bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Kink in DWORF Helical Structure Controls the Activation of the Sarco-plasmic Reticulum Ca2+-ATPase
Authors: Reddy U. Venkateswara , Weber Daniel K. , Wang Songlin , Larsen Erik K. , Gopinath Tata , De Simone Alfonso , Robia Seth , Veglia Gianluigi 
Published: May 2021

SUMMARYThe sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) is a P-type ATPase embedded in the sarcoplasmic reticulum. For each enzymatic cycle, SERCA transports 2 Ca2+ions per ATP hydrolyzed in exchange for 2 to 3 H+ions. SERCA is responsible for approximately 70% of Ca2+transport and plays a central role in muscle relaxation. SERCA’s function is regulated by endogenous regulins, single-pass membrane proteins that bind the ATPase within the membrane. While most of the regulins, such as phospholamban and sarcolipin, inhibit SERCA’s activity, a newly discovered protein DWarf Open Reading Frame (DWORF) has a unique activating effect. DWORF is a 3.8 kDa bitopic membrane protein expressed in cardiac muscle. In this work, we determine the structure, topology, and per-residue lipid interactions of DWORF in lipid bilayers using a combination of high-resolution oriented sample solid-state NMR (OS-ssNMR) spectroscopy and refinement by replica-averaged orientationally-restrained molecular dynamics (RAOR-MD). We found that DWORF’s structural topology consists of a dynamic N-terminal domain, an amphipathic juxtamembrane helix that crosses the lipid groups at an angle of 64° and a transmembrane (TM) C-terminal helix with an angle of 32°. A kink induced by Pro15, unique to DWORF, separated the two helical domains. A single Pro15Ala mutant significantly decreases the kink and eliminates DWORF’s activating effect on SERCA. Overall, our findings directly link DWORF’s structural topology to its unique activating effect on SERCA.
Variation in Ubiquitin System Genes Creates Substrate-Specific Effects on Proteasomal Protein Degradation
Authors: Collins Mahlon A. , Mekonnen Gemechu , Albert Frank W. 
Published: May 2021

AbstractUbiquitin-proteasome system (UPS) protein degradation regulates protein abundance and eliminates mis-folded and damaged proteins from eukaryotic cells. Variation in UPS activity influences numerous cellular and organismal phenotypes. However, to what extent such variation results from individual genetic differences is almost entirely unknown. Here, we developed a statistically powerful mapping approach to characterize the genetic basis of variation in UPS activity. Using the yeastSaccharomyces cerevisiae, we systematically mapped genetic influences on the N-end rule, a UPS pathway that recognizes N-degrons, degradation-promoting signals in protein N-termini. We identified 149 genomic loci that influence UPS activity across the complete set of N-degrons. Resolving four loci to individual causal nucleotides identified regulatory and missense variants in ubiquitin system genes whose products process (NTA1), recognize (UBR1andDOA10), and ubiquitinate (UBC6) cellular proteins. Each of these genes contained multiple causal variants and several individual variants had substrate-specific effects on UPS activity. Acis-acting promoter variant that modulates UPS activity by alteringUBR1expression also alters the abundance of 36 proteins without affecting levels of the corresponding mRNAs. Our results demonstrate that natural genetic variation shapes the full sequence of molecular events in protein ubiquitination and implicate genetic influences on the UPS as a prominent source of post-translational variation in gene expression.
Multiple causal DNA variants in a single gene affect gene expression intrans
Authors: Lutz Sheila , Van Dyke Krisna , Albert Frank W. 
Published: May 2021

AbstractIdentifying the specific causal DNA differences in a genome that contribute to variation in phenotypic traits is a key goal of genetic research.Trans-acting DNA variants that alter gene expression are important sources of genetic variation. Several genes are known to carry single causal variants that affect the expression of numerous genes intrans. Whether these single variants are representative of the architecture oftrans-acting variation is unknown. Here, we studied the geneIRA2, which carries variants with broad,trans-acting effects on gene expression in two strains of the yeastSaccharomyces cerevisiae. We found thatIRA2contains at least seven causal nonsynonymous variants. The causal variants were located throughout the gene body and included a pair of neighboring variants with opposing effects that largely canceled each other out. The causal variants showed evidence for non-additive epistatic interactions, in particular among variants at the 5’ end of the gene. These results show that the molecular basis oftrans-acting variation can involve considerable complexity even within a single gene.
Nuclear NAD+-biosynthetic enzyme NMNAT1 facilitates survival of developing retinal neurons
Authors: Sokolov David , Sechrest Emily , Wang Yekai , Nevin Connor , Du Jianhai , Kolandaivelu Saravanan 
Published: May 2021

ABSTRACTDespite mounting evidence that the mammalian retina is exceptionally reliant on proper NAD+homeostasis for health and function, the specific roles of subcellular NAD+pools in retinal development, maintenance, and disease remain obscure. Here, we show that deletion of the nuclear-localized NAD+synthase nicotinamide mononucleotide adenylyltransferase-1 (NMNAT1) in the developing murine retina causes early and severe degeneration of photoreceptors and select inner retinal neurons via multiple distinct cell death pathways. This severe phenotype is associated with disruptions to retinal central carbon metabolism, purine nucleotide synthesis, and amino acid pathways. Furthermore, large-scale transcriptomics reveals dysregulation of a collection of photoreceptor and synapse-specific genes in NMNAT1 knockout retinas prior to detectable morphological or metabolic alterations. Collectively, our study reveals previously unrecognized complexity in NMNAT1-associated retinal degeneration and suggests a yet-undescribed role for NMNAT1 in gene regulation during photoreceptor terminal differentiation.
Ooids formingin situwithin microbial mats (Kiritimati atoll, central Pacific)
Authors: Suarez-Gonzalez Pablo , Reitner Joachim 
Published: May 2021

AbstractOoids (subspherical particles with a laminated cortex growing around a nucleus) are ubiquitous in the geological record since the Archean and have been widely studied for more than two centuries. However, various questions about them remain open, particularly about the role of microbial communities and organic matter in their formation and development. Although ooids typically occur rolling around in agitated waters, here we describe for the first time aragonite ooids forming statically within microbial mats from hypersaline ponds of Kiritimati (Kiribati, central Pacific). Subspherical particles had been previously observed in these mats and classified as spherulites, but they grow around autochthonous micritic nuclei, and many of them have laminated cortices, with alternating radial fibrous laminae and micritic laminae. Thus, they are compatible with the definition of ‘ooid’ and are in fact identical to many modern and fossil examples. Kiritimati ooids are more abundant and developed in some ponds and in some particular layers of the microbial mats, which has led to the discussion and interpretation of their formation processes as product of mat evolution, through a combination of organic and environmental factors. Radial fibrous laminae are formed during periods of increased supersaturation, either by metabolic or environmental processes. Micritic laminae are formed in closer association with the mat exopolymer (EPS) matrix, probably during periods of lower supersaturation and/or stronger EPS degradation. Therefore, this study represents a step forward in the understanding of ooid development as influenced by microbial communities, providing a useful analogue for explaining similar fossil ooids.
Remus: System for Remote Deep Brain Interventions
Authors: Webb Taylor D. , Wilson Matthew G. , Odéen Henrik , Kubanek Jan 
Published: May 2021

ABSTRACTMotivationTranscranial focused ultrasound brings personalized medicine to the human brain. Ultrasound can modulate neural activity or release drugs in specific neural circuits but this personalized approach requires a system that delivers ultrasound into specified targets flexibly and on command.SummaryWe developed a remote ultrasound system (Remus) that programmatically targets deep brain regions with high spatiotemporal precision and in a multi-focal manner. We validated these functions by safely modulating two deep brain nuclei—the left and right lateral geniculate nucleus–in a task-performing non-human primate. This flexible system will enable researchers and clinicians to diagnose and treat specific deep brain circuits in a noninvasive yet targeted manner, thus embodying the promise of personalized treatments of brain disorders. Animated graphical abstract:onetarget.us/download/rem.
Beneficial and detrimental genes in the cellular response to replication arrest
Authors: Schons-Fonseca Luciane , Lazova Milena D. , Smith Janet L. , Grossman Alan D. 
Published: May 2021

AbstractDNA replication is essential for all living organisms, and a variety of events can perturb replication, including DNA damage (e.g., pyrimidine dimers, crosslinking) and replication arrest due to “roadblocks” such as DNA-binding proteins or transcription. Bacteria have several well-characterized mechanisms for repairing damaged DNA and restoring functional replication forks. However, little is known about the repair of stalled or arrested replication forks in the absence of DNA lesions. Using a library of random transposon insertions inBacillus subtilis, we identified 35 genes that affect the ability of cells to survive arrest of replication elongation, in the absence of DNA damage. Genes identified included those involved in iron-sulfur homeostasis, cell envelope biogenesis, and DNA repair and recombination. InB. subtilis, and many bacteria, two nucleases (AddAB and RecJ) are involved in early steps in repairing replication forks arrested by DNA damage. Loss of either one causes increased sensitivity to DNA damage. These single-strand nucleases resect DNA ends, leading to assembly of the recombinase RecA onto the single stranded DNA. Notably, we found that disruption ofrecJincreased survival of cells following replication arrest, indicating that, in the absence of DNA damage, RecJ is detrimental to surviving replication arrest. In contrast, and as expected, disruption ofaddAdecreased survival of cells following replication arrest, indicating that AddA promotes survival. The different phenotypes ofaddAandrecJmutants appeared to be due to differences in assembly of RecA onto DNA. RecJ promoted too much assembly of RecA, and loss of RecA compensated for the detrimental effects of RecJ. Our results indicate that in the absence of DNA lesions, RecA is dispensable for cells to survive replication arrest and the stable RecA nucleofilaments favored by the RecJ pathway may lead to cell death by preventing proper processing of the arrested replication fork.
A Modified Comprehensive Grading System for Murine Knee Osteoarthritis: Scoring the Whole Joint as an Organ
Authors: Grote Caleb W. , Mackay Matthew J. , Liu Xiangliang , Lu Qinghua , Wang Jinxi 
Published: May 2021

AbstractObjectiveThis study aimed to develop a comprehensive but easy to apply histologic grading system to score osteoarthritic changes in the whole knee joint for both spontaneous and posttraumatic osteoarthritis (OA) mouse models.MethodsThe new OA grading scheme was developed based on extensive literature review and the authors’ experience in mouse OA models with relatively long periods of observation (up to 24 months of age or 24-week post-surgery). Semi-quantitative assessments of the histopathologic OA changes were applied to all four quadrants of the knee. Grading elements per quadrant were defined as follows: cartilage (0-7) including three new grading elements for early- and late-stage OA, respectively; osteophyte (0-2) covering chondro-osteophytes in both outer and inner joint margins; subchondral bone (0-2) containing subchondral bone thickening and destruction; synovitis (0-2) comprised of both synovial plica and intercondylar notch; and peri-articular tissues (0-2) highlighting ectopic chondrogenesis and ossification in the knee capsule, ligament, and musculature.ResultsStatistical analyses showed that the new grading system had high intra- and inter-observer reproducibility (Pearson’s correlation coefficients r >0.9) for both experienced and novice scorers. Sensitivity and reliability analyses confirmed the ability of the new system to detect minimal OA progression between two timepoints with a two-week interval and to accurately identify tissue-specific OA severity within the knee joint.ConclusionsThe comprehensive histologic grading system presented here covers all-stage osteoarthritic changes in all major knee joint tissues of mice, which enable us to score OA severity for the whole joint reproducibly and accurately without software-assisted time-consuming measurements.
Covalent Flexible Peptide Docking in Rosetta
Authors: Tivon Barr , Gabizon Ronen , Somsen Bente A. , Cossar Peter J. , Ottmann Christian , London Nir 
Published: May 2021

AbstractElectrophilic peptides that form an irreversible covalent bond with their target have great potential for binding targets that have been previously considered undruggable. However, the discovery of such peptides remains a challenge. Here, we present CovPepDock, a computational pipeline for peptide docking that incorporates covalent binding between the peptide and a receptor cysteine. We applied CovPepDock retrospectively to a dataset of 115 disulfide-bound peptides and a dataset of 54 electrophilic peptides, for which it produced a top-five scoring, near-native model, in 89% and 100% of the cases, respectively. In addition, we developed a protocol for designing electrophilic peptide binders based on known non-covalent binders or protein-protein interfaces. We identified 7,154 peptide candidates in the PDB for application of this protocol. As a proof-of-concept we validated the protocol on the non-covalent complex of 14-3-3σ and YAP1 phosphopeptide. The protocol identified seven highly potent and selective irreversible peptide binders. The predicted binding mode of one of the peptides was validated using X-ray crystallography. This case-study demonstrates the utility and impact of CovPepDock. It suggests that many new electrophilic peptide binders can be rapidly discovered, with significant potential as therapeutic molecules and chemical probes.
Spatial and ecological drivers of population structure inAlkanna tinctoria(Boraginaceae), a polyploid medicinal herb
Authors: Ahmad Muhammad , Leroy Thibault , Krigas Nikos , Temsch Eva M. , Weiss-Schneeweiss Hanna , Lexer Christian , Sehr Eva Maria , Paun Ovidiu 
Published: May 2021

AbstractBackground and AimsQuantifying genetic variation is fundamental to understand a species’ demographic trajectory and its ability to adapt to future changes. In comparison to diploids, however, genetic variation and factors fostering genetic divergence remains poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploidAlkanna tinctoria(Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies.MethodsWe collected 14 populations ofA. tinctoriawithin its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing (RAD-seq). As an outgroup, we included two populations ofA. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables.Key ResultsWe found support for a marked regional structure inA. tinctoriaalong a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modelling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure inA. tinctoria.ConclusionsCurrent findings provide evidence of strong genetic structure inA. tinctoriamainly driven by neutral processes. The revealed natural genomic variation in GreekAlkannacan be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.
Development of a Cell Surface Display System inChlamydomonas reinhardtii
Authors: Molino João Vitor Dutra , Carpine Roberta , Gademann Karl , Mayfield Stephen , Sieber Simon 
Published: May 2021

AbstractCell-surface display systems are biotechnological techniques used to express heterologous proteins on the cell surface. Their application depends directly on the cell system used, as well as on the anchoring point for the surface displayed protein. To meet most application demands an inexpensive, safe, and scalable production platform, that reduces the economic barriers for large scale use is needed. Towards this goal, we screened three possible cell surface anchoring points in the green algae Chlamydomonas by fusing mVenus to prospective anchors moieties. The vectors harboring mVenus:anchor were screened for mVenus fluorescence and tested for cellular localization by confocal laser scanning microscopy. This strategy allowed the identification of two functional anchors, one for the cytoplasmic membrane using the MAW8 GPI-anchor signal, and one for the cell wall using the GP1 protein. We also exploited GP1 chemical and biological traits to release the fused proteins efficiently during cell wall shedding. Our work provides a foundation for surface engineering ofC reinhardtiisupporting both cell biology studies and biotechnology applications.
Maternal iron deficiency impacts the placental arterial network
Authors: Kalisch-Smith Jacinta I. , Morris Emily C. , Strevens Mary A.A. , Redpath Andia N. , Klaourakis Kostantinos , Szumska Dorota , Outhwaite Jennifer E. , Vieira Joaquim Miguel , Smart Nicola , De Val Sarah , Riley Paul R. , Sparrow Duncan B. 
Published: May 2021

AbstractPlacental vascular gene networks in mammals have been largely unexplored due to a lack of well validated molecular markers to identify them. This is required to study how they form in development, and how they are impacted by embryonic or maternal defects, which in-turn adversely affects the forming heart and vasculature. Such defects are known to be a consequence of maternal iron deficiency (ID), the most common nutrient deficiency world-wide. Here we employed marker analysis to characterise the arterial/arteriole and venous/venule endothelial cells (ECs) during normal placental development, and in the context of maternal ID. We reveal for the first time that placental ECs are unique compared with their embryonic counterparts. In the developing embryo, arterial ECs expressNeuropilin1(Nrp1),Delta-like ligand 4(Dll4) andNotch1, while developing venous ECs expressNeuropilin2(Nrp2),Apj (Aplnr)andEphrinb4 (Ephb4). However, in the E15.5 placenta,Nrp1andNotch1were restricted to arteries, but not continuing arteriole ECs. The arterial tree exclusively expressedDll4. Nrp2showed pan-EC expression at E15.5, whileEphb4was not present at this stage. However, we found the placental venous vascular tree could be distinguished from the arterial tree by high versus low Endomucin (EMCN) andApj (Aplnr)expression respectively. Using EMCN, we reveal that the placental arterial, but not venous, vascular tree is adversely impacted by maternal ID, with reduced area, total length and number of junctions of all vessels without affecting the EMCN high vessels. Defects to the embryonic cardiovascular system can therefore have a significant impact on blood flow delivery and expansion of the placental arterial tree.
The relationship between restrictive human resource practices and salary among working professionals
Authors: Baglione Stephen , Tucci Louis , Smith William , Snead Joanne 
Published: May 2021

PurposeThis study forces respondents to tradeoff between invasive human resource practices and salary.Design/methodology/approachRespondents evaluated 16 calibration profiles to estimate a conjoint model among four categories: pre-employment, employment at the office, employment outside the office, and salary. Each profile included one level from the four categories.FindingsIn a study of mostly full-time employees, conditions at work were paramount. Salary was second followed closely by pre-employment monitoring. Monitoring outside of the office was a distance last.Practical implicationsIn a tight employment market, salary may not be the deciding selection factor for employment.Originality/valueEmployee monitoring is advancing dramatically and making human resource activities commonplace and invasive. This study forces respondents to confront these practices and determine whether salary can compensate for their acceptance.
Effect of information sharing in supply chains: understanding the roles of supply chain visibility, agility, collaboration on supply chain performance
Authors: Baah Charles , Opoku Agyeman Douglas , Acquah Innocent Senyo Kwasi , Agyabeng-Mensah Yaw , Afum Ebenezer , Issau Kassimu , Ofori Daniel , Faibil Daniel 
Published: May 2021

PurposeExploring ways to acquire, sustain and improve competitive positions in supply chains through information sharing, supply chain visibility, collaboration and agility have been essential for scholars and practitioners. Basing on the relational view, resource based view and the extended resource based view, this study assesses the critical role of information sharing in supply chains through emphasizing its effect on supply chain visibility, collaboration, agility and supply chain performance. Particularly, the study proposes that information sharing, supply chain visibility, collaboration and agility collectively have crucial direct and indirect influences on supply chain performance which lead to superior gains, competitiveness and flexibility.Design/methodology/approachThe study adopted a survey research design, a quantitative approach and partial least square structural equation modeling (PLS-SEM) in making data analysis and interpretations due to its suitability for predictive research models.FindingsThe results indicate information sharing positively and significantly influenced supply chain visibility, collaboration, agility and performance. Supply chain visibility presented significant effects on collaboration, agility and performance, while supply chain collaboration and agility had significant impact on supply chain performance. The study findings connote that information sharing is key to enhancing competitive gains and superior supply chain performance.Originality/valueThe study is among the few to probe on how information sharing as a variable interacts with supply chain visibility, collaboration, agility and performance. Although, information sharing has received a lot of attention in supply chains, this study is among the first to capture the study variables in a single model and thus, exposes the vital need for information sharing in improving supply chain performance seeing that it ensured significant and robust impacts on the study variables.