bluuebunny/crossref_metadata_2025_split huggingface dataset:
A synthetic membrane shaper for controlled liposome deformation
Authors: De Franceschi Nicola , Pezeshkian Weria , Fragasso Alessio , Bruininks Bart M.H. , Tsai Sean , Marrink Siewert J. , Dekker Cees 
Published: December 2021

AbstractShape defines the structure and function of cellular membranes. In cell division, the cell membrane deforms into a ‘dumbbell’ shape, while organelles such as the autophagosome exhibit ‘stomatocyte’ shapes. Bottom-up in vitro reconstitution of protein machineries that stabilize or resolve the membrane necks in such deformed liposome structures is of considerable interest to characterize their function. Here we develop a DNA-nanotechnology-based approach that we call Synthetic Membrane Shaper (SMS), where cholesterol-linked DNA structures attach to the liposome membrane to reproducibly generate high yields of stomatocytes and dumbbells. In silico simulations confirm the shape-stabilizing role of the SMS. We show that the SMS is fully compatible with protein reconstitution by assembling bacterial divisome proteins (DynaminA, FtsZ:ZipA) at the catenoidal neck of these membrane structures. The SMS approach provides a general tool for studying protein binding to complex membrane geometries that will greatly benefit synthetic cell research.
A systems approach discovers the role and characteristics of seven LysR type transcription factors inEscherichia coli
Authors: Rodionova Irina A. , Gao Ye , Monk Jonathan , Wong Nicholas , Szubin Richard , Lim Hyun Gyu , Rodionov Dmitry A. , Zhang Zhongge , Saier Milton H. , Palsson Bernhard O. 
Published: December 2021

ABSTRACTAlthoughEscherichia coliK-12 strains represent perhaps the best known model bacteria, we do not know the identity or functions of all of their transcription factors (TFs). It is now possible to systematically discover the physiological function of TFs inE. coliBW25113 using a set of synergistic methods; including ChIP-exo, growth phenotyping, conserved gene clustering, and transcriptome analysis. Among 47 LysR-type TFs (LTFs) found on theE. coliK-12 genome, many regulate nitrogen source utilization or amino acid metabolism. However, 19 LTFs remain unknown. In this study, we elucidated the regulation of seven of these 19 LTFs: YbdO, YbeF, YgfI, YiaU, YneJ, YcaN, YbhD. We show that: 1) YbdO regulation has an effect on bacterial growth at low pH with citrate supplementation. YbdO is a repressor of theybdNMoperon and is implicated in the regulation of citrate lyase genes (citCDEFG); 2) YgfI activates thedhaKLMoperon that encodes the phosphotransferase system involved in glycerol and dihydroxyacetone utilization; 3) YiaU regulates theyiaTgene encoding an outer membrane protein, andwaaPSBOJYZUoperon is also important in determining cell density at the stationary phase; 4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator offnrS(a small RNA molecule). PtrR is important for bacterial growth in the presence of L-glutamate and putrescine as nitrogen sources; and 5) YbhD and YcaN regulate adjacent y-genes on the genome and YbeF is involved in flagella gene regulation. We have thus established the functions for four LTFs and identified the target genes for three LTFs.IMPORTANCEThe reconstruction of the transcriptional regulatory network (TRN) is important for gram-negative bacteria such asE. coli. LysR-type TFs are abundant in Enterobacteria, but many LTF functions still remain unknown. Here we report putative functions of uncharacterized TFs based on multi-omics data related to L-threonine, L-glutamate, and putrescine utilization. Amino acids (AAs) and polyamines are important sources of nitrogen for many microorganisms, but the increase in one amino acid or putrescine concentration in a minimal medium also induces stress. Although polyamine metabolism has been studied, the TRN that controls the putrescine (Ptr) and AA utilization at minimal medium conditions are still poorly understood. The function of previously uncharacterized transcriptional regulators YbdO, YgfI, and YneJ (PtrR) were identified inEscherichia coli. PtrR is important for Ptr and L-glutamate utilization, while YgfI transcriptional regulation was found to be important for growth on L-threonine and glycerol as a carbon source.
Coupled protein quality control during nonsense mediated mRNA decay
Authors: Inglis Alison J. , Guna Alina , Merchán Ángel Gálvez , Pal Akshaye , Esantsi Theodore K. , Keys Heather R. , Frenkel Evgeni M. , Oania Robert , Weissman Jonathan S. , Voorhees Rebecca M. 
Published: December 2021

ABSTRACTTranslation of mRNAs containing premature termination codons (PTCs) can result in truncated protein products with deleterious effects. Nonsense-mediated decay (NMD) is a surveillance path-way responsible for detecting and degrading PTC containing transcripts. While the molecular mechanisms governing mRNA degradation have been extensively studied, the fate of the nascent protein product remains largely uncharacterized. Here, we use a fluorescent reporter system in mammalian cells to reveal a selective degradation pathway specifically targeting the protein product of an NMD mRNA. We show that this process is post-translational, and dependent on an intact ubiquitin proteasome system. To systematically uncover factors involved in NMD-linked protein quality control, we conducted genome-wide flow cytometry-based screens. Our screens recovered known NMD factors, and suggested a lack of dependence on the canonical ribosome-quality control (RQC) pathway. Finally, one of the strongest hits in our screens was the E3 ubiquitin ligase CNOT4, a member of the CCR4-NOT complex, which is involved in initiating mRNA degradation. We show that CNOT4 is involved in NMD coupled protein degradation, and its role depends on a functional RING ubiquitin ligase domain. Our results demonstrate the existence of a targeted pathway for nascent protein degradation from PTC containing mRNAs, and provide a framework for identifying and characterizing factors involved in this process.
Comparison of Three Individual Identification Algorithms for Sperm Whales (Physeter macrocephalus) after Automated Detection
Authors: Blount Drew , Holmberg Jason , Parham Jason , Gero Shane , Gordon Jonathan , Levenson J. Jacob 
Published: December 2021

AbstractPhoto-identification of individual sperm whales (Physeter macrocephalus) is the primary technique for mark-recapture-based population analyses for the species The visual appearance of the fluke — with its distinct nicks and notches — often serves as the primary visual differentiator, allowing humans to make recorded sightings of specific individuals. However, the advent of digital photography and the significant increase in volume of images from multiple projects in combination with pre-existing historical catalogs has made applying the method more challenging.with the required human labor for de-duplication (reduction of Type II errors) and reconciliation of sightings between large datasets too cost- and time-prohibitive. To address this, we trained and evaluated the accuracy of PIE v2 (a triplet loss network) along with two existing fluke trailing edge-matching algorithms, CurvRank v2 and Dynamic Time Warping (DTW), as a mean to speed comparison among a high volume of photographs. Analyzed data were collected from a curated catalog of well-known sperm whales sighted across years (2005-2018) off the island of Dominica. The newly-trained PIE model outperformed the older CurvRank and DTW algorithms, and PIE provided the following top-k individual ID matching accuracy on a standard min-3/max-10 sighting training data set: Rank-1: 87.0%, Rank-5: 90.5%, and Rank-12: 92.5%. An essential aspect of PIE is that it can learn new individuals without network retraining, which can be immediately applied in the presence of (and for the resolution of) duplicate individuals in overlapping catalogs. Overall, our results recommend the use of PIE v2 and CurvRank v2 for ID reconciliation in combination due to their complementary performance.
Habitat deterioration despite protection: long-term declines of littoral area of fishponds in Czech nature reserves
Authors: Kolar Vojtech , Francová Kateřina , Vrba Jaroslav , Grill Stanislav , Boukal David S. 
Published: December 2021

AbstractFishponds play a key role in current pondscapes in many developed countries. Their littoral areas, supporting multiple ecosystem functions including the maintenance of aquatic and riparian biodiversity, have been adversely affected by the move shift towards more intensive aquaculture and widespread eutrophication in the middle 20th century. To counteract these changes, many fishponds received some protection, but its long-term efficiency has not been studied. Here we focus on the role of conservation status in protecting the area of littoral areas of fishponds in Czechia between the years 1950 and 2019. We found that the conservation status of these fishponds did not prevent habitat deterioration in most of the fishponds, especially during the second half of the 20th century. Moreover, we detected no significant effects of the reserve establishment year, fishpond area and conservation target on the littoral areas. This suggests that the conservation measures are insufficient across fishpond reserve types. We attribute the negative trends to persisting high fish stocks, especially of common carp, and eutrophication resulting from additional feeding, pond manuring, and ongoing nutrient inputs from the pond catchments. Sediment dredging and high grazing pressure by waterfowl in some reserves can further aggravate the situation. We conclude that effective protection of the littoral areas requires a paradigm shift towards less intensive fish stock management, more frequent summer drainage, and effective reduction of all nutrient inputs to increase the water quality. Such measures can help recover the littoral areas and the associated biota.Graphical abstractHighlightsLittoral vegetation in ponds supports high biodiversity but often lacks protection.We evaluated long-term changes in the littoral areas of fishponds in Czechia.The areas decreased markedly in both protected and unprotected ponds since 1950.Reserve duration, fishpond area and conservation target did not affect the trends.Changes in fishpond management are recommended for littoral area recovery.
BK channels of five different subunit combinations underlie the de novo KCNMA1 G375R channelopathy
Authors: Geng Yanyan , Li Ping , Butler Alice , Wang Bill , Salkoff Lawrence , Magleby Karl L. 
Published: December 2021

AbstractThe molecular basis of a severe developmental and neurological disorder associated with a de novo G375R variant of the tetrameric BK channel is unknown. Here we address this question by recording from single BK channels expressed for a heterozygous G375R mutation. Five different types of functional BK channels were observed: 3% were WT, 12% were homomeric mutant, and 85% were three different types of hybrid channels. All channel types except WT showed a marked gain-of-function in voltage activation and a smaller loss-of-function in single channel conductance, with both becoming more pronounced as the number of mutant subunits per tetrameric channel increased. The molecular phenotype suggested codominance for the two homomeric channels and partial dominance for the hybrid channels. A model in which BK channels are randomly assembled from mutant and WT subunits, with each subunit contributing increments of activation and conductance, approximated the molecular phenotype of the heterozygous G375R mutation.
De novo serine biosynthesis from glucose predicts sex-specific response to antifolates in non-small cell lung cancer cell lines
Authors: Sponagel Jasmin , Devarakonda Siddhartha , Rubin Joshua B. , Luo Jingqin , Ippolito Joseph E. 
Published: December 2021

SummaryLung cancer is the leading cause of cancer-related death. Intriguingly, males with non-small cell lung cancer (NSCLC), the most common type of lung cancer, have a higher mortality rate than females. Here, we investigated the role of serine metabolism as a predictive marker for sensitivity to the antifolate pemetrexed in male and female NSCLC cell lines. Using [13C6] glucose tracing in NSCLC cell lines, we found that male cells generated significantly more serine from glucose than female cells. Higher serine biosynthesis was further correlated with increased sensitivity to pemetrexed in male cells only. Concordant sex differences in metabolic gene expression were evident in NSCLC and pan-cancer transcriptome datasets, suggesting a potential mechanism with wide-reaching applicability. These data were further validated by integrating antifolate drug cytotoxicity and metabolic pathway transcriptome data from pan-cancer cell lines. Together, these findings highlight the importance of considering sex differences in cancer metabolism to improve treatment for all patients.
Bridging functional annotation gaps in non-model plant genes with AlphaFold, DeepFRI and small molecule docking
Authors: Stephan Georgie , Dugdale Benjamin , Deo Pradeep , Harding Rob , Dale James , Visendi Paul 
Published: December 2021

BackgroundFunctional annotation assigns descriptive biological meaning to genetic sequences. Limited availability of manually curated or experimentally validated plant genes from a diverse range of taxa poses a significant challenge for functional annotation in non-model organisms. Accurate computational approaches are required. We argue that recent breakthroughs in deep learning have the potential to not only narrow the functional annotation gap between non-model and model plant organisms, but also annotate and reveal novel functions even for genes with no homologs in public databases.ResultsDeep learning models were applied to functionally annotate a set of previously published differentially expressed genes. Predicted protein structures and functional annotations were generated using the AlphaFold protein structure and DeepFRI protein language inference models respectively. The resulting structures and functional annotations were validated using small molecule docking experiments. DeepFRI and AlphaFold models not only correctly annotated differentially expressed genes, but also revealed detailed mechanisms involving protein-protein interactions.ConclusionsDeep learning models are capable of inferring novel functions and achieving high accuracy in functional annotation. Their increased use in plant research will result in major improvements in annotations for non-model plants that are underrepresented in genome databases. We illustrate how integrating protein structure prediction, functional residue prediction, and small molecule docking can infer plausible protein-protein interactions and yield additional mechanistic insights. This approach will aid in the selection of candidate genes for further study from differential expression studies that generate large gene lists.
Remote contextual fear retrieval engages activity from salience network regions in rats
Authors: dos Santos Corrêa Moisés , Grisanti Gabriel David Vieira , Franciscatto Isabelle Anjos Fernandes , Tarumoto Tatiana Suemi Anglas , Tiba Paula Ayako , Ferreira Tatiana Lima , Fornari Raquel Vecchio 
Published: December 2021

ABSTRACTThe ability to retrieve contextual fear memories depends on the coordinated activation of a brain-wide circuitry. Transition from recent to remote memories seems to involve the reorganization of this circuitry, a process called systems consolidation that has been associated with time-dependent fear generalization. However, it is unknown whether emotional memories acquired under different stress levels can undergo different systems consolidation processes. Here, we explored the activation pattern and functional connectivity of key brain regions associated with contextual fear conditioning (CFC) retrieval after recent (2 days) or remote (28 days) memory tests performed in rats submitted to strong (1.0mA footshock) or mild (0.3mA footshock) training. We used brain tissue from Wistar rats from a previous study, where we observed that increasing training intensity promotes fear memory generalization over time, possibly due to an increase in corticosterone (CORT) levels during memory consolidation. Analysis of Fos expression across 8 regions of interest (ROIs) allowed us to identify coactivation between them at both timepoints following memory recall. Our results showed that strong CFC elicits higher Fos activation in the anterior insular and prelimbic cortices during remote retrieval, which was positively correlated with freezing along with the basolateral amygdala. Rats trained either with mild or strong CFC showed broad functional connectivity at the recent timepoint whereas only animals submitted to the strong CFC showed a widespread loss of coactivation during remote retrieval. Post-training plasma CORT levels are positively correlated with FOS expression during recent retrieval in strong CFC, but negatively correlated with FOS expression during remote retrieval in mild CFC. Our findings suggest that increasing training intensity results in differential processes of systems consolidation, possibly associated with increased post-training CORT release, and that strong CFC engages activity from the aIC, BLA and PrL – areas associated with the Salience Network in rats – during remote retrieval.
Using Deep Learning for Gene Detection and Classification in Raw Nanopore Signals
Authors: Nykrynova Marketa , Barton Vojtech , Jakubicek Roman , Bezdicek Matej , Lengerova Martina , Skutkova Helena 
Published: December 2021

AbstractRecently, nanopore sequencing has come to the fore as library preparation is rapid and simple, sequencing can be done almost anywhere, and longer reads are obtained than with next-generation sequencing. The main bottleneck still lies in data postprocessing which consists of basecalling, genome assembly, and localizing significant sequences, which is time consuming and computationally demanding, thus prolonging delivery of crucial results for clinical practice. Here, we present a neural network-based method capable of detecting and classifying specific genomic regions already in raw nanopore signals – squiggles. Therefore, the basecalling process can be omitted entirely as the raw signals of significant genes, or intergenic regions can be directly analysed, or if the nucleotide sequences are required, the identified squiggles can be basecalled, preferably to others. The proposed neural network could be included directly in the sequencing run, allowing real-time squiggle processing.
Dual Passive Reactive Brain Computer Interface: a Novel Approach to Human-Machine Symbiosis
Authors: Dehais Frédéric , Ladouce Simon , Darmet Ludovic , Tran-Vu Nong , Ferraro Giuseppe , Tresols Juan Torre , Velut Sébastien , Labedan Patrice 
Published: December 2021

ABSTRACTThe present study proposes a novel concept of neuroadaptive technology, namely a dual passive-reactive Brain-Computer Interface (BCI), that enables bi-directional interaction between humans and machines. We have implemented such a system in a realistic flight simulator using the NextMind classification algorithms and framework to decode pilots’ intention (reactive BCI) and to infer their level of attention (passive BCI). Twelve pilots used the reactive BCI to perform checklists along with an anti-collision radar monitoring task that was supervised by the passive BCI. The latter simulated an automatic avoidance maneuver when it detected that pilots missed an incoming collision. The reactive BCI reached 100% classification accuracy with a mean reaction time of 1.6s when exclusively performing the checklist task. Accuracy was up to 98.5% with a mean reaction time of 2.5s when pilots also had to fly the aircraft and monitor the anti-collision radar. The passive BCI achieved a F1 − score of 0.94. This first demonstration shows the potential of a dual BCI to improve human-machine teaming which could be applied to a variety of applications.
On the assessment of the sources of inoculum of bacterial wilt in Brazil
Authors: Mizubuti Eduardo S. G. , Yamada Jaqueline K. , Santiago Thaís R. , Lopes Carlos Alberto 
Published: December 2021

AbstractDispersal of Ralstonia spp. cells by water and contaminated plant material and the importance of weeds as inoculum sources have been poorly investigated. Water of rivers, soil from fields of diverse crops and areas of natural vegetation both from the Amazônia, Cerrado and Mata Atlântica biomes, besides soil of the rhizosphere of weeds present in tomato fields with records of bacterial wilt were sampled and analyzed to detect Ralstonia spp. Seeds of tomato plants artificially and naturally infected with Ralstonia spp. were also processed. All samples were enriched a priori in selective medium South Africa (SMSA) and colonies were isolated in plates containing solid SMSA. Detection of Ralstonia spp. was confirmed by polymerase chain reaction with specific primers. The Co – operational PCR (CO-PCR) was also used to detect Ralstonia spp. Colonies were obtained from soil samples and from a commercial substrate sample. Five soil samples from eggplant fields, one from coffee field, one substrate from potato seed tuber production, two soil samples from the rhizosphere of Amaranthus spp., one from Bidens pilosa and one from Solanum americanum tested positive for Ralstonia spp. Besides these soil samples, five water samples of rivers were positive for CO-PCR detection: two samples from Amazônia, one from Cerrado and two samples from irrigation water collected from tomato fields located in the Mata Atlântica biome. Ralstonia spp. were not detected in tomato seeds. These results revealed potential inoculum sources, especially weeds, in areas with historical records of bacterial wilt. Additionally, rivers may act as dispersal agents of inoculum of Ralstonia spp.
A spectral demixing method for high-precision multi-color localization microscopy
Authors: Andronov Leonid , Genthial Rachel , Hentsch Didier , Klaholz Bruno P. 
Published: December 2021

AbstractSingle molecule localization microscopy (SMLM) with a dichroic image splitter can provide invaluable multi-color information regarding colocalization of individual molecules, but it often suffers from technical limitations. So far, demixing algorithms give suboptimal results in terms of localization precision and correction of chromatic aberrations. Here we present an image splitter based multi-color SMLM method (splitSMLM) that offers much improved localization precision & drift correction, compensation of chromatic aberrations, and optimized performance of fluorophores in a specific buffer to equalize their reactivation rates for simultaneous imaging. A novel spectral demixing algorithm, SplitViSu, fully preserves localization precision with essentially no data loss and corrects chromatic aberrations at the nanometer scale. Multi-color performance is further improved by using optimized fluorophore and filter combinations. Applied to three-color imaging of the nuclear pore complex (NPC), this method provides a refined positioning of the individual NPC proteins and reveals that Pom121 clusters act as NPC deposition loci, hence illustrating strength and general applicability of the method.