of information about the distribution of each species and metapopulation size and structure could impede effective fisheries management to avoid overexploitation. Here we tested if different life histories in three species of octopus help to predict observed patterns of genetic diversity, population dynamics, structure and connectivity that could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the Pacific coast of the Baja California peninsula. We tested four a priori hypothesis derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We found that the species with low fecundity and without a planktonic larval stage (Octopus bimaculoides) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, suggesting limited dispersal and high local recruitment. In contrast, two species with higher fecundity and planktonic larvae (O. bimaculatus, O. hubbsorum) showed higher effective population size and genetic diversity, and overall lower kinship and population structure, supporting higher levels of gene flow over a larger geographical scale. Even among the latter, there were differences in the calculated parameters possibly associated with increased connectivity in the species with the longest planktonic larval duration (O. bimaculatus). We consider that O. bimaculatus could be more susceptible to over exploitation of small, isolated populations that could have longer recovery times, and suggest that management should take place within each local population. For the two species with pelagic larvae, management should consider metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal between localities driven by ocean currents. The distribution of each species and variations in their reproductive timing should also be considered when establishing marine reserves or seasonal fishing closures.
Life histories predict genetic diversity and population structure within three species of Octopus targeted by small-scale fisheries in Northwest Mexico
Authors: Domínguez-Contreras José F , Munguia-Vega Adrian , Ceballos-Vázquez Bertha P , Arellano-Martínez Marcial , García-Rodríguez Francisco J , Culver Melanie , Reyes-Bonilla Héctor
Published: January 2018

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species with varying life histories targeted by artisanal fisheries in the region, lack of information about the distribution of each species and metapopulation size and structure could impede effective fisheries management to avoid overexploitation. Here we tested if different life histories in three species of octopus help to predict observed patterns of genetic diversity, population dynamics, structure and connectivity that could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the Pacific coast of the Baja California peninsula. We tested four a priori hypothesis derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We found that the species with low fecundity and without a planktonic larval stage (Octopus bimaculoides) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, suggesting limited dispersal and high local recruitment. In contrast, two species with higher fecundity and planktonic larvae (O. bimaculatus, O. hubbsorum) showed higher effective population size and genetic diversity, and overall lower kinship and population structure, supporting higher levels of gene flow over a larger geographical scale. Even among the latter, there were differences in the calculated parameters possibly associated with increased connectivity in the species with the longest planktonic larval duration (O. bimaculatus). We consider that O. bimaculoides could be more susceptible to over exploitation of small, isolated populations that could have longer recovery times, and suggest that management should take place within each local population. For the two species with pelagic larvae, management should consider metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal between localities driven by ocean currents. The distribution of each species and variations in their reproductive timing should also be considered when establishing marine reserves or seasonal fishing closures.
Genetic diversity and population structure in an invasive pantropical earthworm along an altitudinal gradient
Authors: Ortíz-Gamino Diana , Cunha Luis , Martínez-Romero Esperanza , Flores-Estévez Norma , Ortíz-Ceballos Ángel I
Published: January 2018

Population genetic analyses of the invasive pantropical earthworm P. corethrurus populations will contribute significantly to better understand the ecology and especially the reproductive system of this species. Using 34 polymorphic ISSR markers the genetic diversity and population structure was assessed for four populations of P. corethrurus along an altitudinal gradient, ranging from sea level up to ~1667 meters. Nuclear markers were able to distinguish two genetic clusters, probably corresponding to two distinct genetic lineages, herein defined as A and B. Clones were detected in one population (Actopan at 480 masl) and its number was lower than expected for a parthenogenetic species. Nevertheless, low levels of genetic diversity and a high number of intermediary genotypes were detected among the studied P. corethrurus populations with no apparent population structure related to the distinct geographic regions, which may indicate that human-mediated transference is prevalent, in particular, for the lower altitude regions. Hybridisation between the two genetic clusters was tested and pointed to 11 MLGs as being later-generation hybrids (B1 introgression) mainly associated with the three lower altitude regions. Still, most of the individuals seem to belong to lineage A and only five individuals seem to belong exclusively to the lineage B. Interestingly, these parental individuals were only found present at the highest altitude site, Naolinco (1566-1667 masl), which also showed the highest values of genotypic richness. During the biological invasion, multiple introduction of different genetic lineages can provide opportunities for admixture among genetically distinct clusters. The signatures of admixture among P. corethrurus populations along the altitudinal gradient in Mexico may have allowed the invasion success by directly increasing fitness. ISSR markers revealed to be useful for the study of genetic variation in the invasive pantropical earthworm, P. corethrurus.
MiR-92b-3p is induced by advanced glycation end products and involved in the pathogenesis of diabetic nephropathy
Authors: Liping Wang , Nan Geng Jia , Bo Sun , Chengbo Sun , Siyuan Wang , Yan Shi , Xiayan Yu
Published: January 2018

Background. The current study aims to explore the effects of advanced glycation end products (AGEs) on the microRNA (miRNA) expression profile in kidney tissues in a murine diabetic nephropathy (DN) model, and to investigate the possible underlying mechanisms.

Methods. Wister rats were randomly divided into three equal experiment groups, the AGE group, the RSA group and the control group. The rats in the AGE group and the RSA group were administered with AGEs and rat serum albumin (RSA) via the tail vein, respectively, whereas those in the control group received no injection. Following the extraction of total RNA from the murine kidney tissues, miRNA profiling was performed using a miRNA microarray to determine the global differences in miRNA expression between the three experiment groups. The identified panel of aberrantly expressed miRNA candidates were subsequently validated by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Bioinformatics analysis was performed to identify the target genes and enriched signaling pathway for the validated miRNAs.

Results. Compared with RSA group, miR-7d-3p, miR-92b-3p, miR-181b-5p and miR-196c-5p were found to be significantly up-regulated in the AGE group, whereas miR-7a-1-3p, miR-186-5p, miR-192-5P, miR-196b-5p and miR-345-5p were shown to be down-regulated (p<0.05). Among the nine miRNA candidates, miR-92b-3p was validated by qRT-PCR analysis. Subsequent bioinformatic study indicated that SMAD7 could be a potential downstream gene target of miR-92b-3p. Both immunohistochemical staining and western blotting showed that SMAD7 expression was significantly suppressed in the kidney tissues harvested from the AGE group compared to those from the control and the RSA group.

Discussion. The results of the current study revealed a correlation between increased renal level of miR-92b-3p and elevated serum level of AGEs in a murine model of DN.
Satellite tagging highlights the importance of productive Mozambican coastal waters to the ecology and conservation of whale sharks
Authors: Rohner Christoph A , Richardson Anthony J , Jaine Fabrice R A , Bennett Michael B , Weeks Scarla J , Cliff Geremy , Robinson David P , Reeve-Arnold Katie E , Pierce Simon J
Published: January 2018

The whale shark Rhincodon typus is an endangered, highly migratory species with a wide, albeit patchy, distribution through tropical oceans. Ten aerial survey flights along the southern Mozambican coast, conducted between 2004–2008, documented a relatively high density of whale sharks along a ~200 km stretch of the Inhambane Province, with a pronounced hotspot adjacent to Praia do Tofo. To examine the residency and movement of whale sharks in coastal areas around Praia do Tofo, where they may be more susceptible to gill net entanglement, we tagged 15 juveniles with SPOT5 satellite tags and tracked them for 2–88 days (mean = 27 days) as they dispersed from this area. Sharks travelled between 10 and 2,737 km (mean = 738 km) at a mean horizontal speed of 28 ± 17.1 SD km day-1. While several individuals left shelf waters and travelled across international boundaries, most sharks stayed in Mozambican coastal waters over the tracking period. We tested for whale shark habitat preferences, using sea surface temperature, chlorophyll-a concentration and water depth as variables, by computing 100 random model tracks for each real shark based on their empirical movement characteristics. Whale sharks spent significantly more time in cooler, shallower water with higher chlorophyll-a concentrations than model sharks, suggesting that feeding in productive coastal waters is an important driver of their movements. To investigate what this coastal habitat choice means for their conservation in Mozambique, we mapped gill nets during two dedicated aerial surveys along the Inhambane coast and counted gill nets in 1,323 boat-based surveys near Praia do Tofo. Our results show that, while whale sharks are capable of long-distance oceanic movements, they can spend a disproportionate amount of time in specific areas, such as along the southern Mozambique coast. The increasing use of large-mesh gill nets in this coastal hotspot for whale sharks is likely to be a threat to regional populations of this iconic species.