bluuebunny/crossref_metadata_2025_split huggingface dataset:
A myosin II-based nanomachine devised for the study of Ca2+-dependent mechanisms of muscle regulation
Authors: Pertici Irene , Bianchi Giulio , Bongini Lorenzo , Lombardi Vincenzo , Bianco Pasquale 
Published: September 2020

AbstractThe emergent properties of the array arrangement of the molecular motor myosin II in the sarcomere of the striated muscle, generation of steady force and shortening, can be studiedin vitrowith a synthetic nanomachine, made by an ensemble of eight HMM myosin fragments from rabbit psoas muscle carried on a piezoelectric nanopositioner and brought to interact with a properly oriented actin filament attached via gelsolin (a Ca2+-regulated actin binding protein) to a bead trapped by a Dual Laser Optical Tweezers. The application of the original version of the nanomachine to investigation of the Ca2+-dependent regulation mechanisms of the other sarcomeric (regulatory or cytoskeleton) proteins, adding them on at a time, was anyway prevented by the impossibility to preserve Ca2+as a free parameter. Here the nanomachine is implemented by assembling the bead-attached actin filament with the Ca2+-insensitive gelsolin fragment TL40. The performance of the nanomachine is determined either in the absence or in the presence of 0.1 mM Ca2+(the concentration required for BTA preparation with gelsolin). The nanomachine exhibits a maximum power output of 5.4 aW, independently of [Ca2+], opening the possibility for future studies of the Ca2+-dependent function/dysfunction of regulatory and cytoskeletal proteins.
Dispatched conformational dynamics couples transmembrane Na+flux to release of lipid-modified Hedgehog signal
Authors: Wang Qianqian , Asarnow Daniel E. , Ding Ke , Zhang Yunxiao , Ma Yong , Cheng Yifan , Beachy Philip A. 
Published: September 2020

AbstractThe DISP1 protein, related to the NPC1 and PTCH1 cholesterol transporters and to H+-driven transporters of the RND family, enables tissue patterning activity of the lipid-modified Hedgehog protein by releasing it from tightly-localized sites of embryonic expression. A 2.5 Å resolution cryo-EM structure of DISP1 revealed three Na+ions coordinated within a channel that traverses its transmembrane domain. This channel and Na+-binding are disrupted in DISP1-NNN (3.4 Å resolution), a variant with isosteric substitutions for three intramembrane aspartates that each coordinate and neutralize charge for one of the three Na+ions. DISP1-NNN and other variants that singly disrupt the Na+sites retain binding to the lipid-modified Hedgehog protein, but most fail to export Hedgehog. The Sonic hedgehog signal (ShhN) interacts with the DISP1 extracellular domains (2.7 Å complex structure), including an unusual extended DISP1 arm, at a location well above the membrane. Variability analysis reveals a dynamic series of DISP1 conformations, only a restricted subset of which appear to bind ShhN. The bound and unbound DISP1 conformations display distinct Na+site occupancies; these differences, in conjunction with the unusual locations of certain lipids bound to DISP1, suggest a mechanism by which transmembrane Na+flux may power extraction of the lipid-linked Hedgehog signal from the membrane, thus enabling its tissue patterning activity. The Na+-coordinating residues resolved in our DISP1 structures are wholly or partly conserved in some of the other metazoan RND family members, such as PTCH1 and NPC1, suggesting the utilization of Na+flux to power their conformationally-driven activities.
Cloning of Human ABCB11 Gene inE. colirequired the removal of an Intragenic Pribnow-Schaller Box before it’s Insertion into Genomic Safe Harbor AAVS1 Site using CRISPR Cas9
Authors: Vats Nisha , Sanal Madhusudana Girija , Venugopal Senthil Kumar , Taneja Pankaj , Sarin Shiv Kumar 
Published: September 2020

AbstractBackgroundGenomic safe harbors are sites in the genome which are safe for gene insertion such that the inserted gene will function properly, and the disruption of the genomic location doesn’t cause any foreseeable risk to the host. The AAVS1 site is the site which is disrupted upon integration of Adeno Associated Virus (AAV) and is considered a ‘safe-harbor’ in human genome because about one third of humans are infected with AAV and so far there is no apodictic evidence that AAV is pathogenic or disruption of AAVS1 causes any disease in man. Therefore, we chose to target AAVS1 site for the insertion of ABCB11, a bile acid transporter which is defective in Progressive Familial Intra Hepatic Cholestasis Type-2 (PFIC-2), a lethal disease of children where cytotoxic bile salts accumulate inside hepatocytes killing them and eventually the patient.MethodsWe used CRISPR Cas9 a genome editing tool to insert ABCB11 gene at AAVS1 site in human cell-lines.ResultsWe found that human ABCB11 sequence has a “Pribnow- Schaller Box” which allows its expression in bacteria and expression of ABCB11 protein which is toxic toE. coliand the removal of the same was required for successful cloning. We inserted ABCB11 at AAVS1 site in HEK 293T using CRISPR-Cas9 tool. We also found that ABCB11 protein has similarity withE. coliEndotoxin (Lipid A) Transporter MsbA.ConclusionWe inserted ABCB11 at AAVS1 site using CRISPR-Cas9, however, the frequency of homologous recombination was very low for this approach to be successful in-vivo (Figure: pictorial abstract).Pictorial AbstractABCB11 gene (which codes the transporter of human bile salts) is targeted to AAVS1 site using a construct which has 5’ and 3’ overhangs which are homologous to the AAVS1 site. A Pribnow box was detected inside ABCB11 gene which allowed the gene to transcribe in E. Coli causing bacterial lysis probably through competitive replacement of a homologous transporter protein in E. Coli (E. coli Endotoxin (Lipid A) Transporter) MsbA, resulting in Lipid A (L) accumulation inside the bacteria.
Drosophila suzukiiavoidance of microbes in oviposition choice
Authors: Sato Airi , Tanaka Kentaro M. , Yew Joanne Y. , Takahashi Aya 
Published: September 2020

AbstractWhile the majority ofDrosophilaspecies lay eggs onto fermented fruits, females ofD. suzukiipierce the skin and lay eggs into ripening fruits using their serrated ovipositors. The changes of oviposition site preference must have accompanied this niche exploitation. In this study, we established an oviposition assay to investigate the effects of commensal microbes deposited by conspecific and heterospecific individuals, and showed that presence of microbes on the oviposition substrate enhances egg-laying ofD. melanogasterandD. biarmipes, but discourages that ofD. suzukii. This result suggests that a drastic change has taken place in the lineage leading toD. suzukiiin how females respond to chemical cues produced by microbes. We also found that hardness of the substrate affects the response to microbial growth, indicating that mechanosensory stimuli interact with chemosensory invoked decisions to select or avoid oviposition sites.
Poorly expressed alleles of several human immunoglobulin heavy chain variable (IGHV) genes are common in the human population
Authors: Ohlin Mats 
Published: September 2020

ABSTRACTExtensive diversity has been identified in the human heavy chain immunoglobulin locus, including allelic variation, gene duplication, and insertion/deletion events. Several genes have been suggested to be deleted in many haplotypes. Such findings have commonly been based on inference of germline repertoire from data sets covering antibody heavy chain encoding transcripts. The inference process operate under conditions that may limit identification of genes transcribed at low levels. The presence of rare transcripts that would indicate the presence of poorly expressed alleles in haplotypes that otherwise appear to have deleted these genes has now been assessed. Alleles IGHV1-2*05, IGHV1-3*02, IGHV4-4*01, and IGHV7-4-1*01 were all identified as being expressed at very low levels from multiple haplotypes, haplotypes that by inference often appeared not to express these genes at all. These alleles harbor unusual sequence variants that may compromise the functionality of the encoded products. Transcripts of two of these alleles to a large degree do not encode a functional product, suggesting that these alleles might be non-functional. It is proposed that the functionality status of immunoglobulin genes should also include assessment of their ability to encode functional protein products.
Saccharomyces cerevisiaeEcm2 Modulates the Catalytic Steps of pre-mRNA Splicing
Authors: van der Feltz Clarisse , Nikolai Brandon , Schneider Charles , Paulson Joshua C. , Fu Xingyang , Hoskins Aaron A. 
Published: September 2020

ABSTRACTGenetic, biochemical, and structural studies have elucidated the molecular basis for spliceosome catalysis. Splicing is RNA catalyzed and the essential snRNA and protein factors are well-conserved. However, little is known about how non-essential components of the spliceosome contribute to the reaction and modulate the activities of the fundamental core machinery. Ecm2 is a non-essential yeast splicing factor that is a member of the Prp19-related complex of proteins. Cryo-electron microscopy (cryo-EM) structures have revealed that Ecm2 binds the U6 snRNA and is entangled with Cwc2, another non-essential factor that promotes a catalytically active conformation of the spliceosome. These structures also indicate that Ecm2 and the U2 snRNA likely form a transient interaction during 5’ splice site (SS) cleavage. We have characterized genetic interactions between ECM2 and alleles of splicing factors that alter the catalytic steps in splicing. In addition, we have studied how loss of ECM2 impacts splicing of pre-mRNAs containing non-consensus or competing SS. Our results show that ECM2 functions during the catalytic stages of splicing. It facilitates the formation and stabilization of the 1st-step catalytic site, promotes 2nd-step catalysis, and permits alternate 5’ SS usage. We propose that Cwc2 and Ecm2 can each fine-tune the spliceosome active site in unique ways. Their interaction network may act as a conduit through which splicing of certain pre-mRNAs, such as those containing weak or alternate splice sites, can be regulated.
Septal HDAC1 facilitates long-lasting extinction of social fear in male mice
Authors: Bludau Anna , Paul Andreas , Neumann Inga D , Menon Rohit 
Published: September 2020

AbstractSocial anxiety disorder (SAD) is primarily caused by traumatic social events and is characterized by intense fear and avoidance of socially enriched contexts. Formation of such intense social aversion requires learning of the association between trauma and originally neutral social stimuli. Acetylation of histones in response to learning is critical for long-term memory formation. Class I histone deacetylases (HDACs) have emerged as powerful negative regulators of long-term memory formation. However, the lack of clarity in isoform and spatial specificity in HDAC function exists. Utilizing the social fear conditioning (SFC) as well as cued fear conditioning (CFC) paradigms, we aimed to functionally characterize the role of class I HDACs, especially HDAC1, in the regulation of aversive memories in socialversusnon-social contexts. Using cFos expression as a marker of cellular activity, we revealed that the lateral septum (LS) was specifically activated post-acquisition in socially fear conditioned (SFC+) mice. We further measured an increase in activity-inducing HDAC1 phosphorylation at serine residues within the septum of SFC+mice during extinction of social fear. Pharmacological inhibition of HDAC1 within the LS facilitated, while viral overexpression of septal HDAC1 impaired extinction of social fear. Finally, we found that the abovementioned facilitation of extinction memory by HDAC1 inhibition was long-lasting and persists even after 30 days of extinction. Our results show that LS-HDAC1 is a key regulator of long-lasting social fear extinction, which points towards HDAC1 as a potential therapeutic target for SAD.
Limitation of phosphate assimilation maintains cytoplasmic magnesium homeostasis
Authors: Bruna Roberto E. , Kendra Christopher G. , Groisman Eduardo A. , Pontes Mauricio H. 
Published: September 2020

AbstractPhosphorus (P) is an essential component of several core biological molecules. In bacteria, P is mainly acquired as inorganic orthophosphate (Pi). Once in the cytoplasm, Pi is incorporated into adenosine triphosphate (ATP), which exists primarily as a Mg2+salt. Notably, whereas P is essential, excess of cytosolic Pi hinders growth. Here we demonstrate that cytotoxic effects of excessive Pi uptake result from its assimilation into ATP and subsequent disruption of Mg2+dependent processes. We show thatSalmonella entericacells experiencing cytoplasmic Mg2+starvation restrict Pi uptake, thereby limiting the availability of an ATP precursor. This response prevents excessive ATP synthesis, overproduction of ribosomal RNA, chelation of free cytoplasmic Mg2+and the destabilization of Mg2+-dependent core processes that ultimately hinder bacterial growth and leads to loss of cellular viability. We demonstrate that, even when cytoplasmic Mg2+is not limiting, excessive Pi uptake leads to increased ATP synthesis, depletion of free cytoplasmic Mg2+, inhibition of translation and growth. Our results establish that bacteria must restrict Pi uptake to prevent the depletion of cytoplasmic Mg2+. Furthermore, they provide a framework to understand the molecular basis of Pi cytotoxicity and reveal a regulatory logic employed by bacterial cells to control P assimilation.ImportancePhosphorus (P) is essential for life. As the fifth most abundant element in living cells, P is required for the synthesis of an array of biological molecules including (d)NTPs, nucleic acids and membranes. Organisms typically acquire environmental P as inorganic phosphate. While essential for growth and viability, excessive intracellular Pi is toxic for both bacteria and eukaryotes. Using the bacteriumSalmonella entericaas a model, we demonstrate that Pi cytotoxicity is manifested following its assimilation into ATP, which acts as a chelating agent for intracellular cations, most notably, Mg2+. These results identify physiological processes disrupted by excessive Pi and elucidate a regulatory logic employed by bacteria to prevent uncontrollable P assimilation.
Characterizing tissue composition through combined analysis of single-cell morphologies and transcriptional states
Authors: Bao Feng , Deng Yue , Wan Sen , Wang Bo , Dai Qionghai , Altschuler Steven J. , Wu Lani F. 
Published: September 2020

AbstractAdvances in spatial transcriptomics technologies enable optical profiling of morphological and transcriptional modalities from the same cells within tissues. Here, we presentmulti-modalstructuredembedding (MUSE), an approach to deeply characterize tissue heterogeneity through analysis of combined image and transcriptional single-cell measurements. We demonstrate that MUSE can discover cellular subpopulations missed by either modality as well as compensate for modality-specific noise. MUSE identified biologically meaningful cellular subpopulations and stereotyped spatial patterning within heterogeneous mouse cortex brain tissues, profiled by seqFISH+ or STARmap technologies. MUSE provides a framework for combining multi-modal single-cell data to reveal deeper insights into the states, functions and organization of cells in complex biological tissues.
Effect of single‐ versus double‐layer uterine closure during caesarean section on postmenstrual spotting (2Close): multicentre, double‐blind, randomised controlled superiority trial
Authors: Stegwee SI , van der Voet LF , Ben AJ , de Leeuw RA , van de Ven PM , Duijnhoven RG , Bongers MY , Lambalk CB , de Groot CJM , Huirne JAF ,   for the 2Close study group
Published: September 2020

ObjectiveTo evaluate whether double‐layer uterine closure after a first caesarean section (CS) is superior compared with single‐layer uterine closure in terms of postmenstrual spotting and niche development in the uterine caesarean scar.DesignMulticentre, double‐blind, randomised controlled superiority trial.SettingThirty‐two hospitals in the Netherlands.PopulationA total of 2292 women aged ≥18 years undergoing a first CS were randomly assigned to each procedure (1:1): 1144 women were assigned to single‐layer uterine closure and 1148 women were assigned to double‐layer uterine closure.MethodsSingle‐layer unlocked closure and double‐layer unlocked closure, with the second layer imbricating the first.Main outcome measuresNumber of days with postmenstrual spotting during one menstrual cycle 9 months after CS. Secondary outcomes: perioperative and menstrual characteristics; transvaginal ultrasound measurements.ResultsA total of 774 (67.7%) women from the single‐layer group and 770 (67.1%) women from the double‐layer group were evaluable for the primary outcome, as a result of drop‐out and amenorrhoea. The mean number of postmenstrual spotting days was 1.33 (bootstrapped 95% CI 1.12–1.54) after single‐layer closure and 1.26 (bootstrapped 95% CI 1.07–1.45) after double‐layer closure (adjusted mean difference −0.07, 95% CI −0.37 to 0.22, P = 0.810). The operative time was 3.9 minutes longer (95% CI 3.0–4.9 minutes, P < 0.001) and niche prevalence was 4.7% higher (95% CI 0.7–8.7%, P = 0.022) after double‐layer closure.ConclusionsThe superiority of double‐layer closure compared with single‐layer closure in terms of postmenstrual spotting after a first CS was not shown. Long‐term obstetric follow‐up of our trial is needed to assess whether uterine caesarean closure guidelines should be adapted.Tweetable abstractDouble‐layer uterine closure is not superior for postmenstrual spotting after a first caesarean; single‐layer closure performs slightly better on other outcomes.
Why for feed and not for human consumption? The black soldier fly larvae
Authors: Bessa Leah W. , Pieterse Elsje , Marais Jeannine , Hoffman Louwrens C. 
Published: September 2020

AbstractWith the surge in consumption of insects, the search continues to find ways to increase the popularity of insect‐based products in the Western world. The black soldier fly larvae (BSFL), which is mainly utilized for animal feed, has great potential to provide a sustainable source of nutrients for human food. This review aims to discuss some of the key benefits and challenges of BSFL and their potential role as a food ingredient and/or product for human consumption. Few articles specifically discuss BSFL as a food source, therefore a comprehensive literature search strategy consisted of collecting and evaluating published data about BSFL as animal feed that could be relevant to its use in food. The hurdles that need to be overcome in order to introduce BSFL as a viable food option include safety concerns, technofunctional properties, nutritional aspects, consumer attitudes, and product applications for BSFL.
Impact of the COVID‐19 pandemic on patients with chronic rheumatic diseases: A study in 15 Arab countries
Authors: Ziadé Nelly , el Kibbi Lina , Hmamouchi Ihsane , Abdulateef Nizar , Halabi Hussein , Hamdi Wafa , Abutiban Fatemah , el Rakawi Manal , Eissa Mervat , Masri Basel 
Published: September 2020

AbstractAimTo evaluate the impact of the coronavirus disease 2019 pandemic (COVID‐19) on the access to rheumatology care for patients with chronic rheumatic diseases (CRD) in the Arab countries.MethodA web‐based cross‐sectional survey was designed by the Arab Adult Arthritis Awareness group (AAAA) consisting of 16 rheumatologists representing countries from the Arab League of Associations for Rheumatology (ArLAR) and was validated by the ArLAR scientific committee. The survey was disseminated online through social media and patients' association channels between May 8 and May 22, 2020. The steering committee developed recommendations to improve the care of patients with CRD during the COVID‐19 pandemic.ResultsA total of 2163 patients were included in the analysis; 72% were female; mean age was 40 years (SD 11.9). The Levant, the Gulf, and North Africa contributed almost equally to the sample. The pandemic had a significant negative impact on rheumatology visits in 82% of cases, access to hydroxychloroquine (47%), and chronic medication persistency (28%). The negative impact on rheumatology visits was associated with female gender, country, medication non‐persistency, isolation due to COVID‐19, and impact on mental health. Sixty‐one patients (2.8%) stated that they had COVID‐19, 5% said that a close contact was infected, and 47% were in isolation because of COVID‐19.ConclusionThe current study highlights the deleterious consequences of the COVID‐19 pandemic on the continuity of rheumatology care. Therefore, an action plan, including establishing a telemedicine platform, securing drug availability, and promoting medication persistence through the appropriate communication channels, is strongly recommended.
Efficacy of abiraterone acetate in castration‐resistant metastatic prostate cancer: A real‐world data analysis
Authors: Oyman Abdilkerim , Başak Mustafa , Özçelik Melike , Özyükseler Deniz Tataroğlu , Işık Selver , Yıldırım Mahmut Emre 
Published: September 2020

AbstractPurposeThe aim of this study was to evaluate the efficacy of abiraterone in patients with castration‐resistant metastatic prostate cancer.Materials and methodsWe retrospectively analyzed 51 patients with mCRPC treated with abiraterone acetate from January 2014 to August 2018. Clinicopathological information, treatment modalities, treatment responses, and survival times were retrospectively reviewed.ResultsA total of 51 patients who received abiraterone 1000 mg/day + prednisone 10 mg/day between January 2014 and August 2018 were included in the study. Of these patients, 33 (64.7%) had post‐chemotherapy (CT) and 18 (35.3%) had CT‐naive abiraterone receipt. Median overall survival (OS) was 17.3 months (range 9.3‐33.1). Median OS was found to be 12.7 months (range 9.4‐18.3) and 29.4 months (range 9.3‐33.0) in the CT‐naive and post‐CT group, respectively (P = .236). Median radiographic PFS (rPFS) was 10.1 months (range 4.5‐18.4). In the CT‐naive group, rPFS was 10.1 months (IQR 6.0‐14.7) and in the post‐CT group, it was 9.7 months (range 4.0‐18.4) (P = .808). PSA progression‐free survival (PSA‐PFS) was 9.1 months (range 4.6‐13.1). In the CT‐naive group, PSA‐PFS was 7.4 months (range 4.6‐13.4) and in post‐CT, it was 9.1 months (range 4.8‐13.1) (P = .843).ConclusionsThese results show that abiraterone acetate is an effective and reliable agent in real‐life data.