bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization, Comparison, and Optimization of Lattice Light Sheets
Authors: Liu Gaoxiang , Ruan Xiongtao , Milkie Daniel E. , Görlitz Frederik , Mueller Matthew , Hercule Wilmene , Kililea Alison , Betzig Eric , Upadhyayula Srigokul 
Published: July 2022

AbstractLattice light sheet microscopy excels at the non-invasive imaging of three-dimensional (3D) dynamic processes at high spatiotemporal resolution within cells and developing embryos. Recently, several papers have called into question the performance of lattice light sheets relative to the Gaussian sheets most common in light sheet microscopy. Here we undertake a comprehensive theoretical and experimental analysis of various forms of light sheet microscopy which both demonstrates and explains why lattice light sheets provide significant improvements in resolution and photobleaching reduction. The analysis provides a procedure to select the correct light sheet for a desired experiment and specifies the processing that maximizes the use of all fluorescence generated within the light sheet excitation envelope for optimal resolution while minimizing image artifacts and photodamage. Development of a new type of “harmonic balanced” lattice light sheet is shown to improve performance at all spatial frequencies within its 3D resolution limits and maintains this performance over lengthened propagation distances allowing for expanded fields of view.Significance StatementDespite its rapidly growing use, several misconceptions remain concerning the physics of image formation and its optimization in light sheet microscopy, particularly in high resolution variants tailored for subcellular imaging. These include the role of excitation sidelobes, the significance of out-of-focus fluorescence, the importance and optimization of deconvolution, and the perceived advantages of Gaussian beams. Here we attempt to shatter these misconceptions by showing that the professed tradeoffs between axial resolution and background haze, photobleaching rate, phototoxicity, and propensity for image artifacts do not exist for well-crafted lattice light sheets whose data is acquired and processed rigorously. The framework we provide should enable others to optimize light sheets and extract the most information at the lowest cost in their experiments.
Propagation dynamics of electrotactic motility in large epithelial cell sheets
Authors: Zhang Yan , Xu Guoqing , Wu Jiandong , Lee Rachel M , Zhu Zijie , Sun Yaohui , Zhu Kan , Losert Wolfgang , Liao Simon , Zhang Gong , Pan Tingrui , Xu Zhengping , Lin Francis , Zhao Min 
Published: July 2022

SummaryDirectional migration initiated at the wound edge leads epithelial sheets to migrate in wound healing. How such coherent migration is achieved is not well understood. Here we used electric fields to induce robust migration of sheets of human keratinocytes and developed an in silico model to characterize initiation and propagation of epithelial collective migration. Electric fields initiate increase in migrations directionality and speed at the leading edge. The increases propagate across the epithelial sheets, resulting in directional migration of cell sheets as coherent units. Both the experimental and in silico models demonstrated vector-like integration of the electric and default directional cues at the free edge in space and time. The resultant collective migration is remarkably consistent in experiments and modeling, both qualitatively and quantitatively. The keratinocyte model thus faithfully reflects key features of epithelial migration as a coherent tissue in vivo, e.g. that leading cells lead, and that epithelium maintains cell- cell junction.
Acinetobacter baumanniirepresses type VI secretion system through an Mn2+-dependent sRNA-mediated regulation
Authors: Bhowmik Somok , Pathak Avik , Devnath Kuldip , Sett Abhiroop , Pandey Shivam , Jyoti Nishant , Bhando Timsy , Akhter Jawed , Chugh Saurabh , Singh Ramandeep , Sharma Tarun Kumar , Pathania Ranjana 
Published: July 2022

ABSTRACTType VI secretion system (T6SS) is utilized by many Gram negative bacteria for eliminating competing bacterial species and manipulating host cells.Acinetobacter baumanniiATCC 17978 utilizes T6SS at the expense of losing pAB3 plasmid to induce contact-dependent killing of competitor microbes, resulting in the loss of antibiotic resistance carried by pAB3. However, the regulatory network associated with T6SS inA. baumanniiremains poorly understood. Here, we identified an Mn2+-dependent post-transcriptional regulation of T6SS mediated by a bonafide small RNA, AbsR28.A. baumanniiutilizes MumT (Mn2+-uptake inner membrane transporter) for the uptake of extracellular Mn2+during oxidative stress. We demonstrate that the abundance of intracellular Mn2+enables complementary base-pairing of AbsR28-tssMmRNA (that translated to TssM, one of the vital inner membrane components of T6SS), inducing RNase E-mediated degradation oftssMmRNA and resulting in T6SS repression. Thus, AbsR28 mediates a crosstalk between MumT and T6SS inA. baumannii.IMPORTANCESmall RNAs (sRNAs) are identified as critical components within the bacterial regulatory networks involved in fine regulation of virulence-associated factors. The sRNA-mediated regulation ofAcinetobacter baumannii’s T6SS was unchartered. Our findings reveal a novel underlying mechanism of an Mn2+-dependent sRNA-mediated regulation of T6SS inA. baumannii. We show that binding of Mn2+to AbsR28 aids in the complementary base-pairing of AbsR28-tssMmRNA, resulting in RNase E-mediated processing oftssMand T6SS repression. The findings also shed light onA. baumannii’s preference for antibiotic resistance over contact-dependent killing during infection.
High-resolution crystal structure of a metabolic switch protein in a complex with monomeric c-di-GMP reveals a potential mechanism for c-di-GMP dimerization
Authors: Dubey Badri Nath , Shyp Viktoriya , Fucile Geoffrey , Jenal Urs , Schirmer Tilman 
Published: July 2022

AbstractBacterial second messengers c-di-GMP and (p)ppGpp have broad functional repertoires ranging from growth and cell cycle control to the regulation of biofilm formation and virulence. The recent identification of SmbA, an effector protein from Caulobacter crescentus that is jointly targeted by both signaling molecules, has opened up studies on how these global bacterial networks interact. C-di-GMP and (p)ppGpp compete for the same SmbA binding site, with a dimer of the former ligand inducing a conformational change of loop 7 leading to downstream signaling. Here, we report a crystal structure of a partial loop 7 deletion mutant, SmbAΔloop in complex with c-di-GMP determined at 1.4 Å resolution. SmbAΔloop binds monomeric c-di-GMP strengthening the view that loop 7 is required for c-di-GMP dimerization. In the crystal, SmbAΔloop forms a 2-fold symmetric dimer via isologous interactions with the two symmetric halves of c-di-GMP. Structural comparisons of SmbAΔloop with wild-type SmbA in complex with dimeric c-di-GMP or ppGpp support the idea that loop 7 is critical for SmbA function by interacting with downstream partners. These results underscore the flexibility of c-di-GMP in binding to the symmetric interface between protein subunits. It is envisaged that such isologous interactions of c-di-GMP will be observed in hitherto unrecognized targets.
Genetic diversity, population structure and parentage analysis of Brazilian grapevine hybrids after half a century of genetic breeding
Authors: de Oliveira Geovani Luciano , Niederauer Guilherme Francio , de Oliveira Fernanda Ancelmo , Rodrigues Cinthia Souza , Hernandes José Luiz , de Souza Anete Pereira , Moura Mara Fernandes 
Published: July 2022

ABSTRACTIn the 1940s, the Agronomic Institute of Campinas (IAC) started a grapevine breeding program to develop new cultivars adapted to the tropical and subtropical regions of Brazil. More than 2,000 crosses were carried out over 50 years, using 850 varieties as parents. However, among the thousands of hybrids developed by the program, only 130 are still maintained in the IAC grapevine germplasm collection. Little is known about their genetic makeup and usefulness for current breeding programs. In this study, we genotyped 130 Brazilian grape hybrids at 21 polymorphic microsatellite markers to evaluate the genetic diversity and population structure of the hybrids and verified their disclosed pedigrees. The results showed that the hybrid collection is highly diverse, with an expected heterozygosity (HE) of 0.80 and an observed heterozygosity (Ho) of 0.78. Strong structure in three subgroups based mainly on the usage and combination of parental groups was revealed by STRUCTURE software and confirmed by discriminant analysis of principal components (DAPC). Through molecular profiling analysis, fourteen synonyms, one homonym and one duplicate were identified. Parentage analysis confirmed 24 full parentages, as well as 33 half-kinships. In addition, 18 pedigrees were invalidated, and seven mislabeling events were identified. No compatible parent was identified for 33% of the IAC hybrids, highlighting severe genetic erosion in the IAC germplasm. The molecular characterization of the breeding hybrid bank collection contributes to our understanding of the genetic basis of the varieties, guiding the efficient utilization of available genetic diversity. Together, our results could be applied to other breeding programs and assist in the selection of parents, management of the breeding collection, and conservation of grapevine genetic resources.
Cell surface receptors TREM2, CD14 and integrin αMβ2drive sinking engulfment in phosphatidylserine-mediated phagocytosis
Authors: Vorselen Daan , Kamber Roarke A. , Labitigan Ramon Lorenzo D. , van Loon Aaron P. , Peterman Eric , Delgado Melissa K. , Lin Sijie , Rasmussen Jeffrey P. , Bassik Michael C. , Theriot Julie A. 
Published: July 2022

SummaryMacrophages phagocytose and thereby eliminate a wide array of extracellular threats, ranging from antibody-coated bacteria to apoptotic cells. Precision modulation of phagocytosis has emerged as a therapeutic strategy across a range of diseases, but is limited by our incomplete understanding of how macrophages recognize, engulf, and respond to different phagocytic targets. Here, we undertook a systematic investigation of the morphological, biophysical and regulatory differences between two major types of phagocytosis: an immunostimulatory form of phagocytosis triggered by antibody-coated targets and an immunosuppressive form triggered by phosphatidylserine (PS)-coated targets. We confirmed classic observations that antibody-mediated phagocytosis involves the extension of thin actin-rich protrusions around the target, but find that PS-mediated phagocytosis involves an unexpected combination of filopodial probing, piecemeal phagocytosis and a distinct ‘sinking’ mechanism of uptake. Using a genome-wide screening approach, we identified genes specifically required for each form of phagocytosis, including actin regulators, cell surface receptors and intracellular signaling molecules. Three cell surface receptors - TREM2, CD14 and integrin αMβ2- were revealed as essential for PS-mediated uptake. Strikingly, each receptor exhibited a distinct pattern of localization at the plasma membrane and contributed uniquely to the organization of the PS-dependent phagocytic cup. Overall, this work reveals divergent genetic requirements for the morphologically and mechanically distinct forms of PS-mediated and antibody-mediated phagocytosis, thereby informing therapeutic strategies for substrate-specific phagocytosis modulation.
A genetically encoded photo-proximity labeling approach for mapping protein territories
Authors: Hananya Nir , Ye Xuanjia , Koren Shany , Muir Tom W. 
Published: July 2022

AbstractStudying dynamic biological processes requires approaches compatible with the lifetimes of the biochemical transactions under investigation, which can be very short. We describe a genetically encoded system that allows protein interactomes to be captured using visible light. Our approach involves fusing an engineered flavoprotein to a protein of interest. Brief excitation of the fusion protein leads to local generation of reactive radical species within cell-permeable probes. When combined with quantitative proteomics, the system generates ‘snapshots’ of protein interactions with high temporal resolution. The intrinsic fluorescence of the fusion domain permits correlated imaging and proteomics analyses, a capability that is exploited in several contexts, including defining the protein clients of the major vault protein (MVP). The technology should be broadly useful in the biomedical area.
Characterization of norbelladine synthase and noroxomaritidine/norcraugsodine reductase reveals a novel catalytic route for the biosynthesis of Amaryllidaceae alkaloids including the Alzheimer’s drug galanthamine
Authors: Majhi Bharat Bhusan , Gélinas Sarah-Eve , Mérindol Natacha , Desgagné-Penix Isabel 
Published: July 2022

ABSTRACTAmaryllidaceae alkaloids (AAs) are a large group of pharmacological plant-specialized metabolites. Norbelladine is the entry compound in AAs biosynthesis. Two enzymes are capable of catalyzing this reaction in-vitro, both with low-yield; 1) norbelladine synthase (NBS) condenses tyramine and 3,4-dihydroxybenzaldehyde, while 2) noroxomaritidine/norcraugsodine reductase (NR), catalyzes a reduction reaction. To clarify the mechanisms involved in this controversial step, both NBS and NR were characterized from Narcissus papyraceus and Leucojum aestivum. Assays with each enzyme suggested that NBS and NR function together for norbelladine formation. Using molecular-homology modeling and docking studies, we predicted models for the binding of substrates to NBS and NR. Moreover, NBS and NR physically interact, localize to the cell cytoplasm and nucleus and are expressed at high levels in bulbs. Our study establishes that both NBS and NR participate in the biosynthesis of norbelladine, catalyzing the first key steps involved in the biosynthesis of the Alzheimer’s drug galanthamine.
New motifs in Ndc1 mediating interaction with the Nup84 complex and nuclear membranes
Authors: Amm Ingo , Weberruss Marion , Hellwig Andrea , Schwarz Johannes , Tatarek-Nossol Marianna , Lüchtenborg Christian , Kallas Martina , Brügger Britta , Hurt Ed , Antonin Wolfram 
Published: July 2022

ABSTRACTThe nuclear pore complex (NPC) embedded in the double nuclear membrane is built from ~30 different nucleoporins (Nups) in multiple copies, of which a few are integral nuclear membrane proteins. One of these transmembrane Nups is Ndc1, which is thought to play a role in interphase NPC assembly at the fused inner and outer nuclear membrane. In this study, we discovered a direct interaction of Ndc1’s transmembrane domain with Nup120 and Nup133, members of the Y-complex that coats the nuclear pore membrane. In addition, we identified a so far unrecognized amphipathic helix (AH) in the C-terminal domain of Ndc1, which can bind to high curvature liposomes. When overexpressed in yeast this amphipathic motif is toxic and dramatically alters the intracellular membrane organization. Further genetic investigations revealed that Ndc1-AH functionally interacts with related motifs in the C-terminus of Nups Nup53 and Nup59, known to serve in nuclear pore membrane binding and link between NPC modules. This relationship could explain why the essential function of Ndc1 can be suppressed by deleting the amphipathic helix from Nup53. Our data indicate that nuclear membrane biogenesis dependent on a balanced ratio between amphipathic motifs in diverse nucleoporins is essential for interphase NPC biogenesis.
Use of CRISPR‐Cas tools to engineer Trichoderma species
Authors: Wang Ying , Chen Hongyu , Ma Liang , Gong Ming , Wu Yingying , Bao Dapeng , Zou Gen 
Published: July 2022

AbstractGiven their lignocellulose degradability and biocontrol activities, fungi of the ubiquitously distributed genus Trichoderma have multiple industrial and agricultural applications. Genetic manipulation plays a valuable role in tailoring novel engineered strains with enhanced target traits. Nevertheless, as applied to fungi, the classic tools of genetic manipulation tend to be time‐consuming and tedious. However, the recent development of the CRISPR‐Cas system for gene editing has enabled researchers to achieve genome‐wide gene disruptions, gene replacements, and precise editing, and this technology has emerged as a primary focus for novel developments in engineered strains of Trichoderma. Here, we provide a brief overview of the traditional approaches to genetic manipulation, the different strategies employed in establishing CRSIPR‐Cas systems, the utilization of these systems to develop engineered strains of Trichoderma for desired applications, and the future trends in biotechnology.
Detection and elimination of shallot latent virus and onion yellow dwarf virus for potato onion (Allium cepa L. var. aggregatum Don)
Authors: Lou Hu , Liu Zhiqi , Xu Qijiang 
Published: July 2022

AbstractPotato onion (Allium cepa L. var. aggregatum Don) is an important cash crop in northeastern China. It has the characteristics of cold tolerance and high yield and is very popular among consumers in this region. However, shallot latent virus (SLV) and onion yellow dwarf virus (OYDV) reduce the height and yield of potato onion plants. The detection of viruses on potato onion plants and virus elimination of plants are the primary ways to prevent viral infection and spread. We used duplex reverse‐transcription polymerase chain reaction (RT‐PCR) and in situ hybridization to detect SLV and OYDV viruses, and determined that the tissue with the least virus content was the apical meristem. Cultivation of detoxifying plants was by multi‐generation shoot tips. The results showed that duplex RT‐PCR could detect SLV and OYDV in potato onion. By use of multi‐generation shoot tip virus elimination, we have demonstrated that multiple generations of shoot tip virus elimination can produce non‐toxic plants during the third generation of virus elimination, and the elimination rate of virus was 96.2%. This work provides a more convenient method for potato onion virus detection and improves the detection efficiency. This method will in turn aid in the development of virus elimination and rapid propagation methods for potato onion.
Anti‐factor X activity levels with continuous intravenous infusion and subcutaneous administration of enoxaparin after coronary artery bypass grafting: A randomized clinical trial
Authors: Parviainen Maria K. , Vahtera Annukka , Ånäs Niklas , Tähtinen Jutta , Huhtala Heini , Kuitunen Anne , Järvelä Kati 
Published: July 2022

AbstractBackgroundLow‐molecular‐weight heparin enoxaparin is widely used in pharmacological thromboprophylaxis after coronary artery bypass grafting (CABG). The aim of this study was to compare anti‐factor X activity (anti‐Xa) levels when the thromboprophylactic dose of enoxaparin was provided after CABG, with two different administration routes: continuous intravenous infusion (CIV) and subcutaneous bolus (SCB) injection. We hypothesized that the current standard method of SCB administration might lead to lower anti‐Xa levels than recommended in other patient groups, due to reduced bioavailability.MethodsIn this prospective, randomized, controlled clinical trial, 40 patients scheduled for elective CABG were randomized to receive 40 mg of enoxaparin per day either as CIV or SCB for 72 h. Enoxaparin was initiated 6–10 h after CABG. Anti‐Xa levels were measured 12–14 times during the study period. The primary outcome, that is, the maximum anti‐Xa concentration over 0–24 h (Cmax0–24h), was calculated from these measured values. Secondary outcomes were Cmax25–72h and the trough concentration of anti‐Xa after 72 h of enoxaparin initiation (C72h).ResultsTwenty patients were randomized to the CIV‐group and 19 to the SCB‐group. The median anti‐Xa Cmax0–24h was significantly lower in the CIV‐group than in the SCB‐group: 0.15 [interquartile range (IQR) 0.13–0.19] IU/ml versus 0.25 (IQR 0.18–0.32) IU/ml, p < .005. The median anti‐Xa Cmax25–72h was 0.12 (IQR, 0.1–0.17) IU/ml versus 0.23 (IQR 0.19–0.31) IU/ml, respectively, p < .005. At 72 h, there was no difference between the groups in their anti‐Xa levels.ConclusionsIn this low‐risk CABG patient population, SCB administration of a thromboprophylactic dose of enoxaparin provided anti‐Xa levels that are considered sufficient for thromboprophylaxis in other patient groups. CIV administration resulted in lower anti‐Xa levels compared to the SCB route.
Ten‐year trends of adult trauma patients in Central Denmark Region from 2010 to 2019: A retrospective cohort study
Authors: Trier Frederik , Fjølner Jesper , Sørensen Anders Høyer , Søndergaard Rasmus , Kirkegaard Hans , Raaber Nikolaj 
Published: July 2022

AbstractBackgroundTrauma causes significant economic and societal burdens, and the trauma patient population and their prognosis change over time. This study aims to analyze 10‐year trends of trauma patients at a major trauma center in Central Denmark Region.MethodsFive thousand three hundred and sixty‐six patients aged ≥16 years with Injury Severity Score (ISS) > 0 admitted by trauma team activation at a major trauma center between January 1, 2010, and December 31, 2019, were included. An annual percent change with a 95% confidence interval was used to estimate trends in the mechanism of injuries. Multiple logistic regression with mortality as the outcome was adjusted for age, sex, and ISS. Admission year was used as continuous variable in logistic regressions.ResultsThe median age increased from 37 in 2010 to 49 in 2019, and the proportion of patients aged ≥65 doubled. The annual incidence of minor injuries (ISS 1–15) decreased from 181.3/105 inhabitants in 2010 to 112.7/105 in 2019. Severe injuries (ISS > 15) increased from 10.1/105 inhabitants in 2010 to 13.6/105 in 2019. The proportion of patients with ISS > 15 increased from 18.1% in 2010 to 31.1% in 2019. Multivariable logistic regression indicates lower 30‐day mortality for all trauma patients over the study period when adjusting for age, sex, and ISS (odds ratio: 0.94, 95% CI: 0.90–0.99). The 30‐day mortality for severely injured patients with ISS > 15 seems to decrease during the study period when adjusting for age, sex, and ISS (Odds ratio: 0.92, 95% CI: 0.87–0.97). Fall injuries increased by 4.1% annually (95% CI: 2.3%–6.1%).ConclusionsTen‐year trends of trauma patients at a major trauma center show an increasing median age, injury severity, and number of fall injuries. The 30‐day mortality of trauma patients decreased slightly for both minor injuries and severe injuries when adjusting for age, sex, and injury severity.