bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractUnderstanding 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

AbstractEngineering 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.
Computational cognitive neuroscience: Model fitting should not replace model simulation
Authors: Palminteri Stefano , Wyart Valentin , Koechlin Etienne 
Published: October 2016

AbstractCognitive 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

AbstractDue 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

AbstractThe 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.Summary: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.
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

ABSTRACT

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

ABSTRACT

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

ABSTRACTBartonellaspp. 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

ABSTRACT

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

ABSTRACT

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

Abstract
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

Abstract
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 (&lt;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.