bluuebunny/crossref_metadata_2025_split huggingface dataset:
NanoFAST: Structure-based design of a small fluorogen-activating protein with only 98 amino acids
Authors: Mineev Konstantin S. , Goncharuk Sergey A. , Goncharuk Marina V. , Povarova Natalia V. , Baleeva Nadezhda S. , Smirnov Alexander Yu. , Myasnyanko Ivan N , Ruchkin Dmitry A. , Bukhdruker Sergey , Remeeva Alina , Mishin Alexey , Borshchevskiy Valentin , Gordeliy Valentin , Arseniev Alexander S. , Gorbachev Dmitriy A. , Gavrikov Alexey S. , Mishin Alexander S. , Baranov Mikhail S. 
Published: December 2020

AbstractOne of the essential characteristics of any tag used in bioscience and medical applications is its size. The larger the label, the more it may affect the studied object, and the more it may distort its behavior. In this paper, using NMR spectroscopy and X-ray crystallography, we have studied the structure of fluorogen-activating protein FAST both in the apo form and in complex with the fluorogen. We shown that significant change in the protein occurs upon interaction with the ligand. While the protein is completely ordered in the complex, its apo form is characterized by higher mobility and disordering of its N-terminus. We used structural information to design the shortened FAST (which we named nanoFAST) by truncating 26 N-terminal residues. Thus, we created the shortest genetically encoded tag among all known fluorescent and fluorogen-activating proteins, which is composed of only 98 amino acids.
Secondary rewards acquire enhanced incentive motivation via increasing anticipatory activity of the lateral orbitofrontal cortex
Authors: Yang X , Liu X , Zeng Y , Wu R , Zhao W , Xin F , Yao S , Kendrick KM , Ebstein RP , Becker B 
Published: December 2020

AbstractThe motivation to strive for and consume primary rewards such as palatable food is bound by internal satiation and devaluation mechanisms, yet secondary rewards such as money may not be bound by these regulatory mechanisms. The present study therefore aimed at determining diverging devaluation trajectories for primary (chocolate milk) and secondary (money) reinforcers on the behavioral and neural level. Satiation procedures combined with a choice (Experiment 1) and an incentive delay (Experiment 2) paradigm consistently revealed decreased hedonic value for the primary reward as reflected by decreasing hedonic evaluation and choice preference, while hedonic value and preferences for the secondary reward increased. Concomitantly acquired functional near-infrared spectroscopy (fNIRS) data during the incentive delay paradigm revealed that increasing value of the secondary reward was accompanied by increasing anticipatory activation in the lateral orbitofrontal cortex, while during the consummatory phase the secondary reinforcer associated with higher medial orbitofrontal activity irrespective of devaluation stage. Overall, the findings suggest that – in contrast to primary reinforcers - secondary reinforcers can acquire progressively enhanced incentive motivation with repeated receipt, suggesting a mechanism which could promote escalating striving to obtain secondary rewards.
Genetic diversity ofBemisia tabaciGenn. characterized by analysis of ISSR and cytochrome c oxidase subunit I at Qassim, Saudia Arabia
Authors: Abdel-Baky Nagdy F. , Brown J. K. , Aldeghairi M. A. , Motawei M. I. , Rehan Medhat 
Published: December 2020

AbstractProblems of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) that increased and escalated in the last 40 years seem to be related to one or more aggressive biotypes that appeared to spread steadily worldwide. As well, some biological characteristics of B. tabaci have led some entomologists to change and multiply their methodology to update with the change in the pest genetic structures. This study is the 1st of its kind in Qassim region in KSA in respect ofB. tabacibiotypes. Four identification methods (Squash Silverleaf Symptoms (SSL), cross mating, Cytochrome oxidase subunit I (COI) sequences, and ISSR-PCR analysis) were carried out to determine the biotypes of B. tabaci at Qassim regions. Slight SSL symptoms were observed with varying degrees on squash leaves caused byB. tabacipopulation at Qassim, KSA. Cross-mating among the populations that have the same or similar genetic structures produced fertilized offspring, females and males with higher sex ratios in favor of females, and produced a higher number of eggs. Whereas, B. tabaci populations that varied greatly in their genetic structures produced unfertilized eggs, which produce males only. In the same trend, ISSR-PCR analysis revealed that B. tabaci populations at Qassim regions varied genetically and gathered into four genetic groups. In conclusion, COI analysis is a perfect tool for classification between biotypes in B. tabaci. Therefore, this study declares thatB. tabacithat colonized and infest Qassim horticulture has not the same genetic structures but belonging to B biotypes. It could be named asBemisiaspecies complex.
Investigating temporal and spatial variation of eDNA in a nearshore rocky reef environment
Authors: Ely Taylor , Barber Paul H. , Gold Zachary 
Published: December 2020

AbstractEnvironmental DNA (eDNA) is increasingly used to measure biodiversity of marine ecosystems. However, key aspects of spatial and temporal dynamics of eDNA remain unknown. Particularly, it is unclear how long eDNA signals persist locally in dynamic marine environments, since degradation rates have predominantly been quantified through mesocosm studies. To determinein situeDNA residence times, we introduced an eDNA signal from a non-native fish into a Southern California rocky reef ecosystem, and then measured changes in both introduced and background eDNA signals over 96 hours. Foreign eDNA signal could no longer be detected 7.5 hours after introduction, far exceeding disappearance rates quantified in laboratory studies. In addition, native vertebrate eDNA signals varied greatly over the 96 hours of observation, but time of day and tidal direction did not drive this variation in community structure. Species accumulation curves showed that standard sampling protocols using 3 replicate 1 L sea water samples were insufficient to capture full diversity of local marine vertebrates, capturing only 76% of all taxa. Despite this limitation, a single eDNA sample captured greater vertbrate diversity than 18 SCUBA based underwater visual transect surveys conducted at a nearby site. There was no significant difference in species richness between temporal replicates and spatial replicates, suggesting a space for time substitution may be effective for fully capturing the diversity of local marine vertebrate communities in nearshore rocky reef environments. This result is particularly important in designing eDNA metabarcoding sampling protocols to capture local marine species diversity.
Layer-dependent loss and enhancement of geniculostriate and retinotectal pathways in adult human amblyopia
Authors: Wen Wen , Wang Yue , He Sheng , Liu Hong , Zhao Chen , Zhang Peng 
Published: December 2020

AbstractAbnormal visual experience during critical period leads to reorganization of neuroarchitectures in primate visual cortex. However, developmental plasticity of human subcortical visual pathways remains elusive. Using high-resolution fMRI and pathway-selective visual stimuli, we investigated layer-dependent response properties and connectivity of subcortical visual pathways of adult human amblyopia. Stimuli presented to the amblyopic eye showed selective response loss in the parvocellular layers of the lateral geniculate nucleus, and also reduced the connectivity to V1. Amblyopic eye’s response to isoluminant chromatic stimulus was significantly reduced in the superficial layers of the superior colliculus, while the fellow eye’s response robustly increased in the deeper layers associated with increased cortical feedbacks. Therefore, amblyopia led to selective reduction of parvocellular feedforward signals in the geniculostriate pathway, whereas loss and enhancement of parvocellular feedback signals in the retinotectal pathway. These findings shed light for future development of new tools for treating amblyopia and tracking the prognosis.HighlightsAmblyopia impairs feedforward processing in the P layers of the LGNLayer-dependent loss and enhancement of cortical feedback signals in the SCPathway-specific abnormalities explain amblyopic deficits in visual acuity and attentionSignificance statementHow abnormal visual experiences during critical period shape the function and wire the neural circuits of human subcortex remains largely unknown. With high-resolution fMRI and visual stimuli to preferentially activate layer-dependent response in human subcortical pathways, the current study clearly demonstrates that amblyopia shifts the homeostatic interocular balance of human subcortex in a pathway-specific manner. Amblyopia led to selective loss of parvocellular feedforward signals in the geniculostriate pathway, whereas deficit and enhancement of parvocellular feedback signals in the retinotectal pathway. These pathwayspecific functional abnormalities provide the neural basis for amblyopic deficits in visual acuity, control of eye movement and attention. It sheds light for future development of new tools for treating amblyopia and tracking the prognosis.
Engineering large chromosomal deletions by CRISPR-Cas9
Authors: Eleveld Thomas F. , Bakali Chaimaa , Eijk Paul P. , Stathi Phylicia , Poddighe Pino J , Ylstra Bauke 
Published: December 2020

AbstractArm-level chromosomal deletions are a prevalent and defining feature of cancer. A high degree of tumor-type and subtype specific recurrencies suggest a selective oncogenic advantage. However, due to their large size it has been difficult to pinpoint the oncogenic drivers that confer this advantage. Suitable functional genomics approaches to study the oncogenic driving capacity of arm-level deletions are limited. Here we present an effective technique to engineer arm-level deletions by CRISPR-Cas9 and create isogenic cell line models. We simultaneously induce double-strand breaks (DSBs) at two ends of a chromosomal arm and select the cells that have lost the intermittent region. Using this technique, we induce arm-level deletions on chromosome 11q (65 MB) and chromosome 6q (53 MB) in neuroblastoma cell lines. Such isogenic models enable further research on the role of arm-level deletions in tumor development and growth and their possible therapeutic potential.
Global cognitive performance is not influenced by diurnal rhythm
Authors: De Jager Celine H. , Varangis Eleanna , Stern Yaakov 
Published: December 2020

AbstractObjectiveThe human brain is influenced by different biological rhythms, including the daily 24-hour (diurnal) cycle. Past studies have reported evidence of variation in cognitive performance over the course of the day, and of differences in the peak time for cognition in older age. Here, we investigated these questions using two existing longitudinal studies of healthy adults.MethodsTime of neuropsychological battery testing was extracted from study records, and we analyzed cognitive performance measures from 4 domains (Vocabulary, Processing Speed, Fluid Reasoning, and Episodic Memory) in 543 healthy adults between the ages of 20 and 80. Time of day was dichotomized as morning (281 tested before noon), and afternoon (242 tested after noon).ResultsMultivariate analyses controlling for both gender and years of education revealed no significant effect of time of testing (or its interaction with participant age) on cognitive performance. These results suggest that diurnal effects during time periods typically used to test human subjects are unlikely to have a meaningful effect on performance on the neuropsychological tests that are used for standard cognitive assessment.ConclusionThis suggests that the effect of time of day on cognition in the context of aging may not be as ubiquitous as previously suggested, and thus is unlikely to represent a large confound in existing studies of cognition across the adult lifespan.
A cryptic BRCA2 repeated motif binds to HSF2BP oligomers with no impact on meiotic recombination
Authors: Ghouil Rania , Miron Simona , Koornneef Lieke , Veerman Jasper , Paul Maarten W. , Le Du Marie-Hélène , Sleddens-Linkels Esther , van Rossum-Fikkert Sari E. , van Loon Yvette , Felipe-Medina Natalia , Pendas Alberto M. , Maas Alex , Essers Jeroen , Legrand Pierre , Baarends Willy M. , Kanaar Roland , Zinn-Justin Sophie , Zelensky Alex N. 
Published: December 2020

AbstractBRCA2 plays a prominent role in meiotic homologous recombination (HR). Loss of BRCA2 or several of its meiotic partners causes fertility defects. One of these partners, HSF2BP, was recently discovered as expressed physiologically in germline and ectopically produced in cancer cells. It has an N-terminal coiled coil motif involved in direct binding to the protein BRME1, and both HSF2BP and BRME1 are essential for meiotic HR during spermatogenesis. It also interacts through its C-terminal Armadillo (ARM) domain with a conserved region of BRCA2 of unknown function. We analyzed the structural properties and functional consequences of the BRCA2-HSF2BP interaction and tested the emerging model of its involvement in meiosis. We solved the crystal structure of the complex between the BRCA2 fragment that is disordered in solution and the HSF2BP dimeric ARM domain. This revealed two previously unrecognized BRCA2 repeats that each interact with one ARM monomer from two different dimers. BRCA2 binding triggers ARM tetramerization, resulting in a complex containing two BRCA2 fragments connecting two ARM dimers. The 3D structures of the BRCA2 repeats are superimposable, revealing conserved contacts between the BRCA2 residues defining the repeats and the HSF2BP residues lining the groove of the ARM. This large interface is responsible for the nanomolar affinity of the interaction, significantly stronger than any other measured interaction involving BRCA2. Deleting exon 12 fromBrca2, encoding the first repeat, disrupted BRCA2 binding to HSF2BPin vitroand in cells. However,Brca2Δ12/Δ12mice with the same deletion were fertile and did not show any meiotic defects, contrary to the prediction from the model positing that HSF2BP acts as a meiotic localizer of BRCA2. We conclude that the high-affinity interaction between BRCA2 and HSF2BP and the resulting HSF2BP oligomerization are not required for RAD51 and DMC1 recombinase localization to meiotic double strand breaks and for productive meiotic HR.
ACE2 peptide fragment interacts with several sites on the SARS-CoV-2 spike protein S1
Authors: Kuznetsov Aleksei , Arukuusk Piret , Härk Heleri , Juronen Erkki , Langel Ülo , Ustav Mart , Järv Jaak 
Published: December 2020

AbstractThe influence of the peptide QAKTFLDKFNHEAEDLFYQ on the kinetics of the SARS-CoV-2 spike protein S1 binding to angiotensin-converting enzyme 2(ACE2) was studied to model the interaction of the virus with its host cell. This peptide corresponds to the sequence 24-42 of the ACE2 α1 domain, which is the binding site for the S1 protein. The on-rate and off-rate of S1-ACE2 complex formation were measured in the presence of various peptide concentrations using Bio-Layer Interferometry (BLI). The formation of the S1-ACE2 complex was inhibited when the S1 protein was preincubated with the peptide, however, no significant inhibitory effect was observed in the absence of preincubation. Dissociation kinetics revealed that the peptide remained bound to the S1-ACE2 complex and stabilized this complex. Computational mapping of the S1 protein surface for peptide binding revealed two additional sites, located at some distance from the receptor binding domain (RBD) of S1. These additional binding sites affect the interaction between the peptide, the S1 protein, and ACE2.
Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation
Authors: Blassberg Robert , Patel Harshil , Watson Thomas , Gouti Mina , Metzis Vicki , Delás M Joaquina , Briscoe James 
Published: December 2020

AbstractWNT signalling has multiple roles. It maintains pluripotency of embryonic stem cells, assigns posterior identity in the epiblast and induces mesodermal tissue. We provide evidence that these distinct functions are conducted by the transcription factor SOX2, which adopts different modes of chromatin interaction and regulatory element selection depending on its level of expression. At high levels, SOX2 acts as a pioneer factor, displacing nucleosomes from regulatory elements with high affinity SOX2 binding sites and recruiting the WNT effector, TCF/β-catenin, to maintain pluripotent gene expression. Reducing SOX2 levels destabilises pluripotency and reconfigures SOX2/TCF/β-catenin occupancy to caudal epiblast expressed genes. These contain low-affinity SOX2 sites and are co-occupied by T/Bra and CDX. The loss of SOX2 allows WNT induced mesodermal differentiation. These findings define a role for Sox2 levels in dictating the chromatin occupancy of TCF/β-catenin and reveal how context specific responses to a signal are configured by the level of a transcription factor.
Neuronal regulated Ire1-dependent mRNA decay controls germline differentiation inC. elegans
Authors: Levi-Ferber Mor , Shalash Rewayd , Thomas Adrien Le , Salzberg Yehuda , Shurgi Maor , Ashkenazi Avi , Henis-Korenblit Sivan 
Published: December 2020

SummaryUnderstanding the molecular events that regulate cell pluripotency versus acquisition of differentiated somatic cell fate is fundamentally important. Studies inC. elegansdemonstrate that knockout of the germline-specific translation repressorgld-1, causes germ cells within tumorous gonads to form germline-derived teratoma. Previously we demonstrated that ER stress enhances this phenotype to suppress germline tumor progression (Levi-Ferber M, 2015). Here, we identify a neuronal circuit that non-autonomously suppresses germline differentiation, and show that it communicates with the gonad via the neurotransmitter serotonin to limit somatic differentiation of the tumorous germline. ER stress controls this circuit through regulated IRE-1-dependent mRNA decay of transcripts encoding the neuropeptide FLP-6. Depletion of FLP-6 disrupts the circuit’s integrity and hence its ability to prevent somatic-fate acquisition by germline tumor cells. Our findings reveal mechanistically how ER stress enhances ectopic germline differentiation, and demonstrate that RIDD can affect animal physiology by controlling a specific neuronal circuit.
Stable Polymer Bilayers for Protein Channel Recordings at High Guanidinium Chloride Concentrations
Authors: Yu Luning , Kang Xinqi , Alibakhshi Mohammad Amin , Pavlenok Mikhail , Niederweis Michael , Wanunu Meni 
Published: December 2020

AbstractUse of chaotropic reagents is common in biophysical characterization of biomolecules. When the study involves transmembrane protein channels, the stability of the protein channel and supporting bilayer membrane must be considered. In this letter we show that planar bilayers composed of poly(1,2-butadiene)-b-poly(ethylene oxide) diblock copolymer are stable and leak-free at high guanidinium chloride concentrations, in contrast to diphytanoyl phosphatidylcholine bilayers which exhibit deleterious leakage under similar conditions. Further, insertion and functional analysis of channels such as α-hemolysin and MspA are straightforward in these polymer membranes. Finally, we demonstrate that α-hemolysin channels maintain their structural integrity at 2M guanidinium chloride concentrations using blunt DNA hairpins as molecular reporters.
Peptidome profiling for the immunological stratification in sepsis: a proof of concept study
Authors: Ledesma Martín , Todero María Florencia , Maceira Lautaro , Prieto Monica , Vay Carlos , Galas Marcelo , López Beatriz , Yokobori Noemí , Rearte Bárbara 
Published: December 2020

AbstractSepsis has been called “the graveyard of pharmaceutical companies” due to the numerous failed clinical trials. The lack of tools to monitor the immunological status in sepsis constrains the development of immunomodulatory therapies. Here, we evaluated a test based on whole plasma peptidome acquired in a MALDI-TOF-mass spectrometer used for bacterial biotyping and machine-learning algorithms to discriminate the different immunological phases of sepsis. In this proof of concept study, two discrete lipopolysaccharide-(LPS) induced murine models emulating the pro- and anti-inflammatory phases that occur during sepsis were evaluated. The LPS group was inoculated with a single high dose of LPS, recalling the proinflammatory phase, and the IS groups was subjected to increasing doses of LPS to induce the anti-inflammatory/immunosuppression phase. Unstimulated mice served as controls. Both experimental groups showed the hallmarks of pro- and anti- inflammatory phases respectively; the LPS group showed leukopenia and higher levels of cytokines and tissue damage markers, and the IS group showed neutrophilia, lymphopenia and significantly lower antibody titers upon immunization. Principal component analysis of the plasma peptidomes formed three discrete clusters that mostly coincided with the experimental groups. In addition, machine-learning algorithms discriminated the different experimental groups with a sensitivity and specificity of up to 95.7% and 90.9% respectively. Our data reveal the potential of plasma peptidome analysis by MALDI-TOF-mass spectrometry as a simple, speedy and readily transferrable method for sepsis patient stratification that would contribute to therapeutic decision-making based on their immunological status.
The β-Carotene-Oxygen Copolymer: its Relationship to Apocarotenoids and β-Carotene Function
Authors: Mogg Trevor J. , Burton Graham W. 
Published: December 2020

Abstractβ-Carotene spontaneously copolymerizes with molecular oxygen to form a β-carotene-oxygen copolymer compound (“copolymer”) as the main product, together with small amounts of many apocarotenoids. Both the addition and scission products are interpreted as being formed during progression through successive free radical β-carotene-oxygen adduct intermediates. The product mixture from full oxidation of β-carotene, lacking both vitamin A and β-carotene, has immunological activities, some of which derive from the copolymer. However, the copolymer’s chemical makeup is unknown. A chemical breakdown study shows the compound to be moderately stable but nevertheless the latent source of many small apocarotenoids. Although the copolymer alone is only slightly affected by heating at 100°C for 4 h, in methanol solution it is significantly degraded by hydrochloric acid or sodium hydroxide, liberating many apocarotenoids. GC-MS analysis with mass-spectral library matching identified a minimum of 45 structures, while more than 90 others remain unassigned. Thirteen products are Generally Recognized as Safe (GRAS) human flavor agents. Newly identified products include various small keto carboxylic acids and dicarboxylic acids, several of which are central metabolic intermediates. Also present are the dialdehydes glyoxal and methyl glyoxal, recently reported as β-carotene metabolites in plants. Although both compounds at higher concentrations are known to be toxic, at low concentration methyl glyoxal has been reported to be potentially capable of activating an immune response against microbial infection. In plants, advantage is taken of the electrophilic reactivity of specific apocarotenoids derived from β-carotene oxidation to activate protective defenses. Given the copolymer occurs naturally and is a major product of non-enzymatic β-carotene oxidation in stored plants, by partially sequestering apocarotenoid metabolites the copolymer may serve to limit potential toxicity and maintain low cellular apocarotenoid concentrations for signaling purposes. In animals the copolymer may serve as a systemic source of apocarotenoids.