bluuebunny/crossref_metadata_2025_split huggingface dataset:
dbGuide: A database of functionally validated guide RNAs for genome editing in human and mouse cells
Authors: Gooden Alexander A. , Evans Christine N. , Sheets Timothy P. , Clapp Michelle E. , Chari Raj 
Published: August 2020

ABSTRACTWith the technology’s accessibility and ease of use, CRISPR has been employed widely in many different organisms and experimental settings. As a result, thousands of publications have used CRISPR to make specific genetic perturbations, establishing in itself a resource of validated guide RNA sequences. While numerous computational tools to assist in the design and identification of candidate guide RNAs exist, these are still just at best predictions and generally, researchers inevitably will test multiple sequences for functional activity. Here, we presentdbGuide(https://sgrnascorer.cancer.gov/dbguide), a database of functionally validated guide RNA sequences for CRISPR/Cas9-based knockout in human and mouse. Our database not only contains computationally determined candidate guide RNA sequences, but of even greater value, over 4000 sequences which have been functionally validated either through direct amplicon sequencing or manual curation of literature from over 1000 publications. Finally, our established framework will allow for continual addition of newly published and experimentally validated guide RNA sequences for CRISPR/Cas9-based knockout as well as incorporation of sequences from different gene editing systems, additional species, and other types of site-specific functionalities such as base editing, gene activation, repression, and epigenetic modification.
αKG inhibits Regulatory T cell differentiation by coupling lipidome remodelling to mitochondrial metabolism
Authors: Matias Maria I. , Yong Carmen S. , Foroushani Amir , Sezgin Erdinc , Levental Kandice R. , Talebi Ali , Mongellaz Cédric , Dehair Jonas , Wong Madeline , Kinet Sandrina , Zimmermann Valérie S. , Levental Ilya , Yvan-Charvet Laurent , Swinnen Johannes V. , Muljo Stefan A. , Tardito Saverio , Dardalhon Valérie , Taylor Naomi 
Published: August 2020

AbstractThe differentiation of CD4 T cells to a specific effector fate is metabolically regulated, integrating glycolysis and mitochondrial oxidative phosphorylation (OXPHOS) with transcriptional and epigenetic changes. OXPHOS is tightly coordinated with the tricarboxylic acid (TCA) cycle but the precise role of TCA intermediates in CD4 T cell differentiation remain unclear. Here we demonstrate that α-ketoglutarate (αKG) inhibited regulatory T cell (Treg) generation while conversely, increasing Th1 polarization. In accord with these data, αKG promoted the effector profile of Treg-polarized chimeric antigen receptor-engineered T cells against the ErbB2 tumor antigen. Mechanistically, αKG significantly altered transcripts of genes involved in lipid-related processes, inducing a robust lipidome-wide remodelling and decreased membrane fluidity. A massive increase in storage and mitochondria lipids was associated with expression of mitochondrial genes and a significantly augmented OXPHOS. Notably, inhibition of succinate dehydrogenase activity, the bridge between the TCA cycle and the electron transport chain, enforced Treg generation. Thus, our study identifies novel connections between αKG, lipidome remodelling and OXPHOS in CD4 T cell fate decisions.
Discovery and Development of Novel DNA-PK Inhibitors by Targeting the unique Ku-DNA Interaction
Authors: Gavande Navnath S. , VanderVere-Carozza Pamela S. , Pawelczak Katherine S. , Vernon Tyler L. , Hanakahi Leslyn A. , Summerlin Matthew , Dynlacht Joseph R. , Farmer Annabelle H. , Sears Catherine R. , Nasrallah Nawar Al , Garrett Joy , Turchi John J. 
Published: August 2020

ABSTRACTDNA-dependent protein kinase (DNA-PK) plays a critical role in the non-homologous end joining (NHEJ) repair pathway and the DNA damage response (DDR). DNA-PK has therefore been pursued for the development of anti-cancer therapeutics in combination with ionizing radiation (IR). We report the discovery of a new class of DNA-PK inhibitors that act via a novel mechanism of action, inhibition of the Ku-DNA interaction. We have developed a series of highly potent and specific Ku-DNA binding inhibitors (Ku-DBi’s) that block the Ku-DNA interaction and inhibit DNA-PK kinase activity. Ku-DBi’s directly interact with the Ku and inhibitin vitroNHEJ, cellular NHEJ, and potentiate the activity of IR and radiomimetics. Analysis of Ku-null cells demonstrates that Ku-DBi’s cellular activity is a direct result of Ku inhibition, as Ku-null cells are insensitive to Ku-DBi’s. The utility of Ku-DBi’s was also demonstrated in a CRISPR gene-editing model where we demonstrate that the efficiency of gene insertion events was increased in cells pre-treated with Ku-DBi’s, consistent with inhibition of NHEJ and activation of homologous recombination to facilitate gene insertion. These data demonstrate the discovery and application of new series of compounds that modulate DNA repair pathways via a unique mechanism of action.
Optimising tropical forest bird surveys using passive acoustic monitoring and repeated short-duration point counts
Authors: Metcalf Oliver C. , Barlow Jos , Marsden Stuart , de Moura Nárgila Gomes , Berenguer Erika , Ferreira Joice , Lees Alexander C. 
Published: August 2020

AbstractEstimation of avian biodiversity is a cornerstone measure of ecosystem condition, with turnover in avian community composition underpinning many studies of land-use change in tropical forests. Surveys conducted using autonomous recorders have been frequently found to be more efficient than traditional point-count surveys. However, there has been limited research into optimal survey duration, despite autonomous recordings allowing for many more repeats of short-duration surveys with relative ease in comparison to traditional survey methods.We use an acoustic dataset collected from a region of very high avian biodiversity - the eastern Brazilian Amazon - to test the effect of using short-duration surveys to increase temporal coverage without increasing total survey duration. We use this dataset to assess whether a survey protocol consisting of 240 15-second surveys at 29 locations, ‘short-duration surveys’, has an influence on resulting alpha and gamma diversity, and detection frequency, than ‘standard-duration surveys’ of four 15-minute surveys per location.We find that repeated short-duration surveys outperform longer duration surveys in every metric considered herein, with short-duration surveys predicted to detect approximately 50% higher alpha diversity, and 10% higher gamma diversity. Short-duration surveys also detect species more often, at more survey locations. Conversely, standard-duration surveys are almost four times more likely to produce false negatives (i.e. to fail to detect species presence). Whilst there is no difference between the proportion of uncommon species detected by the two methods, when considering species detected multiple times at multiple locations, short-duration surveys detected three times more uncommon species than standard-duration surveys.We conclude that short-duration recorded surveys should be considered the primary method for sampling the species richness of bird communities in tropical forests and is likely to be preferable to longer duration or traditional surveys in most environments.
Emerging Tumor Development by Simulating Single-cell Events
Authors: Rosenbauer Jakob , Berghoff Marco , Schug Alexander 
Published: August 2020

AbstractDespite decades of substantial research, cancer remains a ubiquitous scourge in the industrialized world. Effective treatments require a thorough understanding of macroscopic cancerous tumor growth out of individual cells. Clinical imaging methods, however, only detect late-stage macroscopic tumors, while many quantitative experiments focus on small clusters of cancerous cells in microscopic detail but struggle to grow full tumorsin-vitro. Here, we introduce the critical scale-bridging link between both these scopes. We are able to simulate the growth of mm-sized tumors composed of 1.5 millionμm-resolved individual cells by employing highly parallelized code on a supercomputer. We observe the competition for resources and space, which can lead to hypoxic or necrotic tissue regions. Cellular mutations and tumor stem cells can lead to tissue heterogeneity and change tumor properties. We probe the effects of different chemotherapy and radiotherapy treatments and observe selective pressure. This improved theoretical understanding of cancer growth as emerging behavior from single-cells opens new avenues for various scientific fields, ranging from developing better early-stage cancer detection devices to testing treatment regimesin-silicofor personalized medicine.Author summaryExperimental and microscopy techniques are rapidly advancing biology and the observability of tissue. The theoretical understanding of tissue either focuses on a few cells or continuous tissue. Here we introduce the scale-bridging theoretical link that is able to model single cells as well as tissue consisting of millions of those cells, harvesting the power of modern supercomputers. We close the gap between single-cells and tissue through access to the full time-resolved trajectories of each cell and the emerging behavior of the tissue. We apply our framework on a generalized model for tumor growth. Tumor heterogeneity, as well as tumor stem cells are introduced, and the changes of behavior in response to cancer treatments is observed and validated.
Fertility-LightGBM: A fertility-related protein prediction model by multi-information fusion and light gradient boosting machine
Authors: Yue Lingling , Wang Minghui , Yang Xinhua , Han Yu , Song Lili , Yu Bin 
Published: August 2020

ABSTRACTThe identification of fertility-related proteins plays an essential part in understanding the embryogenesis of germ cell development. Since the traditional experimental methods are expensive and time-consuming to identify fertility-related proteins, the purposes of predicting protein functions from amino acid sequences appeared. In this paper, we propose a fertility-related protein prediction model. Firstly, the model combines protein physicochemical property information, evolutionary information and sequence information to construct the initial feature space ‘ALL’. Then, the least absolute shrinkage and selection operator (LASSO) is used to remove redundant features. Finally, light gradient boosting machine (LightGBM) is used as a classifier to predict. The 5-fold cross-validation accuracy of the training dataset is 88.5%, and the independent accuracy of the training dataset is 91.5%. The results show that our model is more competitive for the prediction of fertility-related proteins, which is helpful for the study of fertility diseases and related drug targets.
Local coupling between sleep spindles and slow oscillations supports the stabilization of motor memories
Authors: Solano Agustín , Riquelme Luis A. , Perez-Chada Daniel , Della-Maggiore Valeria 
Published: August 2020

AbstractRecent studies from us and others suggest that traditionally declarative structures (e.g., hippocampus) mediate some aspects of the encoding and consolidation of procedural memories. This evidence points to the existence of converging physiological pathways across memory systems. Here, we examined whether the coupling between slow oscillations (SO) and spindles, a mechanism well established in the consolidation of declarative memories, is relevant for the stabilization of human motor memories. To this aim, we conducted an EEG study in which we quantified various parameters of these oscillations during a night of sleep that took place immediately after learning a visuomotor adaptation task. We hypothesized that if this coupling is instrumental to motor memory consolidation then spindles locked to the active phase of a slow oscillation would predict long-term memory. We found that visuomotor adaptation increased the overall density of fast (≥12 Hz) but not slow (<12Hz) spindles during NREM3. This modulation was manifested rather locally, over the hemisphere contralateral to the trained hand. Although motor learning did not affect the density of SOs, it substantially enhanced the number of fast spindles locked to the active phase of SOs. The fact that only coupled spindles of the left hemisphere predicted long-term memory overnight, points to the precise phase relationship between these oscillations as a fundamental signature of motor memory consolidation. Our work provides evidence in favor of a common mechanism at the basis of the stabilization of declarative and non-declarative memories.Significance StatementEver since the discovery of memory systems, the study of the mechanisms supporting the consolidation of declarative and procedural memories has progressed somewhat in parallel. In the last few years, however, this framework is starting to change. We now know that structures originally thought of as purely declarative, such as the hippocampus, participate in the consolidation of procedural tasks. Here, we show that sleep modulates the stabilization of motor memories through a mechanism involved in the consolidation of declarative memories, based on the local synchrony between fast sleep spindles and slow oscillations. The fact that only coupled –but not uncoupled- spindles of the contralateral hemisphere predicted long-term memory supports a role of this association in the consolidation of motor memories.
Cdc42 activity is essential for the interplay between cAMP/PKA pathway and CatSper function
Authors: Luque Guillermina M. , Xu Xinran , Romarowski Ana , Gervasi María G. , Orta Gerardo , De la Vega-Beltrán José L. , Stival Cintia , Gilio Nicolás , Dalotto-Moreno Tomás , Krapf Dario , Visconti Pablo E. , Krapf Diego , Darszon Alberto , Buffone Mariano G. 
Published: August 2020

AbstractSperm acquire the ability to fertilize in a process called capacitation and undergo hyperactivation, a change in the motility pattern, which depends on Ca2+transport by CatSper channels. CatSper is essential for fertilization and it is subjected to a complex regulation that is not fully understood. Here, we report that similar to CatSper, Cdc42 distribution in the principal piece is confined to four linear domains and this localization is disrupted in CatSper1-null sperm. Cdc42 inhibition impaired CatSper activity and other Ca2+-dependent downstream events resulting in a severe compromise of the sperm fertilizing potential. We also demonstrate that Cdc42 is essential for CatSper function by modulating cAMP production by sAC, providing a new regulatory mechanism for the stimulation of CatSper by the cAMP/PKA-dependent pathway. These results reveal a broad mechanistic insight into the regulation of Ca2+in mammalian sperm, a matter of critical importance in male infertility as well as in contraception.
Gene families with stochastic exclusive gene choice underlie cell adhesion in mammalian cells
Authors: Iakovlev Mikhail , Faravelli Simone , Becskei Attila 
Published: August 2020

ABSTRACTExclusive stochastic gene choice combines precision with diversity. This regulation enables most T-cells to express exactly one T-cell receptor isoform chosen from a large repertoire, and to react precisely against diverse antigens. Some cells express two receptor isoforms, revealing the stochastic nature of this process. A similar regulation of odorant receptors and protocadherins enable cells to recognize odors and confer individuality to cells in neuronal interaction networks, respectively. We explored whether genes in other families are expressed exclusively by analyzing single cell RNA-seq data with a simple metric. Chromosomal segments and families are more likely to express genes concurrently than exclusively, possibly due to the evolutionary and biophysical aspects of shared regulation. Nonetheless, gene families with exclusive gene choice were detected in multiple cell types, most of them are membrane proteins involved in ion transport and cell adhesion, suggesting the coordination of these two functions. Thus, stochastic exclusive expression extends beyond the prototypical families, permitting precision in gene choice to be combined with the diversity of intercellular interactions.
Knowledge and attitude regarding stem cell research and its application among medical students in Pakistan
Authors: Daud Mashal , Sajid Zaina , Ali Tooba 
Published: August 2020

AbstractBackgroundThe utilization of stem cells (SCs) has led the way into a new era of therapeutics known as regenerative medicine. Their renewal property offers exciting possibilities in reversing tissue damage caused by metabolic and degenerative changes. Research should be conducted increasingly to explore the possibilities of SC utilization in Pakistan.ObjectivesTo assess the level of knowledge, perception, and attitude of medical students regarding stem cell research (SCR) and its application, to obtain a better insight into the future of stem cell therapy in Pakistan as it is a rapidly emerging field in medicine.Materials and MethodsThis cross-sectional study was carried out using a self-administered questionnaire filled by 206 medical students from different medical colleges in Pakistan. A convenience sampling method was used. Knowledge and attitude scores were calculated based on answers to 28 well-structured questions. Data was analyzed using SPSS.ResultsThe mean values of the answers showed that 60.2% (n=124) of the students had a good knowledge and 39.8% (n=82) had poor knowledge of stem cells. Whereas, 56.8% (n=117) expressed a positive attitude and 43.2% (n=89) expressed a negative attitude towards SCR. Independent t-test applied on knowledge score and attitude showed that the mean knowledge score of people with a positive attitude is higher i.e. 21.25 as compared to the mean knowledge score of people with negative attitude i.e. 19.21. And the difference of the means is significant at p=0.007. Thus, the attitude of students was observed to be significantly dependent on their knowledge about SCR.ConclusionThe results show that medical students have baseline knowledge about SC therapy and a positive attitude towards it. Seminars, workshops should be conducted and this topic should be added to their syllabus so that they obtain proper information about SCR and encourage further research.
Water requirement and growth indicators of forest tree species seedlings produced with automated irrigation management
Authors: Bueno Mateus Marques , dos Santos Leles Paulo Sérgio , Abreu João Felício Gonçalves , dos Santos Jaqueline Jesus Santana , de Carvalho Daniel Fonseca 
Published: August 2020

ABSTRACTThe lack of information regarding the water requirement of tree species promotes water waste in the seedlings production in nurseries. Water requirement, the growth plant factors and water efficiencies for height and diameter were determined for Schizolobium parahyba (Vell.) Blake, Cytharexylum myrianthum Cham. and Ceiba speciosa Ravenna seedlings, under greenhouse conditions and automated irrigation management. We used sewage sludge biosolids as substrate in the seedling phase (280 cm-3 tube), and sandy soil material in the initial pot growth phase (18 dm-3 pot). In the seedlings phase, four water replacement levels were applied to the substrate, by drip irrigation, meaning average replacement ranging from 40 (V1) to 100% (V4) of species water requirement. Seedlings developed properly and 80 days after emergency, S. parahyba, C. myrianthum and C. speciosa seedlings received, respectively, 2.40, 1.08 and 0.85 L per plant, for V4. After growth phase (230 DAE), the total water volumes were, respectively, 70.0, 50.3 and 52.7 L per plant. Under adequate water supply, there were rapid recovery and growth of the species, even for the seedlings which showed different height and diameter in the tube phase. The growth plant factors values found were below 0.5 for all species indicating low sensibility to growth, both in height and in diameter, in response to water deficit. Water efficiency indicators point to distinct trends between the two phases, and C. speciosa present higher values of water efficiencies for height (80.7 and 17.0 cm L-1) and diameter (2.1 and 0.5 mm L-1) in both phases.
Repeated multi-domain, but not single-domain, cognitive training prevents cognitive decline and amyloid pathology found in the APPNL-G-Fmouse model of Alzheimer disease
Authors: Mehla Jogender , Deibel Scott H. , Karem Hadil , Hossain Shakhawat , Lacoursiere Sean G. , Sutherland Robert J. , McDonald Robert J. , Mohajerani Majid H. 
Published: August 2020

AbstractEducation, occupation, and an active lifestyle, comprising enhanced social, physical, and mental components are associated with improved cognitive functions in aged people and may prevent/ or delay the progression of various neurodegenerative diseases including Alzheimer’s disease (AD). To investigate this protective effect, APPNL-G-F/NL-G-Fmice at 3 months of age were exposed to repeated, single- or multi-domain cognitive training. Cognitive training was given at the age of 3, 6, 9 & 12 months of age. Single-domain cognitive training was limited to a spatial navigation task. Multi-domain cognitive training consisted of a spatial navigation task, object recognition, and fear conditioning. At the age of 12 months, behavioral tests were completed for cognitive training groups and control group. After completion of behavioral testing, mice were sacrificed, and their brains were assessed for pathology. AppNL-G-Fmice given multi-domain cognitive training compared to APPNL-G-Fcontrol group showed an improvement in cognitive functions, reductions in amyloid load and microgliosis, and a preservation of cholinergic function. There were mild reductions in microglosis in the brain of APPNL-G-Fmice with singledomain cognitive training. These findings provide causal evidence for the potential of certain forms of cognitive training to mitigate the cognitive deficits in Alzheimer disease.
Optimizing accuracy and depth of protein quantification in experiments using isobaric carriers
Authors: Specht Harrison , Slavov Nikolai 
Published: August 2020

The isobaric carrier approach, which combines small isobarically-labeled samples with a larger isobarically-labeled carrier sample, is finding diverse applications in ultrasensitive mass-spectrometry analysis of very small samples, such as single cells. To enhance the growing use of isobaric carriers, we characterized the trade-offs of using isobaric carriers in controlled experiments with complex human proteomes. The data indicate that isobaric carriers directly enhances peptide sequence identification without simultaneously increasing the number of protein copies sampled from small samples. The results also indicate strategies for optimizing the amount of isobaric carrier and analytical parameters, such as ion accumulation time, for different priorities such as improved quantification or increased number of identified proteins. Balancing these trade-offs enables adapting isobaric carrier experiments to different applications, such as quantifying proteins from limited biopsies or organoids, building single-cell atlases, or modeling protein networks in single cells. In all cases, the reliability of protein quantification should be estimated and incorporated in all subsequent analysis. We expect that these guidelines will aid in explicit incorporation of the characterized trade-offs in experimental designs and transparent error propagation in data analysis.Abstract Figure