bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing the effect of small-scale topographic variability on co-existing native and invasive species in a heterogeneous grassland using airborne hyperspectral remote sensing
Authors: Dao Phuong D. , Axiotis Alexander , He Yuhong 
Published: April 2021

AbstractCharacterizing the distribution, mechanism, and behaviour of invasive species is crucial to implementing an effective plan for the protection and management of native grassland ecosystems. Hyperspectral remote sensing has been used for mapping and monitoring invasive species at various spatial and temporal scales. However, most studies focus either on invasive tree species mapping or on the landscape-level using low-spatial resolution remote sensing imagery. These low-resolution images are not fine enough to distinguish individual invasive grasses, especially in a heterogeneous environment where invasive species are small, fragmented, and co-existing with native plants with similar color and texture.To capture the small yet highly dynamic invasive plants at different stages of the growing season and under various topography and hydrological conditions, we use airborne high-resolution narrow-band hyperspectral imagery (HrHSI) to map invasive species in a heterogeneous grassland ecosystem in southern Ontario, Canada.The results show that there is high spectral and textural separability between invasive species and between invasive and native plants, leading to an overall species classification accuracy of up to 89.6%. The combination of resultant species-level maps and the digital elevation model (DEM) showed that seasonality is the dominant factor that drives the distribution of invasive species at the landscape level, while small-scale topographic variations partially explain local patches of invasive species.This study provides insights into the feasibility of using HrHSI in mapping invasive species in a heterogeneous ecosystem and offers the means to understand the mechanism and behaviour of invasive species for a more effective grassland management strategy.
The human sperm basal body is a complex centrosome important for embryo pre-implantation development
Authors: Amargant Farners , Pujol Aïda , Ferrer-Vaquer Anna , Durban Mercè , Martínez Meritxell , Vassena Rita , Vernos Isabelle 
Published: April 2021

AbstractThe mechanism of conversion of the human sperm basal body to a centrosome after fertilization, and its role in supporting human early embryogenesis has not been directly addressed so far. Using proteomics and immunofluorescence studies we show here that the human zygote inherits a basal body enriched with centrosomal proteins from the sperm, establishing the first functional centrosome of the new organism. Injection of human sperm tails containing the basal body into human oocytes followed by parthenogenetically activation, showed that the centrosome contributes to the robustness of the early cell divisions, increasing the probability of parthenotes reaching the compaction stage. In the absence of the sperm-derived centrosome, pericentriolar (PCM) components stored in the oocyte can formde novostructures after genome activation, suggesting a tight PCM expression control in zygotes. Our results reveal that the sperm basal body is a complex organelle which converts to a centrosome after fertilization, ensuring the early steps of embryogenesis and successful compaction. However, more experiments are needed to elucidate the exact molecular mechanisms of centrosome inheritance in humans.
In vitrosynthesis and reconstitution using mammalian cell-free lysates enables the systematic study of the regulation of LINC complex assembly
Authors: Majumder Sagardip , Hsu Yen-Yu , Moghimianavval Hossein , Andreas Michael , Giessen Tobias W. , Luxton G.W. Gant , Liu Allen P. 
Published: April 2021

ABSTRACTMembrane proteins perform numerous important functions in cells and tissues. Approximately 20% of the human genome encodes for membrane proteins, which represent the majority of targets for clinically relevant small molecules. Consequently, understanding their structure and structure-function relationships is a fundamental problem in biomedical research. Given the difficulties inherent to performing mechanistic biochemical and biophysical studies of membrane proteinsin vitro, we previously developed a facile HeLa cell-based cell-free expression (CFE) system that enables the efficient reconstitution of full-length (FL) functional membrane proteins in supported lipid bilayers. Despite having shown the directional reconstitution of CFE-synthesized FL inner nuclear membrane SUN proteins (i.e. SUN1 and SUN2), which directly interact with outer nuclear membrane KASH proteins within the nuclear envelope lumen to form linker of nucleoskeleton and cytoskeleton (LINC) complexes that mechanically couple the cytoskeleton and nucleus, the mechanism underlying regulated LINC complex assembly remains unclear. Here, we provide evidence that suggests that the reconstitution of CFE-synthesized FL membrane proteins in supported lipid bilayers occurs primarily through the fusion of endoplasmic reticulum-derived microsomes present within our CFE reactions with our supported lipid bilayers. In addition, we demonstrate the ease with which our synthetic biology platform can be used to investigate the impact of the chemical environment (e.g. calcium ions and redox state) on the ability of CFE-synthesized FL SUN proteins reconstituted in supported lipid bilayers to interact with the luminal domain of the KASH protein nesprin-2. Moreover, we use our platform to study the molecular requirements for the homo- and hetero-typic interactions that can occur between SUN1 and SUN2. Finally, we show that our platform can be used to simultaneously reconstitute three different CFE-synthesized FL membrane proteins in a single supported lipid bilayer. Overall, these results establish our HeLa cell-based CFE and supported lipid bilayer reconstitution platform as a powerful tool for performing mechanistic dissections of the oligomerization and function of FL membrane proteinsin vitro. While our platform is not a substitute for cell-based studies of membrane protein biochemistry and function, it does provide important mechanistic insights into the biology of difficult-to-study membrane proteins.ABSTRACT GRAPHIC
New insights of glycosylation role on variable domain of antibody structures
Authors: Melo-Braga Marcella Nunes , Carvalho Milene Barbosa , Ferreira Manuela Cristina Emiliano , Felicori Liza Figueiredo 
Published: April 2021

AbstractN-glycosylation at antibody variable domain (FvN-glyco) has emerged as an important modification for antibody function such as stability and antigen recognition, but it is also associated with autoimmune disease and IgE-mediated hypersensitivity reaction. However, the information related to its role and regulation is still scarce. Therefore, we investigated new insights in this regarding using solved antibodies structures presenting in the Protein Data Bank (PDB). From 130 FvN-glycostructures, we observed significant findings as a higher prevalence of N-glycosylation in human and mouse antibodies containing IGHV1-8 and IGHV2-2 germline genes, respectively. We also speculate the influence of activation-induced cytidine deaminase (AID) in introducing N-glycosylation sites during somatic hypermutation, specifically on threonine to asparagine substitution. Moreover, we highlight the enrichment of anti-HIV antibodies containing N-glycosylation at antibody variable domain and where we showed a possible important role of N-glycosylation, besides to antigen-antibody interactions, in antibody chain pair and antibody-antibody interactions. These could be a positive secondary effect of glycosylation to enhance antigen binding and further neutralization, including an additional mechanism to form Fab-dimers. Overall, our findings extend the knowledge on the characteristics and diverse role of N-glycosylation at antibody variable domain.Key PointsPrevalence of FvN-glycoin human IGHV1-8 and mouse IGHV2-2 germline genes.Enrichment of antibody FvN-glycoagainst virus, especially anti-HIV-1.FvN-glycoin the interface with antigen, antibody pair chain, and another antibody.
Glycogen-dependent demixing of frog egg cytoplasm at increased crowding
Authors: Pelletier James F. , Field Christine M. , Coughlin Margaret , Ryazanova Lillia , Sonnett Matthew , Wühr Martin , Mitchison Timothy J. 
Published: April 2021

AbstractCrowding increases the tendency of macromolecules to aggregate and phase separate, and high crowding can induce glass-like states of cytoplasm. To explore the effect of crowding in a well-characterized model cytoplasm we developed methods to selectively concentrate components larger than 25 kDa fromXenopusegg extracts. When crowding was increased 1.4x, the egg cytoplasm demixed into two liquid phases of approximately equal volume. One of the phases was highly enriched in glycogen while the other had a higher protein concentration. Glycogen hydrolysis blocked or reversed demixing. Quantitative proteomics showed that the glycogen phase was enriched in proteins that bind glycogen, participate in carbohydrate metabolism, or are in complexes with especially high native molecular weight. The glycogen phase was depleted of ribosomes, ER and mitochondria. These results inform on the physical nature of a glycogen-rich cytoplasm and suggest a role of demixing in the localization of glycogen particles in tissue cells.
Development of highly potent neutralising nanobodies against multiple SARS-CoV-2 variants including the variant of concern B.1.351
Authors: Sziemel Agnieszka M , Hwa Shi-Hsia , Sigal Alex , Tyson Grace , Logan Nicola , Willett Brian J. , Durcan Peter J 
Published: April 2021

AbstractThe pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. During the years of 2020-2021, millions of humans have died due to SARS-CoV-2 infection and severe economic damage to the global economy has occurred. Unprecedented rapid investments in vaccine development have been made to counter the spread of SARS-CoV-2 among humans. While vaccines are a key pillar of modern medicine, SARS-CoV-2 has mutated as it spread among humans. Vaccines previously developed and approved by regulators are becoming less effective against new variants. One variant of SARS-CoV-2 known as B.1.351 that was first reported to be present in South Africa significantly reduces the efficacy of vaccines developed to date. Therapeutic options that work against the B.1.351 variant are therefore urgently needed to counteract reduced vaccine efficacy. We present here the discovery of recombinant alpaca antibodies that neutralise live virus of B.1.351 and other SARS-CoV-2 variants potently. The antibodies described here may be a useful tool for clinicians who are treating patients infected with B.1.351 and other SARS-CoV-2 for which there is currently no known highly effective treatment.
CST interacts with the cohesin complex and promotes chromosome cohesion
Authors: Schuck P. Logan , Stewart Jason A. 
Published: April 2021

AbstractSister chromatid cohesion (SCC) is established during DNA replication by loading of the cohesin complex on newly replicated chromatids. Cohesin must then be maintained until mitosis to prevent segregation defects and aneuploidy. How SCC is established and maintained until mitosis remains incompletely understood and emerging evidence suggests that replication stress can lead to premature SCC loss. Here, we report that the single-stranded DNA-binding protein CTC1-STN1-TEN1 (CST) aids in SCC. CST primarily functions in telomere length regulation but also has known roles in replication restart and DNA repair. Following depletion of CST subunits, we observed an increase in the complete loss of SCC. Additionally, we determined that CST interacts with the cohesin complex. Unexpectedly, we did not find evidence of defective cohesion establishment or mitotic progression in the absence of CST. However, we did find that treatment with various replication inhibitors increased the association between CST and cohesin. Since replication stress was recently shown to induce SCC loss, we supposed that CST may be required to maintain SCC following fork stalling. In agreement with this idea, SCC loss was greatly increased in CST-depleted cells following exogenous replication stress. Based on our findings, we propose that CST aids in the maintenance of SCC at stalled replication forks to prevent premature cohesion loss.
The Ensemble of Gene Regulatory Networks at Mutation-Selection Balance
Authors: Yang Chia-Hung , Scarpino Samuel V. 
Published: April 2021

AbstractThe evolution of diverse phenotypes both involves and is constrained by molecular interaction networks. When these networks influence patterns of expression, we refer to them as gene regulatory networks (GRNs). Here, we develop a quasi-species model of GRN evolution. With this model, we prove that–across a broad spectrum of viability and mutation functions–the dynamics converge to a stationary distribution over GRNs. Next, we show from first principles how the frequency of GRNs at equilibrium will be proportional to each GRN’s eigenvector centrality in the genotype network. Finally, we determine the structural characteristics of GRNs that are favored in response to a range of selective environments and mutational constraints. Our work connects GRN evolution to quasi-species models, and thus can provide a mechanistic explanation for the topology of GRNs experiencing various evolutionary forces.
Why most Principal Component Analyses (PCA) in population genetic studies are wrong
Authors: Elhaik Eran 
Published: April 2021

AbstractPrincipal Component Analysis (PCA) is a multivariate analysis that allows reduction of the complexity of datasets while preserving data covariance and visualizing the information on colorful scatterplots, ideally with only a minimal loss of information. PCA applications are extensively used as the foremost analyses in population genetics and related fields (e.g., animal and plant or medical genetics), implemented in well-cited packages like EIGENSOFT and PLINK. PCA outcomes are used to shape study design, identify, and characterize individuals and populations, and draw historical and ethnobiological conclusions on origins, evolution, dispersion, and relatedness. The replicability crisis in science has prompted us to evaluate whether PCA results are reliable, robust, and replicable. We employed an intuitive color-based model alongside human population data for eleven common test cases. We demonstrate that PCA results are artifacts of the data and that they can be easily manipulated to generate desired outcomes. PCA results may not be reliable, robust, or replicable as the field assumes. Our findings raise concerns about the validity of results reported in the literature of population genetics and related fields that place a disproportionate reliance upon PCA outcomes and the insights derived from them. We conclude that PCA may have a biasing role in genetic investigations. An alternative mixed-admixture population genetic model is discussed.
Plaque Size Tool: an automated plaque analysis tool for simplifying and standardising bacteriophage plaque morphology measurements
Authors: Trofimova Ellina , Jaschke Paul R 
Published: April 2021

AbstractBacteriophage plaque size measurement is essential for phage characterisation, but their manual size estimation requires a considerable amount of time and effort. In order to ease the work of phage researchers, we have developed an automated command-line application called Plaque Size Tool (PST) that can detect plaques of different morphology on the images of Petri dishes and measure plaque area and diameter. Plaque size measurements using PST showed no difference to those obtained with manual plaque size measurement in Fiji, indicating future results using PST are backwards compatible with prior measurements in the literature. PST can be applied to a range of lytic bacteriophages producing oval-shaped plaques, including bull’s-eye morphology. The application can also be used for titer calculation if most of the plaques are stand-alone. As laboratory automation becomes more commonplace, standardised and flexible open-source analytical tools like PST will be important parts of biofoundry and cloud lab bacteriophage workflows.
Crystal structures of Scone, pseudosymmetric folding of a symmetric designer protein
Authors: Mylemans Bram , Killian Theo , Vandebroek Laurens , Van Meervelt Luc , Tame Jeremy R.H. , Parac-Vogt Tatjana N. , Voet Arnout R.D. 
Published: April 2021

AbstractRecent years have seen a raise in the development of computational proteins including symmetric ones. We recently developed a nine-fold symmetricβ-propeller protein named Cake. Here we wanted to further engineer this protein to a three-fold symmetric nine-bladed propeller using computational design. Two nine-bladed propeller proteins were designed, named Scone-E and Scone-R. Crystallography however revealed the structure of both designs to adopt an eight-fold conformation with distorted termini, leading to a pseudo-symmetric protein. One of the proteins could only be crystallized upon addition of a polyoxometalate highlighting the usefulness of these molecules as a crystallisation additive.
Tourism, environment and hotel management: an innovative perspective to address modern trends in contemporary tourism management
Authors: Huo Chunhui , Hameed Javaria , Sadiq Muhammad Waqas , Albasher Gadah , Alqahtani Wedad 
Published: April 2021

PurposeThis paper aims to provide a valid insight into consumers' minds while considering word of mouth (WOM), brand image and uniqueness as independent variables while considering the tourism industry as the primary stakeholder.Design/methodology/approachThe study adopts qualitative research methods and data collected from 1,033 respondents using convenience sampling methodology. The data are collected from different tourists spots in China and Pakistan. The PROCESS macro was utilized in this study using SPSS version 25.0 to inspect the impacts by using Model 4 and the conditional effects indirectly by utilizing Model 14.FindingsCustomer's intimacy, search for novel and unexplored destinations highlight WOM interactions and perceived service value. Service value, interactional justice and professional attitude of hotel management mediated all the given relationships significantly. The brand image does not mediate any significant associations. Perceived service value and brand image predict customer's loyalty, and WOM is the direct measure of their intentions, and these variables are market trend indicators. A tourist's response toward different destinations is described in this study with comparative analysis of Chinese and Pakistani tourists. The study results showed a significantly positive relationship between hotel management professional behavior, customer's loyalty, customer's intimacy and WOM.Research limitations/implicationsThe recruited population might not be represented as the broader and larger visitor population, resulting in restricting establishing tactics. Moreover, this study's results provide significant insight into a tourism industry, hence providing a chance to manage customer loyalty better.Social, managerial and theoretical implicationsThis study contributes significantly to the body of knowledge and provides remarkable insight from the managerial perspective. Interactional justice results in significant value for hotel management directors and top management, front desk staff and operatives and front level employees and managers. Consumer sensitivity of fairness in interpersonal dealings calls for behavioral changes in frontline employees, especially those directly dealing with hotel visitors. Hotel staff and management should formulate a system to deal with the demands and needs of visitors. It should describe the rights and obligations of visitors and ensure that each customer is treated equally and with respect. Customers should be motivated to read the survey questionnaires kept in their rooms and offer their views on the services provided. This strategy might increase the customers' sense of empowerment and leading to notions of fairness in individual encounters.Originality/valueThis study provides an insight into the customer's minds while considering essential variables that include WOM, brand image, perceived service value and uniqueness.
How supply chain professionals learn at work: an investigation of learning mechanisms
Authors: Derwik Pernilla , Hellström Daniel 
Published: April 2021

PurposeSupply chain (SC) professionals and their competence play a key role in creating value and competitive advantage for companies. A considerable amount of this competence is developed at work, but little is known about how this takes place. Drawing on constructivist learning theory, the authors investigate how SC professionals develop their competence at work.Design/methodology/approachThe study takes off from a theoretical framework of workplace learning mechanisms, followed by a series of in-depth interviews with an expertise panel of profoundly competent and experienced SC professionals.FindingsThe results provide detailed insights into the learning process of SC professionals. The key findings show that SC professionals use a wide range of learning mechanisms throughout their careers, and that the contribution and complexity of these mechanisms differ and change dynamically with seniority. The findings also show that learning mechanisms should not be viewed as isolated phenomena, but closely related to every-day SCM work as well as learning attitude.Research limitations/implicationsBy conceptualizing learning as a process, and congregating the fragmented literature into a framework of workplace learning mechanisms, this research provides a theoretical reference point for future studies. The empirical findings bring a new level of detailed knowledge on how SC professionals learn at work.Practical implicationsThe results can assist SC professionals, HR managers and academic program leaders in their quest to develop competence in the field of SCM.Originality/valueThis paper makes a unique contribution to the human aspects of SCM literature by presenting the first study that investigates in depth the crucial but complex process of how workplace learning takes place for SC professionals in practice.