bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine Learning Optimization of Photosynthetic Microbe Cultivation and Recombinant Protein Production
Authors: Gamble Caitlin , Bryant Drew , Carrieri Damian , Bixby Eli , Dang Jason , Marshall Jacob , Doughty David , Colwell Lucy , Berndl Marc , Roberts James , Frumkin Michael 
Published: August 2021

ABSTRACTBackgroundArthrospira platensis (commonly known as spirulina) is a promising new platform for low-cost manufacturing of biopharmaceuticals. However, full realization of the platform’s potential will depend on achieving both high growth rates of spirulina and high expression of therapeutic proteins.ObjectiveWe aimed to optimize culture conditions for the spirulina-based production of therapeutic proteins.MethodsWe used a machine learning approach called Bayesian black-box optimization to iteratively guide experiments in 96 photobioreactors that explored the relationship between production outcomes and 17 environmental variables such as pH, temperature, and light intensity.ResultsOver 16 rounds of experiments, we identified key variable adjustments that approximately doubled spirulina-based production of heterologous proteins, improving volumetric productivity between 70% to 100% in multiple bioreactor setting configurations.ConclusionAn adaptive, machine learning-based approach to optimize heterologous protein production can improve outcomes based on complex, multivariate experiments, identifying beneficial variable combinations and adjustments that might not otherwise be discoverable within high-dimensional data.
CRISPR-Cas9-mediated Large Cluster Deletion and Multiplex Genome Editing in Paenibacillus polymyxa
Authors: Meliawati Meliawati , Teckentrup Christa , Schmid Jochen 
Published: August 2021

AbstractThe use of molecular tools based on the clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems has rapidly advanced genetic engineering. These molecular biological tools have been applied for different genetic engineering purposes in multiple organisms, including the quite rarely explored Paenibacillus polymyxa. However, only limited studies on large cluster deletion and multiplex genome editing have been described for this highly interesting and versatile bacterium. Here, we demonstrate the utilization of a Cas9-based system to realize targeted deletions of four biosynthetic gene clusters in the range of 12 kb to 41 kb by the use of a single targeting sgRNA. Furthermore, we also harness the system for multiplex editing of genes and large genomic regions. Multiplex deletion was achieved with more than 80 % efficiency, while simultaneous integration at two distantly located sites was obtained with 58 % efficiency. The findings reported in this study are anticipated to accelerate future research in P. polymyxa and related species.
Robust somatic copy number estimation using coarse-to-fine segmentation
Authors: Culibrk Luka , Grewal Jasleen K , Pleasance Erin D , Williamson Laura , Mungall Karen , Laskin Janessa , Marra Marco A , Jones Steven JM 
Published: August 2021

AbstractCancers routinely exhibit chromosomal instability that results in copy number variants (CNVs), namely changes in the abundance of genomic material. Unfortunately, the detection of these variants in cancer genomes is difficult. We present Ploidetect, a software package that effectively identifies CNVs within whole-genome sequenced tumors. Ploidetect utilizes a coarse-to-fine segmentation approach which yields highly contiguous segments while allowing for focal CNVs to be detected with high sensitivity. We benchmark Ploidetect against popular CNV tools using synthetic data, cell line data, and real-world metastatic tumor data, and find an improvement in sensitivity and accuracy while maintaining low levels of oversegmentation. We show that the improved CNV sensitivity enables Ploidetect to recover recurrent homozygous deletions and genes associated with chromosomal instability in a multi-cancer cohort of 687 patients. Using highly contiguous CNV calls afforded by Ploidetect, we also demonstrate the use of segment N50 as a novel metric for the measurement of chromosomal instability within tumor biopsies. We propose that increasingly accurate determination of CNVs is critical for their productive study in cancer, and our work demonstrates advances made possible by progress in this regard.
An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs
Authors: Cook Ashley L. , Wyhs Nicolas , Sur Surojit , Ptak Blair , Popoli Maria , Dobbyn Laura , Papadopoulos Tasos , Bettegowda Chetan , Papadopoulos Nickolas , Vogelstein Bert , Zhou Shibin , Kinzler Kenneth W 
Published: August 2021

SummaryWe describe the creation and characterization of an isogenic cell line panel representing common cancer pathways, with multiple features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cells were generated using CRISPR-technologies. Surprisingly, we discovered most of these lines did not result in complete gene inactivation, despite integration of sgRNA at the desired genomic site. However, a subset of the lines harbored true, biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterize lines covering 19 pathways frequently subject to loss of function in cancers. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a multiplexed high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation ofTP53. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena.
Cryo-EM Structures of Prestin and the Molecular Basis of Outer Hair Cell Electromotility
Authors: Bavi Navid , Clark Michael David , Contreras Gustavo F. , Shen Rong , Reddy Bharat , Milewski Wieslawa , Perozo Eduardo 
Published: August 2021

AbstractThe voltage-dependent motor protein, Prestin (SLC26A5) is responsible for the electromotive behavior of outer hair cells (OHCs). Here, we determined the structure of dolphin Prestin in six distinct states using single particle cryo-electron microscopy. Structural and functional data suggest that Prestin adopts a unique and complex set of states, tunable by the identity of bound anions. Complexes with the inhibitor salicylate show that it competes for the anion-binding site of Prestin. These conformations reveal a novel mechanism of area expansion that depends on the helix flexibility and conformational transitions at the membrane protein interface and putatively affects the physical state of the surrounding membrane. These observations illuminate the structural basis of Prestin electromotility, a key component of the mammalian cochlear amplifier.
Predictive functionality of bacteria in naturally fermented milk products of India using PICRUSt2 and Piphillin pipelines
Authors: Shingling H. Nakibapher Jones , Tamang Jyoti Prakash 
Published: August 2021

AbstractNaturally fermented milk (NFM) products are popular food delicacies in Indian states of Sikkim and Arunachal Pradesh. Bacterial communities in these NFM products of India were previously analysed by high-throughput sequence method. However, predictive gene functionality of NFM products of India has not been studied. In this study, raw sequences of NFM products of Sikkim and Arunachal Pradesh were accessed from MG-RAST/NCBI database server. PICRUSt2 and Piphillin tools were applied to study microbial functional gene prediction. MUSiCC-normalized KOs and mapped KEGG pathways from both PICRUSt2 and Piphillin resulted in higher percentage of the former in comparison to the latter. Though, functional features were compared from both the pipelines, however, there were significant differences between the predictions. Therefore, a consolidated presentation of both the algorithms presented an overall outlook into the predictive functional profiles associated with the microbiota of the NFM products of India.
A red herring in zebrafish genetics: allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
Authors: White Richard J , Mackay Eirinn , Wilson Stephen W , Busch-Nentwich Elisabeth M 
Published: August 2021

AbstractIn model organisms, RNA sequencing is frequently used to assess the effect of genetic mutations on cellular and developmental processes. Typically, animals heterozygous for a mutation are crossed to produce offspring with different genotypes. Resultant embryos are grouped by genotype to compare homozygous mutant embryos to heterozygous and wild-type siblings. Genes that are differentially expressed between the groups are assumed to reveal insights into the pathways affected by the mutation.Here we show that in zebrafish, differentially expressed genes are often overrepresented on the same chromosome as the mutation due to different levels of expression of alleles from different genetic backgrounds. Using an incross of haplotype-resolved wild-type fish, we found evidence of widespread allele-specific expression, which appears as differential expression when comparing embryos homozygous for a region of the genome to their siblings. When analysing mutant transcriptomes, this means that differentially expressed genes on the same chromosome as a mutation of interest may not be caused by that mutation.Typically, the genomic location of a differentially expressed gene is not considered when interpreting its importance with respect to the phenotype. This could lead to pathways being erroneously implicated or overlooked due to the noise of spurious differentially expressed genes on the same chromosome as the mutation. These observations have implications for the interpretation of RNA-seq experiments involving outbred animals and non-inbred model organisms.
Controlled administration of aerosolized SARS-CoV-2 to K18-hACE2 transgenic mice uncouples respiratory infection and anosmia from fatal neuroinvasion
Authors: Fumagalli Valeria , Ravà Micol , Marotta Davide , Di Lucia Pietro , Laura Chiara , Sala Eleonora , Grillo Marta , Bono Elisa , Giustini Leonardo , Perucchini Chiara , Mainetti Marta , Sessa Alessandro , Garcia-Manteiga José M. , Donnici Lorena , Manganaro Lara , Delbue Serena , Broccoli Vania , De Francesco Raffaele , D’Adamo Patrizia , Kuka Mirela , Guidotti Luca G. , Iannacone Matteo 
Published: August 2021

AbstractThe development of a tractable small animal model faithfully reproducing human COVID-19 pathogenesis would arguably meet a pressing need in biomedical research. Thus far, most investigators have used transgenic mice expressing the human ACE2 in epithelial cells (K18-hACE2 transgenic mice) that are intranasally instilled with a liquid SARS-CoV-2 suspension under deep anesthesia. Unfortunately, this experimental approach results in disproportionate high CNS infection leading to fatal encephalitis, which is rarely observed in humans and severely limits this model’s usefulness. Here, we describe the use of an inhalation tower system that allows exposure of unanesthetized mice to aerosolized virus under controlled conditions. Aerosol exposure of K18-hACE2 transgenic mice to SARS-CoV-2 resulted in robust viral replication in the respiratory tract, anosmia, and airway obstruction, but did not lead to fatal viral neuroinvasion. When compared to intranasal inoculation, aerosol infection resulted in a more pronounced lung pathology including increased immune infiltration, fibrin deposition and a transcriptional signature comparable to that observed in SARS-CoV-2- infected patients. This model may prove useful for studies of viral transmission, disease pathogenesis (including long-term consequences of SARS-CoV-2 infection) and therapeutic interventions.
Resistance to amitraz in the parasitic honey bee mite Varroa destructor is associated with mutations in the β−adrenergic-like octopamine receptor
Authors: Hernández-Rodríguez Carmen Sara , Moreno-Martí Sara , Almecija Gabrielle , Christmon Krisztina , Johnson Josephine D. , Ventelon Marie , vanEngelsdorp Dennis , Cook Steven C. , González-Cabrera Joel 
Published: August 2021

AbstractVarroa destructor is considered a major reason for high loss rate of Western honey bee (Apis mellifera) colonies. To prevent colony losses caused by V. destructor it is necessary to actively manage the mite population. Beekeepers, particularly commercial beekeepers, have few alternative treatments other than synthetic acaricides to control the parasite, resulting in intensive treatment regimens that led to the evolution of resistance in mite populations.To investigate the mechanism of the resistance to amitraz detected in V. destructor mites from French and U.S. apiaries, we identified and characterized octopamine and tyramine receptors (the known targets of amitraz) in this species. The comparison of sequences obtained from mites collected from different apiaries with different treatment regimens, showed that the amino acid substitutions N87S or Y215H in the OctβR were associated with treatment failures reported in French or U.S. apiaries, respectively. Based on our findings, we have developed and tested two high throughput diagnostic assays based on TaqMan® able to accurately detect mites carrying the mutations in this receptor. This valuable information may be of help for beekeepers when selecting the most suitable acaricide to manage V. destructor.
Older adults generalize their movements across walking contexts more than young during gradual and abrupt split-belt walking
Authors: Aucie Yashar , Harket Harrison. M. , Sombric Carly. J. , Torres-Oviedo Gelsy 
Published: August 2021

AbstractGeneralization of movements from experienced to novel situations is a critical aspect of motor learning. It has been demonstrated that the training period when a movement is learned influences the movement’s generalization to untrained situations. However, little is known about how healthy aging affects these processes. For example, young adults exhibit greater generalization of movements learned on a device (e.g. split-belt treadmill or robotic arm) to movements without it (e.g, overground walking or unconstrained reaching) when participants experience small vs. large perturbations on the training device. Here, we investigated whether a similar effect would be observed in older adults. To this end, we compared the generalization of split-belt adaptation to overground walking in older (75.9±4.8 years old) and young adults (24.7±5.9 years old) when adapted gradually (i.e., small perturbations) vs. abruptly (i.e., large perturbations). We found that both age groups adapted more to the abrupt condition compared to the gradual condition, which resulted in greater adaptation effects (i.e., aftereffects) on the treadmill in the abrupt than the gradual groups. We also found that older adults generalize more than young adults, regardless of the perturbation schedule (i.e., gradual or abrupt). Our results suggest that abrupt perturbations during adaptation do not limit the generalization of movement in older adults-perhaps because they are more likely to attribute them to their own faulty movements. These results suggest that large perturbations are better than small when training older clinical populations since abrupt disturbances would lead to more adaptation and generalization of corrected movements in older people.
Learning torus PCA based classification for multiscale RNA backbone structure correction with application to SARS-CoV-2
Authors: Wiechers Henrik , Eltzner Benjamin , Mardia Kanti V. , Huckemann Stephan F. 
Published: August 2021

AbstractMotivationReconstructions of structure of biomolecules, for instance via X-ray crystallography or cryo-EM frequently contain clashes of atomic centers. Correction methods are usually based on simulations approximating biophysical chemistry, making them computationally expensive and often not correcting all clashes.ResultsWe propose a computationally fast data-driven statistical method yielding suites free from within-suite clashes: From such a clash free training data set, devising mode hunting after torus PCA on adaptive cutting average linkage tree clustering (MINTAGE), we learn RNA suite shapes. With classification based on multiscale structure enhancement (CLEAN), for a given clash suite we determine its neighborhood on a mesoscopic scale involving several suites. As corrected suite we propose the Fréchet mean on a torus of the largest classes in this neighborhood. We validate CLEAN MINTAGE on a benchmark data set, compare it to a state of the art correction method and apply it, as proof of concept, to two exemplary suites adjacent to helical pieces of the frameshift stimulation element of SARS-CoV-2 which are difficult to reconstruct. In contrast to a recent reconstruction proposing several different structure models, CLEAN MINTAGE unanimously proposes structure corrections within the same clash free class for all suites.Code Availabilityhttps://gitlab.gwdg.de/henrik.wiechers1/clean-mintage-code
Increased PHOSPHO1 expression mediates cortical bone mineral density in renal osteodystrophy
Authors: Hsu Shun-Neng , Stephen Louise A , Dillon Scott , Milne Elspeth , Javaheri Behzad , Pitsillides Andrew A , Novak Amanda , Millán Jose Luis , Macrae Vicky E , Staines Katherine A , Farquharson Colin 
Published: August 2021

ABSTRACTPatients with advanced chronic kidney disease (CKD) often present with skeletal abnormalities; a condition known as renal osteodystrophy (ROD). While Tissue-nonspecific alkaline phosphatase (TNAP) and PHOSPHO1 are recognized to be critical for bone mineralization, their role in the etiology of ROD is unclear. To address this, ROD was induced in both wild-type and Phospho1 knockout (P1KO) mice using dietary adenine supplementation. The mice presented with hyperphosphatemia, hyperparathyroidism, and elevated levels of FGF23 and bone turnover markers. In particular, we noted that in CKD mice, bone mineral density (BMD) was increased in cortical bone (p < 0.05) but decreased in trabecular bone (p < 0.05). These changes were accompanied by decreased TNAP (p < 0.01) and increased PHOSPHO1 (p < 0.001) expression in wild-type CKD bones. In P1KO CKD mice, the cortical BMD phenotype was rescued, suggesting that the increased cortical BMD of CKD mice was driven by increased PHOSPHO1 expression. Other structural parameters were also improved in P1KO CKD mice. We further investigated the driver of the mineralization defects, by studying the effects of FGF23, PTH, and phosphate administration on PHOSPHO1 and TNAP expression by primary murine osteoblasts. We found both PHOSPHO1 and TNAP expression to be down-regulated in response to phosphate and PTH. While matrix mineralization was increased with phosphate (Pi), it decreased with PTH and FGF23 had no effect. The in vitro data suggest that the TNAP reduction in CKD-MBD is driven by the hyperphosphatemia and/or hyperparathyroidism noted in these mice, while the higher PHOSPHO1 expression may be a compensatory mechanism in an attempt to protect the bone from hypomineralization. We propose that increased PHOSPHO1 expression in ROD may contribute to the disordered skeletal mineralization characteristic of this progressive disorder.
Measuring the double-drift illusion and its resets with hand trajectories
Authors: ’t Hart Bernard Marius , Henriques Denise Y.P. , Cavanagh Patrick 
Published: August 2021

AbstractIf a gabor pattern drifts in one direction while its internal texture drifts in the orthogonal direction, its perceived position deviates further and further away from its true path. We first evaluated the illusion using manual tracking. Participants followed the gabor with a stylus on a drawing tablet that coincided optically with the horizontal monitor surface. Their hand and the stylus were not visible during the tracking. The magnitude of the tracking illusion corresponded closely to previous perceptual and pointing measures indicating that manual tracking is a valid measure for the illusion. This allowed us to use it in a second experiment to capture the behavior of the illusion as it eventually degrades and breaks down in single trials. Specifically, the deviation of the gabor stops accumulating at some point and either stays at a fixed offset or resets toward the veridical position. To report the perceived trajectory of the gabor, participants drew it after the gabor was removed from the monitor. Resets were detected and analyzed and their distribution matches neither a temporal nor a spatial limit, but rather a broad gamma distribution over time. This suggests that resets are triggered randomly, about once per 1.3 s, possible by extraneous distractions or eye movements.
Multispecies phase diagram of biofilm architectures reveals biophysical principles of biofilm development
Authors: Jeckel Hannah , Díaz-Pascual Francisco , Skinner Dominic J. , Song Boya , Jiménez-Siebert Eva , Jelli Eric , Vaidya Sanika , Dunkel Jörn , Drescher Knut 
Published: August 2021

AbstractBacterial biofilms are among the most abundant multicellular structures on Earth and play essential roles in a wide range of ecological, medical, and industrial processes. However, general principles that govern the emergence of biofilm architecture across different species remain unknown. Here, we combine experiments, simulations and statistical analysis to identify shared biophysical mechanisms that determine biofilm architecture development at the single-cell level, for the speciesVibrio cholerae, Escherichia coli, Salmonella enterica, andPseudomonas aeruginosa. Our data-driven analysis reveals that despite the many molecular differences between these species, the biofilm architecture differences can be described by only two control parameters: cellular aspect ratio and cell density. Further experiments using single-species mutants for which the cell aspect ratio and the cell density are systematically varied, and mechanistic simulations, show that tuning these two control parameters reproduces biofilm architectures of different species. Altogether, our results show that early-stage biofilm architecture is determined by mechanical cell-cell interactions which are conserved across different species and, therefore, provide a unifying understanding of biofilm architecture development.
Deep learning basedkcatprediction enables improved enzyme constrained model reconstruction
Authors: Li Feiran , Yuan Le , Lu Hongzhong , Li Gang , Chen Yu , Engqvist Martin K. M. , Kerkhoven Eduard J , Nielsen Jens 
Published: August 2021

AbstractEnzyme turnover numbers (kcatvalues) are key parameters to understand cell metabolism, proteome allocation and physiological diversity, but experimentally measuredkcatdata are sparse and noisy. Here we provide a deep learning approach to predictkcatvalues for metabolic enzymes in a high-throughput manner with the input of substrate structures and protein sequences. Our approach can capturekcatchanges for mutated enzymes and identify amino acid residues with great impact onkcatvalues. Furthermore, we applied the approach to predict genome scalekcatvalues for over 300 yeast species, demonstrating that the predictedkcatvalues are consistent with current evolutional understanding. Additionally, we designed an automatic pipeline using the predictedkcatvalues to parameterize enzyme-constrained genome scale metabolic models (ecGEMs) facilitated by a Bayesian approach, which outperformed the default ecGEMs in predicting phenotypes and proteomes and enabled to explain phenotype differences among yeast species. The deep learningkcatprediction approach and automatic ecGEM construction pipeline would thus be a valuable tool to uncover the global trend of enzyme kinetics and physiological diversity, and to further elucidate cell metabolism on a large scale.