bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic Information Relationship Network (GIRN): A Force-directed graphing tool for gene expression analysis
Authors: Rondeau Gaelle , Welsh John
Published: October 2016

We present a web-based tool, Genetic Information Relationship Network (GIRN), for mapping genes to a global protein interaction network for humans, and for further annotating this map with gene ontology, pathway, disease, and user-generated terms. These annotations can be adjusted according to enrichment within a subset of genes. Additionally, drugs that interact with genes in the subset can be added to the graph. The maps are force-directed graphs in which highly connected nodes tend toward the center, and highly interconnected nodes tend toward each other. Icons of different shapes and colors are employed to indicate whether the node represents a protein, a gene, or one of the various types of annotation. Coordinated interaction of genes and functional inference can be identified by visual inspection. Each node in the graph is associated with a menu of links to external data sources. Collectively, these tools provide an efficient portal to gene-associated public data for any group of genes specified by the user. The site can be found atwww.voxvill.org/relnet.
Atmospheric deposition exposes pandas to toxic pollutants
Authors: Chen Yi-ping , Zheng Ying-juan , Liu Qiang , Song Yi , An Zhi-sheng , Ma Qing-yi , Ellison Aaron M.
Published: October 2016

The giant panda (Ailuropoda melanoleuca) is one of the most endangered animals in the world, and it is recognized worldwide as a symbol for conservation. A previous study showed that wild and captive pandas were exposed to toxins in their diet of bamboo, but the ultimate origin of these toxins is unknown. Here we show that atmospheric deposition is the origin of heavy metals and persistent organic pollutants (POPs) in the diets of captive and wild Qinling giant pandas. Atmospheric deposition averaged 115 and 49 g⋅m−2⋅yr−1at China’s Shaanxi Wild Animal Research Center (SWARC) and Foping National Nature Reserve (FNNR), respectively. Atmospheric deposition of heavy metals (As, Cd, Cr, Pb, Hg, Co, Cu, Zn, Mn and Ni) and POPs at SWARC was higher than at FNNR. Soil concentrations of the aforementioned heavy metals other than As and Zn also were significantly higher at SWARC than at FNNR. We conclude that efforts to conserve the Qinling subspecies of panda may be compromised by air pollution attendant to China’s economic development. Improvement of air quality and reductions of toxic emissions are urgently required to protect China’s iconic species.
Reproductive Isolation through Experimental Manipulation of Sexually Antagonistic Coevolution inDrosophila melanogaster
Authors: Zeeshan Ali Syed , Chatterjee Martik , Samant Manas Arun , Prasad Nagaraj Guru
Published: October 2016

Promiscuity can drive the evolution of sexual conflict before and after mating occurs. Post-mating, the male ejaculate can selfishly manipulate female physiology leading to a chemical arms race between the sexes. Theory suggests that drift and sexually antagonistic coevolution can cause allopatric populations to evolve different chemical interactions between the sexes, thereby leading to postmating reproductive barriers and speciation. There is, however, little empirical evidence supporting this form of speciation. We tested this theory by creating an experimental evolutionary model ofDrosophila melanogasterpopulations undergoing different levels of interlocus sexual conflict. We found that allopatric populations under elevated sexual conflict show assortative mating indicating premating reproductive isolation. Further, these allopatric populations also show reduced copulation duration and sperm defense ability when mating happens between individuals between individuals across populations compared to that within the same population, indicating postmating prezygotic isolation. Sexual conflict can cause reproductive isolation in allopatric populations through the coevolution of chemical (postmating prezygotic) as well as behavioural (premating) interaction between the sexes. Thus, to our knowledge, we provide the first comprehensive evidence of postmating (as well as premating) reproductive isolation due to sexual conflict.
Control mechanisms for stochastic biochemical systems via computation of reachable sets
Authors: Lakatos Eszter , Stumpf Michael P.H.
Published: October 2016

Controlling the behaviour of cells by rationally guiding molecular processes is an overarching aim of much of synthetic biology. Molecular processes, however, are notoriously noisy and frequently non-linear. We present an approach to studying the impact of control measures on motifs of molecular interactions, that addresses the problems faced in biological systems: stochasticity, parameter uncertainty, and non-linearity. We show that our reachability analysis formalism can describe the potential behaviour of biological (naturally evolved as well as engineered) systems, and provides a set of bounds on their dynamics at the level of population statistics: for example, we can obtain the possible ranges of means and variances of mRNA and protein expression levels, even in the presence of uncertainty about model parameters.
Genome-Wide Association Study of Ionomic Traits on Diverse Soybean Populations from Germplasm Collections
Authors: Ziegler Greg , Nelson Randall , Granada Stephanie , Krishnan Hari B. , Gillman Jason D. , Baxter Ivan
Published: October 2016

The elemental content of a soybean seed is a determined by both genetic and environmental factors and is an important component of its nutritional value. The elemental content is chemically stable, making the samples stored in germplasm repositories an intriguing source of experimental material. To test the efficacy of using samples from germplasm banks for gene discovery, we analyzed the elemental profile of seeds from 1653 lines in the USDA Soybean Germplasm Collection. We observed large differences in the elemental profiles based on where the lines were grown, which lead us to break up the genetic analysis into multiple small experiments. Despite these challenges, we were able to identify candidate SNPs controlling elemental accumulation as well as lines with extreme elemental accumulation phenotypes. Our results suggest that elemental analysis of germplasm samples can identify SNPs in linkage disequilibrium to genes, which can be leveraged to assist in crop improvement efforts.
Considerations and complications of mapping small RNA libraries to transposable elements
Authors: Bousios Alexandros , Gaut Brandon S. , Darzentas Nikos
Published: October 2016

The advent of high-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. Often coupled with the availability of fully sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), and especially when such genomes are large as is often the case in plants. Here, to shed light on the challenges of mapping sRNAs to TEs, we focus on the 2,300Mb maize genome, of which >85% is derived from TEs. We compare various methodological strategies that are commonly employed in TE studies. These include choices for the reference dataset, the normalization of multiple mapping sRNAs, and the selection among different types of sRNA metrics. We further examine how these choices influence the relationship between sRNAs and the critical feature of TE age, and explore and contrast their effect on low copy regions (exons) and other popular HTS data (RNA-seq). Finally, based on our analysis, we share a series of take-home messages to help guide TE epigenetic studies specifically, but our conclusions may also apply to any work that involves mapping and analysis of HTS data.
A causal role of the right superior temporal sulcus in emotion recognition from biological motion
Authors: Basil Rochelle A. , Westwater Margaret L. , Wiener Martin , Thompson James C.
Published: October 2016

Understanding the emotions of others through nonverbal cues is critical for successful social interactions. The right posterior superior temporal sulcus (rpSTS) is one brain region thought to be key in the recognition of the mental states of others based on body language and facial expression. In the present study, we temporarily disrupted functional activity of the rpSTS by using continuous, theta-burst transcranial magnetic stimulation (cTBS) to test the hypothesis that the rpSTS plays a causal role in emotion recognition from body movements. Participants (N=23) received cTBS of the rpSTS, which was individually localized using fMRI, and a vertex control site. Before and after cTBS, we tested the ability of participants to identify emotions from point-light biological motion stimuli and a non-biological global motion identification task. Results revealed that the ability of participants to accurately identify emotional states from biological motion was reduced following cTBS stimulation to the rpSTS, but was unimpaired following vertex stimulation. Accuracy on the global motion tasks was unaffected by cTBS to either site. These results support the causal role of the rpSTS in decoding information about other’s emotional state from their body movements and gestures.
QTL-guided metabolic engineering of a complex trait
Authors: Maurer Matthew J. , Sutardja Lawrence , Pinel Dominic , Bauer Stefan , Muehlbauer Amanda L. , Ames Tyler D. , Skerker Jeffrey M. , Arkin Adam P.
Published: October 2016

Engineering complex phenotypes for industrial and synthetic biology applications is difficult and often confounds rational design. Bioethanol production from lignocellulosic feedstocks is a complex trait that requires multiple host systems to utilize, detoxify, and metabolize a mixture of sugars and inhibitors present in plant hydrolysates. Here, we demonstrate an integrated approach to discovering and optimizing host factors that impact fitness ofSaccharomyces cerevisiaeduring fermentation of aMiscanthus x giganteusplant hydrolysate. We first used high-resolution Quantitative Trait Loci (QTL) mapping and systematic Bulk Reciprocal Hemizygosity analysis (bRHA) to discover 17 loci that differentiate hydrolysate tolerance between an industrially related (JAY291) and a laboratory (S288C) strain. We then used this data to identify a subset of favorable allelic loci that were most amenable for strain engineering. Guided by this “genetic blueprint”, and using a dual-guide Cas9-based method to efficiently perform multi-kilobase locus replacements, we engineered an S288C strain with superior hydrolysate tolerance than JAY291. Our methods should be generalizable to engineering any complex trait inS. cerevisiae, as well as other organisms.
Hosts, parasites, and their interactions respond to climatic variables
Authors: Poisot Timothée , Guéveneux-Julien Cynthia , Fortin Marie-Josée , Gravel Dominique , Legendre Pierre
Published: October 2016

Aim: Although there is a vast body of literature on the causes of variation in species composition in ecological communities, less effort has been invested in understanding how interactions between these species vary. Since interactions are crucial to the structure and functioning of ecological communities, we need to develop a better understanding of their spatial distribution. Here, we investigate whether species interactions vary more in response to different climate variables, than individual species do. Location: Eurasia. Time period: 2000s. Major taxa: Animalia. Methods: We used a measure of Local Contribution to Beta-Diversity to evaluate the compositional uniqueness of 51 host–parasite communities of rodents and their ectoparasitic fleas across Eurasia, using publicly available data. We measured uniqueness based on the species composition, and based on potential and realized biotic interactions (here, host-parasite interactions). Results: We show that species interactions vary more, across space, than species do. In particular, we show that species interactions respond to some climatic variables that have no effect on species distributions or dissimilarity. Main conclusions: Species interactions capture some degree of variation which is not apparent when looking at species occurrences only. In this system, this appeared as hosts and parasites interacting in different ways as a reponse to different environments, especially the temperature and dryness. We discuss the implications of this finding for the amount of information that should be considered when measuring community dissimilarity.
Computational cognitive neuroscience: Model fitting should not replace model simulation
Authors: Palminteri Stefano , Wyart Valentin , Koechlin Etienne
Published: October 2016

Cognitive neuroscience, especially in the fields of learning and decision-making, is witnessing the blossoming of computational model-based analyses. Several methodological and review papers have indicated how and why candidate models should becomparedby trading off their ability to predict the data as a function of their complexity. However, the importance ofsimulatingcandidate models has been so far largely overlooked, which entails several drawbacks and leads to invalid conclusions. Here we argue that the analysis of model simulations is often necessary to support the specific claims about behavioral function that most of model-based studies make. We defend this argument both informally by providing a large-scale (N>300) review of recent studies, and formally by showing how model simulations are necessary to interpret model comparison results. Finally, we propose guidelines for future work, which combine model comparison and simulation.
Alzheimer-related pathogenesis is dependent on neuronal receptor PTPσ
Authors: Gu Yuanzheng , Shu Yaoling , Corona Angela W. , Xu Kui , Yi Allen F. , Chen Shannon , Luo Man , Tremblay Michel L. , Nelson Randy J. , Landreth Gary E. , Silver Jerry , Shen Yingjie
Published: October 2016

Due to limited understanding of disease mechanisms and the lack of molecular targets, translational research for Alzheimer disease has not been fruitful hitherto. Here we report findings that indicate neuronal receptor phosphatase PTPσ as a potential therapeutic target for this dementia. In two TgAPP mouse models, a spectrum of Alzheimer-related pathologies, including aged-induced progression of β-amyloidosis, Tau aggregation, neuroinflammation, synaptic loss, as well as behavioral deficits, all show unambiguous dependency on PTPσ. APP amyloidogenic metabolites diminish upon PTPσ genetic depletion or pharmacological inhibition. Binding to APP in the brain, PTPσ regulates APP proteolytic metabolism via its phosphatase activity, likely through downstream signaling that modulates APP membrane localization and affinity to the β-secretase, in a specific manner that does not broadly affect β- and γ-secretase processing of other major substrates. Together, these findings unveil a gatekeeping role of PTPσ upstream in Alzheimer-like pathogenic pathway.
A Novel function for Cactus/IκB inhibitor to promote Toll signals in theDrosophilaembryo
Authors: Cardoso Maira Arruda , Fontenele Marcio , Lim Bomyi , Bisch Paulo Mascarello , Shvartsman Stanislav , Araujo Helena Marcolla
Published: October 2016

The evolutionarily conserved Toll signaling pathway controls innate immunity across phyla and embryonic patterning in insects. In the Drosophila embryo Toll is required to establish gene expression domains along the dorsal-ventral axis. Pathway activation induces degradation of the IκB inhibitor Cactus resulting in a nuclear gradient of the NFκB effector Dorsal. Here we investigate howcactusmodulates Toll signals through its effects on the Dorsal gradient and Dorsal target genes. Quantitative analysis using a series of loss and gain-of-function conditions shows that the ventral and lateral aspects of the Dorsal gradient behave differently respective to Cactus fluctuations. Unexpectedly, Cactus favors Dorsal nuclear localization required as response to high Toll signals at the ventral side of the embryo. Furthermore, N-terminal deleted Cactus mimics these effects, indicating that the ability of Cactus to favor Toll stems from mobilization of a free Cactus pool induced by the Calpain A protease. These results indicate that unexplored mechanisms are at play to ensure a correct response to high Toll signals.

The IκB protein Cactus favors high Toll signals, revealing that the ventral and lateral aspects of the Dorsal/NFκB nuclear gradient behave differently respective to Cactus concentrations in the Drosophila embryo.
Improved assembly of noisy long reads by k-mer validation
Authors: Carvalho Antonio Bernardo , Dupim Eduardo G. , Goldstein Gabriel
Published: October 2016

Genome assembly depends critically on read length. Two recent technologies, from Pacific Biosciences (PacBio) and Oxford Nanopore, produce read lengths >20 kb, which yield de novo genome assemblies with vastly greater contiguity than those based on Sanger, Illumina, or other technologies. However, the very high error rates of these two new technologies (∼15% per base) makes assembly imprecise at repeats longer than the read length and computationally expensive. Here we show that the contiguity and quality of the assembly of these noisy long reads can be significantly improved at a minimal cost, by leveraging on the low error rate and low cost of Illumina short reads. Namely, k-mers from the PacBio raw reads that are not present in Illumina reads (which account for ∼95% of the distinct k-mers) are deemed sequencing errors and ignored at the seed alignment step. By focusing on the ∼5% of k-mers that are error free, read overlap sensitivity is dramatically increased. Of equal importance, the validation procedure can be extended to exclude repetitive k-mers, which prevents read miscorrection at repeats and further improves the resulting assemblies. We tested the k-mer validation procedure using one long-read technology (PacBio) and one assembler (MHAP/Celera Assembler), but it is very likely to yield analogous improvements with alternative long-read technologies and assemblers, such as Oxford Nanopore and BLASR/DALIGNER/Falcon, respectively.
Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region
Authors: Mohajeri Kiana , Cantsilieris Stuart , Huddleston John , Nelson Bradley J. , Coe Bradley P. , Campbell Catarina D. , Baker Carl , Harshman Lana , Munson Katherine M. , Kronenberg Zev N. , Kremitzki Milinn , Raja Archana , Catacchio Claudia Rita , Graves Tina A. , Wilson Richard K. , Ventura Mario , Eichler Evan E.
Published: October 2016

Recurrent rearrangements of Chromosome 8p23.1 are associated with congenital heart defects and developmental delay. The complexity of this region has led to inconsistencies in the current reference assembly, confounding studies of genetic variation. Using comparative sequence-based approaches, we generated a high-quality 6.3-Mbp alternate reference assembly of an inverted Chromosome 8p23.1 haplotype. Comparison with nonhuman primates reveals a 746-kbp duplicative transposition and two separate inversion events that arose in the last million years of human evolution. The breakpoints associated with these rearrangements map to an ape-specific interchromosomal core duplicon that clusters at sites of evolutionary inversion (P = 7.8 × 10−5). Refinement of microdeletion breakpoints identifies a subgroup of patients that map to the same interchromosomal core involved in the evolutionary formation of the duplication blocks. Our results define a higher-order genomic instability element that has shaped the structure of specific chromosomes during primate evolution contributing to rearrangements associated with inversion and disease.
Combinatorial microfluidic droplet engineering for biomimetic material synthesis
Authors: Bawazer Lukmaan A. , McNally Ciara S. , Empson Christopher J. , Marchant William J. , Comyn Tim P. , Niu Xize , Cho Soongwon , McPherson Michael J. , Binks Bernard P. , deMello Andrew , Meldrum Fiona C.
Published: October 2016

Combinatorial chemical evolution is used to select oil-water droplet interfaces that drive inorganic nanoparticle synthesis.
Maintenance of leukemic cell identity by the activity of the Polycomb complex PRC1 in mice
Authors: Rossi Alessandra , Ferrari Karin J. , Piunti Andrea , Jammula SriGanesh , Chiacchiera Fulvio , Mazzarella Luca , Scelfo Andrea , Pelicci Pier Giuseppe , Pasini Diego
Published: October 2016

The Polycomb complex PRC1 is a gatekeeper of leukemic cell identity in the presence of distinct oncogenic signals.
Scalable solution-phase epitaxial growth of symmetry-mismatched heterostructures on two-dimensional crystal soft template
Authors: Lin Zhaoyang , Yin Anxiang , Mao Jun , Xia Yi , Kempf Nicholas , He Qiyuan , Wang Yiliu , Chen Chih-Yen , Zhang Yanliang , Ozolins Vidvuds , Ren Zhifeng , Huang Yu , Duan Xiangfeng
Published: October 2016

Lin
et al.
report 2D layered materials as a soft template for symmetry-mismatched epitaxial growth of PbSe/Bi
2
Se
3
heterostructures.
Infrared vibrational nanocrystallography and nanoimaging
Authors: Muller Eric A. , Pollard Benjamin , Bechtel Hans A. , van Blerkom Peter , Raschke Markus B.
Published: October 2016

Nanoscale spectroscopy and imaging of organic materials reveal heterogeneity in molecular orientation in crystalline domains.
Tunable and label-free virus enrichment for ultrasensitive virus detection using carbon nanotube arrays
Authors: Yeh Yin-Ting , Tang Yi , Sebastian Aswathy , Dasgupta Archi , Perea-Lopez Nestor , Albert Istvan , Lu Huaguang , Terrones Mauricio , Zheng Si-Yang
Published: October 2016

Aligned carbon nanotube–integrated device can effectively trap and enrich viruses from field samples without using antibodies.
Effects of In-Feed Chlortetracycline Prophylaxis in Beef Cattle on Animal Health and Antimicrobial-Resistant Escherichia coli
Authors: Agga Getahun E. , Schmidt John W. , Arthur Terrance M.
Published: October 2016

Concerns have been raised that in-feed chlortetracycline (CTC) may increase antimicrobial resistance (AMR), specifically tetracycline-resistant (TET
r
)
Escherichia coli
and third-generation cephalosporin-resistant (3GC
r
)
E. coli
. We evaluated the impact of a 5-day in-feed CTC prophylaxis on animal health, TET
r
E. coli
, and 3GC
r
E. coli
. A control group of cattle (
n
= 150) received no CTC, while a CTC group (
n
= 150) received in-feed CTC (10 mg/lb of body weight/day) from the 5th to the 9th day after feedlot arrival. Over 25% (38/150) of the animals in the control group developed illnesses requiring therapeutic treatment with antimicrobials critically important to human medicine. Only two animals (1.3%) in the CTC group required such treatments. Fecal swab and pen surface occurrences of generic
E. coli
(isolated on media that did not contain antimicrobials of interest and were not isolated based on any specific resistance), TET
r
E. coli
, and 3GC
r
E. coli
were determined on five sampling occasions: arrival at the feedlot, 5 days posttreatment (5 dpt), 27 dpt, 75 dpt, and 117 dpt. On 5 dpt, TET
r
E. coli
concentrations were higher for the CTC group than the control group (
P
< 0.01). On 27 dpt, 75 dpt, and 117 dpt, TET
r
E. coli
concentrations did not differ between groups. 3GC
r
E. coli
occurrences did not differ between control and CTC groups on any sampling occasion. For both groups, generic, TET
r
, and 3GC
r
E. coli
occurrences were highest on 75 dpt and 117 dpt, suggesting that factors other than in-feed CTC contributed more significantly to antimicrobial-resistant
E. coli
occurrence.

IMPORTANCE
The occurrence of human bacterial infections resistant to antimicrobial therapy has been increasing. It has been postulated that antimicrobial resistance was inevitable, but the life span of the antimicrobial era has been prematurely compromised due to the misuse of antimicrobials in clinical and agricultural practices. Direct evidence relating the use of antimicrobials in livestock production to diminished human health outcomes due to antimicrobial resistance is lacking, and the U.S. Food and Drug Administration has taken an approach to maximize therapeutic efficacy and minimize the selection of resistant microorganisms through judicious use of antimicrobials. This study demonstrated that prophylactic in-feed treatment of chlortetracycline administered for 5 days to calves entering feedlots is judicious, as this therapy reduced animal morbidity, reduced the use of antimicrobials more critical to human health, and had no long-term impact on the occurrence of antimicrobial-resistant
E. coli
.
Engineering of a Highly Efficient Escherichia coli Strain for Mevalonate Fermentation through Chromosomal Integration
Authors: Wang Jilong , Niyompanich Suthamat , Tai Yi-Shu , Wang Jingyu , Bai Wenqin , Mahida Prithviraj , Gao Tuo , Zhang Kechun
Published: October 2016

Chromosomal integration of heterologous metabolic pathways is optimal for industrially relevant fermentation, as plasmid-based fermentation causes extra metabolic burden and genetic instabilities. In this work, chromosomal integration was adapted for the production of mevalonate, which can be readily converted into β-methyl-δ-valerolactone, a monomer for the production of mechanically tunable polyesters. The mevalonate pathway, driven by a constitutive promoter, was integrated into the chromosome of
Escherichia coli
to replace the native fermentation gene
adhE
or
ldhA
. The engineered strains (CMEV-1 and CMEV-2) did not require inducer or antibiotic and showed slightly higher maximal productivities (0.38 to ∼0.43 g/liter/h) and yields (67.8 to ∼71.4% of the maximum theoretical yield) than those of the plasmid-based fermentation. Since the glycolysis pathway is the first module for mevalonate synthesis,
atpFH
deletion was employed to improve the glycolytic rate and the production rate of mevalonate. Shake flask fermentation results showed that the deletion of
atpFH
in CMEV-1 resulted in a 2.1-fold increase in the maximum productivity. Furthermore, enhancement of the downstream pathway by integrating two copies of the mevalonate pathway genes into the chromosome further improved the mevalonate yield. Finally, our fed-batch fermentation showed that, with deletion of the
atpFH
and
sucA
genes and integration of two copies of the mevalonate pathway genes into the chromosome, the engineered strain CMEV-7 exhibited both high maximal productivity (∼1.01 g/liter/h) and high yield (86.1% of the maximum theoretical yield, 30 g/liter mevalonate from 61 g/liter glucose after 48 h in a shake flask).

IMPORTANCE
Metabolic engineering has succeeded in producing various chemicals. However, few of these chemicals are commercially competitive with the conventional petroleum-derived materials. In this work, chromosomal integration of the heterologous pathway and subsequent optimization strategies ensure stable and efficient (i.e., high-titer, high-yield, and high-productivity) production of mevalonate, which demonstrates the potential for scale-up fermentation. Among the optimization strategies, we demonstrated that enhancement of the glycolytic flux significantly improved the productivity. This result provides an example of how to tune the carbon flux for the optimal production of exogenous chemicals.
Association of Bartonella Species with Wild and Synanthropic Rodents in Different Brazilian Biomes
Authors: Gonçalves Luiz Ricardo , Favacho Alexsandra Rodrigues de Mendonça , Roque André Luiz Rodrigues , Mendes Natalia Serra , Fidelis Junior Otávio Luiz , Benevenute Jyan Lucas , Herrera Heitor Miraglia , D'Andrea Paulo Sérgio , de Lemos Elba Regina Sampaio , Machado Rosangela Zacarias , André Marcos Rogério
Published: October 2016

Bartonellaspp. comprise an ecologically successful group of microorganisms that infect erythrocytes and have adapted to different hosts, which include a wide range of mammals, besides humans. Rodents are reservoirs of about two-thirds ofBartonellaspp. described to date; and some of them have been implicated as causative agents of human diseases. In our study, we performed molecular and phylogenetic analyses ofBartonellaspp. infecting wild rodents from five different Brazilian biomes. In order to characterize the genetic diversity ofBartonellaspp., we performed a robust analysis based on three target genes, followed by sequencing, Bayesian inference, and maximum likelihood analysis.Bartonellaspp. were detected in 25.6% (117/457) of rodent spleen samples analyzed, and this occurrence varied among different biomes. The diversity analysis ofgltAsequences showed the presence of 15 different haplotypes. Analysis of the phylogenetic relationship ofgltAsequences performed by Bayesian inference and maximum likelihood showed that theBartonellaspecies detected in rodents from Brazil was closely related to the phylogenetic group A detected in other cricetid rodents from North America, probably constituting only one species. Last, theBartonellaspecies genogroup identified in the present study formed a monophyletic group that includedBartonellasamples from seven different rodent species distributed in three distinct biomes. In conclusion, our study showed that the occurrence ofBartonellabacteria in rodents is much more frequent and widespread than previously recognized.

IMPORTANCEIn the present study, we reported the occurrence ofBartonellaspp. in some sites in Brazil. The identification and understanding of the distribution of this important group of bacteria may allow the Brazilian authorities to recognize potential regions with the risk of transmission of these pathogens among wild and domestic animals and humans. In addition, our study accessed important gaps in the biology of this group of bacteria in Brazil, such as its low host specificity, high genetic diversity, and relationship with otherBartonellaspp. detected in rodents trapped in America. Considering the diversity of newly discoveredBartonellaspecies and the great ecological plasticity of these bacteria, new studies with the aim of revealing the biological aspects unknown until now are needed and must be performed around the world. In this context, the impact ofBartonellaspp. associated with rodents in human health should be assessed in future studies.
Geographic Impact on Genomic Divergence as Revealed by Comparison of Nine Citromicrobial Genomes
Authors: Zheng Qiang , Liu Yanting , Jeanthon Christian , Zhang Rui , Lin Wenxin , Yao Jicheng , Jiao Nianzhi
Published: October 2016

Aerobic anoxygenic phototrophic bacteria (AAPB) are thought to be important players in oceanic carbon and energy cycling in the euphotic zone of the ocean. The genus
Citromicrobium
, widely found in oligotrophic oceans, is a member of marine alphaproteobacterial AAPB. Nine
Citromicrobium
strains isolated from the South China Sea, the Mediterranean Sea, or the tropical South Atlantic Ocean were found to harbor identical 16S rRNA sequences. The sequencing of their genomes revealed high synteny in major regions. Nine genetic islands (GIs) involved mainly in type IV secretion systems, flagellar biosynthesis, prophage, and integrative conjugative elements, were identified by a fine-scale comparative genomics analysis. These GIs played significant roles in genomic evolution and divergence. Interestingly, the coexistence of two different photosynthetic gene clusters (PGCs) was not only found in the analyzed genomes but also confirmed, for the first time, to our knowledge, in environmental samples. The prevalence of the coexistence of two different PGCs may suggest an adaptation mechanism for
Citromicrobium
members to survive in the oceans. Comparison of genomic characteristics (e.g., GIs, average nucleotide identity [ANI], single-nucleotide polymorphisms [SNPs], and phylogeny) revealed that strains within a marine region shared a similar evolutionary history that was distinct from that of strains isolated from other regions (South China Sea versus Mediterranean Sea). Geographic differences are partly responsible for driving the observed genomic divergences and allow microbes to evolve through local adaptation. Three
Citromicrobium
strains isolated from the Mediterranean Sea diverged millions of years ago from other strains and evolved into a novel group.

IMPORTANCE
Aerobic anoxygenic phototrophic bacteria are a widespread functional group in the upper ocean, and their abundance could be up to 15% of the total heterotrophic bacteria. To date, a great number of studies display AAPB biogeographic distribution patterns in the ocean; however, little is understood about the geographic isolation impact on the genome divergence of marine AAPB. In this study, we compare nine
Citromicrobium
genomes of strains that have identical 16S rRNA sequences but different ocean origins. Our results reveal that strains isolated from the same marine region share a similar evolutionary history that is distinct from that of strains isolated from other regions. These
Citromicrobium
strains diverged millions of years ago. In addition, the coexistence of two different PGCs is prevalent in the analyzed genomes and in environmental samples.
Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing
Authors: Taylor D. Lee , Walters William A. , Lennon Niall J. , Bochicchio James , Krohn Andrew , Caporaso J. Gregory , Pennanen Taina
Published: October 2016

While high-throughput sequencing methods are revolutionizing fungal ecology, recovering accurate estimates of species richness and abundance has proven elusive. We sought to design internal transcribed spacer (ITS) primers and an Illumina protocol that would maximize coverage of the kingdom Fungi while minimizing nontarget eukaryotes. We inspected alignments of the 5.8S and large subunit (LSU) ribosomal genes and evaluated potential primers using PrimerProspector. We tested the resulting primers using tiered-abundance mock communities and five previously characterized soil samples. We recovered operational taxonomic units (OTUs) belonging to all 8 members in both mock communities, despite DNA abundances spanning 3 orders of magnitude. The expected and observed read counts were strongly correlated (
r
= 0.94 to 0.97). However, several taxa were consistently over- or underrepresented, likely due to variation in rRNA gene copy numbers. The Illumina data resulted in clustering of soil samples identical to that obtained with Sanger sequence clone library data using different primers. Furthermore, the two methods produced distance matrices with a Mantel correlation of 0.92. Nonfungal sequences comprised less than 0.5% of the soil data set, with most attributable to vascular plants. Our results suggest that high-throughput methods can produce fairly accurate estimates of fungal abundances in complex communities. Further improvements might be achieved through corrections for rRNA copy number and utilization of standardized mock communities.

IMPORTANCE
Fungi play numerous important roles in the environment. Improvements in sequencing methods are providing revolutionary insights into fungal biodiversity, yet accurate estimates of the number of fungal species (i.e., richness) and their relative abundances in an environmental sample (e.g., soil, roots, water, etc.) remain difficult to obtain. We present improved methods for high-throughput Illumina sequencing of the species-diagnostic fungal ribosomal marker gene that improve the accuracy of richness and abundance estimates. The improvements include new PCR primers and library preparation, validation using a known mock community, and bioinformatic parameter tuning.
A carbonate-based proxy for sulfate-driven anaerobic oxidation of methane
Authors: Feng Dong , Peng Yongbo , Bao Huiming , Peckmann Jörn , Roberts Harry H. , Chen Duofu
Published: October 2016

Sulfate-driven anaerobic oxidation of methane (SD-AOM) supports chemosynthesis-based communities and limits the release of methane from marine sediments. Formation of authigenic carbonates at active methane seeps is promoted by SD-AOM stoichiometry. While distinctively small δ18O/δ34S slopes of pore fluid sulfate have been shown to typify modern methane-rich environments, identification of such environments has been difficult for the geological past due to the lack of sedimentary pore fluids. However, if the isotopic composition of sulfate were archived in authigenic carbonate during early diagenesis, carbonate-associated sulfate (CAS) should display the characteristic δ18O-δ34S pattern. To test this hypothesis, we investigated the δ18OCAS, δ34SCAS, and 87Sr/86Sr signatures of authigenic carbonate minerals from three modern and two ancient methane-seep provinces. The data obtained demonstrate that all deposits regardless of age or location display consistently small δ18OCAS/δ34SCAS slopes (∼0.3) and CAS does not represent ambient seawater but pore-water sulfate. This finding confirms the utility of CAS as a recorder of SD-AOM in methane-rich environments. In addition, we report that aragonites bear higher CAS contents, 87Sr/86Sr ratios closer to that of contemporary seawater, and a larger δ18OCAS/δ34SCAS slope than calcites, reflecting the shallower formation depth of aragonite where pore-water has a composition close to that of seawater with high concentrations of sulfate. The new proxy can be used to constrain the record of SD-AOM through most of Earth history by measuring the δ18O and δ34S values of CAS of methane-derived diagenetic carbonates including but not limited to seep carbonates.
Tracing subducted black shales in the Lesser Antilles arc using molybdenum isotope ratios
Authors: Freymuth Heye , Elliott Tim , van Soest Matthijs , Skora Susanne
Published: October 2016

Lesser Antilles arc lavas have trace element and radiogenic isotope characteristics indicative of a continent-derived contribution. It is debated vigorously whether this continental signature represents terrigenous sediment that has been subducted with the Atlantic plate and added to the magma sources in the mantle wedge, or portions of the subarc crust that are assimilated during magma ascent. Here we present Mo isotope data for Lesser Antilles arc lavas and sediments offboard the Lesser Antilles trench. Sequences of black shales, present in the subducting sediment piles, are highly enriched in Mo and have unusually high 98Mo/95Mo. Despite their low mass fraction in the sediment package (<10% in Deep Sea Drilling Project Site 144), they dominate the Mo content and isotopic composition of the bulk sediment subducting at the Lesser Antilles trench. We show that lavas from the southern part of the Lesser Antilles arc also have high 98Mo/95Mo ratios, implicating the addition of Mo derived from the subducted black shales to their mantle sources. This establishes a new link between the composition of subducted material and the arc lava output.
Pseudotachylyte increases the post-slip strength of faults
Authors: Proctor B. , Lockner D.A.
Published: October 2016

Solidified frictional melts, or pseudotachylytes, are observed in exhumed faults from across the seismogenic zone. These unique fault rocks, and many experimental studies, suggest that frictional melting can be an important process during earthquakes. However, it remains unknown how melting affects the post-slip strength of the fault and why many exhumed faults do not contain pseudotachylyte. Analyses of triaxial stick-slip events on Westerly Granite (Rhode Island, USA) sawcuts at confining pressures from 50 to 400 MPa show evidence for frictional heating, including some events energetic enough to generate surface melt. Total and partial stress drops were observed with slip as high as 6.5 mm. We find that in dry samples following melt-producing stick slip, the shear failure strength increased as much as 50 MPa, while wet samples had <10 MPa strengthening. Microstructural analysis indicates that the strengthening is caused by welding of the slip surface during melt quenching, suggesting that natural pseudotachylytes may also strengthen faults after earthquakes. These results predict that natural pseudotachylyte will inhibit slip reactivation and possibly generate stress heterogeneities along faults. Wet samples do not exhibit melt welding, possibly because of thermal pressurization of water reducing frictional heating during slip.
Transitions in coral reef accretion rates linked to intrinsic ecological shifts on turbid-zone nearshore reefs
Authors: Morgan Kyle M. , Perry Chris T. , Smithers Scott G. , Johnson Jamie A. , Gulliver Pauline
Published: October 2016

Nearshore coral communities within turbid settings are typically perceived to have limited reef-building capacity. However, several recent studies have reported reef growth over millennial time scales within such environments and have hypothesized that depth-variable community assemblages may act as equally important controls on reef growth as they do in clear-water settings. Here, we explicitly test this idea using a newly compiled chronostratigraphic record (31 cores, 142 radiometric dates) from seven proximal (but discrete) nearshore coral reefs located along the central Great Barrier Reef (Australia). Uniquely, these reefs span distinct stages of geomorphological maturity, as reflected in their elevations below sea level. Integrated age-depth and ecological data sets indicate that contemporary coral assemblage shifts, associated with changing light availability and wave exposure as reefs shallowed, coincided with transitions in accretion rates at equivalent core depths. Reef initiation followed a regional ∼1 m drop in sea level (1200–800 calibrated yr B.P.) which would have lowered the photic floor and exposed new substrate for coral recruitment by winnowing away fine seafloor sediments. We propose that a two-way feedback mechanism exists where past growth history influences current reef morphology and ecology, ultimately driving future reef accumulation and morphological change. These findings provide the first empirical evidence that nearshore reef growth trajectories are intrinsically driven by changes in coral community structure as reefs move toward sea level, a finding of direct significance for predicting the impacts of extrinsically driven ecological change (e.g., coral-algal phase shifts) on reef growth potential within the wider coastal zone on the Great Barrier Reef.
Single-stage temporomandibular joint arthroplasty in a patient with complete bony ankylosis and previous extradural haematoma
Authors: Brown Emma , Wilson Mark H , Revington Peter
Published: October 2016

We present a case of a man aged 20 years who was referred with the inability to open his mouth as a consequence of severe ankylosis of his temporomandibular joint. He had previously undergone an attempt to release the ankylosis at the referring institution; however, this was complicated by an extradural haematoma as a result of iatrogenic injury. We describe a one-stage procedure which provided safe excision of the ankylotic mass along with immediate total joint replacement with a custom implant. We advocate the use of preoperative vascular imaging along with the use of custom-made cutting guides to minimise vascular injury.
Schwannoma of the tongue
Authors: Kavčič Jakob , Božič Marko
Published: October 2016

Schwannoma, neurilemmoma or neurinoma is a rare, benign nerve sheath neoplasm composed of Schwann cells. It is usually solitary, slow growing and asymptomatic. Approximately 1–12% of the tumours occur intraorally with the tongue being the most common location. We report a rare case of lingual schwannoma in a 20-year-old female patient involving the tip of the tongue, which was slow growing and asymptomatic. For diagnosis histopathological examination and also immunohistochemistry testing were carried out to confirm the nature of tissue fragments. The treatment was complete surgical excision.
Rare cause of bilateral sudden deafness
Authors: Vos F I , Merkus P , van Nieuwkerk E B J , Hensen E F
Published: October 2016

In this paper, we describe the case of a 62-year-old female with recurring episodes of sudden deafness with vertigo and facial paresis. Within a month's time, this resulted in bilateral deafness and vestibular areflexia. Erroneously, the patient was diagnosed with sudden deafness of unknown origin and subsequently with neuroborreliosis (Lyme disease). The true diagnosis of relapsing polychondritis (RP) was revealed 9 months after initial presentation. The diagnostic delay is in part explained by the fact that, by definition, the disease has to relapse before the diagnosis can be made, but also by its pluriform clinical presentation. Timely identification of RP as the cause of this profound sensorineural hearing loss proved to be important. It was key in instigating adequate follow-up, and allowed for cochlear implantation before total cochlear obliteration, which might have hampered optimal hearing rehabilitation.
Bilateral brachiocephalic vein compression: an unusual and rare presentation of multinodular goitre
Authors: McNeill Caitlin Jane , Sinnott Joseph Dalby , Howlett David
Published: October 2016

An interesting and rare case where a longstanding multinodular goitre causes sudden onset symptoms of superior vena cava obstruction. The symptoms were caused by bilateral brachiocephalic vein compression against the first rib. The patient's symptoms included upper limb and facial swelling, whereas her lower limbs were not oedematous (figure 1). The patient underwent CT imaging which showed a multinodular retrosternal thyroid filling the space created by the first rib, sometimes known as the thoracic outlet. The goitre expanded sufficiently to compress the brachiocephalic vein on both sides as shown in figures 2 and 3. This prevented venous drainage from the upper limbs and head. The goitre was also large enough to cause deviation of the trachea although there was no airway compromise. This case is interesting as it is very rare for a benign condition such as a multinodular goitre to cause symptoms of superior vena cava obstruction.
‘Women and babies are dying but not of Ebola’: the effect of the Ebola virus epidemic on the availability, uptake and outcomes of maternal and newborn health services in Sierra Leone
Authors: Jones Susan A , Gopalakrishnan Somasundari , Ameh Charles A , White Sarah , van den Broek Nynke R
Published: October 2016

Background

We sought to determine the impact of the Ebola virus epidemic on the availability, uptake and outcome of routine maternity services in Sierra Leone.

Methods

The number of antenatal and postnatal visits, institutional births, availability of emergency obstetric care (EmOC), maternal deaths and stillbirths were assessed by month, by districts and by level of healthcare for 10 months during, and 12 months prior to, the Ebola virus disease (EVD) epidemic. All healthcare facilities designated to provide comprehensive (n=13) or basic (n=67) EmOC across the 13 districts of Sierra Leone were included.

Results

Preservice students were not deployed during the EVD epidemic. The number of healthcare providers in facilities remained constant (incidence rate ratio (IRR) 1.03, 95% CI 1.00 to 1.07). Availability of antibiotics, oxytocics, anticonvulsants, manual removal of placenta, removal of retained products of conception, blood transfusion and caesarean section were not affected by the EVD epidemic. Across Sierra Leone, following the onset of the EVD epidemic, there was a 18% decrease in the number of women attending for antenatal (IRR 0.82, 95% CI 0.79 to 0.84); 22% decrease in postnatal attendance (IRR 0.78, 95% CI 0.75 to 0.80) visits and 11% decrease in the number of women attending for birth at a healthcare facility (IRR 0.89, 95% CI 0.87 to 0.91). There was a corresponding 34% increase in the facility maternal mortality ratio (IRR 1.34, 95% CI 1.07 to 1.69) and 24% increase in the stillbirth rate (IRR 1.24, 95% CI 1.14 to 1.35).

Conclusions

During the EVD epidemic, fewer pregnant women accessed healthcare. For those who did, an increase in maternal mortality and stillbirth was observed. In the post-Ebola phase, ‘readiness’ (or not) of the global partners for large-scale epidemics has been the focus of debate. The level of functioning of the health system with regard to ability to continue to provide high-quality effective routine care needs more attention.