bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digital Manufacturing of Functional Ready-to-Use Microfluidic Systems
Authors: Karamzadeh Vahid , Sohrabi-Kashani Ahmad , Shen Molly , Juncker David 
Published: May 2023

AbstractDigital manufacturing (DM) strives for the seamless manufacture of a functional device from a digital file. DM holds great potential for microfluidics, but requirements for embedded conduits and high resolution beyond the capability of common manufacturing equipment, and microfluidic systems’ dependence on peripherals (e.g. connections, power supply, computer), have limited its adoption. Microfluidic capillaric circuits (CCs) are structurally-encoded, self-contained microfluidic systems that operate and self-fill thanks to precisely tailored hydrophilicity. CCs were heretofore hydrophilized in a plasma chamber, but which only produces transient hydrophilicity, lacks reproducibility, and limits CC design to open surface channels sealed with a tape. Here we introduce the additive DM of monolithic, fully functional and intrinsically hydrophilic CCs. CCs were 3D printed with commonly available light engine-based 3D printers using polyethylene(glycol)diacrylate-based ink co-polymerized with hydrophilic acrylic acid crosslinkers and optimized for hydrophilicity and printability. A new, robust capillary valve design and embedded conduits with circular cross-sections that prevent bubble trapping are presented, and complex interwoven circuit architectures created, and their use illustrated with an immunoassay. Finally, the need for external paper capillary pumps is eliminated by directly embedding the capillary pump in the chip as a porous gyroid structure, realizing fully functional, monolithic CCs. Thence, a computer-aided design file can be made into a CC by commonly available 3D printers in less than 30 minutes enabling low-cost, distributed, DM of fully functional ready-to-use microfluidic systems.
Hybrid vesicle and reaction-diffusion modeling with STEPS
Authors: Hepburn Iain , Lallouette Jules , Chen Weiliang , Gallimore Andrew R. , Nagasawa Sarah Y. , De Schutter Erik 
Published: May 2023

AbstractVesicles carry out many essential functions within cells through the processes of endocytosis, exocytosis, and passive and active transport. This includes transporting and delivering molecules between different parts of the cell, and storing and releasing neurotransmitters in neurons. To date, computational simulation of these key biological players has been rather limited and has not advanced at the same pace as other aspects of cell modeling. As computational power advances and researchers want to add new realism to their models an important advance in the field of computational biology is to simulate vesicles in a realistic yet efficient manner. We describe a general vesicle modeling tool that has been designed for wide application to a variety of cell models, implemented within our voxel-based approach to modeling reaction-diffusion processes in realistic mesh reconstructions of cell tissue in our software STEPS. The implementation is validated in an extensive test suite, parallel performance demonstrated in a realistic synaptic bouton model, and example models are visualized in a Blender extension module.
Genome ofPhyllanthus emblica: the medicinal plant Amla with super antioxidant properties
Authors: Mahajan Shruti , Bisht Manohar S. , Chakraborty Abhisek , Sharma Vineet K 
Published: May 2023

AbstractPhyllanthus emblicaor Indian gooseberry, commonly known as amla, is an important medicinal horticultural plant used in traditional and modern medicines. It bears stone fruits with immense antioxidant properties due to being one of the richest natural sources of vitamin C and numerous flavonoids. This study presents the first genome sequencing of this species performed using 10x Genomics and Oxford Nanopore Technology. The draft genome assembly was 519 Mbp in size and consisted of 4,384 contigs, N50 of 597 Kbp, 98.4% BUSCO score and 37,858 coding sequences. This study also reports the genome-wide phylogeny of this species with 26 other plant species that resolved the phylogenetic position ofP. emblica. The presence of three ascorbate biosynthesis pathways including L-galactose, galacturonate and myo-inositol pathways was confirmed in this genome. A comprehensive comparative evolutionary genomic analysis including gene family expansion/contraction and identification of multiple signatures of adaptive evolution provided evolutionary insights into ascorbate and flavonoid biosynthesis pathways and stone fruit formation through lignin biosynthesis. The availability of this genome will be beneficial for its horticultural, medicinal, dietary, and cosmetic applications and will also help in comparative genomics analysis studies.
A single-cell strategy for the identification of intronic variants related to mis-splicing in pancreatic cancer
Authors: Duman Emre Taylan , Sitte Maren , Conrads Karly , Makay Adi , Ludewig Fabian , Ströbel Philipp , Ellenrieder Volker , Hessman Elisabeth , Papantonis Argyris , Salinas Gabriela 
Published: May 2023

AbstractMost clinical diagnostic and genomic research setups focus almost exclusively on coding regions and essential splice sites, thereby overlooking other non-coding variants. As a result, intronic variants that can promote mis-splicing events across a range of diseases, including cancer, are yet to be systematically investigated. Such investigations would require both genomic and transcriptomic data, but there currently exist very few datasets that satisfy these requirements. We address this by developing a single-nucleus full-length RNA-sequencing approach that allows for the detection of potentially pathogenic intronic variants. We exemplify the potency of our approach by applying pancreatic cancer tumor and tumor-derived specimens and linking intronic variants to splicing dysregulation. We specifically find that prominent intron retention and pseudo-exon activation events are shared by the tumors and affect genes encoding key transcriptional regulators. Our work paves the way for the assessment and exploitation of intronic mutations as powerful prognostic markers and potential therapeutic targets in cancer.Graphical Abstract
Histone H3.3 lysine 9 and 27 control repressive chromatin states at crypticcis-regulatory elements and bivalent promoters in mouse embryonic stem cells
Authors: Trovato Matteo , Bunina Daria , Yildiz Umut , Marx Nadine Fernandez-Novel , Uckelmann Michael , Levina Vita , Kori Yekaterina , Janeva Ana , Garcia Benjamin A. , Davidovich Chen , Zaugg Judith B. , Noh Kyung-Min 
Published: May 2023

AbstractHistone modifications are associated with distinct transcriptional states, but it is unclear whether they instruct gene expression. To investigate this, we mutated histone H3.3 K9 and K27 residues in mouse embryonic stem cells (mESCs). Here, we find that H3.3K9 is essential for controlling specific distal intergenic regions and for proper H3K27me3 deposition at promoters. The H3.3K9A mutation resulted in decreased H3K9me3 at regions encompassing endogenous retroviruses and induced a gain of H3K27ac and nascent transcription. These changes in the chromatin environment unleashed cryptic enhancers, resulting in the activation of distinctive transcriptional programs and culminating in protein expression normally restricted to specialized immune cell types. The H3.3K27A mutant disrupted deposition and spreading of the repressive H3K27me3 mark, particularly impacting bivalent genes with higher basal level of H3.3 at promoters. Therefore, H3.3K9 and K27 crucially orchestrate repressive chromatin states atcis-regulatory elements and bivalent promoters, respectively, and instruct proper transcription in mESCs.
An Atypical E3 Ligase Module in UBR4 Mediates Destabilization of N-degron Substrates
Authors: Barnsby-Greer Lucy , Mabbitt Peter D. , Dery Marc-Andre , Squair Daniel R. , Wood Nicola T. , Lange Sven , Virdee Satpal 
Published: May 2023

AbstractUBR4 is an E3 ligase (E3) of the N-degron pathway and is involved in neurodevelopment, age-associated muscular atrophy and cancer progression. The location and mechanistic classification of the E3 module within the 600 kDa protein UBR4 remains unknown. Herein, we identify and characterize, at a biochemical and structural level, a distinct E3 module within human UBR4 consisting of a novel “hemiRING” zinc finger, a helical-rich UBR Zinc-finger Interacting (UZI) subdomain, and a predicted backside interacting N-terminal helix. A structure of an E2 conjugating enzyme (E2)-E3 complex provides atomic level insight into the exquisite specificity of the hemiRING towards the E2s UBE2A/B. The UZI subdomain can be considered a component of the E3 module as it has a modest activating effect on the ubiquitin loaded E2 (E2∼Ub), which is complemented by the intrinsically high lysine reactivity of UBE2A. These findings reveal the mechanistic underpinnings of a neuronal N-degron E3 ligase, its specific recruitment of UBE2A, and highlight the underappreciated architectural diversity of cross-brace domains associated with ubiquitin E3 activity.
Rapid evolution of piRNA clusters in theDrosophila melanogasterovary
Authors: Srivastav Satyam , Feschotte Cédric , Clark Andrew G. 
Published: May 2023

AbstractAnimal genomes are parasitized by a horde of transposable elements (TEs) whose mutagenic activity can have catastrophic consequences. The piRNA pathway is a conserved mechanism to repress TE activity in the germline via a specialized class of small RNAs associated with effector Piwi proteins called piwi-associated RNAs (piRNAs). piRNAs are produced from discrete genomic regions called piRNA clusters (piCs). While piCs are generally enriched for TE sequences and the molecular processes by which they are transcribed and regulated are relatively well understood inDrosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC evolution, we use a population genomics approach to compare piC activity and sequence composition across 8 geographically distant strains ofD. melanogasterwith high quality long-read genome assemblies. We perform extensive annotations of ovary piCs and TE content in each strain and test predictions of two proposed models of piC evolution. The‘de novo’model posits that individual TE insertions can spontaneously attain the status of a small piC to generate piRNAs silencing the entire TE family. The ‘trap’ model envisions large and evolutionary stable genomic clusters where TEs tend to accumulate and serves as a long-term “memory” of ancient TE invasions and produce a great variety of piRNAs protecting against related TEs entering the genome. It remains unclear which model best describes the evolution of piCs. Our analysis uncovers extensive variation in piC activity across strains and signatures of rapid birth and death of piCs in natural populations. Most TE families inferred to be recently or currently active show an enrichment of strain-specific insertions into large piCs, consistent with the trap model. By contrast, only a small subset of active LTR retrotransposon families is enriched for the formation of strain-specific piCs, suggesting that these families have an inherent proclivity to formde novopiCs. Thus, our findings support aspects of both‘de novo’and ‘trap’ models of piC evolution. We propose that these two models represent two extreme stages along an evolutionary continuum, which begins with the emergence of piCsde novofrom a few specific LTR retrotransposon insertions that subsequently expand by accretion of other TE insertions during evolution to form larger ‘trap’ clusters. Our study shows that piCs are evolutionarily labile and that TEs themselves are the major force driving the formation and evolution of piCs.
SeMOE allows for quantitative glycan perception and exhibits anti-cancer potentiality
Authors: Tian Xiao , Zheng Lingna , Wang Changjiang , Han Yida , Li Yujie , Cui Tongxiao , Liu Jialin , Liu Chuanming , Jia Guogeng , Yang Lujie , Zeng Chen , Ding Lijun , Wang Chu , Cheng Bo , Wang Meng , Xie Ran 
Published: May 2023

AbstractMetabolic oligosaccharide engineering (MOE) is a classical chemical approach to perturb, profile and perceive glycans in physiological systems, but probes upon bioorthogonal reaction require accessibility and background signal readout makes it challenging to achieve absolute glycan quantification. Here we develop SeMOE, a selenosugar-based metabolic oligosaccharide engineering strategy that combines elemental analysis and MOE to enable the absolute quantification and mass spectrometric imaging of glycome in a concise procedure. We demonstrate that SeMOE probes allow for perception, absolute quantification and visualization of glycans in diverse biological contexts. We demonstrate that chemical reporters on conventional MOE can be integrated into a bifunctional SeMOE probe to provide multimodality signal readouts. We further show the anti-cancer potentiality of SeMOE probes. SeMOE thus provides a convenient and simplified method to “see more” of the glyco-world.
“When I talk about it, my eyes light up!” Impacts of a national laboratory internship on community college student success
Authors: Coté Laleh E. , Van Doren Seth , Zamora Astrid N. , Jaramillo Salcido Julio , Law Esther W. , Otero Munoz Gabriel , Manocha Aparna , Flood Colette L. , Baranger Anne M. 
Published: May 2023

AbstractParticipation in technical/research internships may improve undergraduate graduation rates and persistence in science, technology, engineering, and mathematics (STEM), yet little is known about the benefits of these activities a) for community college students, b) when hosted by national laboratories, and c) beyond the first few years after the internship. We applied Social Cognitive Career Theory (SCCT) to investigate alumni perspectives about how CCI at Lawrence Berkeley National Laboratory (LBNL) impacted their academic/career activities. We learned that alumni had low confidence and expectations of success in STEM as community college students. Participation in CCI increased their professional networks, expectations of success, and STEM skills, identity, and self-efficacy/confidence. Hispanic/Latinx alumni recalled the positive impact of mentors who prioritized personal connections, and women valued “warm” social environments. We propose several additions to the SCCT model, to better reflect the supports and barriers to STEM persistence for community college students.
Conformational stability and order of Hoogsteen base pair induced by protein binding
Authors: Kole Kanika , Gupta Aayatti Mallick , Chakrabarti Jaydeb 
Published: May 2023

AbstractSeveral experimental studies have shown that in the presence of proteins, the Hoogsteen (HG) base pair (bp) becomes stabilized. The molecular mechanism underlying this stabilization is not well known. This leads us to use all-atom molecular dynamics simulation to examine the stability of the HG bp in duplex DNA in both the absence and presence of proteins. We use conformational thermodynamics to investigate the stability of a HG bp in duplex DNA at the molecular level. We also compute the changes in the conformational free energy and entropy of DNA when DNA adopts a HG bp in its bp sequence rather than a Watson–Crick (WC) bp in both naked DNA and protein-bound DNA complex. We observe that the HG bp and the entire DNA duplex conformation are stabilized and ordered in the presence of proteins. Sugar-phosphate, sugar-base, and sugar-pucker torsion angles play key roles in stabilizing and ordering the HG bp in the protein-bound DNA complex.
The association of a streamlined and updated stroke protocol with improved secondary prevention and outcome
Authors: Leung Almond , Fong Richard J , Mahawish Karim M 
Published: May 2023

AbstractBackgroundStroke recurrence rates following an index event remain high compared with the baseline population. Evidence-based stroke treatments reduce this risk.AimsTo determine the effect of an updated and streamlined hospital stroke guideline on prescribing practices and stroke recurrence rates at 3 months.MethodsHospital registries were searched for ICD-10 codes for transient ischaemic attack (TIA) and ischaemic stroke between July 2019 and July 2020. Data on patient demographics, discharge documentation, and other outcomes of interest were dichotomised into pre and post-intervention.Results396 patients were identified. There was a significant reduction in the stroke recurrence rate at 3 months post guideline update (8.3% vs 2.2%, OR 0.24, p<0.01). There were significant improvements in prescriptions for statins (66.5% vs 81.2%, p≤0.01) and antihypertensives (40.7% vs 50.7%, p=0.05), and documentation of lipid and blood pressure targets in discharge letters. There was a trend towards greater use of dual antiplatelet therapy (25.2% vs 34.1%, p=0.057).ConclusionIn this audit, we found an association between the guideline update and improved patient outcomes and prescribing practices. We were unable to directly attribute the reduction in stroke recurrence to any single factor. This may be a chance finding and warrants investigation in other settings.
The developmental timing of spinal touch processing alterations and its relation to ASD-associated behaviors in mouse models
Authors: Tasnim Aniqa , Alkislar Ilayda , Hakim Richard , Turecek Josef , Abdelaziz Amira , Orefice Lauren L. , Ginty David D. 
Published: May 2023

ABSTRACTAltered somatosensory reactivity is frequently observed among individuals with autism spectrum disorders (ASDs). Here, we report that while multiple mouse models of ASD exhibit aberrant somatosensory behaviors in adulthood, some models exhibit altered tactile reactivity as early as embryonic development, while in others, altered reactivity emerges later in life. Additionally, tactile over-reactivity during neonatal development is associated with anxiety-like behaviors and social interaction deficits in adulthood, whereas tactile over-reactivity that emerges later in life is not. The locus of circuit disruption dictates the timing of aberrant tactile behaviors: altered feedback or presynaptic inhibition of peripheral mechanosensory neurons leads to abnormal tactile reactivity during neonatal development, while disruptions in feedforward inhibition in the spinal cord lead to touch reactivity alterations that manifest later in life. Thus, the developmental timing of aberrant touch processing can predict the manifestation of ASD-associated behaviors in mouse models, and differential timing of sensory disturbance onset may contribute to phenotypic diversity across individuals with ASD.
NMR Resonance Assignment of the LA Motif of Human LA-Related Protein 1
Authors: Smith Benjamin C. , Silvers Robert 
Published: May 2023

AbstractHuman La-related protein 1 (HsLARP1) is involved in post-transcriptional regulation of certain 5’ s terminal oligopyrimidine (5’TOP) mRNAs as well as other mRNAs and binds to both the 5’TOP motif and the 3’-poly(A) tail of certain mRNAs. HsLARP1 is heavily involved in cell proliferation, cell cycle defects, and cancer, where HsLARP1 is significantly upregulated in malignant cells and tissues. Like all LARPs, HsLARP1 contains a folded RNA binding domain, the La motif (LaM). Our current understanding of post-transcriptional regulation that emanates from the intricate molecular framework of HsLARP1 is currently limited to small snapshots, obfuscating our understanding of the full picture on HsLARP1 functionality in post-transcriptional events. Here, we present the nearly complete resonance assignment of the LaM of HsLARP1, providing a significant platform for future NMR spectroscopic studies.
Interplay of macromolecular interactions during assembly of human DNA polymerase δ holoenzymes and initiation of DNA synthesis
Authors: Norris Jessica L. , Rogers Lindsey O. , Pytko Kara G. , Dannenberg Rachel L. , Perreault Samuel , Kaushik Vikas , Kuppa Sahiti , Antony Edwin , Hedglin Mark 
Published: May 2023

ABSTRACTIn humans, DNA polymerase δ (Pol δ) holoenzymes, comprised of Pol δ and the processivity sliding clamp, proliferating cell nuclear antigen (PCNA), carry out DNA synthesis during lagging strand DNA replication, initiation of leading strand DNA replication, and the major DNA damage repair and tolerance pathways. Pol δ holoenzymes are assembled at primer/template (P/T) junctions and initiate DNA synthesis in a coordinated process involving the major single strand DNA-binding protein complex, replication protein A (RPA), the processivity sliding clamp loader, replication factor C (RFC), PCNA, and Pol δ. Each of these factors interact uniquely with a P/T junction and most directly engage one another. Currently, the interplay between these macromolecular interactions is largely unknown. In the present study, novel Förster Resonance Energy Transfer (FRET) assays reveal that dynamic interactions of RPA with a P/T junction during assembly of a Pol δ holoenzyme and initiation of DNA synthesis maintain RPA at a P/T junction and accommodate RFC, PCNA, and Pol δ, maximizing the efficiency of each process. Collectively, these studies significantly advance our understanding of human DNA replication and DNA repair.
Simultaneous enhancement of multiple functional properties using evolution-informed protein design
Authors: Fram Benjamin , Truebridge Ian , Su Yang , Riesselman Adam J. , Ingraham John B. , Passera Alessandro , Napier Eve , Thadani Nicole N. , Lim Samuel , Roberts Kristen , Kaur Gurleen , Stiffler Michael , Marks Debora S. , Bahl Christopher D. , Khan Amir R. , Sander Chris , Gauthier Nicholas P. 
Published: May 2023

AbstractDesigning optimized proteins is important for a range of practical applications. Protein design is a rapidly developing field that would benefit from approaches that enable many changes in the amino acid primary sequence, rather than a small number of mutations, while maintaining structure and enhancing function. Homologous protein sequences contain extensive information about various protein properties and activities that have emerged over billions of years of evolution. Evolutionary models of sequence co-variation, derived from a set of homologous sequences, have proven effective in a range of applications including structure determination and mutation effect prediction. In this work we apply one of these models (EVcouplings) to computationally design highly divergent variants of the model protein TEM-1 β-lactamase, and characterize these designs experimentally using multiple biochemical and biophysical assays. Nearly all designed variants were functional, including one with 84 mutations from the nearest natural homolog. Surprisingly, all functional designs had large increases in thermostability and most had a broadening of available substrates. These property enhancements occurred while maintaining a nearly identical structure to the wild type enzyme. Collectively, this work demonstrates that evolutionary models of sequence co-variation (1) are able to capture complex epistatic interactions that successfully guide large sequence departures from natural contexts, and (2) can be applied to generate functional diversity useful for many applications in protein design.