bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graphene-enabled, spatially controlled electroporation of adherent cells for live-cell super-resolution microscopy
Authors: Moon Seonah , Li Wan , Xu Ke 
Published: May 2019

AbstractThe incorporation of exogenous molecules into live cells is essential for both biological research and therapeutic applications. In particular, for the emerging field of super-resolution microscopy of live mammalian cells, reliable fluorescent labeling of intracellular targets remains a challenge. Here, utilizing the unique mechanical, electrical, and optical properties of graphene, a single layer of bonded carbon atoms, we report a facile approach that enables both high-throughput delivery of fluorescent probes into adherent live cells andin situsuper-resolution microscopy on the same device. ∼90% delivery efficiencies are achieved for free dyes and dye-tagged affinity probes, short peptides, and whole antibodies, thus enabling high-quality super-resolution microscopy. Moreover, we demonstrate excellent spatiotemporal controls, which, in combination with the ready patternablity of graphene, allow for the spatially selective delivery of two different probes for cells at different locations on the same substrate. We thus open up a new pathway to the microscopic manipulation and visualization of live cells.
Evolution of vascular plants through redeployment of ancient developmental regulators
Authors: van ’t Wout Hofland Nicole , Lu Kuan-Ju , Mor Eliana , Mutte Sumanth , Abrahams Paul , Kato Hirotaka , Vandepoele Klaas , Weijers Dolf , De Rybel Bert 
Published: May 2019

AbstractVascular plants provide most of the biomass, food and feed on earth; yet the molecular innovations that led to the evolution of their conductive tissues are unknown. Here, we reveal the evolutionary trajectory for the heterodimeric TMO5/LHW transcription factor complex, which is rate-limiting for vascular cell proliferation in Arabidopsis thaliana. Both regulators have origins predating vascular tissue emergence, and even terrestrialization. We further show that TMO5 evolved its modern function, including dimerization with LHW, at the origin of land plants. A second innovation in LHW, coinciding with vascular plant emergence, conditioned obligate heterodimerization and generated the critical function in vascular development. In summary, our results suggest that division potential of vascular cells may have been a major driver in the evolution of vascular plants.
Epigenetic loss of heterozygosity of Apc and an inflammation-associated mutational signature detected in Lrig1+/--driven murine colonic adenomas
Authors: Preston Jessica 
Published: May 2019

AbstractMurine colonic adenomas induced by the loss of a single copy of the tumor suppressor gene Apc in Lrig1+/- expressing progenitor cells grow rapidly, with high penetrance and tumor multiplicity. This study investigates the prevalence of intertumoral genetic heterogeneity and phenotypic variation across tumors, and attempts to identify the genomic cause of the unusual phenotype. Adult Lrig1-CreERT2/+; Apc-flox/+ mice were intraperitoneal injected with 2mg tamoxifen for 3 consecutive days which induced highly penetrant, dysplastic adenomas in the distal colon ∼100 days later. Whole tumors (n=14) from 8 mice were excised and tumor exome DNA and mRNA were sequenced. Somatic mutations present in the tumor exome DNA were compared with adjacent normal colon (n=9 tumors from 3 mice). Putative somatic mutations were called after stringent filtering using SeuratSomatic, a Genome Analysis Toolkit software module. RNA-Seq was performed on tumor mRNA (n=5 tumors from 5 mice) compared to wildtype colon (n=3). Differential gene expression was profiled using the R package DESeq2. Copy number variations and splicing defects were assessed using custom tracks on the UCSC genome browser.Adenomas resulting from the loss of Apc in Lrig1+/-- expressing colonic progenitor cells are genetically heterogeneous and hypermutated, containing ∼25-30 high-quality somatic mutations per megabase. A loss of heterozygosity of Apc was not observed in the tumor genomes, however evidence of an epigenetic loss of heterozygosity was readily apparent in the tumor transcriptome. The tumors display a strong bias toward G: C > A: T point mutations, which are a signature of guanine adducts, associated with tobacco tar and H. pylori infections. Putative tumor-driving mutations were detected and thousands of differentially expressed genes were identified including several UDP glucuronosyltransferases. Abnormal splicing patterns characterized by a loss of intron retention were detected in several RNA-binding genes throughout the tumor transcriptome. The widespread defects in gene expression, genomic stability, and splicing patterns implies that an early epigenetic loss of Apc in Lrig1+/--expressing progenitor cells causes a rapid formation of guanine adducts and a corresponding accumulation of mutation C>A point mutations. This study demonstrates that randomly-appearing oncogenic mutations can become fixed into a latent genomic reservoir prior to advanced disease.
Systematic exploration of protein conformational space using a Distance Geometry approach
Authors: Malliavin Thérèse E. , Mucherino Antonio , Lavor Carlile , Liberti Leo 
Published: May 2019

AbstractThe optimisation approaches classically used during the determination of protein structure encounter various diffculties, specially when the size of the conformational space is large. Indeed, in such case, algorithmic convergence criteria are more difficult to set up. Moreover, the size of the search space makes it difficult to achieve a complete exploration. The interval Branch-and-Prune (iBP) approach, based on the reformulating of the Distance Geometry Problem (DGP) provides a theoretical frame for the generation of protein conformations, by systematically sampling the conformational space. When an appropriate subset of inter-atomic distances is known exactly, this worst-case exponential-time algorithm is provably complete and fixed-parameter tractable. These guarantees, however, immediately disappear as distance measurement errors are introduced. Here we propose an improvement of this approach: the threading-augmented interval Branch-and-Prune (TAiBP), where the combinatorial explosion of the original iBP approach arising from its exponential complexity is alleviated by partitioning the input instances into consecutive peptide fragments and by using Self-Organizing Maps (SOMs) to obtain clusters of similar solutions. A validation of the TAiBP approach is presented here on a set of proteins of various sizes and structures. The calculation inputs are: a uniform covalent geometry extracted from force field covalent terms, the backbone dihedral angles with error intervals, and a few long-range distances. For most of the proteins smaller than 50 residues and interval widths of 20°, the TAiBP approach yielded solutions with RMSD values smaller than 3 Å with respect to the initial protein conformation. The efficiency of TAiBP approach for proteins larger than 50 residues will require the use of non-uniform covalent geometry, and may have benefits from the recent development of residue-specific force-fields.
Unfolded protein-independent IRE1 activation contributes to multifaceted developmental processes in Arabidopsis
Authors: Mishiba Kei-ichiro , Iwata Yuji , Mochizuki Tomofumi , Matsumura Atsushi , Nishioka Nanami , Hirata Rikako , Koizumi Nozomu 
Published: May 2019

AbstractAs an initial step for the unfolded protein response (UPR) pathway, the luminal domain of inositol requiring enzyme 1 (IRE1) senses unfolded proteins in the endoplasmic reticulum (ER). Recent findings in yeast and metazoans suggest alternative IRE1 activation without the sensor domain, although its mechanism and physiological significance remain to be elucidated. In Arabidopsis, the IRE1A and IRE1B double mutant (ire1a/b) is unable to activate cytoplasmic splicing of bZIP60 mRNA and regulated IRE1-dependent decay (RIDD) under ER stress, while the mutant does not exhibit severe developmental defects and is fertile under non-stress conditions. In this study, we focused on a third Arabidopsis IRE1 gene, designated as IRE1C, whose product lacks a sensor domain. We found that even though ire1c and ire1a/c mutants did not exhibit defective bZIP60 splicing and RIDD under ER stress, the ire1a/b/c triple mutant is lethal. Heterozygous IRE1C (ire1c/+) mutation in the ire1a/b mutants resulted in growth defects and reduction of the number of pollen grains. Genetic analysis revealed that IRE1C is required for male gametophyte development in the ire1a/b mutant background. Expression of a mutant form of IRE1B that lacks the luminal sensor domain (ΔLD) in the ire1a/b mutant did not complement defects in ER stress-dependent bZIP60 splicing and RIDD. Nevertheless, expression of ΔLD complemented a developmental defect in the male gametophyte in ire1a/b/c haplotype. In vivo, the ΔLD protein was activated by glycerol treatment that increases the composition of saturated lipid and was able to activate RIDD but not bZIP60 splicing. Phenotypes of IRE1B mutants lacking the sensor domain produced by CRISPR/Cas9-mediated gene editing in the ire1a/c mutant background were essentially same as those of ΔLD-expressing ire1a/b mutant. These observations suggest that IRE1 contributes to plant development, especially male gametogenesis, using an alternative activation mechanism that bypasses the unfolded protein-sensing luminal domain.
Selective Affimers Recognize BCL-2 Family Proteins Through Non-Canonical Structural Motifs
Authors: Miles Jennifer A. , Hobor Fruzsina , Taylor James , Tiede Christian , Rowell Philip R. , Trinh Chi H. , Jackson Brian , Nadat Fatima , Kyle Hannah F. , Wicky Basile I. M. , Clarke Jane , Tomlinson Darren C. , Wilson Andrew J. , Edwards Thomas A. 
Published: May 2019

AbstractThe BCL-2 family is a challenging set of proteins to target selectively due to sequence and structural homologies across the family. Selective ligands for the BCL-2 family regulators of apoptosis are desirable as probes to understand cell biology and apoptotic signalling pathways, and as starting points for inhibitor design. We have used phage display to isolate Affimer reagents (non-antibody binding proteins based on a conserved scaffold) to identify ligands for MCL-1, BCL-xL, BCL-2, BAK and BAX, then used multiple biophysical characterisation methods to probe the interactions. We established that purified Affimers elicit selective and potent recognition of their target BCL-2 protein. For anti-apoptotic targets, competitive inhibition of their canonical protein-protein interactions is demonstrated. Co-crystal structures reveal an unprecedented mode of molecular recognition; where a BH3 helix is normally bound, flexible loops from the Affimer dock into the BH3 binding cleft. Moreover, the Affimers induce a change in the target proteins towards a desirable drug bound like conformation. These results indicate Affimers can be used as alternative templates to inspire design of selective BCL-2 family modulators, and provide proof-of-concept for the elaboration of selective non-antibody binding reagents for use in cell-biology applications.
Accelerating Sequence Alignment to Graphs
Authors: Jain Chirag , Dilthey Alexander , Misra Sanchit , Zhang Haowen , Aluru Srinivas 
Published: May 2019

AbstractAligning DNA sequences to an annotated reference is a key step for genotyping in biology. Recent scientific studies have demonstrated improved inference by aligning reads to a variation graph, i.e., a reference sequence augmented with known genetic variations. Given a variation graph in the form of a directed acyclic string graph, the sequence to graph alignment problem seeks to find the best matching path in the graph for an input query sequence. Solving this problem exactly using a sequential dynamic programming algorithm takes quadratic time in terms of the graph size and query length, making it difficult to scale to high throughput DNA sequencing data. In this work, we propose the first parallel algorithm for computing sequence to graph alignments that leverages multiple cores and single-instruction multiple-data (SIMD) operations. We take advantage of the available inter-task parallelism, and provide a novel blocked approach to compute the score matrix while ensuring high memory locality. Using a 48-core Intel Xeon Skylake processor, the proposed algorithm achieves peak performance of 317 billion cell updates per second (GCUPS), and demonstrates near linear weak and strong scaling on up to 48 cores. It delivers significant performance gains compared to existing algorithms, and results in run-time reduction from multiple days to three hours for the problem of optimally aligning high coverage long (PacBio/ONT) or short (Illumina) DNA reads to an MHC human variation graph containing 10 million vertices.AvailabilityThe implementation of our algorithm is available at https://github.com/ParBLiSS/PaSGAL. Data sets used for evaluation are accessible using https://alurulab.cc.gatech.edu/PaSGAL.
Pathogen susceptibility and fitness costs explain variation in immune priming across natural populations of flour beetles
Authors: Khan Imroze , Prakash Arun , Agashe Deepa 
Published: May 2019

Abstract

In many insects, individuals primed with low doses of pathogens early in life have higher survival after exposure to the same pathogen later in life. Yet, our understanding of the evolutionary and ecological history of priming of immune response in natural insect populations is limited. Previous work demonstrated population‐, sex‐ and stage‐specific variation in the survival benefit of priming response in flour beetles (Tribolium castaneum) infected with their natural pathogen Bacillus thuringiensis. However, the evolutionary forces responsible for this natural variation remained unclear.

In the present work, we tested whether the strength of the priming response (measured as the survival benefit after priming and subsequent infection, relative to unprimed controls) was associated with multiple fitness parameters and immune components across 10 flour beetle populations collected from different locations in India.

Our results suggest two major selective pressures that may explain the observed inter‐population variation in priming: (a) Basal pathogen susceptibility – populations that were more susceptible to infection produced a stronger priming response, and (b) Short‐term early reproductive success – populations where primed females produced more offspring early in life (measured over 2 days) had lower survival benefit (measured over 120 days), suggesting a potential trade‐off between early reproduction and priming response. However, the negative association between survival and reproduction is limited to priming and infection in adults, but not in larvae. While other components of beetle fitness (starvation resistance and larval development) and immune function (haemolymph antibacterial activity and antimicrobial quinone secretion) also varied widely across populations, none of them was correlated with the variation in priming responses across populations.

Our work is the first systematic empirical demonstration of multiple selective pressures that may govern the evolution of immune priming in the wild. We hope that this motivates further experiments to establish the role of pathogen‐imposed selection and fitness costs in the evolution of priming in natural insect populations.
Grape Peel Extract and Resveratrol Inhibit Wrinkle Formation in Mice Model Through Activation of Nrf2/HO‐1 Signaling Pathway
Authors: Kim Jungeun , Oh Jisun , Averilla Janice N. , Kim Hyo Jung , Kim Jae‐Sik , Kim Jong‐Sang 
Published: May 2019

AbstractConsidering the anti‐photoaging effect of antioxidant compounds, we investigated the protective capacity of grape peel extract (GPE) and resveratrol on ultraviolet (UV)‐induced skin wrinkle formation. Total phenolic, total anthocyanin, and total flavonoid content in GPE prepared from peel of Campbell Early variety were 23.96 ± 0.09, 3.27 ± 0.40, and 1.24 ± 0.09 mg/g dry weight, respectively. Additionally, trans‐resveratrol and piceid content of the resulting GPE were 117.14 ± 19.97 and 85.23 ± 8.89 µg/g dry weight, respectively. Oral administration of either 2 g GPE or 2 mg resveratrol per kg body weight in mice attenuated UVB‐induced epidermal thickening (the thickness was reduced by about 63% and 55% with GPE and resveratrol consumption prior to exposure to UVB, respectively, compared to only UVB‐treated condition) and had marginally protective effect on wrinkle formation of skin exposed to UVB. As introduction of either GPE or resveratrol induced Nrf2‐dependent antioxidant enzymes including heme oxygenase‐1 (HO‐1) in liver and skin as well as inhibited metalloproteinases, it is highly probable that the extract or resveratrol mitigated UVB‐induced photoaging through activation of Nrf2/HO‐1 signaling pathway.Practical ApplicationThis study proved that resveratrol and the extract of grape peel, a common by‐product of grape juice processing, provide effective protection from UV‐induced skin wrinkle formation. Therefore, grape peel extract, which contains an appreciable amount of bioactive compound resveratrol, can be utilized as functional food ingredient for the manufacture of inner beauty products.
Life cycle models of women's body mass index and probability of being obese: Evidence from panel data
Authors: Huang Ying , Huffman Wallace E. 
Published: May 2019

AbstractThe objective of this paper is to develop a multiperiod, finite‐life, life cycle models of household decisions on food, leisure, and health (body mass index [BMI] or being obese) and to estimate econometric versions of these models treating SNAP (Supplemental Nutrition Assistance Program) participation as endogenous. A key insight from the economic models is that households allocate their wealth over the multiperiod life cycle to equalize the marginal utility of wealth in each period. The observations for this study are a balanced panel of over 1,600 women from the National Longitudinal Survey of Youth, 1979 Cohort (NLSY79). We focus on the 20‐year period starting in 1986, when SNAP data first became available. Women of all ages are included in the study because at the beginning of adulthood women cannot accurately predict over their life cycle labor and marriage market and health shocks that can thrust them into an economic position where they would qualify for SNAP. New findings include that a woman's household SNAP participation with or without updating for last periods health status and higher local dairy product prices reduce significantly her BMI and probability of being obese.
Involvement of STAT3 in the synergistic induction of 11β‐HSD1 by SAA1 and cortisol in human amnion fibroblasts
Authors: Lu Yi , Zhou Qiong , Lu Jiang‐Wen , Wang Wang‐Sheng , Sun Kang 
Published: May 2019

AbstractProblemCortisol, which is regenerated from biologically inactive cortisone by 11β‐hydroxysteroid dehydrogenase type 1 (11β‐HSD1) in human fetal membranes, may play an important role in human parturition. Recently, we have demonstrated that human fetal membranes are capable of de novo synthesis of serum amyloid A1 (SAA1), an acute‐phase protein of inflammation, and SAA1 may be engaged in multiple actions associated with human parturition. It remains to be determined whether SAA1 can interact with cortisol in the regulation of 11β‐HSD1 in the fetal membranes.Method of StudyIn the current study, we examined the regulation of 11β‐HSD1 expression by SAA1, and the interaction between SAA1 and cortisol in the regulation of 11β‐HSD1 expression in primary human amnion fibroblasts and amnion tissue.ResultsEither SAA1 or cortisol induced 11β‐HSD1 expression in a concentration‐dependent manner. Combination of SAA1 and cortisol synergistically enhanced 11β‐HSD1 expression. Mechanism studies revealed that SAA1 and cortisol induced the phosphorylation of the transcription factor STAT3 in a sequential order with the induction by SAA1 preceding the induction by cortisol. Furthermore, the induction of 11β‐HSD1 expression by either SAA1 or cortisol or combination of SAA1 and cortisol was blocked by STAT3 inhibition with its antagonist S3I‐201 or siRNA‐mediated knockdown.ConclusionThis study has demonstrated that SAA1 and cortisol can reinforce each other in the induction of 11β‐HSD1 expression through sequential phosphorylation of STAT3. The synergistic enhancement of 11β‐HSD1 expression by SAA1 and cortisol may lead to excessive cortisol accumulation in the fetal membranes at parturition.
Early childhood infections and the use of antibiotics and antipyretic‐analgesics in Finland, Estonia and Russian Karelia
Authors: Mustonen Neea , Siljander Heli , Peet Aleksandr , Tillmann Vallo , Härkönen Taina , Ilonen Jorma , Hyöty Heikki , Knip Mikael ,   the DIABIMMUNE Study Group
Published: May 2019

AbstractAimInfections in early childhood are common reasons to seek medical attention. This study compares the prevalence of infections, and the use of antibiotics and antipyretic–analgesics, in children from Finland, Estonia and Russian Karelia.MethodsChildren with a genetically increased risk for type 1 diabetes (N = 797) were observed from birth up to 3 years of age. Illnesses and medications were reported by parents continuously. All reported infections, antibiotics and antipyretic–analgesics were compared between Finland and Estonia, and to a lesser extent with Russian Karelia, due to poor study compliance.ResultsCompared with Estonians, Finns reported more infections during the first and second years of life. During the follow‐up, Finnish children had 10 infections while Estonians only had 8 (p < 0.001). Finns also used more antibiotics and antipyretic–analgesics in each year during the follow‐up. Russian Karelians reported the lowest frequency of infections and the most infrequent use of antibiotics and antipyretic–analgesics in the first two years of life.ConclusionInfections and the use of antibiotics and antipyretic–analgesics in early childhood were most frequent in Finland, where socio‐economic conditions are the most developed and microbial encounters are sparse. This may reflect on the hygiene hypothesis, a less effective immune system that allows normally harmless microbes to attack and cause clinical infections.
Pharmacology and function of the orphan GPR139 G protein‐coupled receptor
Authors: Vedel Line , Nøhr Anne Cathrine , Gloriam David E. , Bräuner‐Osborne Hans 
Published: May 2019

AbstractG protein‐coupled receptors (GPCRs) constitute the largest family of receptors and membrane proteins in the human genome with ~800 members of which half are olfactory. GPCRs are activated by a very broad range of endogenous signalling molecules and are involved in a plethora of physiological functions. All GPCRs contain a transmembrane domain, consisting of a bundle of seven α‐helices spanning the cell membrane, and forming the majority of the known ortho‐ or allosteric ligand binding sites. Due to their many physiological functions and the accessible and druggable transmembrane pocket, GPCRs constitute the largest family of drug targets mediating the actions of 34% of currently marketed drugs. GPCRs activate one or more of the four G protein families (Gq/11, Gi/o, Gs and G12/13) and/or ß‐arrestin. About a third of the non‐olfactory GPCRs are referred to as orphan receptors which means that their endogenous agonist(s) have not yet been found or firmly established. In this MiniReview, we focus on the orphan GPR139 receptor, for which the aromatic amino acids L‐Trp and L‐Phe as well as ACTH/α‐MSH‐related peptides have been proposed as endogenous agonists. GPR139 has been reported to activate several G protein pathways of which Gq/11 is the primary one. The receptor shows the highest expression in the striatum, thalamus, hypothalamus, pituitary and habenula of the human, rat and mouse CNS. We review the surrogate agonists and antagonists that have been published as well as the agonist pharmacophore and binding site. Finally, the putative physiological functions and therapeutic potential are outlined.