bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of CD73 as the antigen of an antigen-unknown monoclonal antibody established by exosome immunization, and its antibody-drug conjugate exerts an antitumor effect on glioblastoma cell lines
Authors: anzai Takahiro , Saijou Shinji , Takashima Hiroki , Hara Misato , Hanaoka Shingo , Matsumura Yasuhiro , Yasunaga Masahiro 
Published: October 2021

AbstractDevelopment of antibodies against the native structure of membrane proteins with multiple transmembrane domains is challenging because it is difficult to prepare antigens with native structures. Previously, we successfully developed a monoclonal antibody against multi-pass membrane protein TMEM180 by exosome immunization in rats. This approach yielded antibod-ies that recognized cancer-specific antigens on the exosome. In this study, we performed im-munoprecipitation using magnetic beads to identify the antigen of one of the rat antibody clones, 0614, as CD73. We then converted antibody 0614 to human chimeric antibody 0614-5 and found that the humanized antibody did not inhibit CD73 enzymatic activity. Glioblastoma (GB) was the cancer type with the highest expression of CD73 in the tumor relative to healthy tissue. An antibody–drug conjugate (ADC) of 0614-5 exerted an antitumor effect on GB cell lines according to expression of CD73. The 0614-5-ADC could be used to treat cancers with high CD73 expression. In addition, our strategy could be used to determine the antigen of any antibody produced by exosome immunization.
A systematic evaluation of data processing and problem formulation of CRISPR off-target site prediction
Authors: Yaish Ofir , Asif Maor , Orenstein Yaron 
Published: October 2021

AbstractCRISPR/Cas9 system is widely used in a broad range of gene-editing applications. While this gene-editing technique is quite accurate in the target region, there may be many unplanned off-target edited sites. Consequently, a plethora of computational methods have been developed to predict off-target cleavage sites given a guide RNA and a reference genome. However, these methods are based on small-scale datasets (only tens to hundreds of off-target sites) produced by experimental techniques to detect off-target sites with a low signal-to-noise ratio. Recently, CHANGE-seq, a new in vitro experimental technique to detect off-target sites, was used to produce a dataset of unprecedented scale and quality (more than 200,000 off-target sites over 110 guide RNAs). In addition, the same study included GUIDE-seq experiments for 58 of the guide RNAs to produce in vivo measurements of off-target sites. Here, we fill the gap in previous computational methods by utilizing these data to perform a systematic evaluation of data processing and formulation of the CRISPR off-target site prediction problem. Our evaluations show that data transformation as a pre-processing phase is critical prior to model training. Moreover, we demonstrate the improvement gained by adding potential inactive off-target sites to the training datasets. Furthermore, our results point to the importance of adding the number of mismatches between the guide RNA and the off-target site as a feature. Finally, we present predictive off-target in vivo models based on transfer learning from in vitro. Our conclusions will be instrumental to any future development of an off-target predictor based on high-throughput datasets.
New tools for automated cryo-EM single-particle analysis in RELION-4.0
Authors: Kimanius Dari , Dong Liyi , Sharov Grigory , Nakane Takanori , Scheres Sjors H.W. 
Published: October 2021

1AbstractWe describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in the fourth major release of the RELION software. In particular, we introduce VDAM, a Variable-metric gradient Descent algorithm with Adaptive Moments estimation, for image refinement; a convolutional neural network for unsupervised selection of 2D classes; and a flexible framework for the design and execution of multiple jobs in pre-defined workflows. In addition, we present a stand-alone utility called MDCatch that links the execution of jobs within this framework with metadata gathering during microscope data acquisition. The new tools are aimed at providing fast and robust procedures for unsupervised cryo-EM structure determination, with potential applications for on-the-fly processing and the development of flexible, high-throughput structure determination pipelines. We illustrate their potential on twelve publicly available cryo-EM data sets.
Prime Editing Efficiency and Fidelity are Enhanced in the Absence of Mismatch Repair
Authors: Ferreira da Silva J , Oliveira GP , Arasa-Verge EA , Kagiou C , Moretton A , Timelthaler G , Jiricny J , Loizou JI 
Published: October 2021

AbstractPrime editing (PE) is a powerful genome engineering approach that enables the introduction of base substitutions, insertions and deletions into any given genomic locus. However, the efficiency of PE varies widely and depends not only on the genomic region targeted, but also on the genetic background of the edited cell. To determine which cellular factors affect PE efficiency, we carried out a focused genetic screen targeting 32 DNA repair factors, spanning all reported repair pathways. We show that, depending on cell line and type of edit, ablation of mismatch repair (MMR) affords a 2-17 fold increase in PE efficiency, across several human cell lines, types of edits and genomic loci. The accumulation of the key MMR factors MLH1 and MSH2 at PE sites argues for direct involvement of MMR in PE control. Our results shed new light on the mechanism of PE and suggest how its efficiency might be optimised.
Enhancers of host immune tolerance to bacterial infection discovered using linked computational and experimental approaches
Authors: Sperry Megan M. , Novak Richard , Keshari Vishal , Dinis Alexandre L. M. , Cartwright Mark J. , Camacho Diogo M. , Paré Jean-François , Super Mike , Levin Michael , Ingber Donald E. 
Published: October 2021

AbstractCurrent therapeutic strategies against bacterial infections focus on reduction of pathogen load through antibiotics; however, stimulation of host tolerance to infection might offer an alternative approach. Here we used computational transcriptomics and a Xenopus embryo infection model to rapidly discover infection response pathways, identify potential tolerance inducer drugs, and validate their ability to induce broad tolerance. Xenopus embryos exhibit natural tolerance to A. baumanii, K. pneumoniae, S. aureus, and S. pneumoniae bacteria, whereas A. hydrophila and P. aeruginosa produce infection that leads to death. Transcriptional profiling led to definition of a 20-gene signature that allows for discrimination between tolerant and susceptible states, as well as identification of active and passive tolerance responses based on the degree of engagement of gene transcription modulation. Upregulation of metal ion transport and hypoxia pathways reminiscent of responses observed in primate and mouse infection models were identified as tolerance mediators, and drug screening in the susceptible A. hydrophila infection model confirmed that a metal chelator (deferoxamine) and HIF-1α agonist (1,4-DPCA) increase embryo survival despite high pathogen load. These data demonstrate the value of combining the Xenopus embryo infection model with multi-omics analyses for mechanistic discovery and drug repurposing to induce host tolerance to bacterial infection.
Efficient Fluorescence-Based Localization Technique for Real-Time Tracking Endophytes Route in Host-Plants Colonization
Authors: Ondzighi-Assoume Christine A. , Bhusal Bandana , Traore Adam , Ouma Wilson K. , Mmbaga Margaret , Swiggart Ethan 
Published: October 2021

ABSTRACTBacterial isolates that enhance plant growth and suppress plant pathogens growth are essential tools for reducing pesticide applications in plant production systems. The objectives of this study were to develop a reliable fluorescence-based technique for labeling bacterial isolates selected as biological control agents (BCAs) to allow their direct tracking in the host-plant interactions, understand the BCA localization within their host plants, and the route of plant colonization. Objectives were achieved by developing competent BCAs transformed with two plasmids, pBSU101 and pANIC-10A, containing reporter genes eGFP and pporRFP, respectively. Our results revealed that the plasmid-mediated transformation efficiencies of antibiotic-resistant competent BCAs identified as PSL, IMC8, and PS were up 84%. Fluorescent BCA-tagged reporter genes were associated with roots and hypocotyls but not with leaves or stems and were confirmed by fluoresence microscopy and PCR analyses in colonized Arabidopsis and sorghum. This fluorescence-based technique’s high resolution and reproducibility make it a platform-independent system that allows tracking of BCAs spatially within plant tissues, enabling assessment of the movement and niches of BCAs within colonized plants. Steps for producing and transforming competent fluorescent BCAs, as well as the inoculation of plants with transformed BCAs, localization, and confirmation of fluorescent BCAs through fluorescence imaging and PCR, are provided in this manuscript. This study features host-plant interactions and subsequently biological and physiological mechanisms implicated in these interactions. The maximum time to complete all the steps of this protocol is approximately three months.SENTENCE SUMMARYWe describe a novel fluorescence localization technique as a powerful tool to directly visualize and determine the route in-situ of BCAs in host-plants interaction. The study features the host-plant interactions, biological and physiological responses implicated.
Ready-to-eat foods: A potential vehicle for spread of coagulase-positive staphylococci and antibiotic-resistant Staphylococcus aureus in Buea municipality, South West Cameroon
Authors: Esemu Seraphine Nkie , Njoh Sally Tabe , Ndip Lucy M. , Keneh Nene Kaah , Kfusi Jerome Achah , Njukeng Achiangia Patrick 
Published: October 2021

AbstractBackgroundThe consumption of ready-to-eat (RTE) foods contaminated with coagulase-positive staphylococci (CoPS) and especially Staphylococcus aureus puts consumers at potential risk of foodborne disease or colonization and subsequent infection. This cross-sectional study determined the levels of CoPS and the presence of S. aureus in RTE foods sold in Buea municipality.MethodA total of 420 RTE food samples comprising 70 each of cake, bread, fruit salad, meat-hot-pot, suya and boiled rice were randomly purchased from February to August 2020. The CoPS counts were determined by culturing on Baird-Parker agar and S. aureus identified by amplification of the nuc gene using polymerase chain reaction. All S. aureus isolates were screened for the presence of classical staphylococcal enterotoxin genes and each isolate challenged with 11 antibiotics to determine their antibiotic susceptibility profiles. Oxacillin-resistant S. aureus were analyzed for the presence of mecA gene.ResultOverall, 161 (38.3%) samples had detectable levels of coagulase-positive staphylococci ranging from 2.0-5.81 log10CFU/g. Based on CoPS levels, 37 (8.81%) of the 420 RTE food samples, only fruit salad and meat-hot-pot, had unsatisfactory microbiological quality. A total of 72 S. aureus isolates, comprising 52.78% from fruit salad, 16.67% from meat-hot-pot, 12.5% from boiled rice, 9.72% from suya, 5.56% from bread and 4.17% from cake were recovered. None of the S. aureus isolates possessed any of the classical enterotoxin genes. All the isolates were sensitive to vancomycin and ofloxacin while 68 (94.44%) and 66 (91.67%) were sensitive to oxacillin and ciprofloxacin, respectively. Resistance to penicillin (93.06%) was highest followed by amoxicillin (91.67%) and erythromycin (79.17%). Four isolates were identified as methicillin-resistant S. aureus all of which carried the mecA gene. A total of 24 antibiotypes were identified.ConclusionOur findings showed that RTE foods sold in the Buea municipality are likely vehicles for transmission of CoPS and antibiotic-resistant S. aureus.
Fast and ultra-sensitive glycoform analysis by supercritical fluid chromatography-tandem mass spectrometry
Authors: Haga Yoshimi , Yamada Masaki , Fujii Risa , Saichi Naomi , Yokokawa Takashi , Hama Toshihiro , Hayakawa Yoshihiro , Ueda Koji 
Published: October 2021

AbstractTherapeutic monoclonal antibodies (mAbs) are currently the largest and fastest growing category of biopharmaceuticals. Glycosylation of mAbs has a significant impact on their effector functions, as well as on their safety and pharmacokinetics. Heterogeneity of glycoforms is affected by various factors such as the producing cells and cell culture process. Therefore, accurate glycoform characterization is essential for drug design, process optimization, manufacturing, and quality control of therapeutic mAbs. In this study, we developed a fast, quantitative, and highly sensitive analytical platform for mAb glycan profiling by supercritical fluid chromatography-tandem mass spectrometry (SFC-MS/MS). An 8-minute analysis of bevacizumab, nivolumab, ramucirumab, rituximab, and trastuzumab by SFC-MS detected a total of 102 glycoforms, with a detection limit of 5 attomole. The dynamic range of glycan abundance was over 6 orders of magnitude for bevacizumab analysis by SFC-MS, compared to 3 orders of magnitude for conventional fluorescence HPLC analysis. This method revealed the glycan profile characteristics and lot-to-lot heterogeneity of various therapeutic mAbs. We were also able to detect a series of structural variations in pharmacologically important glycan structures. SFC-MS-based glycoform profiling method will provide an ideal platform for in-depth analysis of precise glycan structure and abundance.
Chemotherapy-Induced Cachexia and Model-Informed Dosing to Preserve Lean Mass in Cancer Treatment
Authors: Farhang-Sardroodi Suzan , La Croix Michael A. , Wilkie Kathleen P. 
Published: October 2021

AbstractAlthough chemotherapy is a standard treatment for cancer, it comes with significant side effects. In particular, certain agents can induce severe muscle loss, known as cachexia, worsening patient quality of life and treatment outcomes. 5-fluorouracil, an anti-cancer agent used to treat several cancers, has been shown to cause muscle loss. Experimental data indicates a non-linear dose-dependence for muscle loss in mice treated with daily or week-day schedules. We present a mathematical model of chemotherapy-induced muscle wasting that captures this non-linear dose-dependence. Area-under-the-curve metrics are proposed to quantify the treatment’s effects on lean mass and tumour control. Model simulations are used to explore alternate dosing schedules, aging effects, and morphine use in chemotherapy treatment with the aim of better protecting lean mass while actively targeting the tumour, ultimately leading to improved personalization of treatment planning and improved patient quality of life.Author SummaryIn this paper we present a novel mathematical model for muscle loss due to cancer chemotherapy treatment. Loss of muscle mass relates to increased drug toxicity and side-effects, and to decreased patient quality of life and survival rates. With our model, we examine the therapeutic efficacy of various dosing schedules with the aim of controlling a growing tumour while also preserving lean mass. Preservation of body composition, in addition to consideration of inflammation and immune interactions, the gut microbiome, and other systemic health measures, may lead to improved patient-specific treatment plans that improve patient quality of life.
Mycobacterial resistance to zinc poisoning requires assembly of P-ATPase-containing membrane metal efflux platforms
Authors: Boudehen Yves-Marie , Faucher Marion , Maréchal Xavier , Miras Roger , Rech Jérôme , Sénèque Olivier , Wallat Maximilian , Demange Pascal , Bouet Jean-Yves , Saurel Olivier , Catty Patrice , Gutierrez Claude , Neyrolles Olivier 
Published: October 2021

ABSTRACTTransition metals are toxic at high concentrations. The P1B-ATPase metal exporter CtpC/Rv3270 is required for resistance to zinc poisoning in the human pathogen Mycobacterium tuberculosis. Here, we discovered that zinc resistance also depends on the chaperone-like protein PacL1/Rv3269. PacL1 bound Zn2+, but unlike PacL1 and CtpC, the PacL1 metal-binding motif (MBM) was required only at high zinc concentrations. PacL1 co-localized with CtpC in dynamic microdomains within the mycobacterial plasma membrane. Microdomain formation did not require flotillins nor the PacL1 MBM. Instead, loss of the PacL1 Glutamine/Alanine repeats led to loss of CtpC and sensitivity to zinc. PacL1 and CtpC are within the same operon, and homologous PacL1-P1B-ATPase pairs are widely distributed within and across prokaryotes. PacL1 colocalized and functioned redundantly with PacL orthologs in Mycobacterium tuberculosis. Overall, our study suggests that PacL proteins are scaffolds that assemble P-ATPase-containing metal efflux platforms, a novel type of functional membrane microdomain that underlies bacterial resistance to metal poisoning.
Nup358 regulates remodelling of ER-mitochondrial contact sites and autophagy
Authors: Kalarikkal Misha , Saikia Rimpi , Varshney Pallavi , Dhamale Prathamesh , Majumdar Amitabha , Joseph Jomon 
Published: October 2021

AbstractThe contact sites between ER and mitochondria regulate several cellular processes including inter-organelle lipid transport, calcium homeostasis and autophagy. However, the mechanisms that regulate the dynamics and functions of these contact sites remain unresolved. We show that annulate lamellae (AL), a relatively unexplored subcellular structure representing subdomains of ER enriched with a subset of nucleoporins, are present at ER-mitochondria contact sites (ERMCS). Depletion of one of the AL-resident nucleoporins, Nup358, results in increased contacts between ER and mitochondria. Mechanistically, Nup358 modulates ERMCS dynamics by restricting mTORC2/Akt signalling. Our results suggest that growth factor-mediated remodelling of ERMCS depends on a reciprocal binding of Nup358 and mTOR to the ERMCS tethering complex consisting of VAPB and PTPIP51. Furthermore, Nup358 also interacts with IP3R, an ERMCS-enriched Ca2+ channel, and controls Ca2+ release from the ER. Consequently, depletion of Nup358 leads to elevated cytoplasmic Ca2+ and autophagy via activation of Ca2+/CaMKK2/AMPK axis. Our study thus uncovers a novel role for AL, particularly for Nup358, in regulating mTORC2-mediated ERMCS remodelling and Ca2+-directed autophagy, possibly via independent mechanisms.
FGF signalling is involved in cumulus migration in the common house spider Parasteatoda tepidariorum
Authors: Wang Ruixun , Karadas Linda , Schiffer Philipp , Pechmann Matthias 
Published: October 2021

AbstractCell migration is a fundamental component during the development of most multicellular organisms. In spiders, the collective migration of a signalling centre, known as the cumulus, is required to set the dorsoventral body axis of the embryo.Here, we show that FGF signalling plays an important role during cumulus migration in the spider Parasteatoda tepidariorum. Spider embryos with reduced FGF signalling lack cumulus migration and display dorsoventral patterning defects. Our study reveals that cumulus expression of several FGF signalling components is regulated by the transcription factor Ets4. In conjunction with a previous study, we show that the expression of fgf8 in the germ-disc is regulated via the Hedgehog signalling pathway. We also demonstrate that FGF signalling influences the BMP signalling pathway activity in the region around cumulus cells.Finally, we show that FGF signalling might also influence cumulus migration in basally branching spiders and we propose a hypothetical model in which fgf8 acts a chemo-attractant to guide cumulus cells towards the future dorsal pole of the spider embryo.
Reconceptualizing disaster phases through aMetis-based approach
Authors: Pérodin Joanne , Adefris Zelalem , Cruz Mayra , Matos Rondon Nahomi , Hermantin Leonie , De la Cruz Guadalupe , Ganapati Nazife Emel , Ganapati Sukumar 
Published: October 2021

PurposeThis paper aims to call for change in disaster research through ametis-based approach that values practical skills and knowledge (vs technical knowledge) derived from responding to ongoing changes in the natural and human environment.Design/methodology/approachThis paper is based onmetisfrom Miami-Dade County that is prone to an array of climate-related disasters.Metisis supplemented by a review of secondary sources (e.g. newspaper articles, government reports).FindingsThere is a need to reconceptualize disaster phases in disaster research—preparedness, response, recovery and mitigation. For many members of marginalized communities of color, this paper depicts preparedness and mitigation as luxuries and response as a time of worry about financial obligations and survival after the disaster. It suggests that even communities that are not on a hurricane's path could have post-disaster experiences. It also highlights ongoing risks to marginalized communities' physical and mental well-being that are in addition to the mental health impacts of the disaster during the recovery phase.Originality/valueThis paper's originality is twofold: (1) underlining the importance ofmetis, a less studied and understood concept in disaster risk reduction, prevention and management literature and (2) questioning disaster researchers' technical knowledge with respect to each of the four disaster phases in light ofmetis.
Knowledge and implementation gaps in disaster risk reduction and spatial planning: Palu City, Indonesia
Authors: Sagala Saut Aritua Hasiholan , Suroso Djoko Santoso Abi , Puspitasari Novi , Suroso Avicennia Azzahra , Rizqika Khaza Allaya 
Published: October 2021

PurposeThis paper aims to explore the involvement of various actors in the preparation of Palu City's spatial plan before the multi-hazard events of 2018. In addition, it evaluates the extent to which disaster risk reduction (DRR) is mainstreamed in the spatial plan.Design/methodology/approachThe study uses qualitative methods of analysis with a risk-based planning approach and stakeholder analysis.FindingsIt is critical that DRR is mainstreamed in spatial planning from the preparation to the implementation. Disasters can take place when there is a knowledge gap in the planning process. This results in developments in disaster-prone areas and even in high-risk areas. Therefore, mainstreaming DRR into spatial planning requires national guidelines that offer planners at the local level clear and detailed guidance on what they must prepare, consider and do in a risk-based spatial planning process.Practical implicationsSpatial planning that does not mainstream DRR can lead to catastrophic consequences in the form of casualties and losses when multi-hazards occur.Originality/valueThe study provides evidence-based findings on the importance of mainstreaming DRR into spatial planning, particularly in areas prone to multi-hazards, which can be optimized through a risk-based planning approach.