bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community structure – ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function
Authors: Meyer Kyle M. , Hopple Anya M. , Klein Ann M. , Morris Andrew H. , Bridgham Scott , Bohannan Brendan J. M. 
Published: May 2019

ABSTRACTBelowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here we argue that this stems from at least three issues: 1) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge, 2) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge and 3) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH4)-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and include environmental covariates in statistical analyses to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH4oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.
Dissection of central clock function inDrosophilathrough cell-specific CRISPR-mediated clock gene disruption
Authors: Delventhal Rebecca , Pantalia Meghan , O’Connor Reed M. , Ulgherait Matthew , Kim Han X. , Basturk Maylis , Canman Julie C. , Shirasu-Hiza Mimi 
Published: May 2019

AbstractInDrosophila, ~150 neurons expressing molecular clock proteins regulate circadian behavior. Sixteen of these clock neurons secrete the neuropeptide Pdf and have been called “master pacemakers” because they are essential for circadian rhythms. A subset of Pdf+neurons (the morning oscillator) regulates morning activity and communicates with other non-Pdf+neurons, including a subset called the evening oscillator. It is assumed that the molecular clock in Pdf+neurons is required for these functions. To test this, we developed and validated Gal4-UAS based CRISPR tools for cell-specific disruption of key molecular clock components,periodandtimeless. While loss of the molecular clock in both the morning and evening oscillators eliminates circadian locomotor activity, the molecular clock in either oscillator alone is sufficient for circadian locomotor activity. This suggests that clock neurons do not act in a hierarchy but as a distributed network to regulate circadian activity.
Diffuse TBI-induced expression of anxiety-like behavior coincides with altered glutamatergic function, TrkB protein levels and region-dependent pathophysiology in amygdala circuitry
Authors: Beitchman Joshua A. , Griffiths Daniel R. , Hur Yerin , Ogle Sarah B. , Hair Caitlin E. , Morrison Helena W. , Lifshitz Jonathan , Adelson P. David , Thomas Theresa Currier 
Published: May 2019

AbstractUp to 50% of traumatic brain injury (TBI) survivors demonstrate persisting affective symptoms indicative of limbic system dysregulation, yet the pathophysiology underlying the symptoms is unclear. We hypothesize that TBI-induced pathophysiologic changes within distinct amygdala nuclei contribute to the expression of late-onset anxiety-like behavior. Adult, male Sprague-Dawley rats underwent midline fluid percussion injury or sham surgery. Anxiety-like behavior was assessed at 7 and 28 days post-injury (DPI) followed by assessment of real-time glutamate neurotransmission in the basolateral amygdala (BLA) and central nucleus of the amygdala (CeA) using glutamate-selective microelectrode arrays. In separate animal cohorts, the presence of neuropathology, astrocytosis, and microglial activation were assessed at 1, 7, and 28DPI. Protein levels of glutamatergic transporters (Glt-1, GLAST) and presynaptic modulators of glutamate release (mGluR2, TrkB, BDNF, and glucocorticoid receptors) were quantified using automated capillary western techniques at 28DPI. The expression of anxiety-like behavior at 28DPI coincided with decreased glutamate release and slower glutamate clearance in the CeA, not BLA. Changes in glutamate neurotransmission were independent of protein levels of glutamate transporters and mGluR2 receptors, neuropathology, and astrocytosis. At 1DPI, microglia in the CeA demonstrated a neuroinflammatory response. BDNF and TrkB were decreased at 28DPI in the amygdala. These data indicate that diffuse axonal injury instigates sequences of molecular, structural and functional changes in the amygdala that contribute to circuit dysregulation relevant to the expression of affective disorders. Translationally, diffuse axonal injury can influence severity and incidence of affective symptoms and should be addressed in the history of patients with affective disorders.
Distinct sensorimotor feedback loops for dynamic and static control of primate precision grip
Authors: Oya Tomomichi , Takei Tomohiko , Seki Kazuhiko 
Published: May 2019

AbstractVolitional limb motor control involves dynamic and static muscle actions. It remains elusive how such distinct actions are controlled through separated or shared neural circuits. Here we explored the potential separation for dynamic and static controls in the primate hand actions, by investigating the neuronal coherence between local 1eld potentials (LFPs) of the spinal cord and the forelimb electromyographic activity (EMGs), and LFPs of the motor cortex and the EMGs during the performance of a precision grip in macaque monkeys. We observed the emergence of beta-range coherence with EMGs at spinal cord and motor cortex in the separated phases; spinal coherence during the grip phase and cortical coherence during the hold phase. Further, both of the coherence were influenced by bidirectional interactions with reasonable latencies as beta oscillatory cycles. These results indicate that dedicated feedback circuits comprising spinal and cortical structures underlie dynamic and static controls of dexterous hand actions.
Overexpression ofMedicago sativa glutamate-semialdehyde aminotransferase(GSA) gene in tobacco increased photosynthesis efficiency
Authors: Ghasemzadeh Maryam , Khozeai Mahdi , Amiri Hamzeh 
Published: May 2019

AbstractTo investigate the effect of increasedglutamate-semialdehyde aminotransferase (GSA)on photosynthetic capacity and growth, tobacco (Nicoliana tabacumL. Xanti) plants with increased levels of glutamate-semialdehyde aminotransferase protein were produced. This was achieved using a cassette composed of a full-lengthMedicago sativecDNA under the control of the cauliflower mosaic virus 35S promoter. The results revealed distinct impacts of GSA activity on photosynthesis rate and growth inGSAover expression tobacco plants. In transgenic plants with increased GSA activity, an increase in soluble and insoluble sugars accumulation was evident. Total biomass, leaf area, plant height and internode 3-4 were increased inGSAsense plants, compared with equivalent wild-type tobacco plants. Moreover, transgenic tobacco plants with increased GSA activity exhibit higher levels of 5-aminolevulinic acid (ALA) accumulation and increased in content of chlorophyll and carotenoids pigments. Collectively, our data suggest that higher level of GSA activity gives an advantage to photosynthesis, growth in tobacco plants. This work also provides a case study that an individual enzyme in the biosynthesis of chlorophyll pathway may serve as a useful target for genetic engineering to improve photosynthesis and growth in plants.HighlightOverexpression ofglutamate-semialdehyde aminotransferase (GSA) increasephotosynthetic capacity, growth in tobacco.
Root microbiota assembly and adaptive differentiation among European Arabidopsis populations
Authors: Thiergart Thorsten , Durán Paloma , Ellis Thomas , Garrido-Oter Ruben , Kemen Eric , Roux Fabrice , Alonso-Blanco Carlos , Ågren Jon , Schulze-Lefert Paul , Hacquard Stéphane 
Published: May 2019

SummaryFactors that drive continental-scale variation in root microbiota and plant adaptation are poorly understood. We monitored root-associated microbial communities in Arabidopsis thaliana and co-occurring grasses at 17 European sites across three years. Analysis of 5,625 microbial community profiles demonstrated strong geographic structuring of the soil biome, but not of the root microbiota. Remarkable similarity in bacterial community composition in roots of A. thaliana and grasses was explained by the presence of a few diverse and geographically widespread taxa that disproportionately colonize roots across sites. In a reciprocal transplant between two A. thaliana populations in Sweden and Italy, we uncoupled soil from location effects and tested their respective contributions to root microbiota variation and plant adaptation. The composition of the root microbiota was affected by location and soil origin, and to a lesser degree by host genotype. The filamentous eukaryotes were particularly strongly affected by location. Strong local adaptation between the two A. thaliana populations was observed, with difference in soil properties and microbes of little importance for the observed magnitude of adaptive differentiation. Our results suggest that, across large spatial scales, climate is more important than are soil conditions for plant adaptation and variation in root-associated filamentous eukaryotic communities.
A rationally designed and highly versatile epitope tag for nanobody-based purification, detection and manipulation of proteins
Authors: Götzke Hansjörg , Kilisch Markus , Martínez-Carranza Markel , Sograte-Idrissi Shama , Rajavel Abirami , Schlichthaerle Thomas , Engels Niklas , Jungmann Ralf , Stenmark Pål , Opazo Felipe , Frey Steffen 
Published: May 2019

AbstractSpecialized epitope tags are widely used for detecting, manipulating or purifying proteins, but often their versatility is limited. Here, we introduce the ALFA-tag, a novel, rationally designed epitope tag that serves an exceptionally broad spectrum of applications in life sciences while outperforming established tags like the HA, FLAG or myc tags. The ALFA-tag forms a small and stable α-helix that is functional irrespective of its position on the target protein in prokaryotic and eukaryotic hosts. We developed a nanobody (NbALFA) binding ALFA-tagged proteins from native or fixed specimen with low picomolar affinity. It is ideally suited for super-resolution microscopy, immunoprecipitations and Western blotting, and also allows in-vivo detection of proteins. By solving the crystal structure of the complex we were able to design a nanobody mutant (NbALFAPE) that permits efficient one-step purifications of native ALFA-tagged proteins, complexes and even entire living cells using peptide elution under physiological conditions.
Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure
Authors: Suma Antonio , Stopar Alex , Nicholson Allen W. , Castronovo Matteo , Carnevale Vincenzo 
Published: May 2019

ABSTRACTWe used coarse-grained molecular dynamics simulations to characterize the global and local mechanical properties of a DNA origami triangle nanostructure. The structure presents two metastable conformations separated by a free energy barrier that is lowered upon omission of four specific DNA staples (defect). In contrast, only one stable conformation is present upon removing eight staples. The metastability is explained in terms of the intrinsic conformations of the three trapezoidal substructures. We computationally modeled the local accessibility to endonucleases, to predict the reactivity of twenty sites, and found good agreement with the experimental data. We showed that global fluctuations affect local reactivity: the removal of the DNA staples increased the computed accessibility to a restriction enzyme, at sites as distant as 40nm, due to an increase in global fluctuation. These results raise the intriguing possibility of the rational engineering of allosterically modulated DNA origami.
Live-cell STED microscopy of mitochondrial cristae
Authors: Stephan Till , Roesch Axel , Riedel Dietmar , Jakobs Stefan 
Published: May 2019

AbstractMitochondria are highly dynamic organelles that exhibit a complex inner architecture. They exhibit a smooth outer membrane and a highly convoluted inner membrane that forms invaginations called cristae. Imaging cristae in living cells poses a formidable challenge for light microscopy. Relying on a cell line stably expressing the mitochondrial protein Cox8A fused to the SNAP-tag and using STED (stimulated emission depletion) super-resolution microscopy, we demonstrate the visualization of cristae dynamics in cultivated human cells.
Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells
Authors: Kohyama Shunshi , Yoshinaga Natsuhiko , Yanagisawa Miho , Fujiwara Kei , Doi Nobuhide 
Published: May 2019

AbstractMin system, which determines the cell division plane of bacteria, uses the localization change of protein (Min wave) emerged by a reaction-diffusion coupling. Although previous studies have shown that cell-sized space and boundaries modulate shape and speed of Min waves, its effects on Min wave emergence was still elusive. Here, by using a fully confined microsized space as a mimic of live cells, we revealed that confinement changes conditions for Min wave emergence. In the microsized space, an increase of surface-to-volume ratio changed the localization efficiency of proteins on membranes, and therefore, suppression of the localization change was necessary to produce stable Min wave generations. Furthermore, we showed that the cell-sized space more strictly limits parameters for wave emergence because confinement inhibits instability and excitability of the system. These results illuminate that confinement of reaction-diffusion systems works as a controller of spatiotemporal patterns in live cells.
Paraoxonase and acylated homoserine lactones in urine from patients with urinary tract infections
Authors: Lafleur John , Amdur Richard L. 
Published: May 2019

AbstractParaoxonases are mammalian enzymes that have a number of roles including the inhibition of bacterial virulence and biofilm formation by microorganisms that quorum sense with acylated homoserine lactones. Paraoxonases have previously been reported to inhibit P. aeruginosa biofilm formation in mammalian airways and skin. An innate immune role for paraoxonases in urinary tract infection has not previously been reported. We performed western blots for paraoxonase1 in urine from patients with urinary tract infection; we also tested urinary tract infection urine for the presence of acylated homoserine lactones using a cellular reporter system. We report here that paraoxonase1 was not found with our western blot assay in the urine of normal control patients; in those with urinary tract infection, paraoxonase1 was associated with E. coli UTI. Acylated homoserine lactones, but not paraoxonases, were found in the bulk urine of those with P. aeruginosa urinary tract infection. We hypothesize that paraoxonase may play a similar innate immune role in infected urine as has previously described in skin and airways.
Trypanosoma bruceiJ protein 2 functionally cooperates with the cytosolic Hsp70.4 and Hsp70 proteins
Authors: Bentley Stephen J. , Boshoff Aileen 
Published: May 2019

AbstractThe etiological agent of African trypanosomiasis,Trypanosoma brucei, has been identified to possess an expanded and diverse group of heat shock proteins, that have been implicated in cytoprotection, differentiation, and subsequently progression and transmission of the disease. Heat shock protein 70 is a highly conserved and ubiquitous molecular chaperone that is important in maintaining protein homeostasis in the cell. Its function is regulated by a wide range of co-chaperones; and inhibition of these functions and interactions with co-chaperones are emerging as potential therapeutic targets for numerous diseases. This study sought to biochemically characterize the cytosolic Hsp70 and Hsp70.4 proteins and to investigate if they form a functional partnership with the Type I J-protein, Tbj2. The cytosolic localisation of the proteins was confirmed by accessing the TrypTag endogenous tagging microscopy database. Expression of TbHsp70 was shown to be heat inducible, whilst TbHsp70.4 was constitutively expressed. The basal ATPase activities of TbHsp70.4 and TbHsp70 were stimulated by Tbj2. It was further determined that Tbj2 forms a functional partnership with TbHsp70 and TbHsp70.4 as the J-protein was shown to stimulate the ability of both proteins to mediate the refolding of chemically denatured β-galactosidase. This study provides further insight into this important class of proteins which may contribute to the development of new therapeutic strategies to combat African Trypanosomiasis.
Landscape of tumor-infiltrating immune cells in human immunogenic cancers:B cells are inversely associated with CD8T cells, but positively correlated with Treg cells
Authors: Chae Young Kwang , Bae William Han , Jung Minji , Kim Young Suk , Anker Jonathan Forrest , Tamragouri Keerthi , Matsangou Maria , Giles Francis Joseph 
Published: May 2019

AbstractThe composition of tumor-infiltrating immune cells may be a strong predictor of cancer treatment responses and survival outcomes. While B cells have been suggested to suppress T cell cytotoxicity in preclinical studies, it has been less understood whether B cells will exert immune-regulatory roles in human cancers. We explored immune cell landscapes in six human immunogenic cancers, including bladder cancer, head and neck cancer, lung adenocarcinoma, lung squamous cell carcinoma, melanoma, and renal cell carcinoma by calculating gene expression patterns of immune cell-specific metagenes in a total of 2951 cancers. We demonstrated that tumor-infiltrating activated B cells was correlated with regulatory T cell (Treg) infiltration, but had an inverse association with activated CD8 T cell infiltration consistently across all six human cancers. Tumors infiltrated by activated B cells (ActB+ tumors) demonstrated an elevated expression of regulatory cytokines and immune checkpoints, compared to tumors without infiltration by activated B cells (ActB-tumors). Activated B infiltration was not significantly associated with survival outcomes.PrécisThis human cancer tissue analysis showed that tumor infiltration by activated B cells correlates with decreased infiltration by activated CD8 T cells in immunogenic solid tumors, implicating B cell inhibition may enhance T cell-mediated cytotoxicity.
A general approach for identifying protein epitopes targeted by antibody repertoires using whole proteomes
Authors: Paull Michael L. , Johnston Tim , Ibsen Kelly N. , Bozekowski Joel D. , Daugherty Patrick S. 
Published: May 2019

AbstractAntibodies are essential to functional immunity, yet the epitopes targeted by antibody repertoires remain largely uncharacterized. To aid in characterization, we developed a generalizable strategy to identify antibody-binding epitopes within individual proteins and entire proteomes. Specifically, we selected antibody-binding peptides for 273 distinct sera out of a random library and identified the peptides using next-generation sequencing. To identify antibody-binding epitopes and the antigens from which these epitopes were derived, we tiled the sequences of candidate antigens into short overlapping subsequences of length k (k-mers). We used the enrichment over background of these k-mers in the antibody-binding peptide dataset to identify antibody-binding epitopes. As a positive control, we used this approach, termed K-mer Tiling of Protein Epitopes (K-TOPE), to identify epitopes targeted by monoclonal and polyclonal antibodies of well-characterized specificity, accurately recovering their known epitopes. K-TOPE characterized a commonly targeted antigen fromRhinovirus A, identifying three epitopes recognized by antibodies present in 83% of sera (n = 250). An analysis of 2,908 proteins from 400 viral taxa that infect humans revealed seven enterovirus epitopes and five Epstein-Barr virus epitopes recognized by >30% of specimens. Analysis ofStaphylococcusandStreptococcusproteomes similarly revealed six epitopes recognized by >40% of specimens. These common viral and bacterial epitopes exhibited excellent agreement with previously mapped epitopes. Additionally, we identified 30 HSV2-specific epitopes that were 100% specific against HSV1 in novel and previously reported antigens. The K-TOPE approach thus provides a powerful new tool to elucidate the organisms, antigens, and epitopes targeted by human antibody repertoires.
Mediterranean Diet adherence in emerging adults in Izmir
Authors: Genc Mahmut , Genc Seda 
Published: May 2019

Purpose
The purpose of this paper is to evaluate the adherence and abandonment of the Turkish emerging adults in an Izmir University located at western Mediterranean coast of Turkey and to assess potential associations with anthropometric characteristics.

Design/methodology/approach
A cross-sectional survey (n=494, 18–27 years) carried out in 2017 among emerging adults in University. KIDMED Index was used to assess the degree of adherence Mediterranean Diet (MedDiet). The associations of KIDMED scores with demographic, residency and anthropometric were separately reported. The data were collected through standardized questionnaires directly from participants.

Findings
The average KIDMED score was calculated 4.86±2.5. Optimum adherence to the MedDiet was found only in 13.0 percent of participants, whereas 32.6 percent had poor adherence levels. Considering self-reported anthropometric data, the BMI values of the population was calculated as 22.3±3.9 kg/m2. In population, 13.9 percent of the subjects were underweight, while 16.0 percent were overweight and 3.9 percent obese. A significant association was found between BMI and KIDMED scores both in genders and residency.

Originality/value
This is the first study reporting the level of adherence to the MedDiet among Turkish emerging adults in terms of residency during education and the first KIDMED study conducted in Izmir located at Aegean Sea. The results support previously proposed transition concept by several scholar from different Mediterranean countries: it was found that only 13 percent of young adults having desired dietary habits in an Aegean city with local traditional cuisine highly affected by Cretan cuisine. These results are significant for University managements and health authorities in order to take actions for returning this transition contrariwise beginning with these groups.