bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single molecule analysis reveals the role of regulatory light chains in fine-tuning skeletal myosin-II function
Authors: Nayak Arnab , Wang Tianbang , Franz Peter , Steffen Walter , Chizhov Igor , Tsiavaliaris Georgios , Amrute-Nayak Mamta 
Published: January 2020

AbstractMyosin II is the main force generating motor during muscle contraction. Myosin II exists as different isoforms, involved in diverse physiological functions. The outstanding question is whether the myosin heavy chain (MHC) isoforms alone account for the distinct physiological properties. Unique sets of essential and regulatory light chains (RLCs) assembled with specific MHCs raises an interesting possibility of specialization of myosin functions via light chains (LCs). Here, we ask whether different RLCs contribute to the functional diversification. To investigate this, we generated chimeric motors by reconstituting MHC fast isoform (MyHC-IId) and slow isoform (MHC-I) with different light chain variants. As a result of RLCs swapping, actin filament sliding velocity increased by ∼ 10 fold for the slow myosin and decreased by >3 fold for the fast myosin. Ensemble molecule solution kinetics and single molecule optical trapping measurements provided in-depth insights into altered chemo mechanical properties of the myosin motors, thereby affecting the sliding speed. We find that both slow and fast myosins mechanical output is sensitive to the RLC isoform and propose that RLCs are crucial in fine-tuning of the myosin function.
High Force Catch Bond Mechanism of Bacterial Adhesion in the Human Gut
Authors: Liu Zhaowei , Liu Haipei , Vera Andrés M. , Bernardi Rafael C. , Tinnefeld Philip , Nash Michael A. 
Published: January 2020

AbstractBacterial colonization of the human intestine requires firm adhesion of bacteria to insoluble targets under hydrodynamic flow. Here we report the molecular mechanism behind an mechanostable protein complex responsible for resisting high shear forces and adhering bacteria to cellulose fibers in the human gut. Using single-molecule force spectroscopy (SMFS), single-molecule FRET (smFRET), and molecular dynamics (MD) simulations, we resolved two binding modes and three unbinding reaction pathways of a mechanically ultrastableR. champanellensis(Rc) Dockerin-Cohesin (Doc-Coh) complex. The complex assembles in two discrete binding modes with significantly different mechanical properties, with one breaking at ~500 pN and the other at ~200 pN at loading rates from 1-100 nN/sec. A neighboring X-module domain allosterically regulates the binding interaction and inhibits one of the low-force pathways at high loading rates, giving rise to a new mechanism of catch bonding that manifests under force ramp protocols. Multi-state Monte Carlo simulations show strong agreement with experimental results, validating the proposed kinetic scheme. These results explain mechanistically how gut microbes regulate cell adhesion strength at high shear stress through intricate molecular mechanisms including dual-binding modes, mechanical allostery and catch bonds.
Deep learning based behavioral analysis enables high precision rodent tracking and is capable of outperforming commercial solutions
Authors: Sturman Oliver , von Ziegler Lukas , Schläppi Christa , Akyol Furkan , Grewe Benjamin , Bohacek Johannes 
Published: January 2020

AbstractTo study brain function, preclinical research relies heavily on animal monitoring and the subsequent analyses of behavior. Commercial platforms have enabled semi high-throughput behavioral analyses by providing accurate tracking of animals, yet they often struggle with the analysis of ethologically relevant behaviors and lack the flexibility to adapt to variable testing environments. In the last couple of years, substantial advances in deep learning and machine vision have given researchers the ability to take behavioral analysis entirely into their own hands. Here, we directly compare the performance of commercially available platforms (Ethovision XT14, Noldus; TSE Multi Conditioning System, TSE Systems) to cross-verified human annotation. To this end, we provide a set of videos - carefully annotated by several human raters - of three widely used behavioral tests (open field, elevated plus maze, forced swim test). Using these data, we show that by combining deep learning-based motion tracking (DeepLabCut) with simple post-analysis, we can track animals in a range of classic behavioral tests at similar or even greater accuracy than commercial behavioral solutions. In addition, we integrate the tracking data from DeepLabCut with post analysis supervised machine learning approaches. This combination allows us to score ethologically relevant behaviors with similar accuracy to humans, the current gold standard, thus outperforming commercial solutions. Moreover, the resulting machine learning approach eliminates variation both within and between human annotators. In summary, our approach helps to improve the quality and accuracy of behavioral data, outperforming commercial systems at a fraction of the cost.
Toxic effect of 2,2’-bis(bicyclo[2.2.1] heptane) on bacterial cells
Authors: Kessenikh A. G. , Yaguzhinsky L. S. , Bermeshev M. V. , Pevgov V. G. , Samoilov V. O. , Shorunov S. V. , Maksimov A. L. , Yaguzhinsky L. S. , Manukhov I. V. 
Published: January 2020

ABSTRACTHere we present the study of the genotoxic effect of a 2,2’-bis(bicyclo[2.2.1]heptane) (BBH), which is promising as a fuel component for liquid rocket engines. The use ofEscherichia coli lux-biosensors showed that in addition to DNA damage causing SOS-response, there is also an oxidative effect on cells. The greatest toxicity is determined by the mechanism of formation of superoxide anion radical and is detected by the lux biosensorE. colipSoxS-lux, in which the genes of bacterial luciferases are transcriptionally crosslinked with the promoter of thesoxSgene. It is assumed that the oxidation of BBH leads to the formation of reactive oxygen species, which should give the main contribution to the toxicity of this substance.
What causes different coronal curve patterns in idiopathic scoliosis?
Authors: Pasha Saba 
Published: January 2020

AbstractBackgroundAdolescent idiopathic scoliosis (AIS) is a three-dimensional deformity of the spinal column in otherwise healthy adolescents. The underlying mechanisms associated with the spinal deformity development have been explored which delineated the role of the sagittal curvature of the spine. The patterns of the spinal deformity vary between the AIS patients as shown in several classification systems. It remains to further investigate how variations in sagittal profiles result in different coronal plane deformities in AIS and how these deformation patterns are intrinsically different.MethodsA total of 71 Lenke 1 and 52 Lenke 5 AIS patients were included retrospectively. The 3D models of the spine were generated from biplanar radiographs to calculate the clinical spinal parameters, vertebral axial rotations, and the 3D centerline of the spinal curvature. A classification based on the centerlines’ axial plane projection was developed. The 3D curvature of the centerline was calculated at each point. A 2D elastic rod finite element model (FEM) of the sagittal spinal curvature for each axial subtype was developed to calculate the 3D deformity of the spine under gravity and axial torsion. Differences in the axial clusters’ clinical parameters, curvature of the spine, and the deformation patterns of the FEM were compared. The characteristics of the sagittal curvature of these axial clusters were determined.ResultsLenke1 was divided into two axial groups (I and II) whereas the Lenke 5 cohort all had the same axial projection pattern (loop shape). T5-T12 kyphosis was significantly different between Lenke1-Group I and the other two groups, p=0.04. The vertebral rotation in both Lenke1-Group I and Lenke 5 had only one maximum value and the FEM deformed in a loop shaped whereas Lenke1-group II showed two maximum values for vertebral rotation and the FEM of the centerline deformed in a lemniscate shape. The ratio of the spinal arc lengths above and below the sagittal inflection points for Lenke1-Groups I and II and Lenke 5 were 0.52, 1.16, and 3.24, respectively.ConclusionVariations in the axial plane projection of the curve were observed within Lenke types. Lenke 1- Group I and Lenke 5 showed similar 3D curve characteristics suggesting one 3D curve whereas Lenke1-Group II, with two 3D curves, behaved differently. The length of the spinal arcs above and below the sagittal inflection point related to the patterns of axial deformity.
Can early exposure to stress enhance resilience to ocean warming in two oyster species?
Authors: Pereira Roberta R. C. , Scanes Elliot , Gibbs Mitchell , Byrne Maria , Ross Pauline M. 
Published: January 2020

ABSTRACTSecuring economically and ecologically significant molluscs, as our oceans warm and acidify due to climate change, is a global priority. South eastern Australia receives warm water in a strengthening East Australia Current and so resident species are vulnerable to elevated temperature and marine heat waves. This study tested whether oysters pre exposed to elevated temperature or heat stress enhances resilience to ocean warming later in life. Two Australian species, the flat oyster,Ostrea angasi,and the Sydney rock oyster,Saccostrea glomerata, were given a mild dose of warm water or “heat shock” stress in the laboratory and then transferred to elevated temperature conditions where we used the thermal outfall from power generation as a proxy to investigate the impacts of ocean warming. Shell growth, condition index, lipid content and profile and survival of oysters was impacted by elevated temperature in the field, with flat oysters being more impacted than Sydney rock oysters. Flat oysters grew faster than Sydney rock oysters at ambient temperature, but were more sensitive to elevated temperature. Early exposure to heat stress did little to ameliorate the negative effects of increased temperature, although the survival of heat shocked flat oysters was greater than non-heat shocked oysters. Further investigations are required to determine if early exposure to heat stress can act to inoculate oysters to future stress and overall enhance resilience of oysters to ocean warming.
Mitigating ecosystem impacts of bottom trawl fisheries for North Sea soleSolea soleaby replacing mechanical by electrical stimulation
Authors: Rijnsdorp A.D. , Depestele J. , Eigaard O.R. , Hintzen N.T. , Ivanovic A. , Molenaar P. , O’Neill F. , Polet H. , Poos J.J. , van Kooten T. 
Published: January 2020

AbstractEcosystem effects of bottom trawl fisheries are a major concern. We analysed whether the replacement of mechanical stimulation by electrical stimulation may reduce the adverse impacts on the benthic ecosystem in the beam trawl fishery for sole. Although the use of electricity is not allowed to catch fish in European Union waters, a number of beam trawlers got derogation and switched to pulse trawling to explore the potential to reduce impacts. We extended a recently developed assessment framework and showed that the switch to pulse trawling substantially reduced benthic impacts when exploiting the Total Allowable Catch of sole in the North Sea. We applied the framework to Dutch beam trawl logbook data from 2009 to 2017 and estimated that the trawling footprint decreased by 23%; the precautionary impact indicator of the benthic community decreased by 39%; the impact on median longevity decreased by 20%; the impact on benthic biomass decreased by 61%; the amount of sediment mobilised decreased by 39%. The decrease is due to the replacement of tickler chains by electrode arrays, a lower towing speed and higher catch efficiency for sole. The effort and benthic impact of the beam trawl fishery targeting plaicePleuronectes platessain the central North Sea increased with the recovery of the plaice stock. This study illustrates the usefulness of a standardized methodological framework to assess the differences in time trends and trawling impact between gears.
ADrosophilamodel of oral peptide therapeutics for adult Intestinal Stem Cell tumors
Authors: Bajpai Anjali , Ahmad Quazi Taushif , Tang Hong-Wen , Manzar Nishat , Singh Virender , Thakur Ashwani , Ateeq Bushra , Perrimon Norbert , Sinha Pradip 
Published: January 2020

ABSTRACTThe proto-oncogene YAP /Yki, a transcription co-factor of the Hippo pathway, has been linked to many cancers. YAP interacts with DNA-binding TEAD/Sd proteins to regulate expression of its transcriptional targets. Disruption of YAP-TEAD therefore offers a potential therapeutic strategy. The mammalian Vestigial Like (VGLL) protein, specifically its TONDU domain, has been shown to competitively inhibit YAP-TEAD interaction and a TONDU peptide can suppress YAP-induced cancer. As TONDU could potentially be developed into a therapeutic peptide for multiple cancers, we evaluated its efficacy in Yki-driven adult Intestinal Stem Cell (ISC) tumors in Drosophila. We show that oral uptake of the TONDU peptide is highly effective at inhibiting Yki-driven gut tumors by suppressing YAP-TEAD interaction. Comparative proteomics of early and late stage Yki-driven ISC tumors revealed enrichment of a number of proteins, including members of the integrin signaling pathway, such as Talin, Vinculin and Paxillin. These, in turn displayed a decrease in their levels in TONDU-peptide treated tumors. Further, we show that Sd binds to the regulatory region of integrin-coding gene, mew, which codes for αPS1, a key integrin of the ISCs. In support to a possible role of integrins in Yki-driven ISC tumors, we show that genetic downregulation ofmewarrests Yki-driven ISC proliferation, reminiscent of the effects of TONDU peptide. Altogether, our findings present a novel platform for screening therapeutic peptides and provide insights into tumor suppression mechanisms.SIGNIFICANCE STATEMENTDiscovering novel strategies to inhibit oncogene activity is a priority in cancer biology. As signaling pathways are widely conserved between mammals and Drosophila, these questions can be effectively addressed in this model organism. Here, we show that progression ofDrosophilaIntestinal Stem Cell (ISC) tumors induced by gain of an oncogenic form of the transcription co-factor Yki can be suppressed by feeding a peptide corresponding to the conserved TONDU domain of Vestigial (Vg), which blocks binding of Yki to the Sd transcription factor. Further, we show that down regulation of the integrin signaling pathway is causally linked to TONDU-peptide-mediated ISC tumor suppression. Our findings reveal thatDrosophilacan be successfully used to screen peptides for their therapeutic applications.
The photoreceptor UVR8 mediates the perception of both UV-B and UV-A wavelengths up to 350 nm of sunlight with responsivity moderated by cryptochromes
Authors: Rai Neha , O’Hara Andrew , Farkas Daniel , Safronov Omid , Ratanasopa Khuanpiroon , Wang Fang , Lindfors Anders V. , Jenkins Gareth I. , Lehto Tarja , Salojärvi Jarkko , Brosché Mikael , Strid Åke , Aphalo Pedro J. , Morales Luis O. 
Published: January 2020

AbstractThe photoreceptors UV RESISTANCE LOCUS 8 (UVR8) and CRYPTOCHROMES 1 and 2 (CRYs) play major roles in the perception of UV-B (280–315 nm) and UV-A/blue radiation (315–500 nm), respectively. However, it is poorly understood how they function in sunlight. The roles of UVR8 and CRYs were assessed in a factorial experiment withArabidopsis thalianawild-type and photoreceptor mutants exposed to sunlight for 6 h or 12 h under five types of filters with cut-offs in UV and blue-light regions. Transcriptome-wide responses triggered by UV-B and UV-A wavelengths shorter than 350 nm (UV-Asw) required UVR8 whereas those induced by blue and UV-A wavelengths longer than 350 nm (UV-Alw) required CRYs. UVR8 modulated gene expression in response to blue light while lack of CRYs drastically enhanced gene expression in response to UV-B and UV-Asw. These results agree with our estimates of photons absorbed by these photoreceptors in sunlight and within vitromonomerization of UVR8 by wavelengths up to 335 nm. Motif enrichment analysis predicted complex signaling downstream of UVR8 and CRYs. Our results highlight that it is important to use UV waveband definitions specific to plants’ photomorphogenesis as is routinely done in the visible region.
Dynamic evolution of great ape Y chromosomes
Authors: Cechova Monika , Vegesna Rahulsimham , Tomaszkiewicz Marta , Harris Robert S. , Chen Di , Rangavittal Samarth , Medvedev Paul , Makova Kateryna D. 
Published: January 2020

AbstractThe mammalian male-specific Y chromosome plays a critical role in sex determination and male fertility. However, because of its repetitive and haploid nature, it is frequently absent from genome assemblies and remains enigmatic. The Y chromosomes of great apes represent a particular puzzle: their gene content is more similar between human and gorilla than between human and chimpanzee, even though human and chimpanzee shared a more recent common ancestor. To solve this puzzle, here we constructed a dataset including Ys from all extant great ape genera. We generated assemblies of bonobo and orangutan Ys, from short and long sequencing reads, and aligned them with the publicly available human, chimpanzee and gorilla Y assemblies. Analyzing this dataset, we found that the genusPan, including chimpanzee and bonobo, experienced accelerated substitution rates. Additionally,Panalso exhibited elevated gene death rates. These observations are consistent with high levels of sperm competition inPan. Furthermore, we inferred that the great ape common ancestor already possessed multi-copy sequences homologous to most human and chimpanzee palindromes. Nonetheless, each species also acquired distinct ampliconic sequences. We also detected increased chromatin contacts between and within palindromes (from Hi-C data), likely facilitating gene conversion and structural rearrangements. Moreover, our ENCODE data analysis suggested that Y palindromes exist to promote gene conversion preventing degradation of not only genes, as is commonly believed, but also gene regulatory sites. Our results highlight the dynamic mode of Y chromosome evolution, and open avenues for studies of male-specific dispersal in endangered great ape species.
Membrane-mediated ligand unbinding of the PK-11195 ligand from TSPO
Authors: Dixon Tom , Uyar Arzu , Ferguson-Miller Shelagh , Dickson Alex 
Published: January 2020

ABSTRACTThe translocator protein (TSPO), previously known as the peripheral benzodiazepine receptor, is of longstanding medical interest as both a biomarker for neuroinjury and a potential drug target for neuroinflammation and other disorders. Recently it was shown that ligand residence time is a key factor determining steroidogenic efficacy of TSPO-binding compounds. This spurs interest in simulations of (un)binding pathways of TSPO ligands, which could reveal the molecular interactions governing ligand residence time. In this study, we use a weighted ensemble algorithm to determine the unbinding pathway for different poses of PK-11195, a TSPO ligand used in neuroimaging. In contrast with previous studies, our results show that PK-11195 does not dissociate directly into the solvent but instead dissociates via the lipid membrane by going between the transmembrane helices. We analyze this path ensemble in detail, constructing descriptors that can facilitate a general understanding of membrane-mediated ligand binding. We construct a Markov state model using additional straightforward simulations to determine pose stability and kinetics of ligand unbinding. Together we combine over 40µs of trajectory data to form a coherent picture of the ligand binding landscape. We find that all poses are able to interconvert before unbinding, leading to single mean first passage time estimate for all starting poses which roughly agrees with the experimental quantity. The ligand binding transition state predicted by our combined model occurs when PK-11195 is already in the membrane and does not involve direct ligand-protein interactions. This has implications for the design of new long residence-time TSPO ligands.SIGNIFICANCEKinetics-oriented drug design is an emerging objective in drug discovery. However, while ligand binding affinity (or the binding free energy) is purely a function of the bound and unbound states, the binding kinetics depends on the nature of the paths by which the (un)binding occurs. This underscores the importance of approaches that can reveal information about the ensemble of (un)binding paths. Here we used advanced molecular dynamics approaches to study the unbinding of PK-11195 from TSPO and find it dissociates from the protein by dissolving into the membrane, and that the transition state occurs after the PK-11195 molecule has already separated from TSPO. These results motivate the design of future long-residence time TSPO ligands that destabilize the membrane-solvated transition state.
Human iPS Cells Derived Skeletal Muscle Progenitor Cells Promote Myoangiogenesis and Restore Dystrophin in Duchenne Muscular Dystrophic Mice
Authors: Xuan Wanling , Khan Mahmood , Ashraf Muhammad 
Published: January 2020

AbstractBackground and ObjectiveDuchenne muscular dystrophy (DMD) is caused by mutations of the gene that encodes the protein dystrophin. Loss of dystrophin leads to severe and progressive muscle-wasting in both skeletal and heart muscles. Human induced pluripotent stem cells (hiPSCs) and their derivatives offer important opportunities to treat a number of diseases. Here, we investigated whether givinostat, a histone deacetylase inhibitor (HDACi), could reprogram hiPSCs into muscle progenitor cells (MPC) for DMD treatment.Methods and ResultsMPC generated by CHIR99021 and givinostat (Givi) small molecules from multiple hiPSCs expressed myogenic makers (Pax7, desmin) and were differentiated into myotubes expressing MF20 upon culture in specific differentiation medium. These MPC exhibited superior proliferation and migration capacity determined by CCK-8, colony and migration assays compared to control-MPC generated by CHIR99021 and fibroblast growth factor (FGF). Upon transplantation in hind limb of Mdx/SCID mice with cardiotoxin (CTX) induced injury, these MPC showed higher engraftment and restoration of dystrophin than treatment with control-MPC and human myoblasts. In addition, treated muscle with these MPC showed significantly limited infiltration of inflammatory cells and reduced muscle necrosis and fibrosis. A number of these cells were engrafted under basal lamina expressing Pax7, which were capable of generating new muscle fibers after additional injury. Extracellular vesicles released from these cells promoted angiogenesis after reinjury.ConclusionWe successfully generated integration free MPC from multiple hiPS cell lines using CHIR99021 and Givi. Givinostat induced MPC showed marked and impressive regenerative capabilities and restored dystrophin in injured tibialis muscle compared to control MPC. Additionally, MPC generated by Givi also seeded the stem cell pool in the treated muscle. It is concluded that hiPSCs pharmacologically reprogrammed into MPC with a small molecule, Givi with anti-oxidative, anti-inflammatory and muscle gene promoting properties might be an effective cellular source for treatment of muscle injury and restoration of dystrophin in DMD.