bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ginsentides: Cysteine and Glycine-rich Peptides from the Ginseng Family with Unusual Disulfide Connectivity
Authors: Tam James P. , Nguyen Giang K. T. , Loo Shining , Wang Shujing , Yang Daiwen , Kam Antony 
Published: October 2018

AbstractGinseng, a popular and valuable traditional medicine, has been used for centuries to maintain health and treat disease. Here we report the discovery and characterization of ginsentides, a novel family of cysteine and glycine-rich peptides derived from the three most widely-used ginseng species: Panax ginseng, Panax quinquefolius, and Panax notoginseng. Using proteomic and transcriptomic methods, we identified 14 ginsentides, TP1-TP14 which consist of 31–33 amino acids and whose expression profiles are species- and tissues-dependent. Ginsentides have an eight-cysteine motif typical of the eight-cysteine-hevein-like peptides (8C-HLP) commonly found in medicinal herbs, but lack a chitin-binding domain. Transcriptomic analysis showed that the three-domain biosynthetic precursors of ginsentides differ from known 8C-HLP precursors in architecture and the absence of a C-terminal protein-cargo domain. A database search revealed an additional 50 ginsentide-like precursors from both gymnosperms and angiosperms. Disulfide mapping and structure determination of the ginsentide TP1 revealed a novel disulfide connectivity that differs from the 8C-HLPs. The structure of ginsentide TP1 is highly compact, with the N- and C-termini topologically fixed by disulfide bonds to form a pseudocyclic structure that confers resistance to heat, proteolysis, and acid and serum-mediated degradation. Together, our results expand the chemical space of natural products found in ginseng and highlight the occurrence, distribution, disulfide connectivity, and precursor architectures of cysteine- and glycine-rich ginsentides as a class of novel non-chitin-binding, non-cargo-carrying 8C-HLPs.
Reduction in nutritional quality and growing area suitability of common bean under climate change induced drought stress in Africa
Authors: Hummel Marijke , Hallahan Brendan F. , Brychkova Galina , Ramirez-Villegas Julian , Guwela Veronica , Chataika Bartholomew , Curley Edna , McKeown Peter C. , Morrison Liam , Talsma Elise F. , Beebe Steve , Jarvis Andy , Chirwa Rowland , Spillane Charles 
Published: October 2018

AbstractClimate change impacts on food security will involve negative impacts on crop yields, and potentially on the nutritional quality of staple crops. Common bean is the most important grain legume staple crop for human diets and nutrition worldwide. We demonstrate by crop modeling that the majority of current common bean growing areas in southeastern Africa will become unsuitable for bean cultivation by the year 2050. We further demonstrate reductions in yields of available common bean varieties in a field trial that is a climate analogue site for future predicted drought conditions. Little is known regarding the impact of climate change induced abiotic stresses on the nutritional quality of common beans. Our analysis of nutritional and antinutritional compounds reveals that iron levels in common bean grains are reduced under future climate-scenario relevant drought stress conditions. In contrast, the levels of protein, zinc, lead and phytic acid increase in the beans under such drought stress conditions. This indicates that under climate-change induced drought scenarios, future bean servings by 2050 will likely have lower nutritional quality, posing challenges for ongoing climate-proofing of bean production for yields, nutritional quality, human health, and food security.
Efficacy and Resistance Management Potential of a Modified Vip3C Protein for Control of Spodoptera frugiperda in Maize
Authors: Kahn Theodore W. , Chakroun Maissa , Williams Jayme , Walsh Tom , James Bill , Monserrate Jessica , Ferré Juan 
Published: October 2018

AbstractA modified Vip3C protein has been developed that has a spectrum of activity that has the potential to be commercially useful for pest control, and shows good efficacy against Spodoptera frugiperda in insect bioassays and field trials. For the first time Vip3A and Vip3C proteins have been compared to Cry1 and Cry2 proteins in a complete set of experiments from insect bioassays to competition binding assays to field trials, and the results of these complementary experiments are in agreement with each other. Binding assays with radiolabelled toxins and brush border membrane vesicles from S. frugiperda and Helicoverpa armigera show that the modified Vip3C protein shares binding sites with Vip3A, and does not share sites with Cry1F or Cry2A. In agreement with the resulting binding site model, Vip3A-resistant insects were also cross-resistant to the modified Vip3C protein. Furthermore, maize plants expressing the modified Vip3C protein, but not those expressing Cry1F protein, were protected against Cry1F-resistant S. frugiperda in field trials.
Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations
Authors: Mateo Lidia , Rech Gabriel E. , González Josefa 
Published: October 2018

AbstractSignatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. In Drosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, several studies based mainly in North American populations showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection might be challenging when analyzing these populations. European populations could help identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden) and Castellana Grotte (Southern Italy). We found low levels of population structure and no evidence of recent African admixture in these two populations. We thus look for patterns of spatially varying selection affecting individual genes and gene sets. Besides single nucleotide polymorphisms, we also investigated the role of transposable elements in local adaptation. We concluded that European populations are a good dataset to identify candidate loci under spatially varying selection. The analysis of the two populations sequenced in this work in the context of all the available D. melanogaster data allowed us to pinpoint genes and biological processes likely to be relevant for local adaptation. Identifying and analyzing populations with low levels of population structure and admixture should help to disentangle selective from non-selective forces underlying patterns of population differentiation in other species as well.
The effect of LTP- and LTD-like visual stimulation on modulation of human orientation discrimination
Authors: Marzoll Andreas , Saygi Tan , Dinse Hubert R. 
Published: October 2018

AbstractStudies showing that repetitive visual stimulation protocols alter perception and induce cortical reorganization, as well-reported for the tactile domain, have been sparse. In this study, we investigated how “long-term potentiation [LTP]-like” and “long-term depression [LTD]-like” repetitive visual stimulation affects orientation discrimination ability in human observers. LTP-like stimulation with features most closely resembling the stimuli used during behavioral assessment evoked the largest improvement, while the effects were smaller in protocols that differed in shape or orientation features. This gradient suggests lower learning specificity than classical perceptual learning experiments, possibly because of an interplay of task- and feature-based factors. All modulatory effects of repetitive stimulation were superimposed on top of spontaneous task learning. Moreover, blockwise analysis revealed that LTP-like stimulation, in contrast to LTD-like or sham stimulation, prevented a loss of practice-related gain of orientation discrimination thresholds. This observation highlights a critical role of LTP-like stimulation for consolidation, typically observed during sleep.
Strategic allocation of working memory resource
Authors: Yoo Aspen H. , Klyszejko Zuzanna , Curtis Clayton E. , Ma Wei Ji 
Published: October 2018

AbstractVisual working memory (VWM), the brief retention of past visual information, supports a range of cognitive functions. One of the defining, and largely studied, characteristics of VWM is how resource-limited it is, raising questions about how this resource is shared or split across memoranda. Since objects are rarely equally important in the real world, we ask how people split this resource in settings where objects have different levels of importance. In a psychophysical experiment, participants remembered the location of four targets with different probabilities of being tested after a delay. We then measured their memory accuracy of one of the targets. We found that participants allocated more resource to memoranda with higher priority, but underallocated resource to high- and overallocated to low-priority targets relative to the true probability of being tested. These results are well explained by a computational model in which resource is allocated to minimize expected estimation error. We replicated this finding in a second experiment in which participants bet on their memory fidelity after making the location estimate. The results of this experiment show that people have access to and utilize the quality of their memory when making decisions. Furthermore, people again allocate resource in a way that minimizes memory errors, even in a context in which an alternative strategy was incentivized. Our study not only shows that people are allocating resource according to behavioral relevance, but suggests that they are doing so with the aim of maximizing memory accuracy.
Incorporation of Hydroxyethylcellulose-Functionalized Halloysite as a Means of Decreasing the Thermal Conductivity of Oilwell Cement
Authors: Cho Junsang , Waetzig Gregory R. , Udayakantha Malsha , Hong Claire Y. , Banerjee Sarbajit 
Published: October 2018

AbstractThe significant heat loss and severe thermal fluctuations inherent in steam-assisted gravity drainage (SAGD) and cyclic steam stimulation (CSS) impose considerable constraints on well cementing. In order to obtain better energy efficiency and mechanical robustness, there is considerable interest in the development of low-thermal-conductivity cement that can provide a combination of enhanced thermal insulation and mechanical resilience upon thermal cycling. However, the current palette of thermal cements is exceedingly sparse. In this article, we illustrate a method for decreasing the thermal conductivity of cement by inclusion of hydroxyethylcellulose-functionalized halloysite nanotubes. Halloysite/hydroxyethylcellulose inclusions offer an abundance of disparate interfaces and void space that can effectively scatter phonons, thereby bringing about a pronounced reduction of thermal conductivity. The microstructure of the nanocomposite cementitious matrix is strongly modified even as the compositional profile remains essentially unaltered. Modified cement nanocomposites incorporating halloysite nanotubes along with hydroxyethylcellulose in a 8:1 ratio with an overall loading of 2 wt.% exhibit the lowest measured thermal conductivity of 0.212 ± 0.003 W/m.K, which is substantially reduced from the thermal conductivity of unmodified cement (1.252 W/m.K). The ability to substantially decrease thermal conductivity without deleterious modification of mechanical properties through alteration of microstructure, inclusion of encapsulated void spaces, and introduction of multiple phonon-scattering interfaces suggests an entirely new approach to oilwell cementing based on the design of tailored nanocomposites.
The synthesis, crystal, hydrogen sulfide detection and cell assement of novel chemsensors based on coumarin derivatives
Authors: Chen Yanmei , Shang Xuefang , Li Congshu , Xue Zhenzhen , Chen Hongli , Wu Hongwei , Wang Tianyun 
Published: October 2018

AbstractA series of chemsensors (1–4) containing fluorobenzene group based on coumarin derivatives have been developed for the selective and sensitive detection of H2S. The advantages of the synthesized fluorescent probe (compound 1) were the low detection limit (4 × 10−6 mol·L−1), good selectivity and high sensitivity which had been demonstrated through UV-vis, fluorescent titration experiments. Besides cytotoxicity test of compounds (1 and 2) was studied and the results indicated that compounds (1 and 2) showed almost no cytotoxicityat at a concentration of 150 μg·mL−1. The interacted mechanism was the thiolysis reaction of dinitrophenyl ether which had been confirmed by fluorescence and HRMS titration experiment. In addition, probe 1 can also detect HS− selectively by naked eye in pure DMSO solvent.
Characterization of a recurrent missense mutation in the forkhead DNA-binding domain of FOXP1
Authors: Johnson Tyler B. , Mechels Keegan , Anderson Ruthellen H. , Cain Jacob T. , Sturdevant David A. , Braddock Stephen , Pinz Hailey , Wilson Mark A. , Landsverk Megan , Roux Kyle J. , Weimer Jill M. 
Published: October 2018

AbstractHaploinsufficiency of Forkhead box protein P1 (FOXP1), a highly conserved transcription factor, leads to developmental delay, intellectual disability, autism spectrum disorder, speech delay, and dysmorphic features. Most of the reported FOXP1 mutations occur on the C-terminus of the protein and cluster around to the forkhead domain. All reported FOXP1 pathogenic variants result in abnormal cellular localization and loss of transcriptional repression activity of the protein product. Here we present three patients with the same FOXP1 mutation, c.1574G>A (p.R525Q), that results in the characteristic loss of transcription repression activity. This mutation, however, represents the first reported FOXP1 mutation that does not result in cytoplasmic or nuclear aggregation of the protein but maintains normal nuclear localization.
RETRACTED ARTICLE: TET2 inhibits tumorigenesis of breast cancer cells by regulating caspase-4
Authors: Zhu Xuguo , Li Shuangqi 
Published: October 2018

AbstractEpigenetic regulators have been shown to influence breast cancer progression. However, the detailed mechanism by which TET2 plays the suppressive role in tumorigenesis remains not completely understood. We employed RT-qPCR and westernblot to examine genes expression. Next, the bisulphite sequencing PCR was used to determine the methylation level at CASP4 promoter in the cells. Phenotypically, we utilized growth curve analysis, colony formation in soft agar and xenograft tumor assay to assess tumorigenesis of MCF-7 cell. We found that TET2 knockout enhanced colony formation ability and in vivo tumor formation ability of MCF-7 cell, whereas TET2 depletion not affected the growth rate of MCF-7 cell in the culture. Mechanistically, TET2 loss led to a significant decrease in caspase-4 expression possibly via increasing DNA methylation of CASP4 promoter in MCF-7 cell. To validate, TET2 overexpression led to higher level of caspase-4 in MDA-MB-231 and 293T cells, which was dependent on TET2 enzymatic activity. Finally, we observed that caspase-4 could revert, at least partially, TET2 deletion-induced tumorigenesis of MCF-7. In summary, we reveal a novel mechanism that TET2 suppresses tumorigenesis of breast cancer cells through caspase-4. Our findings will facilitate development of new diagnostic markers or therapeutical therapies for breast cancer.
Impact of Escherichia coli K12 and O18:K1 on human platelets: Differential effects on platelet activation, RNAs and proteins
Authors: Fejes A. V. , Best M. G. , van der Heijden W. A. , Vancura A. , Verschueren H. , de Mast Q. , Wurdinger T. , Mannhalter C. 
Published: October 2018

AbstractBlood platelets can interact with bacteria, possibly leading to platelet activation, cytokine and microparticle release and immune signalling. Besides, bacteria can also affect the platelet RNA content. We investigated the impact of non-pathogenic K12 and pathogenic O18:K1Escherichia (E.) colistrains on platelet activation, RNA expression patterns, and selected proteins. Depending on bacteria concentration, contact of platelets withE. coliK12 lead to an increase of P-selectin (24–51.3%), CD63 (15.9–24.3%), PAC-1 (3.8–14.9%) and bound fibrinogen (22.4–39%) on the surface.E. coliO18:K1 did not affect these markers. Sequencing analysis of total RNA showed thatE. coliK12 caused a significant concentration change of 103 spliced mRNAs, of which 74 decreased. For the RNAs ofHMBS(logFC = +5.73),ATP2C1(logFC = −3.13) andLRCH4(logFC = −4.07) changes were detectable by thromboSeq and Tuxedo pipelines. By Western blot we observed the conversion of HMBS protein from a 47 kDA to 40 kDa product byE. coliK12, O18:K1 and by purified lipopolysaccharide. While ATP2C1 protein was released from platelets,E. colieither reduced the secretion or broke down the released protein making it undetectable by antibodies. Our results demonstrate that differentE. colistrains influence activation, RNA and protein levels differently which may affect platelet-bacteria crosstalk.
Overexpression of CD98 in intestinal epithelium dysregulates miRNAs and their targeted proteins along the ileal villus-crypt axis
Authors: Han Moon K. , Baker Mark , Zhang Yuchen , Yang Chunhua , Zhang Mingzhen , Garg Pallavi , Viennois Emilie , Merlin Didier 
Published: October 2018

AbstractCD98 has been implicated in the experimental model of inflammatory bowel disease. We have previously shown that IEC-specific overexpression of CD98 mediates intestinal inflammation and intestinal epithelial barrier dysfunction. Mice overexpressing CD98 exhibited severe colitis and a greater susceptibility to CAC. Here we demonstrated CD98 overexpression to dysregulate homeostatic gradient profile of miRNA and protein expression along the ileal villus-crypt axis. Using miRNA-target gene prediction module, we observed differentially expressed miRNAs to target proteins of villus and crypt profoundly affected by CD98 overexpression. We have utilized online bioinformatics as methods to further scrutinize the biological meanings of miRNA-target data. We identified significant interactions among the differentially regulated proteins targeted by altered miRNAs in Tg mice. The biological processes affected by the predicted targets of miRNAs deviate from the homeostatic functions of the miRNA-gene-protein axis of the wildtype mice. Our results emphasize a dynamic perturbation of miRNA and protein expression in villus-crypt axis contributing to potential biological consequences of altering CD98 expression. Our findings also suggest the need for a consideration of arrays of interacting biological entities (i.e. miRNAs-mRNAs, protein-protein interaction) or a combination comparison for a better understanding of the disease pathology which is necessary for an effective therapeutic target development.
Ophirina amphinema n. gen., n. sp., a New Deeply Branching Discobid with Phylogenetic Affinity to Jakobids
Authors: Yabuki Akinori , Gyaltshen Yangtsho , Heiss Aaron A. , Fujikura Katsunori , Kim Eunsoo 
Published: October 2018

AbstractWe report a novel nanoflagellate, Ophirina amphinema n. gen. n. sp., isolated from a lagoon of the Solomon Islands. The flagellate displays ‘typical excavate’ morphological characteristics, such as the presence of a ventral feeding groove with vanes on the posterior flagellum. The cell is ca. 4 µm in length, bears two flagella, and has a single mitochondrion with flat to discoid cristae. The flagellate exists in two morphotypes: a suspension-feeder, which bears flagella that are about the length of the cell, and a swimmer, which has longer flagella. In a tree based on the analysis of 156 proteins, Ophirina is sister to jakobids, with moderate bootstrap support. Ophirina has some ultrastructural (e.g. B-fibre associated with the posterior basal body) and mtDNA (e.g. rpoA–D) features in common with jakobids. Yet, other morphological features, including the crista morphology and presence of two flagellar vanes, rather connect Ophirina to non-jakobid or non-discobid excavates. Ophirina amphinema has some unique features, such as an unusual segmented core structure within the basal bodies and a rightward-oriented dorsal fan. Thus, Ophirina represents a new deeply-branching member of Discoba, and its mosaic morphological characteristics may illuminate aspects of the ancestral eukaryotic cellular body plan.
Systems pharmacology reveals the unique mechanism features of Shenzhu Capsule for treatment of ulcerative colitis in comparison with synthetic drugs
Authors: Feng Wuwen , Ao Hui , Yue Shijun , Peng Cheng 
Published: October 2018

AbstractIn clinic, both synthetic drugs and Shenzhu Capsule (SZC), one kind of traditional Chinese medicines (TCMs), are used to treat ulcerative colitis (UC). In our study, a systems pharmacology approach was employed to elucidate the chemical and mechanism differences between SZC and synthetic drugs in treating UC. First, the compound databases were constructed for SZC and synthetic drugs. Then, the targets of SZC were predicted with on-line tools and validated using molecular docking method. Finally, chemical space, targets, and pathways of SZC and synthetic drugs were compared. Results showed that atractylenolide I, atractylone, kaempferol, etc., were bioactive compounds of SZC. Comparison of SZC and synthetic drugs showed that (1) in chemical space, the area of SZC encompasses the area of synthetic drugs; (2) SZC can act on more targets and pathways than synthetic drugs; (3) SZC can not only regulate immune and inflammatory reactions but also act on ulcerative colitis complications (bloody diarrhea) and prevent UC to develop into colorectal cancer whereas synthetic drugs mainly regulate immune and inflammatory reactions. Our study could help us to understand the compound and mechanism differences between TCM and synthetic drugs.
Magnetocardiography on an isolated animal heart with a room-temperature optically pumped magnetometer
Authors: Jensen Kasper , Skarsfeldt Mark Alexander , Stærkind Hans , Arnbak Jens , Balabas Mikhail V. , Olesen Søren-Peter , Bentzen Bo Hjorth , Polzik Eugene S. 
Published: October 2018

AbstractOptically pumped magnetometers are becoming a promising alternative to cryogenically-cooled superconducting magnetometers for detecting and imaging biomagnetic fields. Magnetic field detection is a completely non-invasive method, which allows one to study the function of excitable human organs with a sensor placed outside the human body. For instance, magnetometers can be used to detect brain activity or to study the activity of the heart. We have developed a highly sensitive miniature optically pumped magnetometer based on cesium atomic vapor kept in a paraffin-coated glass container. The magnetometer is optimized for detection of biological signals and has high temporal and spatial resolution. It is operated at room- or human body temperature and can be placed in contact with or at a mm-distance from a biological object. With this magnetometer, we detected the heartbeat of an isolated guinea-pig heart, which is an animal widely used in biomedical studies. In our recordings of the magnetocardiogram, we can detect the P-wave, QRS-complex and T-wave associated with the cardiac cycle in real time. We also demonstrate that our device is capable of measuring the cardiac electrographic intervals, such as the RR- and QT-interval, and detecting drug-induced prolongation of the QT-interval, which is important for medical diagnostics.