bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is graphite lithiophobic or lithiophilic?
Authors: Duan Jian , Zheng Yuheng , Luo Wei , Wu Wangyan , Wang Tengrui , Xie Yong , Li Sa , Li Ju , Huang Yunhui 
Published: December 2019

Abstract
Graphite and lithium metal are two classic anode materials and their composite has shown promising performance for rechargeable batteries. However, it is generally accepted that Li metal wets graphite poorly, causing its spreading and infiltration difficult. Here we show that graphite can either appear superlithiophilic or lithiophobic, depending on the local redox potential. By comparing the wetting performance of highly ordered pyrolytic graphite, porous carbon paper (PCP), lithiated PCP and graphite powder, we demonstrate that the surface contaminants that pin the contact-line motion and cause contact-angle hysteresis have their own electrochemical-stability windows. The surface contaminants can be either removed or reinforced in a time-dependent manner, depending on whether the reducing agents (C6→LiC6) or the oxidizing agents (air, moisture) dominate in the ambient environment, leading to bifurcating dynamics of either superfast or superslow wetting. Our findings enable new fabrication technology for Li–graphite composite with a controllable Li-metal/graphite ratio and present great promise for the mass production of Li-based anodes for use in high-energy-density batteries.
An experimental workflow identifies nitrogenase proteins ready for expression in plant mitochondria
Authors: Okada S. , Gregg C. M. , Allen R. S. , Menon A. , Hussain D. , Gillespie V. , Johnston E. , Byrne K. , Colgrave M. , Wood C. C. 
Published: December 2019

AbstractIndustrial nitrogen fertilizer is intrinsic to modern agriculture yet expensive and environmentally harmful. We aim to reconstitute bacterial nitrogenase function within plant mitochondria to reduce nitrogen fertilizer usage. Many nitrogen fixation (Nif) proteins are required for biosynthesis and function of the mature nitrogenase enzyme, and these will need to be correctly processed and soluble within mitochondria as a pre-requisite for function. Here we present our workflow that assessed processing, solubility and relative abundance of 16Klebsiella oxytocaNif proteins targeted to the plant mitochondrial matrix using an Arabidopsis mitochondrial targeting peptide (MTP). The functional consequence of the N-terminal modifications required for mitochondrial targeting of Nif proteins was tested using bacterial nitrogenase assays. We found that despite the use of the same constitutive promoter and MTP, MTP::Nif processing and relative abundance in plant leaf varied considerably. Assessment of solubility for all MTP::Nif proteins found NifF, M, N, S, U, W, X, Y and Z were soluble, while NifB, E, H, J, K, Q and V were mostly insoluble. Although most Nif proteins tolerated the N-terminal extension as a consequence of mitochondrial processing, this extension in NifM reduced nitrogenase activity to 10% of controls. Using proteomics, we detected a ∼50-fold increase in the abundance of NifM when it contained the N-terminal MTP extension, which may account for this reduction seen in nitrogenase activity. Based on plant mitochondrial processing and solubility, and retention of function in a bacterial assay, our workflow has identified that NifF, N, S, U, W, Y and Z satisfied all these criteria. Future work can now focus on improving these parameters for the remaining Nif components to assemble a complete set of plant-ready Nif proteins for reconstituting nitrogen fixation in plant mitochondria.
Separation of Bioactive Small Molecules, Peptide from Natural Products and Proteins from Pathogenic Microbe by Rotofor-based Preparative Isoelectric Focusing (IEF) Method
Authors: Veerapandian Raja , Paudyal Anuja , Chang Adeline , Vediyappan Govindsamy 
Published: December 2019

AbstractThe primary purpose of purifying the bioactive small molecules is obtaining enough amount of specific molecules for their downstream applications. There are various methods available for serving this purpose. However, not all can afford for cost-effective purification methods, especially for complex biological samples. Here we demonstrate, the Rotofor based preparative IEF separation which shows the high possibility of separating and enriching desired molecules, including small molecules and peptides from the complex plant extract. This method is well-suited for use at any stage of a purification scheme and has been used for complex biological samples quantification and characterization. As a proof of concept, we fractionatedGymnema sylvestreplant extract and isolated a family of terpenoid saponin molecules at the acidic end and small peptide molecule near the basic end. To our knowledge, this is a first report that Rotofor can be used to fractionate bioactive small molecules from natural product sources. We also showed effective microbial protein separation usingCandida albicansfungus as a model system. The Rotofor based IEF has appealing features such as low cost, simplicity, high application potential and can be performed in any laboratory with the instrument setup.
Capture and visualization of liveMycobacterium tuberculosisbacilli from tuberculosis bioaerosols
Authors: Dinkele Ryan , Gessner Sophia , Koch Anastasia S. , Morrow Carl , Gqada Melitta , Kamariza Mireille , Bertozzi Carolyn R. , Smith Brian , McLoud Courtney , Kamholz Andrew , Bryden Wayne , Call Charles , Mizrahi Valerie , Wood Robin , Warner Digby F. 
Published: December 2019

AbstractThe tuberculosis (TB) pandemic demands urgent interventions such as those designed to interruptMycobacterium tuberculosis(Mtb) transmission, a challenge exacerbated by our poor understanding of the events enabling successful transfer of infectious bacilli between hosts. To address this problem, we developed the Respiratory Aerosol Sampling Chamber (RASC), a personal clean-room equipped with high-efficiency filtration and sampling technologies that allow biosafe capture and isolation of particulate matter – includingMtbbacilli – released by patients during natural breathing and (non-induced) cough. Here, we demonstrate the use of DMN-trehalose labelling to detect and quantify liveMtbbacilli among complex bioaerosol samples arrayed in a bespoke nanowell device following capture in the RASC. A pilot study identifiedMtbin more than 85 % of known TB patients, improving significantly on previous work which has relied on animal infection and cough sampling to estimate transmission events. Moreover, intra-patient comparisons of bioaerosol and sputum samples indicated thatMtbaerosols likely derive from a compartment other than sputum. These results support the utility of the RASC platform for research aimed at interruptingMtbtransmission, including the non-invasive detection ofMtb-infected individuals who are predicted to contribute to bacillary spread despite the absence of clinical symptoms.
A genome wide analysis ofEscherichia coliresponses to fosfomycin using TraDIS-Xpress reveals novel roles for phosphonate and phosphate transport systems
Authors: Yasir Muhammad , Turner Keith , Bastkowski Sarah , Charles Ian , Webber Mark A. 
Published: December 2019

AbstractFosfomycin is an antibiotic which has seen a revival in use due to its unique mechanism of action and resulting efficacy against isolates resistant to many other antibiotics. Mechanisms of resistance have been elucidated and loss of function mutations within the genes encoding the sugar importers, GlpT and UhpT are commonly selected for by fosfomycin exposure inE. coli. There has however not been a genome wide analysis of the basis for fosfomycin sensitivity reported to date. Here we used ‘TraDIS-Xpress’ a high-density transposon mutagenesis approach to assay the role of all genes inE. coliin fosfomycin sensitivity. The data confirmed known mechanisms of action and resistance as well as identifying a set of novel loci involved in fosfomycin sensitivity. The assay was able to identify sub domains within genes of importance and also revealed essential genes with roles in fosfomycin sensitivity based on expression changes. Novel genes identified included those involved in glucose metabolism, the phosphonate import and breakdown system,phnC-Mand the phosphate importer,pstSACB. The impact of these genes in fosfomycin sensitivity was validated by measuring the susceptibility of defined inactivation mutants. This work reveals a wider set of genes contribute to fosfomycin sensitivity including core sugar metabolism genes and two transport systems previously unrecognised as having a role in fosfomycin sensitivity. The work also suggests new routes by which drugs with a phosphonate moiety may be transported across the inner membrane of Gram-negative bacteria.ImportanceThe emergence and spread of antibiotic resistant bacteria had resulted in increased use of alternative drugs which retain efficacy against isolates resistant to other classes of drugs. One example is fosfomycin; an old drug which has found greatly increased use in recent years. We studied the mechanisms of fosfomycin resistance by applying a genome wide screen based on comparing the fitness of a massive library of transposon mutants in the presence of fosfomycin. This approach identified the previously known mechanisms of resistance but also identified a number of new pathways which contribute to fosfomycin sensitivity including two importer systems. This information advances our knowledge about an increasingly important antibiotic and identifies new potential routes to resistance.
A method to determine the double bond position in unsaturated fatty acids by solvent plasmatization using liquid chromatography-mass spectrometry
Authors: Takashima Shigeo , Toyoshi Kayoko , Yamamoto Takuhei , Shimozawa Nobuyuki 
Published: December 2019

AbstractFatty acids (FAs) are the central components of life: they constitute biological membranes in the form of lipid, act as signaling molecules, and are used as energy sources. FAs are classified according to their chain lengths and the number and position of carbon-carbon double bond, and their physiological character is largely defined by these structural properties. Determination of the precise structural properties is crucial for characterizing FAs, but pinpointing the exact position of carbon-carbon double bond in FA molecules is challenging. Herein, a new analytical method is reported for determining the double bond position of mono- and poly-unsaturated FAs using liquid chromatography-mass spectrometry (LC-MS) coupled with solvent plasmatization. With the aid of plasma on ESI capirally, epoxidation or peroxidation of carbon-carbon double bond in FAs is facilitated. Subsequently, molecular fragmentation occurs at or beside the epoxidized or peroxidized double bond via collision-induced dissociation (CID), and the position of the double bond is elucidated. In this method, FAs are separated by LC, modified by plasma, fragmented via CID, and detected using a time-of-flight mass spectrometer in a seamless manner such that the FA composition in a mixture can be determined. Our method enables thorough characterization of FA species with distinguishing multiple isomers, and therefore can uncover the true diversity of FAs for their application in food, health, and medical sciences.
Redox-mediated regulation of a labile, evolutionarily conserved cross-β structure formed by the TDP43 low complexity domain
Authors: Lin Yi , Zhou Xiaoming , Kato Masato , Liu Daifei , Ghaemmaghami Sina , Tu Benjamin P. , McKnight Steven L. 
Published: December 2019

SummaryAn evolutionarily conserved low complexity (LC) domain is found within a 152 residue segment localized to the carboxyl-terminal region of the TDP43 RNA-binding protein. This TDP43 LC domain contains ten conserved methionine residues. Self-association of this domain leads to the formation of liquid-like droplets composed of labile, cross-β polymers. Exposure of polymers to low concentrations of H2O2leads to a phenomenon of droplet melting that can be reversed upon exposure of the oxidized protein to the MsrA and MsrB methionine sulfoxide reductase enzymes, thioredoxin, thioredoxin reductase and NADPH. Morphological features of the cross-β polymers were revealed by a method of H2O2-mediated footprinting. Similar TDP43 LC domain footprints were observed in highly polymerized, hydrogel samples, liquid-like droplet samples, and living cells. The ability of H2O2to impede cross-β polymerization was abrogated by a prominent ALS-causing mutation that changes methionine residue 337 to valine. These observations offer potentially useful insight into the biological role of TDP43 in facilitating synapse-localized translation, as well as aberrant aggregation of the protein in neurodegenerative disease.
Interactive mapping of language and memory with the GE2REC protocol
Authors: Banjac Sonja , Roger Elise , Cousin Emilie , Perrone-Bertolotti Marcela , Haldin Célise , Pichat Cédric , Lamalle Laurent , Minotti Lorella , Kahane Philippe , Baciu Monica 
Published: December 2019

AbstractPrevious studies have highlighted the importance of considering cognitive functions in a dynamic and interactive perspective and multiple evidence was brought for a language and memory interaction. In this study performed in healthy participants, we developed a new protocol entitled GE2REC that interactively accesses the neural representation of language-and-memory network. This protocol consists of three runs related to each other, providing a link between tasks, in order to assure an interactive measure of linguistic and episodic memory processes. GE2REC consists of a sentence generation (GE) in auditory modality and two recollecting (2REC) memory tasks, one recognition performed in visual modality, and another one recall performed in auditory modality. Its efficiency was evaluated in 20 healthy volunteers using a 3T MR imager. Our results corroborate the ability of GE2REC to robustly activate a fronto-temporo-parietal language network as well as temporal mesial, prefrontal and parietal cortices during encoding and recognition. GE2REC is useful because: (a) requires simultaneous and interactive language-and-memory processes and jointly maps their neural basis; (b) explores encoding and retrieval, managing to elicit activation of mesial temporal structures; (c) is short and easy to perform, hence being suitable for more restrictive settings, and (d) has an ecological dimension of tasks and stimuli. Overall, GE2REC can provide valuable information in terms of the practical foundation of exploration language and memory interconnection.
Disconnectome Associated with Progressive Ischemic Periventricular White Matter Lesions
Authors: Li Zhengjun , Dolui Sudipto , Habes Mohamad , Bassett Danielle S. , Wolk David , Detre John A. 
Published: December 2019

AbstractPeriventricular white matter (PVWM) hyperintensities on T2-weighted MRI are ubiquitous in older adults and associated with dementia. Efforts to determine how PVWM lesions impact structural connectivity to impinge on brain function remain challenging in part because white matter tractography algorithms for diffusion tensor imaging (DTI) may lose fidelity in the presence of lesions. We used a “virtual lesion” approach to characterize the “disconnectome” associated with periventricular white matter (PVWM) lesions. We simulated progressive ischemic PVWM lesions using sub-threshold cerebral blood flow (CBF) masks derived from a previously published group-averaged map acquired from N=436 middle aged subjects in which the lowest CBF values were seen in PVWM and morphologically recapitulated the spatial pattern of PVWM hyperintensities seen in typical aging. We mimicked the age-dependent evolution of PVWM lesion burden by varying the threshold applied to the CBF map. We found that the optic radiations, inferior fronto-occipital fasciculus, inferior longitudinal fasciculus, corpus callosum, temporopontine tract and fornix were affected in early simulated PVWM lesion burdens, and that the connectivity of subcortical, cerebellar, and visual regions were significantly disrupted with increasing simulated PVWM lesion burdens. We also validated the use of virtual lesions to simulate the disconnectome due to WM hyperintensities in a cognitively normal elderly cohort (N=46) by evaluating correlations between structural and functional connectomes. The virtual lesion approach provides new insights into the spatial-temporal changes of the brain structural connectome under progressive PVWM burdens during normal aging.Significance StatementWe determined the disconnectomes caused by periventricular white matter (PVWM) lesions using the “virtual lesion” approach. We validated the approach using lesions, DTI and resting-state fMRI data from elderly subjects. We simulated disconnectome of progressive PVWM lesions using cerebral blood flow (CBF) masks in PVWM region with normative DTI data, which provides specificity for an ischemic mechanism and begins to address the possibility that connectivity may be affected by reduced CBF prior to the development of overt lesions on T2-weighted FLAIR MRI. The current study presented new insights into the spatial-temporal evolutions of the brain structural connectome under progressive PVWM burdens under normal aging.
G-domain prediction across the diversity of G protein families
Authors: Sanghavi Hiral M. , Rashmi Richa , Dasgupta Anirban , Majumdar Sharmistha 
Published: December 2019

AbstractGuanine nucleotide binding proteins are characterized by a structurally and mechanistically conserved GTP-binding domain, indispensable for binding GTP. The G domain comprises of five adjacent consensus motifs called G boxes, which are separated by amino acid spacers of different lengths. Several G proteins, discovered over time, are characterized by diverse function and sequence. This sequence diversity is also observed in the G box motifs (specifically the G5 box) as well as the inter-G box spacer length. The Spacers and Mismatch Algorithm (SMA) introduced in this study, can predict G-domains in a given G protein sequence, based on user-specified constraints for approximate G-box patterns and inter-box gaps in each G protein family. The SMA parameters can be customized as more G proteins are discovered and characterized structurally. Family-specific G box motifs including the less characterized G5 motif as well as G domain boundaries were predicted with higher precision. Overall, our analysis suggests the possible classification of G protein families based on family-specific G box sequences and lengths of inter-G box spacers.Significance StatementIt is difficult to define the boundaries of a G domain as well as predict G boxes and important GTP-binding residues of a G protein, if structural information is not available. Sequence alignment and phylogenetic methods are often unsuccessful, given the sequence diversity across G protein families. SMA is a unique method which uses approximate pattern matching as well as inter-motif separation constraints to predict the locations of G-boxes. It is able to predict all G boxes including the less characterized G5 motif which marks the carboxy-terminal boundary of a G domain. Thus, SMA can be used to predict G domain boundaries within a large multi-domain protein as long as the user-specified constraints are satisfied.ClassificationBiological Sciences/Biophysics and Computational Biology
Chloroplast SRP43 subunit Prevents Aggregation of Proteins
Authors: Furr Mercede , Okoto Patience , Moradi Mahmoud , Heyes Colin , Henry Ralph , Suresh Kumar Thallapuranam Krishnaswamy 
Published: December 2019

AbstractIntegration of light-harvesting chlorophyll binding proteins into the thylakoid membrane requires a specific chaperone, being the cpSRP43 subunit, of the signal recognition particle pathway in chloroplasts. cpSRP43, unique to the chloroplast, is responsible for transport of LHCPs through the stroma as well as assisting in the correct folding, assembly and disaggregation of these proteins for the acquisition of light energy. cpSRP43 is a highly flexible, multidomain protein capable of binding distinct partners in the cpSRP pathway. cpSRP43 is an irreplaceable component, necessary for the accurate and successful integration of LHCPs. It can act as a disaggregase without any input of external energy. Its action is based on the ability to associate with variable regions of different proteins owing to the domains and flexibility within its distinctive structure. Understanding the unique capabilities of cpSRP43 in the chloroplast begs the question of its usefulness outside of the plant cell, as well as its yet unknown roles still within the plant cell. Although the capabilities of cpSRP43 as a hub protein, adept to binding many unknown partners, has been alluded to in other works, it has yet to be thoroughly investigated. In this study we discover that cpSRP43 can act as a generic chaperone for proteins other than LHCP/not native to the chloroplast. The high thermal stability of cpSRP43 has been demonstrated in the previous chapter by its ability to retain its secondary structure as well as withstand aggregation upon heating and cooling cycles as confirmed by absorbance, intrinsic tryptophan fluorescence and far UV circular dichroism spectroscopy. This property gives cpSRP43 the basis to act as a generic chaperone and provide protection like that of typical heat shock proteins. Carbonic anhydrase, Concanavalin A and hFGF1 (acidic human fibroblast growth factor), were selected as candidates for chaperoning activity by cpSRP43. In all three cases, heat-induced aggregation of the candidate protein was either eliminated or significantly reduced in the presence of cpSRP43. In the case of hFGF1, the bioactivity was preserved after heat-treatment in the presence of cpSRP43. We have proposed a mechanism by which cpSRP43 is able to execute this action however further investigation is warranted to determine the exact mechanism(s) which may vary dependent on the target protein.
No title, no theme: The joined neural space between speakers and listeners during production and comprehension of multi-sentence discourse
Authors: Heidlmayr Karin , Weber Kirsten , Takashima Atsuko , Hagoort Peter 
Published: December 2019

AbstractSpeakers and listeners usually interact in larger discourses than single words or even single sentences. The goal of the present study was to identify the neural bases reflecting how the mental representation of the situation denoted in a multi-sentence discourse (situation model) is constructed and shared between speakers and listeners. An fMRI study using a variant of the ambiguous text paradigm was designed. Speakers produced ambiguous texts in the scanner and listeners subsequently listened to these texts in different states of ambiguity: preceded by a highly informative, intermediately informative or no title at all. Conventional BOLD activation analyses in listeners, as well as inter-subject correlation analyses between the speakers’ and the listeners’ hemodynamic time courses were performed. Critically, only the processing of disambiguated, coherent discourse with an intelligible situation model representation involved (shared) activation in bilateral lateral parietal and medial prefrontal regions. This shared spatiotemporal pattern of brain activation between the speaker and the listener suggests that the process of memory retrieval in medial prefrontal regions and the binding of retrieved information in the lateral parietal cortex constitutes a core mechanism underlying the communication of complex conceptual representations.