bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibodies against Elapidae and Viperidae snake venoms: in vivo neutralization and mechanistic insights
Authors: Kumar Amit , Madni Zaid Kamal , Chaturvedi Shivam , Salunke Dinakar M. 
Published: June 2023

AbstractSnake envenomation results in a range of clinical sequelae, and effective therapy is yet to be discovered. Anti-snake venom antibodies are being considered as a potent strategy. We developed venom-neutralizing humanized antibody scFvs and elucidated biochemical and structural mechanisms associated with the inhibition of toxicity. Tomlinson I and J human antibody scFv libraries were screened againstNaja najaandEchis carinatusvenoms, and seven unique antibody scFvs were obtained. Further, specific toxins of snake venom interacting with each of these scFvs were identified, and phospholipase A2 (PLA2) was found to be prominently captured by the phage-anchored antibody scFvs. Proteomic analysis of whole venom also revealed PLA2 to be the most abundant toxin in both venom samples. The scFvs binding to PLA2 were used to performin vivosurvival assay using the mouse model andin vitrotoxin inhibition assays. scFv N194, which binds to acidic PLA2, showed considerable survival inNaja najavenom-challenged mice and conferred up to 50% protection. A combination of two scFvs, E113 and E10, both interacting with basic PLA2, exhibited synergistically enhanced survival of 33% inEchis carinatusvenom-challenged mice, compared to 16% survival conferred by an equal amount of individual scFvs. Furthermore, these scFvs demonstrated inhibition of venom-induced myotoxicity and hemolysis which corroborate the survival data. Structural studies highlighted possible modes of PLA2 neutralization by scFv through the engagement of CDRs with C-terminal myotoxic loop and interfacial region, which are crucial for PLA2 toxicity.
High-confidence placement of difficult-to-fit fragments into electron density by using anomalous signals - a case study using hits targeting SARS-CoV-2 non-structural protein 1
Authors: Ma Shumeng , Mykhaylyk Vitaliy , Bowler Matthew W. , Pinotsis Nikos , Kozielski Frank 
Published: June 2023

AbstractThe identification of multiple simultaneous orientations of small molecule inhibitors binding to a protein target is a common challenge. It has recently been reported that the conformational heterogeneity of ligands is widely underreported in the Protein Data Bank, which is likely to impede optimal exploitation to improve affinity of these ligands1. Significantly less is even known about multiple binding orientations for fragments (< 300 Da) although this information would be essential for subsequent fragment optimisation using growing, linking or merging and rational structure-based design. Here we use recently reported fragment hits for the SARS-CoV-2 non-structural protein 1 (nsp1) N-terminal domain to propose a general procedure for unambiguously identifying binding orientations of 2-dimensional fragments containing either sulphur or chloro substituents within the wavelength range of most tunable beamlines. By measuring datasets at two energies, using a tuneable beamline operating in vacuum and optimised for data collection at very low X-ray energies, we show that the anomalous signal can be used to identify multiple orientations in small fragments containing sulphur and/or chloro substituents or to verify recently reported conformations. Although in this specific case we identified the positions of sulphur and chlorine in fragments bound to their protein target, we are confident that this work can be further expanded to additional atoms or ions which often occur in fragments. Finally, our improvements in the understanding of binding orientations will also serve to advance the rational optimisation of SARS-CoV-2 nsp1 targeting fragment hits.
Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide Activated SIRT7
Authors: Bolding Julie E. , Nielsen Alexander L. , Jensen Iben , Hansen Tobias N. , Ryberg Line A. , Jameson Samuel T. , Harris Pernille , Peters Günther H. J. , Denu John M. , Rogers Joseph M. , Olsen Christian A. 
Published: June 2023

AbstractThe sirtuins are NAD+-dependent lysine deacylases, comprising seven isoforms (SIRT1–7) in humans, which are involved in the regulation of a plethora of biology, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ε-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms; in part, because of a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well asde novocyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms and stabilize SIRT7 in cells.
Notch signalling influences cell fate decisions and HOX gene induction in axial progenitors
Authors: Cooper Fay , Souilhol Celine , Haston Scott , Gray Shona , Boswell Katy , Gogolou Antigoni , Frith Thomas , Stavish Dylan , James Bethany M , Bose Dan , Dale Jacqueline Kim , Tsakiridis Anestis 
Published: June 2023

ABSTRACTThe generation of the post-cranial embryonic body relies on the coordinated production of spinal cord neurectoderm and presomitic mesoderm cells from neuromesodermal progenitors (NMPs). This process is orchestrated by pro-neural and pro-mesodermal transcription factors that are co-expressed in NMPs together with Hox genes, which are critical for axial allocation of NMP derivatives. NMPs reside in a posterior growth region, which is marked by the expression of Wnt, FGF and Notch signalling components. While the importance of Wnt and FGF in influencing the induction and differentiation of NMPs is well established, the precise role of Notch remains unclear. Here, we show that the Wnt/FGF-driven induction of NMPs from human embryonic stem cells (hESCs) relies on Notch signalling. Using hESC-derived NMPs and chick embryo grafting, we demonstrate that Notch directs a pro-mesodermal character at the expense of neural fate. We show that Notch also contributes to activation ofHOXgene expression in human NMPs, partly in a non cell-autonomous manner. Finally, we provide evidence that Notch exerts its effects via the establishment of a negative feedback loop with FGF signalling.
Structure and dynamics of differential ligand binding in the human ρ-type GABAAreceptor
Authors: Cowgill John , Fan Chen , Haloi Nandan , Tobiasson Victor , Zhuang Yuxuan , Howard Rebecca J. , Lindahl Erik 
Published: June 2023

SUMMARYThe neurotransmitter γ-aminobutyric acid (GABA) drives critical inhibitory processes in and beyond the nervous system, partly via ionotropic type-A receptors (GABAARs). Pharmacological properties of ρ-type GABAARs are particularly distinctive, yet the structural basis for their specialization remains unclear. Here we present cryo-EM structures of a lipid-embedded human ρ1 GABAAR, including a partial intracellular domain, under apo, inhibited, and desensitized conditions. An apparent resting state, determined first in the absence of modulators, was recapitulated with the specific inhibitor (1,2,5,6-tetrahydropyridin-4-yl)methylphosphinic acid and blocker picrotoxin, and provided a rationale for bicuculline insensitivity. Comparative structures, mutant recordings, and molecular simulations with and without GABA further explained the sensitized but slower activation of ρ1 relative to canonical subtypes. Combining GABA with picrotoxin also captured an apparent uncoupled intermediate state. This work reveals structural mechanisms of gating and modulation with applications to ρ-specific pharmaceutical design, and to our biophysical understanding of ligand-gated ion channels.
Mapping the architecture of the initiating phosphoglycosyl transferase fromS. entericaO-antigen biosynthesis in a liponanoparticle
Authors: Dodge Greg J. , Anderson Alyssa J. , He Yi , Liu Weijing , Viner Rosa , Imperiali Barbara 
Published: June 2023

AbstractBacterial cell surface glycoconjugates are critical for cell survival and for interactions between bacteria and their hosts. Consequently, the pathways responsible for their biosynthesis have untapped potential as therapeutic targets. The localization of many glycoconjugate biosynthesis enzymes to the membrane represents a significant challenge for expressing, purifying, and characterizing these enzymes. Here, we leverage cutting-edge methods to stabilize, purify, and structurally characterize WbaP, a phosphoglycosyl transferase (PGT) fromSalmonella enterica(LT2) O-antigen biosynthesis without detergent solubilization from the lipid bilayer. From a functional perspective, these studies establish WbaP as a homodimer, reveal the structural elements responsible for oligomerization, shed light on the regulatory role of a domain of unknown function embedded within WbaP, and identify conserved structural motifs between PGTs and functionally unrelated UDP-sugar dehydratases. From a technological perspective, the strategy developed here is generalizable and provides a toolkit for studying small membrane proteins embedded in liponanoparticles beyond PGTs.
Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing
Authors: Zhang Annie , Friedman Larry J. , Gelles Jeff , Bell Stephen P 
Published: June 2023

AbstractDuring origin licensing, the eukaryotic replicative helicase Mcm2-7 forms head-to-head double hexamers to prime origins for bidirectional replication. Recent single-molecule and structural studies revealed that one molecule of the helicase loader ORC can sequentially load two Mcm2-7 hexamers to ensure proper head-to-head helicase alignment. To perform this task, ORC must release from its initial high-affinity DNA binding site and “flip” to bind a weaker, inverted DNA site. However, the mechanism of this binding-site switch remains unclear. In this study, we used single-molecule Förster resonance energy transfer (sm-FRET) to study the changing interactions between DNA and ORC or Mcm2-7. We found that the loss of DNA bending that occurs during DNA deposition into the Mcm2-7 central channel increases the rate of ORC dissociation from DNA. Further studies revealed temporally-controlled DNA sliding of helicase-loading intermediates, and that the first sliding complex includes ORC, Mcm2-7, and Cdt1. We demonstrate that sequential events of DNA unbending, Cdc6 release, and sliding lead to a stepwise decrease in ORC stability on DNA, facilitating ORC dissociation from its strong binding site during site switching. In addition, the controlled sliding we observed provides insight into how ORC accesses secondary DNA binding sites at different locations relative to the initial binding site. Our study highlights the importance of dynamic protein-DNA interactions in the loading of two oppositely-oriented Mcm2-7 helicases to ensure bidirectional DNA replication.Significance StatementBidirectional DNA replication, in which two replication forks travel in opposite directions from each origin of replication, is required for complete genome duplication. To prepare for this event, two copies of the Mcm2-7 replicative helicase are loaded at each origin in opposite orientations. Using single-molecule assays, we studied the sequence of changing protein-DNA interactions involved in this process. These stepwise changes gradually reduce the DNA-binding strength of ORC, the primary DNA binding protein involved in this event. This reduced affinity promotes ORC dissociation and rebinding in the opposite orientation on the DNA, facilitating the sequential assembly of two Mcm2-7 molecules in opposite orientations. Our findings identify a coordinated series of events that drive proper DNA replication initiation.
The principles of peptide selection by the transporter associated with antigen processing
Authors: Lee James , Oldham Michael L. , Manon Victor , Chen Jue 
Published: June 2023

AbstractThe adaptive immune response eliminates infected and cancer cells through the recognition of antigenic peptides displayed by major compatibility complex class I (MHC-I) molecules1, 2. A single transporter, the transporter associated with antigen processing (TAP), supplies nearly the entire peptide repertoire for the many MHC-I alleles3–5. A fundamental unresolved question is how TAP transports peptides with vast sequence diversity. Here, using cryo-electron microscopy (cryo-EM), we determined seven structures of human TAP in the presence and absence of peptides with different sequences and lengths. We observe that peptides are suspended in the transmembrane cavity of TAP with the peptide N-and C-termini anchored at two distal binding pockets. The central residues of the peptide are unrestricted, making few contacts with TAP. A minimum of eight residues is required to bridge the two binding pockets, aligning with the lower length limit for MHC-I binding6, 7. Mutations in TAP that disrupt hydrogen bonds with the peptide termini nearly abolish MHC-I surface expression, indicating that binding depends on interactions with mainchain atoms at the two termini. By utilizing two spatially separated binding pockets and concentrating interactions at the two ends of the peptide, TAP functions as a molecular caliper, selecting peptides for length while permitting sequence diversity.
Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes
Authors: Seeber PA , Batke L , Dvornikov Y , Schmidt A , Wang Y , Stoof-Leichsenring KR , Moon KL , Vohr SH , Shapiro B , Epp LS 
Published: June 2023

AbstractAncient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions of late survival of extinct species. However, translocation and lateral inflow of DNA in sediments can potentially distort the stratigraphic signal of the DNA. Using three different approaches on two short lake sediment cores of the Yamal peninsula, West Siberia, with ages spanning only the past hundreds of years, we detect DNA and identified mitochondrial genomes of multiple mammoth and woolly rhinoceros individuals—both species that have been extinct for thousands of years on the mainland. The occurrence of clearly identifiable aeDNA of extinct Pleistocene megafauna (e.g., > 400K reads in one core) throughout these two short subsurface cores, along with specificities of sedimentology and dating, confirm that processes acting on regional scales, such as extensive permafrost thawing, can influence the aeDNA record and should be accounted for in aeDNA paleoecology.
Leveraging the Adolescent Brain Cognitive Development Study to improve behavioral prediction from neuroimaging in smaller replication samples
Authors: Makowski Carolina , Brown Timothy T. , Zhao Weiqi , Hagler Donald J. , Parekh Pravesh , Garavan Hugh , Nichols Thomas E. , Jernigan Terry L. , Dale Anders M. 
Published: June 2023

ABSTRACTMagnetic resonance imaging (MRI) is a popular and useful non-invasive method to map patterns of brain structure and function to complex human traits. Recently published observations in multiple large scale studies cast doubt upon these prospects, particularly for prediction of cognitive traits from structural and resting state functional MRI, which seems to account for little behavioral variability. We leverage baseline data from thousands of children in the Adolescent Brain Cognitive DevelopmentSM(ABCD®) Study to inform the replication sample size required with both univariate and multivariate methods across different imaging modalities to detect reproducible brain-behavior associations. We demonstrate that by applying multivariate methods to high-dimensional brain imaging data, we can capture lower dimensional patterns of structural and functional brain architecture that correlate robustly with cognitive phenotypes and are reproducible with only 41 individuals in the replication sample for working memory-related functional MRI, and ∼100 subjects for structural MRI. Even with 100 random re-samplings of 50 subjects in the discovery sample, prediction can be adequately powered with 98 subjects in the replication sample for multivariate prediction of cognition with working memory task functional MRI. These results point to an important role for neuroimaging in translational neurodevelopmental research and showcase how findings in large samples can inform reproducible brain-behavior associations in small sample sizes that are at the heart of many investigators’ research programs and grants.
Deciphering Phage-Host Specificity Based on the Association of Phage Depolymerases and Bacterial Surface Glycan with Deep Learning
Authors: Yang Yiyan , Dufault-Thompson Keith , Yan Wei , Cai Tian , Xie Lei , Jiang Xiaofang 
Published: June 2023

AbstractPhage tailspike proteins are depolymerases that target diverse bacterial surface glycans with high specificity, determining the host-specificity of numerous phages. To address the challenge of identifying tailspike proteins due to their sequence diversity, we developed SpikeHunter, an approach based on the ESM-2 protein language model. Using SpikeHunter, we successfully identified 231,965 tailspike proteins from a dataset comprising 8,434,494 prophages found within 165,365 genomes of five common pathogens. Among these proteins, 143,035 tailspike proteins displayed strong associations with serotypes. Moreover, we observed highly similar tailspike proteins in species that share closely related serotypes. We found extensive domain swapping in all five species, with the C-terminal domain being significantly associated with host serotype highlighting its role in host range determination. Our study presents a comprehensive cross-species analysis of tailspike protein to serotype associations, providing insights applicable to phage therapy and biotechnology.
Good practices in COVID-19 risk reduction adopted by Australian construction enterprises
Authors: Seneviratne Krisanthi , Perera Srinath , Ginigaddara Buddhini , Jin Xiaohua , Tang Liyaning , Osei Kyei Robert 
Published: June 2023

PurposeThis research investigated the impacts of COVID-19 on construction enterprises and good practices adopted by the enterprises in reducing COVID-19 risks. The Sendai Framework (TSF) is widely accepted as a strategic roadmap to reduce disaster risks throughout the life cycle of a disaster. As such, with the aim of enhancing the resilience of Australian construction enterprises, the identified good practices were mapped with TSF priorities to consolidate COVID-19 risk reduction practices that can be adopted by Australian construction enterprises.Design/methodology/approachCase study research approach was used, and three case studies were conducted with small, medium and large construction enterprises. Small, medium and large enterprises were selected based on the Australian Bureau of Statistics classification of the business size. Data were collected through semi-structured interviews conducted with three executive members from the three enterprises. Data were analysed using content analysis.FindingsThe study found that construction enterprises faced demand and supply side impacts. Infrastructure projects, funded by public sector clients and larger enterprises were least affected. Investments and demand for residential and other building projects were reduced by private sector clients, affecting small and medium enterprises. Findings also show that the construction enterprises adopted good practices in identifying, managing, investing on resilience and recovery that align with TSF priorities. All three enterprises agreed on some common good practices on risk identification, risk management and effective recovery. Different views were shared on investments related to disaster resilience.Practical implicationsThis study contributes to mitigate the COVID-19 impacts on construction enterprises and subsequent economic and social impacts.Originality/valueThis research found how Australian construction enterprises survived during COVID-19. The study adopted TSF to construction and COVID-19 context while consolidating COVID-19 risk reduction practices.
Prospects, drivers of and barriers to artificial intelligence adoption in project management
Authors: Shang Gao , Low Sui Pheng , Lim Xin Ying Valen 
Published: June 2023

PurposeThe rise of artificial intelligence (AI) and differing attitudes towards its adoption in the building and environment (B&E) industry has an impact upon whether companies can meet changing demand and remain relevant and competitive. The emergence of Industry 4.0 technologies, coupled with the repercussions of COVID-19, increases the urgency and opportunities offered that companies must react to, as disruptive technologies impact how project management (PM) professionals work and necessitate acquisition of new skills. This paper attempts to identify the drivers of and barriers to, as well as the general perception and receptiveness of local PM professionals towards, AI adoption in PM and thereby propose potential strategies and recommendations to drive AI adoption in PM.Design/methodology/approachThis study employs both quantitative and qualitative approaches to examine the findings gathered. A survey questionnaire was used as the primary method of gathering quantitative data from 60 local PM professionals. Statistical tests were performed to analyse the data. To substantiate and validate the findings, in-depth interviews with several experienced industry professionals were performed.FindingsIt is found that top drivers include support from top management and leadership, organisational readiness and the need for greater work productivity and efficiency. Top barriers were found to be the high cost of AI implementation and maintenance and the lack of top-down support and skilled employees trained in AI. These findings could be attributed to the present state of AI technologies being new and considerably underutilised in the industry. Hence, substantial top-down support with the right availability of resources and readiness, both in terms of cost and skilled employees, is paramount to kick-start AI implementation in PM.Originality/valueLittle research has been done on the use of AI in PM locally. AI's potential to improve the productivity and efficiency of PM processes in the B&E industry cannot be overlooked. An understanding of the drivers of, barriers to and attitudes towards AI adoption can facilitate more intentional and directed oversight of AI's strategic roll-out at both the governmental and corporate levels and thus mitigate potential challenges that may hinder the implementation process in the future.