bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pooled genome-wide CRISPR activation screening for rapamycin resistance genes inDrosophilacells
Authors: Xia Baolong , Viswanatha Raghuvir , Hu Yanhui , Mohr Stephanie E. , Perrimon Norbert 
Published: December 2022

AbstractLoss-of-function and gain-of-function genetic perturbations provide valuable insights into gene function. InDrosophilacells, while genome-wide loss-of-function screens have been extensively used to reveal mechanisms of a variety of biological processes, approaches for performing genome-wide gain-of-function screens are still lacking. Here, we describe a pooled CRISPR activation (CRISPRa) screening platform inDrosophilacells and apply this method to both focused and genome-wide screens to identify rapamycin resistance genes. The screens identified three genes as novel rapamycin resistance genes: a member of SLC16 family of monocarboxylate transporters (CG8468), a member of the lipocalin protein family (CG5399), and a zinc finger C2H2 transcription factor (CG9932). Mechanistically, we demonstrate thatCG5399overexpression activates the RTK-Akt-mTOR signaling pathway and that activation of InR byCG5399requires cholesterol and clathrin-coated pits at the cell membrane. This study establishes a novel platform for functional genetic studies inDrosophilacells.
How woodcocks produce the most brilliant white plumage patches among the birds
Authors: Dunning Jamie , Patil Anvay , D’Alba Liliana , Bond Alexander L , Debruyn Gerben , Dhinojwala Ali , Shawkey Matthew , Jenni Lukas 
Published: December 2022

AbstractUntil recently, and when compared with diurnal birds that use contrasting plumage patches and complex feather structures to convey visual information, communication in nocturnal species was considered to follow acoustic and chemical channels. However, many nocturnal birds have evolved intensely white plumage patches within otherwise inconspicuous plumages. We used spectrophotometry, electron microscopy, and optical modelling to explain the mechanisms producing bright white tail feather tips of the Eurasian woodcockScolopax rusticola. Their diffuse reflectance was ∼30% higher than any previously measured feather. This intense reflectance is the result of incoherent light scattering from a disordered nanostructure composed of keratin and air within the barb rami. In addition, the flattening, thickening, and arrangement of those barbs creates a Venetian-blind-like macrostructure that enhances the surface area for light reflection. We suggest that the woodcocks have evolved these bright white feather patches for long-range visual communication in dimly lit environments.
Propagated circulating tumor cells uncovers the role of NFκB and COP1 in metastasis
Authors: Xiao Jerry , Sharma Utsav , Arab Abolfazl , Miglani Sohit , Bhalla Sonakshi , Suguru Shravanthy , Suter Robert , Mukherji Reetu , Lippman Marc E. , Pohlmann Paula R. , Zeck Jay , Marshall John L. , Weinberg Benjamin A. , He Aiwu Ruth , Noel Marcus S. , Schlegel Richard , Goodarzi Hani , Agarwal Seema 
Published: December 2022

AbstractCirculating tumor cells (CTCs), a population of cancer cells that represents the seeds of metastatic nodules, are a promising model system for studying metastasis. However, expansion of patient-derived CTCsex vivois challenging and dependent on the collection of high numbers of CTCs, which are ultra-rare. Here, we report the development of a combined CTC and CTC-derived xenograft (CDX) platform for expanding and studying patient-derived CTCs from metastatic colon, lung, and pancreatic cancers. Propagated CTCs yielded a highly aggressive population of cells that could be used to routinely and robustly establish primary tumors and metastatic lesions in CDXs. Differential gene analysis of the resultant CTC models emphasized a role for NF-kB signaling as a pan-cancer signaling pathway involved in metastasis. Furthermore, metastatic CTCs were identified through a prospective 5-gene signature (BCAR1, COL1A1, IGSF3, RRAD, and TFPI2). Whole-exome sequencing of CDX models and metastases further identified mutations in constitutive photomorphogenesis protein 1 (COP1) as a potential driver of metastasis. These findings illustrate the utility of the combined patient-derived CTC model and provide a glimpse of the promise of CTCs in identifying drivers of cancer metastasis.
Daily membrane capacitance changes in mouse neurons
Authors: Severin Daniel , Moreno Cristián , Tran Trinh , Wesselborg Christian , Shirley Sofia , Kirkwood Alfredo , Golowasch Jorge 
Published: December 2022

AbstractCapacitance of biological membranes is determined by the properties of the lipid portion of the membrane, as well as morphological features of a cell. In neurons, membrane capacitance is a determining factor of synaptic integration, action potential propagation speed and firing frequency due to its direct effect on the membrane time constant. Besides slow changes associated with increased morphological complexity during postnatal maturation, neuron membrane capacity is largely considered a stable, non-regulated constant magnitude. Here we report that in two excitatory neuronal cell types, pyramidal cells of mouse primary visual cortex and granule cells of the hippocampus, the membrane capacitance significantly changes between the start and the end of a daily light cycle. The changes are large, nearly two-fold in magnitude in pyramidal cells, but are not observed in cortical parvalbumin-expressing inhibitory interneurons. We discuss potential functional implications and plausible mechanisms.
Computing Absolute Binding Affinities by Streamlined Alchemical Free Energy Perturbation (SAFEP)
Authors: Santiago-McRae Ezry , Ebrahimi Mina , Sandberg Jesse W. , Brannigan Grace , Hénin Jérôme 
Published: December 2022

AbstractFree Energy Perturbation (FEP) is a powerful but challenging computational technique for estimating differences in free energy between two or more states. This document is intended both as a tutorial and as an adaptable protocol for computing free energies of binding using free energy perturbations in NAMD. We present the Streamlined Alchemical Free Energy Perturbation (SAFEP) framework. SAFEP shifts the computational frame of reference from the ligand to the binding site itself. This both simplifies the thermodynamic cycle and makes the approach more broadly applicable to superficial sites and other less common geometries. As a practical example, we give instructions for calculating the absolute binding free energy of phenol to lysozyme. We assume familiarity with standard procedures for setting up, running, and analyzing molecular dynamics simulations using NAMD and VMD. While simulation times will vary, the human tasks should take no more than 3 to 4 hours for a reader without previous training in free energy calculations or experience with the VMD Colvars Dashboard. Sample data are provided for all key calculations both for comparison and readers’ convenience.
The role of human superior colliculus in affective experiences during visual and somatosensory stimulation
Authors: Chen Danlei , Kragel Philip A. , Savoca Paul W. , Wald Lawrence L. , Bianciardi Marta , Wager Tor D. , Quigley Karen S. , Satpute Ajay B. , Barrett Lisa Feldman , Theriault Jordan E. 
Published: December 2022

AbstractThe superior colliculus is often studied for its role in visually guided behaviors, but research in non-human animals indicates it is a midbrain hub for processing sensory information from multiple domains, including interoception (which is associated with affect). We used ultra-high field 7-Tesla fMRI to extend this work to humans, modeling superior colliculus BOLD signal intensity during visual or somatosensory stimulation (N = 40 in each sensory modality), both under aversive and neutral affective intensity. As hypothesized, the superior colliculus showed increased BOLD signal intensity in the dorsal and ventral subregions during visual and somatosensory stimulation, respectively. The entire superior colliculus also showed increased BOLD signal intensity during aversive compared to neural conditions. The superior colliculus BOLD signal intensity also correlated with a preregistered set of brain regions involved in visual, somatosensory, and interoceptive processing.
Supercomputer framework for reverse engineering firing patterns of neuron populations to identify their synaptic inputs
Authors: Chardon Matthieu K. , Wang Y. Curtis , Garcia Marta , Besler Emre , Beauchamp J. Andrew , D’Mello Michael , Powers Randall K. , Heckman Charles J. 
Published: December 2022

AbstractIn this study, we develop new reverse engineering (RE) techniques to identify the organization of the synaptic inputs generating firing patterns of populations of neurons. We tested these techniquesin silicoto allow rigorous evaluation of their effectiveness, using remarkably extensive parameter searches enabled by massively-parallel computation on supercomputers. We chose spinal motoneurons as our target neural system, since motoneurons process all motor commands and have well established input-output properties. One set of simulated motoneurons was driven by 300,000+ simulated combinations of excitatory, inhibitory, and neuromodulatory inputs. Our goal was to determine if these firing patterns had sufficient information to allow RE identification of the input combinations. Like other neural systems, the motoneuron input-output system is likely non-unique. This non-uniqueness could potentially limit this RE approach, as many input combinations can produce similar outputs. However, our simulations revealed that firing patterns contained sufficient information to sharply restrict the solution space. Thus, our RE approach successfully generated estimates of the actual simulated patterns of excitation, inhibition, and neuromodulation, with variances accounted for ranging from 75% to 90%. It was striking that nonlinearities induced in firing patterns by the neuromodulation inputs did not impede RE, but instead generated distinctive features in firing patterns that aided RE. These simulations demonstrate the potential of this form of RE analysis. It is likely that the ever-increasing capacity of supercomputers will allow increasingly accurate RE of neuron inputs from their firing patterns from many neural systems.
Genetic and phylogenetic features of the repetitive ITS copies in theHirsutella sinensisgenome and the genomically independent AT-biasedOphiocordyceps sinensisgenotypes
Authors: Li Xiu-Zhang , Li Yu-Ling , Wang Ya-Nan , Zhu Jia-Shi 
Published: December 2022

AbstractIt has been hypothesized that AT-biased genotypes ofOphiocordyceps sinensisare generated through repeat-induced point mutation (RIP) and coexist as permanently nonfunctional internal transcribed spacer (ITS) pseudogenes in the genome ofHirsutella sinensis(GC-biased Genotype #1 ofO. sinensis). This study examined theH. sinensisgenome, which contains multiple repetitive ITS copies (GC content: 64.7±0.33%) with multiple insertion/deletion and transversion alleles, which were not generated through RIP mutagenesis that theoretically causes cytosine-to-thymine (C-to-T) and guanine-to-adenine (G-to-A) transitions. The repetitive ITS copies in theH. sinensisgenome were found to be genetically and phylogenetically distinct from the AT-biasedO. sinensisgenotypes (GC content: 51.1±1.69%), which possess multiple transition alleles. The sequences of Genotypes #2–17, both GC- and AT-biased, are absent from theH. sinensisgenome; these genotypes belong to interindividualO. sinensisfungi and differentially occur in different compartments of naturalCordyceps sinensis,with dynamic alterations in abundance occurring in an asynchronous, disproportional manner duringC. sinensismaturation. Metatranscriptomic analyses of naturalC. sinensisrevealed the transcriptional silencing of 5.8S genes in allC. sinensis- colonizing fungi, includingH. sinensis. The transcription assay reported by Liet al. [1] provided unsound, controversial evidence indicating that the 5.8S genes of AT-biased genotypes are nonfunctional pseudogenes. In addition to the single ITS locus analysis, repetitive genomic copies were also examined at multiple loci in theH. sinensisgenome, and approximately 8.2% of the authentic genes had repetitive copies, including various transitions, transversions, and insertions/deletions. The transcripts for the repetitive copies, regardless of the decreases, increases, or bidirectional changes in the AT content, were identified in theH. sinensistranscriptome. These results are inconsistent with those of RIP mutagenesis, which generates pseudogenic, nonfunctional, repetitive copies. In conclusion, AT-biased genotypes ofO. sinensismight have evolved through evolutionary mechanisms from a common ancestor over the long course of evolution, in parallel with GC-biased Genotype #1H. sinensis.
Investigation on the Effectiveness ofLactobacillus plantarumin Enhancing the Folate content ofInjeramade with Different Cereals
Authors: Tamene Aynadis , Baye Kaleab , Mekuriyaw Tesfaye 
Published: December 2022

ABSTRACTInjera is an Ethiopian fermented pancake-like flatbread made from different cereals. The aim of the study was to investigate the effect of injera making process using different cereals (tef, sorghum, wheat and barley) on folate content and to evaluate the effectiveness of Lactobacillus plantarum (L. plantarum) in enhancing folate of injera made with different cereals. Cereals were used alone or in combination (tef and sorghum (1:1), wheat and sorghum (3:1), sorghum (100 %) and Barley (100 %). L. plantarum previously isolated from tef dough and ersho were used as starters. Folate content of flour, dough and injera was determined by microbiological assay. The contribution of consumption of injera made with different cereals to the folate requirement of children and women of reproductive age was evaluated. Acceptability of injera was estimated by 30 adult healthy volunteers using a 9-point hedonic scale. Among the studied cereals, the highest average folate content (49.9 μg/100 g) was observed in 100 % sorghum flour and the least (32.2 μg/100 g) in 100 % barley flour, on dry weight basis. After fermentation, the highest average folate content (60.1 μg/100 g) was observed in 100 % sorghum dough fermented with L. plantarum and the least (27.6 μg/100 g) was observed in the same dough but fermented with ersho. The average folate contents (fresh weight basis) of 100 % sorghum, wheat & sorghum (3:1), tef & sorghum (1:1) and 100 % barley injeras fermented with L. plantarum were 14.48 μg/100 g, 15.45 μg/100 g, 13.23 μg/100 g and 13.13 μg/100 g, respectively. Consumption of L. plantarum fermented injera made with different cereals can contribute up to 8 % of the recommended folate intake of women of reproductive age. Injera made with tef and sorghum blend (1:1) and fermented with L. plantarum was highly accepted.
Unconditioned and Conditioned Anxiolytic Effects of Sodium Valproate on Flavor Neophobia and Fear Conditioning
Authors: Cintado María Ángeles , González-Tirado Gabriel , Cárcel Lucía , De la Casa Luis Gonzalo 
Published: December 2022

AbstractIn three experiments with rats, we analyzed the potential anxiolytic effects of sodium valproate, an anticonvulsant drug that has shown additional pharmacodynamic effects in animal models, including anxiolytic action. Since previous results have revealed that injecting valproate before allowing animals to consume a novel flavor solution resulted in an attenuation of neophobia, we predicted a similar effect when the novel flavor is presented on a drug-free trial in the presence of a context previously associated with the drug. In line with this hypothesis, in our first experiment we observed a reduction in neophobia to a novel flavor for those animals tested in the presence of the context associated with Sodium Valproate. However, a control group that received the drug before being allowed access to the novel flavor showed a significant reduction in consumption. Experiment 2 revealed that the unconditioned effects of the drug include a deleterious effect on the animals’ locomotor activity that probably interferes with drinking behavior. Finally, in a third experiment, we directly tested the potential anxiolytic properties of sodium valproate by injecting the drug before implementing a fear conditioning procedure. These findings are explained in terms of the unconditioned anxiolytic action of the drug and the formation of an association between the context and the effects of the drug that evokes a conditioned response reminiscent of such anxiolytic effect.
Rapid Audiovisual Integration Guides Predictive Actions
Authors: Kreyenmeier Philipp , Schroeger Anna , Cañal-Bruland Rouwen , Raab Markus , Spering Miriam 
Published: December 2022

AbstractNatural movements, such as catching a ball or capturing prey, typically involve multiple senses. Yet, laboratory studies on human movements commonly focus solely on vision and ignore sound. Here we ask how visual and auditory signals are integrated to guide interceptive movements. Human observers tracked the brief launch of a simulated baseball, randomly paired with batting sounds of varying intensities, and made a quick pointing movement at the ball. Movement endpoints revealed systematic overestimation of target speed when ball launch was paired with a loud versus a quiet sound, even though sound was never informative. This effect was modulated by the availability of visual information: sounds biased interception when ball presentation time was short. Continuous eye movements uncovered that sound affected interception within 125 ms of ball launch and revealed a correction of the sound-induced bias when more visual information was available. Our findings suggest that auditory and visual signals are integrated to guide interception and that this integration process must occur early at a site that receives auditory and visual signals within an ultrashort timespan.
Global soil metagenomics reveals ubiquitous yet previously-hidden predominance ofDeltaproteobacteriain nitrogen-fixing microbiome
Authors: Masuda Yoko , Mise Kazumori , Xu Zhenxing , Zhang Zhengcheng , Shiratori Yutaka , Senoo Keishi , Itoh Hideomi 
Published: December 2022

AbstractBiological nitrogen fixation is a fundamental process sustaining all life on earth. In the soil,Alphaproteobacteria, Betaproteobacteria, andCyanobacteriaare traditionally considered the major groups of nitrogen fixation population. This conventional knowledge has been accumulated by numerous PCR amplicon surveys for nitrogenase genes. However, this prevalent view appears to be inconsistent with results of recent PCR-free meta-omics investigations. Here, we show the global distribution and diversity of terrestrial diazotrophic microbiome, updated by fully leveraging the planetary collections of soil metagenomes along with recently expanded culture collections. After extensive analysis of 1,445 soil metagenomic samples, we proved that the previously-undervaluedAnaeromyxobacteraceaeandGeobacteraceaewithinDeltaproteobacteriaare ubiquitous and predominant groups of diazotrophic microbiome in the soils, spanning a broad spectrum of environments, with different geographic origins and land usage types, including aerobic (croplands, grasslands) and anaerobic ones (paddy soils, sediments). Our results delineate a revised scheme of soil nitrogen fixation, which is inclusive of both conventional diazotrophs and the so far undervaluedDeltaproteobacteria.
A weighted quantile sum regression with penalized weights and two indices
Authors: Renzetti Stefano , Gennings Chris , Calza Stefano 
Published: December 2022

AbstractBackgroundNew statistical methodologies were developed in the last decade to face the challenges of estimating the effects of exposure to multiple chemicals. Weighted Quantile Sum (WQS) regression is a recent statistical method that allows estimating a mixture effect associated with a specific health effect and identifying the components that characterize the mixture effect.ObjectivesIn this study, we propose an extension of WQS regression that estimates two mixture effects of chemicals on a health outcome in the same model through the inclusion of two indices with the introduction of a penalization term.MethodsTo evaluate the performance of this new model we performed both a simulation study and a real case study where we assessed the effects of nutrients on obesity among adults using the National Health and Nutrition Examination Survey (NHANES) data.ResultsThe method showed good performance in estimating both the regression parameter and the weights associated with the single elements when the penalized term was set equal to the magnitude of the Akaike information criterion of the unpenalized WQS regression. The two indices further helped to give a better estimate of the parameters (Positive direction Median Error (PME): 0.017; Negative direction Median Error (NME): -0.023) compared to the standard WQS (PME: -0.141; NME: 0.078). In the case study, WQS with two indices was able to find a significant effect of nutrients on obesity in both directions identifying caffeine and magnesium as the main actors in the positive and negative association respectively.DiscussionThrough this work, we introduced an extension of the WQS regression that showed the possibility to improve the accuracy of the parameter estimates when considering a mixture of elements that can have both a protective and a harmful effect on the outcome; and the advantage of adding a penalization term when estimating the weights.
Artificial intelligence-assisted meta-analysis of the frequency ofACEI/D polymorphisms in centenarians and other long-lived individuals
Authors: Li Lingxuan , Murakami Shin 
Published: December 2022

AbstractCurrent research on the angiotensin-converting-enzyme (ACE) gene has yielded controversial results on whether different ACE polymorphisms are linked with human longevity. ACE polymorphisms are a risk factor for Alzheimer’s disease and age-onset diseases that may contribute to the mortality of older people. Our goal is to consolidate existing studies with assistance from artificial intelligence and machine-learning-assisted software to come to a more precise understanding of the role of the ACE gene in human longevity. The I (insertion) and D (deletion) polymorphisms in the intron are correlated with the levels of circulating ACE; homozygous D (DD) is high and homozygous I (II) is low. Here, we performed a detailed meta-analysis of the I and D polymorphisms using centenarians (100+ years old), long-lived subjects (85+ years old), and control groups. ACE genotype distribution was analyzed across a total of 2,054 centenarians and 12,074 controls, as well as 1,367 long-lived subjects between the ages of 85-99, using the inverse variance and random effects methods. The ACE DD genotype was found to be favored in centenarians (OR: 1.41 [95% CI: 1.19-1.67], P < 0.0001) with a heterogeneity of 32%, and the II genotype slightly favored the control groups (OR: 0.81 [95% CI: 0.66-0.98], P = 0.03) with a heterogeneity of 28%, corroborating results from previous meta-analyses. Novel to our meta-analysis, the ID genotype was found to be favored in control groups (OR: 0.86 [95% CI: 0.76-0.97], P = 0.01) with a heterogeneity of 0%. The long-lived group showed a similar positive association between the DD genotype and longevity (OR: 1.34 [95% CI: 1.21-1.48, P < 0.0001) and a negative association between the II genotype and longevity (OR: 0.79 [95% CI: 0.70-0.88], P < 0.0001). The long-lived ID genotype did not show significant findings (OR: 0.93 [95% CI: 0.84-1.02], P = 0.79). In conclusion, the results suggest a significant positive association of the DD genotype with human longevity. However, despite the previous study, the results do not confirm a positive association of the ID genotype with human longevity. We suggest a few paradoxical observations: (1) inhibition of ACE can increase longevity in model systems from nematodes to mammals, seemingly opposite to the finding in humans; (2) exceptional longevity associated with homozygous DD is also associated age-related diseases with higher mortality risks in homozygous DD. We discuss ACE, longevity, and age-related diseases.