bluuebunny/crossref_metadata_2025_split huggingface dataset:
Video-rate remote refocusing through continuous oscillation of a membrane deformable mirror
Authors: Wright Terry , Sparks Hugh , Paterson Carl , Dunsby Chris 
Published: April 2021

AbstractThis paper presents the use of a deformable mirror (DM) configured to rapidly refocus a microscope employing a high numerical aperture objective lens. An Alpao DM97-15 membrane DM was used to refocus a 40×/0.80 NA water-immersion objective through a defocus range of −50 to 50 μm at 26.3 sweeps per second. We achieved imaging with a mean Strehl metric of > 0.6 over a field of view in the sample of 200×200 μm2over a defocus range of 77 μm. We describe an optimisation procedure where the mirror is swept continuously in order to avoid known problems of hysteresis associated with the membrane DM employed. This work demonstrates that a DM-based refocusing system could in the future be used in light-sheet fluorescence microscopes to achieve video-rate volumetric imaging.
Metaviromes reveal the dynamics of Pseudomonas host-specific phages cultured and uncultured by plaque assay
Authors: Skov Alanin Katrine Wacenius , Forero Junco Laura Milena , Jørgensen Jacob Bruun , Kjærgaard Nielsen Tue , Rasmussen Morten Arendt , Kot Witold , Hansen Lars Hestbjerg 
Published: April 2021

AbstractIsolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or the ones with highest ability to plaque on solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in envi-ronmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community’s shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media corresponds to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum 2-fold change above 0 in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, was highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlights how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.
Kinase activity of TBK1 is required for its binding to STING, but not for its recruitment to the Golgi
Authors: Kemmoku Haruka , Kuchitsu Yoshihiko , Mukai Kojiro , Taguchi Tomohiko 
Published: April 2021

AbstractStimulator of interferon genes (STING) is an innate immune protein for DNA pathogens. In response to the emergence of DNA in the cytosol, STING relocates from the endoplasmic reticulum (ER) to the Golgi and induces the type I interferon response through cytosolic TANK-binding kinase 1 (TBK1). The molecular mechanism underlying TBK1 activation by STING remains poorly understood. Here we report a cell system by which STING and TBK1 are simultaneously monitored. The system utilizes STING/TBK1-double knockout (KO) cells, fluorescent protein-tagged TBK1 and STING, and super-resolution microscopy. After STING stimulation, TBK1 is directly recruited to the trans-Golgi network (TGN), not to the other parts of the Golgi. The recruitment of TBK1 does not require its kinase activity. C-terminal STING variants (ΔC9 and L373A), in which the TBK1-STING binding interface is mutated or deleted, induce the recruitment of TBK1. These results indicate that the kinase activity of TBK1 or the C-terminal motif of STING is not required for its recruitment to TGN, but rather for the formation of the stable STING signalling complex at TGN.
A nanoscale reciprocating rotary mechanism with coordinated mobility control
Authors: Bertosin Eva , Maffeo Christopher M. , Drexler Thomas , Honemann Maximilian N. , Aksimentiev Aleksei , Dietz Hendrik 
Published: April 2021

AbstractBiological molecular motors transform chemical energy into mechanical work by coupling a cycle of catalytic reactions to large scale structural transitions. Mechanical deformation can be surprisingly efficient in realizing such coupling, as demonstrated by the celebrated example of F1FoATP synthase. Here, we describe a synthetic molecular mechanism that transforms a rotary motion of an asymmetric camshaft into reciprocating large-scale transitions in the structure of the surrounding stator orchestrated by mechanical deformation. We designed the mechanism using DNA origami, characterized the structure of the components and the entire mechanism using cryo-electron microscopy, and examined the mechanism’s dynamic behavior using single-particle fluorescence microscopy and molecular dynamics simulations. The data indicates that, while the camshaft can rotate inside the stator by diffusion, mechanical deformation of the stator makes the camshaft pause at a set of preferred orientations. By changing the mechanical stiffness of the stator, we could accelerate or suppress the Brownian rotation within the mechanism, thereby demonstrating an allosteric coupling between the movement of the camshaft and of the stator, and the ability to tailor the free energy landscape that governs the rotary motion. Our mechanism provides a framework for the manufacture of artificial nanomachines that, just like the man-made machines in the macroscopic world, function because of coordinated movements of their components.
Failure to mate enhances investment in behaviors that may promote mating reward and impairs the ability to cope with stressors via a subpopulation of Neuropeptide F receptor neurons
Authors: Ryvkin Julia , Omesi Liora , Kim Yong-Kyu , Levi Mali , Pozeilov Hadar , Barak-Buchris Lital , Agranovich Bella , Abramovich Ifat , Gottlieb Eyal , Jacob Avi , Nässel Dick R. , Heberlein Ulrike , Shohat-Ophir Galit 
Published: April 2021

AbstractLiving in dynamic environments such as the social domain, where interaction with others determines the reproductive success of individuals, requires the ability to recognize opportunities to obtain natural rewards and cope with challenges that are associated with achieving them. As such, actions that promote survival and reproduction are reinforced by the brain reward system, whereas coping with the challenges associated with obtaining these rewards is mediated by stress-response pathways, the activation of which can impair health and shorten lifespan. While much research has been devoted to understanding mechanisms underlying the way by which natural rewards are processed by the reward system, less attention has been given to the consequences of failure to obtain a desirable reward. As a model system to study the impact of failure to obtain a natural reward, we used the well-established courtship suppression paradigm inDrosophila melanogasteras means to induce repeated failures to obtain sexual reward in male flies. We discovered that beyond the known reduction in courtship actions caused by interaction with non-receptive females, repeated failures to mate induce a stress response characterized by persistent motivation to obtain the sexual reward, reduced male-male social interaction, and enhanced aggression. This frustrative-like state caused by the conflict between high motivation to obtain sexual reward and the inability to fulfill their mating drive impairs the capacity of rejected males to tolerate stressors such as starvation and oxidative stress. We further show that sensitivity to starvation and enhanced social arousal is mediated by the disinhibition of a small population of neurons that express receptors for the fly homologue of neuropeptide Y. Our findings demonstrate for the first time the existence of social stress in flies and offers a framework to study mechanisms underlying the crosstalk between reward, stress, and reproduction in a simple nervous system that is highly amenable to genetic manipulation.
Endosomes deliver ceramide phosphoethanolamine with unique acyl chain anchors to the cleavage furrow during male meiotic cytokinesis
Authors: Kunduri Govind , Le Si-Hung , Baena Valentina , Vijaykrishna Nagampalli , Harned Adam , Nagashima Kunio , Blankenberg Daniel , Izumi Yoshihiro , Narayan Kedar , Bamba Takeshi , Acharya Usha , Acharya Jairaj K. 
Published: April 2021

AbstractCell division, wherein one cell divides into two daughter cells, is fundamental to all living organisms. Cytokinesis, the final step in cell division, begins with the formation of an actomyosin contractile ring, positioned midway between the segregated chromosomes. Constriction of the ring with concomitant membrane deposition in a spatiotemporal manner generates a cleavage furrow that physically separates the cytoplasm. Unique lipids with specific biophysical properties have been shown to localize to intercellular bridges (also called midbody) connecting the two dividing cells; however, their biological roles and delivery mechanisms remain largely unknown. In this study, we show that Ceramide phosphoethanolamine (CPE), the structural analog of sphingomyelin, has unique acyl chain anchors in spermatocytes and is essential for meiotic cytokinesis. The head group of CPE is also important for spermatogenesis. We find that aberrant central spindle and contractile ring behavior but not mislocalization of phosphatidylinositol phosphates (PIPs) at the plasma membrane is responsible for the male meiotic cytokinesis defect in CPE deficient animals. Further, we demonstrate the enrichment of CPE in multivesicular bodies marked by Rab7, which in turn localize to cleavage furrow. Volume electron microscopy analysis using correlative light and focused ion beam scanning electron microscopy shows that CPE enriched Rab7 positive endosomes are juxtaposed on contractile ring material. Correlative light and transmission electron microscopy reveal Rab7 positive endosomes as a multivesicular body-like organelle that releases its intraluminal vesicles in the vicinity of ingressing furrows. Genetic ablation of Rab7 or expression of dominant negative Rab11 results in significant meiotic cytokinesis defects. Our results imply that endosomal delivery of CPE to ingressing membranes is crucial for meiotic cytokinesis.
A pan-cancer analysis of matrisome proteins reveals CTHRC1and LOXL2 as major ECM regulators across cancers
Authors: Harikrishnan Keerthi , Prabhu Srinivas Seshagiri , Balasubramanian Nagaraj 
Published: April 2021

AbstractThe extracellular matrix as part of the tumor microenvironment can regulate cancer cell growth and progression. Using TCGA data from 30 cancer types, the top 5% of matrisome genes with amplifications or deletions that affect survival in cancers were identified. Eight of these genes show altered expression in ~50% or more cancers affecting survival in ~20% or more. Among them SNED1 is the most downregulated and CTHRC1 and LOXL2 most upregulated. Differential gene expression analysis of SNED-1 did not identify any genes it regulates across cancers, while CTHRC1 and LOXL2 affected 19 and 5 genes respectively in 3 or more cancers. STRING analysis of these genes classified them as ‘extracellular’, involved prominently in ECM organization. Their correlation and co-occurrence in context of their effect on survival and staging of the disease identified MMP13, POSTN and SFRP4 along with COL11A1, COL10A1, COL1A1, ADAMTS12 and PPAPDC1A as possible interactors of CTHRC1 and LOXL2 in cancers. These are implicated in collagen organization, making it vital to matrisome regulation of cancers. Clinical Proteomic Tumor Analysis Consortium data confirms the changes in expression of these genes along with CTHRC1 and LOXL2 in breast and lung cancer, further supporting their implication as vital pan-cancer matrisome mediators.HighlightsCTHRC1 and LOXL2 are prominently upregulated pan-cancer matrisome genes.High CTHRC1 and LOXL2 expression is associated with disease progression and poor survival in cancers.CTHRC1 with POSTN, MMP13 and SFRP4 and LOXL2 with COL11A1, COL10A1, COL1A1, ADAMTS12 and PPAPDC1A drive matrisome regulation of cancers.CTHRC1 and LOXL2 could prominently drive collagen organization and function across cancers.
Neurotrophic control of size regulation during axolotl limb regeneration
Authors: Wells-Enright Kaylee M. , Kelley Kristina , Baumel Mary , Vieira Warren A. , McCusker Catherine D. 
Published: April 2021

AbstractThe mechanisms that regulate the sizing of the regenerating limb in tetrapods such as the Mexican axolotl are unknown. Upon the completion of the developmental stages of regeneration, when the regenerative organ known as the blastema completes patterning and differentiation, the limb regenerate is proportionally small in size. It then undergoes a phase of regeneration that we have called the “tiny-limb” stage, that is defined by rapid growth until the regenerate reaches the proportionally appropriate size. In the current study we have characterized this growth and have found that signaling from the limb nerves is required for its maintenance. Using the regenerative assay known as the Accessory Limb Model, we have found that the size of the limb can be positively and negatively manipulated by nerve abundance. We have additionally developed a new regenerative assay called the Neural Modified-ALM (NM-ALM), which decouples the source of the nerve from the regenerating host environment. Using the NM-ALM we discovered that non-neural extrinsic factors from differently sized host animals do not play a prominent role in determining the size of the regenerating limb. We have also discovered that the regulation of limb size is not autonomously regulated by the limb nerves. Together, these observations show that the limb nerves provide essential and instructive cues to regulate the final size of the regenerating limb.
The nature of intraspecific genome size variation in taxonomically complex eyebrights
Authors: Becher Hannes , Powell Robyn F. , Brown Max R. , Metherell Chris , Pellicer Jaume , Leitch Ilia J. , Twyford Alex D. 
Published: April 2021

SummaryGenome size (GS) is a key trait related to morphology, life history, and evolvability. Although GS is, by definition, affected by presence/absence variants (PAVs), which are ubiquitous in population sequencing studies, GS is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific GS variation in taxonomically complex British eyebrights (Euphrasia).We generated GS data for 192 individuals of diploid and tetraploidEuphrasiaand analysed GS variation in relation to ploidy, taxonomy, population affiliation, and geography. We further compared the genomic repeat content of 30 samples.We found considerable genuine intraspecific GS variation, and observed isolation-by-distance for GS in outcrossing diploids. TetraploidEuphrasiashowed contrasting patterns, with GS increasing with latitude in outcrossingEuphrasia arctica, but little GS variation in the highly selfingEuphrasia micrantha. Interspecific differences in GS genomic repeat percentages were small.We show the utility of treating GS as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, GS variation may be increased through hybridisation and population subdivision. In addition to selection on associated traits, GS is predicted to be affected indirectly by selection due to pleiotropy of the underlying PAVs.
Simultaneous profiling of multiple chromatin proteins in the same cells
Authors: Gopalan Sneha , Wang Yuqing , Harper Nicholas W. , Garber Manuel , Fazzio Thomas G. 
Published: April 2021

AbstractMethods derived from CUT&RUN and CUT&Tag enable genome-wide mapping of the localization of proteins on chromatin from as few as one cell. These and other mapping approaches focus on one protein at a time, preventing direct measurements of colocalization of different chromatin proteins in the same cells and requiring prioritization of targets where samples are limiting. Here we describe multi-CUT&Tag, an adaptation of CUT&Tag that overcomes these hurdles by using antibody-specific barcodes to simultaneously map multiple proteins in the same cells. Highly specific multi-CUT&Tag maps of histone marks and RNA Polymerase II uncovered sites of co-localization in the same cells, active and repressed genes, and candidate cis-regulatory elements. Single-cell multi-CUT&Tag profiling facilitated identification of distinct cell types from a mixed population and characterization of cell type-specific chromatin architecture. In sum, multi-CUT&Tag increases the information content per cell of epigenomic maps, facilitating direct analysis of the interplay of different proteins on chromatin.
Fascin limits Myosin activity withinDrosophilaborder cells to control substrate stiffness and promote migration
Authors: Lamb Maureen C. , Kaluarachchi Chathuri P. , Lansakara Thiranjeewa I. , Lan Yiling , Tivanski Alexei V. , Tootle Tina L. 
Published: April 2021

AbstractA key regulator of collective cell migrations, which drive development and cancer metastasis, is substrate stiffness. Increased substrate stiffness promotes migration and is controlled by Myosin. UsingDrosophilaborder cell migration as a model of collective cell migration, we identify, for the first time, that the actin bundling protein Fascin limits Myosin activityin vivo. Loss of Fascin results in: increased activated Myosin on the border cells and their substrate, the nurse cells; decreased border cell Myosin dynamics; and increased nurse cell stiffness as measured by atomic force microscopy. Reducing Myosin restores on-time border cell migration infascinmutant follicles. Further, Fascin’s actin bundling activity is required to limit Myosin activation. Surprisingly, we find that Fascin regulates Myosin activity in the border cells to control nurse cell stiffness to promote migration. Thus, these data shift the paradigm from a substrate stiffness-centric model of regulating migration, to uncover that collectively migrating cells play a critical role in controlling the mechanical properties of their substrate in order to promote their own migration. This new means of mechanical regulation of migration is likely conserved across contexts and organisms, as Fascin and Myosin are common regulators of cell migration.
The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis
Authors: Rivero-Hinojosa Samuel , Pugacheva Elena M. , Kang Sungyun , Méndez-Catalá Claudia Fabiola , Kovalchuk Alexander L. , Strunnikov Alexander V. , Loukinov Dmitri , Lee Jeannie T. , Lobanenkov Victor V. 
Published: April 2021

ABSTRACTCTCF is a key organizer of the 3D genome. Its specialized paralog, BORIS, heterodimerizes with CTCF but is expressed only in male germ cells and in cancer states. Unexpectedly, BORIS-null mice have only minimal germ cell defects. To understand the CTCF-BORIS relationship, mouse models with varied CTCF and BORIS levels were generated. WhereasCtcf+/+Boris+/+,Ctcf+/-Boris+/+, andCtcf+/+Boris-/-males are fertile,Ctcf+/-Boris-/-(Compound Mutant; CM) males are sterile. Testes with combined depletion of both CTCF and BORIS show reduced size, defective meiotic recombination, increased apoptosis, and malformed spermatozoa. Although CM germ cells exhibit only 25% of CTCF WT expression, chromatin binding of CTCF is preferentially lost from CTCF-BORIS heterodimeric sites. Furthermore, CM testes lose the expression of a large number of spermatogenesis genes and gain the expression of developmentally inappropriate genes that are “toxic” to fertility. Thus, a combined action of CTCF and BORIS is required to both repress pre-meiotic genes and activate post-meiotic genes for a complete spermatogenesis program.
Rapid Structure-Function Insights via Hairpin-Centric Analysis of Big RNA Structure Probing Datasets
Authors: Radecki Pierce , Uppuluri Rahul , Aviran Sharon 
Published: April 2021

ABSTRACTThe functions of RNA are often tied to its structure, hence analyzing structure is of significant interest when studying cellular processes. Recently, large-scale structure probing (SP) studies have enabled assessment of global structure-function relationships via standard data summarizations or local folding. Here, we approach structure quantification from a hairpin-centric perspective where putative hairpins are identified in SP datasets and used as a means to capture local structural effects. This has the advantage of rapid processing of big (e.g., transcriptome-wide) data as RNA folding is circumvented, yet it captures more information than simple data summarizations. We reformulate a statistical learning algorithm we previously developed to significantly improve precision of hairpin detection, then introduce a novel nucleotide-wise measure, termed the hairpin-derived structure level (HDSL), which captures local structuredness by accounting for the presence of likely hairpin elements. Applying HDSL to data from recent studies recapitulates, strengthens, and expands on their findings which were obtained by more comprehensive folding algorithms, yet our analyses are orders of magnitude faster. These results demonstrate that hairpin detection is a promising avenue for global and rapid structure-function analysis, furthering our understanding of RNA biology and the principal features which drive biological insights from SP data.
Bioconversion of pomegranate residues into biofuels and bioactive lipids
Authors: Dourou Marianna , Economou Christina N. , Aggeli Lida , Janák Miroslav , Valdés Gabriela , Elezi Nefeli , Kakavas Dimitrios , Papageorgiou Theodore , Vayenas Dimitrios V. , Certik Milan , Aggelis George 
Published: April 2021

AbstractPomegranate residues (PRs) (i.e. the solid residues remaining after juice extraction), generated currently in abundance in Greece, contain a variety of carbon sources and therefore can be regarded as a potential feedstock for chemical and biotechnological processes rather than as waste materials. In the current project, the polysaccharides contained in PRs were extracted and hydrolyzed in a one-step process without the use of chemical reagents and the resulting broth was used as substrate in biotechnological applications, including ethanol and single cell oil (SCO) production. The yeastsMeyerozyma guilliermondii,Scheffersomyces coipomoensis,Sugiyamaella paludigenaand especiallySaccharomyces cerevisiae, were able to efficiently convert PR derived reducing sugars into bioethanol. Ethanol production under anaerobic conditions ranged from 3.6 to 12.5 g/L. In addition, the oleaginous yeastsLipomyces lipoferandYarrowia lipolyticaas well asM. guilliermondii,S. coipomoensisandS. paludigenawere tested for their ability to accumulate lipids suitable as feedstock for biodiesel production. Lipids were accumulated at concentrations up to 18% and were rich in palmitic acid (C16:0) and oleic acid (C18:1). Finally, the oleaginous fungusCunnichamella echinulatawas cultivated on PR based solid substrates for γ-linolenic acid (GLA) production. The fermented bio-products (i.e. fermented substrate plus fungal mycelia) contained up to 4.8 mg GLA/g of dry weight. Phenolic removal (up to 30%) was achieved by several of the above mentioned microorganisms, includingC. echinulata,L. lipofer,M. guilliermondii,S. paludigenaandY. lipolytica. We conclude that PRs can be used as a raw material for microbial growth, ethanol and SCO production, which is of economic and environmental importance.