Specific Sites Research Articles

Computer-Aided Molecular Modifications for Enhanced Activity and Thermal Stability of d-Allulose 3-Epimerase.

D-Allulose 3-epimerase (DAE) can convert D-fructose into D-allulose, but its lower activity and poor thermal stability restrict its application in industrial production. This study utilized a semi-rational design and specific site mutations to enhance the enzyme activity and thermal stability of a DAE from Clostridium scindens ATCC 35704 (Csc-DAE) at the same time. Notably, the activities of six mutants (V22I, A25V, Q46I, C212N, G165A, and G267D) and the orderly superimposed double-point mutants were increased by 1.08-1.31 and 1.28-1.64 times that of the wild type (553.7 U/mg), respectively. In addition, A25V/C212N showed good thermal stability, and its optimum temperature (Topt) was 65 °C and half-life (t1/2) was 3.997 h at 60 °C, which increased by 5 °C and 5.76 times, respectively. The conversion ratio reached 30.62 and 31.22% at 65 and 70 °C, respectively, and the structural changes of the mutants were analyzed using molecular docking. These studies provide a beneficial mutation for industrial applications.

Geometry based prediction of tau protein sites and motifs associated with misfolding and aggregation

Recent studies of tau proteins point to specific sites or motifs along the protein related to its misfolding and aggregation propensity, which is associated with neurodegenerative diseases of structure-dependent pathology. In this manuscript we employ topology and geometry to analyze the local structure of tau proteins obtained from the Protein Data Bank. Our results show that mathematical topology/geometry of cryo-EM structures alone identify the PGGG motifs, and the PHF6(*) motifs as sites of interest and reveal a geometrical hierarchy of the PGGG motifs that differs for 3R+4R and 4R tauopathies. By employing the Local Topological Free Energy (LTE), we find that progressive supranuclear palsy (PSP) and globular glial tauopathy (GGT) have the highest LTE values around residues 302–305, which are inside the jR2R3 peptide and in the vicinity of the 301 site, experimentally associated with aggregation. By extending the LTE definition to estimate a global topological free energy, we find that the jR2R3 peptide of PSP and GGT, has in fact the lowest global topological free energy among other tauopathies. These results point to a possible correlation between the global topological free energy of parts of the protein and the LTE of specific sites.

SARS-CoV-2 neutralizing antibody specificities differ dramatically between recently infected infants and immune-imprinted individuals.

The immune response to viral infection is shaped by past exposures to related virus strains, a phenomenon known as imprinting. For severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), much of the population has been imprinted by a viral spike from an early strain, either through vaccination or infection during the early stages of the COVID-19 pandemic. As a consequence of this imprinting, infection with more recent SARS-CoV-2 strains primarily boosts cross-reactive antibodies elicited by the imprinting strain. Here we compare the neutralizing antibody specificities of imprinted individuals versus infants infected with a recent strain. Specifically, we use pseudovirus-based deep mutational scanning to measure how spike mutations affect neutralization by the serum antibodies of adults and children imprinted by the original vaccine versus infants with a primary infection by an XBB* variant. While the serum neutralizing activity of the imprinted individuals primarily targets the spike receptor-binding domain (RBD), the serum neutralizing activity of infants infected with only XBB* mostly targets the spike N-terminal domain. In these infants, secondary exposure to the XBB* spike via vaccination shifts more of the neutralizing activity toward the RBD, although the specific RBD sites targeted are different from imprinted adults. The dramatic differences in neutralization specificities among individuals with different exposure histories likely impact SARS-CoV-2 evolution.IMPORTANCEWe show that a person's exposure history to different SARS-CoV-2 strains strongly affects which regions on the viral spike that their neutralizing antibodies target. In particular, infants who have just been infected once with a recent viral strain make neutralizing antibodies that target different regions of the viral spike than adults or children who have been exposed to both older and more recent strains. This person-to-person heterogeneity means that the same viral mutation can have different impacts on the antibody immunity of different people.

Genome-Wide Analysis of Stable RNA Secondary Structures across Multiple Organisms Using Chemical Probing Data: Insights into Short Structural Motifs and RNA-Targeting Therapeutics.

Small molecules targeting specific RNA-binding sites, including stable and transient RNA structures, are emerging as effective pharmacological approaches for modulating gene expression. However, little is understood about how stable RNA secondary structures are shared across organisms, which is an important factor in controlling drug selectivity. In this study, I provide an analytical pipeline named RNA secondary structure finder (R2S-Finder) to discover short, stable RNA structural motifs in humans, Escherichia coli (E. coli), SARS-CoV-2, and Zika virus by leveraging existing in vivo and in vitro genome-wide chemical RNA-probing datasets. I found several common features across the organisms. For example, apart from the well-documented tetraloops, AU-rich tetraloops are widely present in different organisms. I also validated that the 5' untranslated region (UTR) contains a higher proportion of stable structures than the coding sequences in humans and Zika virus. In general, stable structures predicted from in vitro (protein-free) and in vivo datasets are consistent across different organisms, indicating that stable structure formation is mostly driven by RNA folding, while a larger variation was found between in vitro and in vivo data for certain RNA types, such as human long intergenic noncoding RNAs (lincRNAs). Finally, I predicted stable three- and four-way RNA junctions that exist under both in vivo and in vitro conditions and can potentially serve as drug targets. All results of stable structures, stem-loops, internal loops, bulges, and n-way junctions have been collated in the R2S-Finder database (https://github.com/JingxinWangLab/R2S-Finder), which is coded in hyperlinked HTML pages and tabulated in CSV files.

Hollow MOF‐derived layered NiS2/Mxene composites for high‐performance supercapacitors

MXene, characterized by its unique layered structure, shows great promise as an electrode material for energy storage devices. MXene‐based electrode materials, with their excellent metallic conductivity, high packing density, and large specific surface area, efficiently store high‐rate Faradaic pseudocapacitive energy. This study successfully synthesized a layered NiS2/Mxene composite using a self‐assembly method. The structural design significantly increases the composite material’s specific surface area and active sites while effectively suppressing the restacking of MXene nanosheets. Furthermore, the MXene layer wrapped around NiS2 not only improves electrical conductivity but also stabilizes the hollow structure to prevent collapse. Test results reveal that the NiS2/Mxene composite demonstrates a specific capacitance of 1016 F g‐1 at a current density of 1 A g‐1. The asymmetric supercapacitor (ACS) achieves an energy density of 46.6 Wh kg‐1 at a power density of 698.7 W kg‐1, with excellent cycling stability. This study proposes a novel design strategy for asymmetric supercapacitor electrodes incorporating MOFs and MXene composites.

The landscape of N6-methyladenosine in localized primary prostate cancer.

N6-methyladenosine (m6A), the most abundant internal RNA modification in humans, regulates most aspects of RNA processing. Prostate cancer is characterized by widespread transcriptomic dysregulation; therefore, we characterized the m6A landscape of 162 localized prostate tumors with matched DNA, RNA and protein profiling. m6A abundance varied dramatically across tumors, with global patterns emerging via complex germline-somatic cooperative regulation. Individual germline polymorphisms regulated m6A abundance, cooperating with somatic mutation of cancer driver genes and m6A regulators. The resulting complex patterns were associated with prognostic clinical features and established the biomarker potential of global and locus-specific m6A patterns. Tumor hypoxia dysregulates m6A profiles, bridging prior genomic and proteomic observations. Specific m6A sites, such as those in VCAN, drive disease aggression, associating with poor outcomes, tumor growth and metastasis. m6A dysregulation is thus associated with key events in the natural history of prostate cancer: germline risk, microenvironmental dysregulation, somatic mutation and metastasis.

Velocity Model Construction and Time-to-Depth Conversion of a Vintage Seismic Reflection Profile for Improving the Constraints on a Subsurface Geological Model: An Example from the Sicily Channel (Central Mediterranean Sea)

The well-known uncertainties in subsurface velocity field definition call for the integration of all the available data, including vintage seismic profiles, which, despite typically being in raster or paper format, often contain velocities derived from stacking and associated interval velocities. This study aims to build a velocity model for the time-to-depth conversion of an interpreted seismic reflection profile by using the interval velocity reported on a vintage, paper-format seismic profile and contribute to improving the subsurface geological model of the Sicily Channel, Central Mediterranean. Spline interpolation is used for velocity model building of the shallower part (3.5 sec TWT) of the seismic profile CS89-01, derived from the stacking velocities of 31 Common Depth Point (CDP) gathers. This was followed by the Gaussian convolution operator and a data exclusion filter to improve the accuracy of the velocity model. The time-to-depth-converted seismic reflection profile is a regional cross-section that covers almost the entire Sicily Channel, crossing part of the northern margin of the African Plate, from Tunisia to eastern Sicily. This study provides a new subsurface velocity field that can be applied, or taken into account, to most parts of the Sicily Channel when structural and stratigraphic interpretations are carried out at specific sites and where uncertainties in subsurface geological model exist (e.g., in the present study, the volcanic bodies in the Pantelleria Graben and Lampedusa High).

Access Intimacy and Humanness in CART Captioning Relationships

This article engages with the nuanced experience of auditory disability and Communication Access Realtime Translation (CART) captioning by exploring how access to the soundscape as provided by a human captioner creates a unique intimacy –and unique, often unintended benefits—for disability access. Bringing together the concepts of access intimacy, contact zones, and disability theory, this article focuses on personal experiences as a hard of hearing (HoH), disabled individual and investigates the formation of access intimacy within a formal accommodation structure. Through reflective autoethnography, this article (re)defines access intimacy as a learned skill that can result from formal academic partnerships. First, the article will define and explore CART captioning as a specific site where the human interactions necessitated by this specific accommodation create opportunities to expand out conversations of access and accommodation. Next, it will analyze the author's personal experiences with CART captioning through the lens of access intimacy, expanding on how this intimacy can be developed through institutional relationships. The article ends with a personal vignette with the goal of illustrating this access intimacy –and the additional access conferred through this intimacy.

Harnessing Bio-Inspired Axial Coordination to Boost Synergistic Effects for Enhanced Bifunctional Oxygen Electrocatalysis.

Strategic alteration of the chelating atoms around the metal center can modify the electronic band structure of the electrocatalyst, improving its performance in oxygen evolution and reduction reactions (OER/ORR). Advancements in the development of catalysts with heteroatoms and axial modifications in the coordination sphere are mostly limited to single-molecule electrocatalysts or elevated temperature-mediated pyrolysis approaches for oxygen electrocatalysis. Inspired by biological catalytic systems with axial coordination, a pyrolysis-free strategic methodology is adopted for the synthesis of an iron-metaled covalent organic polymer matrix axially laminated over cobalt-based metal-organic framework through an imidazole moiety. Precise engineering of coordination atoms in synthesized core-shell material, featuring dual metal sites with distinct neighboring atom exhibits mutual synergy due to the presence of bridging imidazole moiety between two metal sites. Modulated synergism navigates the electronic structure such that it favors specific reactant adsorption on specific metal sites during bifunctional O2 electrocatalysis as confirmed through in situ Raman spectroscopy and in situ attenuated total reflection infrared (ATR-IR) spectroscopy. Through dynamic correlation between the in-situ studies and modified d-band center obtained theoretically, the pivotal role of axial coordination linkage mediated synergism favoring ORR/OER process via target-specific reactant adsorption is demonstrated.

Pore Space Partition Enabled by Lithium(I) Chelation of a Metal-Organic Framework for Benchmark C2H2/CO2 Separation.

Adsorptive separation of acetylene (C2H2) from carbon dioxide (CO2) offers a promising approach to purify C2H2 with low-energy footprints. However, the development of ideal adsorbents with simultaneous high C2H2 adsorption and selectivity remains a great challenge due to their very small molecular sizes and physical properties. Herein, we report a lithium(I)-chelation strategy for pore space partition (PSP) in a microporous MOF (Li+@NOTT-101-(COOH)2) to achieve simultaneous high C2H2 uptake and selectivity. The chelation model of Li+ ions within the framework was visually identified by single-crystal X-ray diffraction studies. The immobilized Li+ ions were found to have two functions: (1) partitioning large pore cages into smaller ones while maintaining high surface area and (2) providing specific binding sites to selectively take up C2H2 over CO2. The resulting Li+@NOTT-101-(COOH)2 exhibits a rare combination of a simultaneous high C2H2 capture capacity (205 cm3 g-1) and C2H2/CO2 selectivity (13) at ambient conditions, far surpassing that of NOTT-101-(COOH)2 (148 cm3 g-1 and 3.8, respectively) and most top-tier materials reported. Theoretical calculations and gas-loaded SCXRD studies reveal that the chelated Li+ ions combined with the segmented small cages can selectively bind with a large amount of C2H2 through the unique π-complexation, accounting for the improved C2H2 uptake and selectivity. Breakthrough experiments validated its excellent separation capacity for actual C2H2/CO2 mixtures, providing one of the highest C2H2 productivities of 118.9 L kg-1 (>99.5% purity) in a single adsorption-desorption cycle.

Modulation of C=O groups concentration in carbon-based materials to enhance peroxymonosulfate activation towards degradation of organic contaminant: mechanism of the non-radical oxidation pathway.

Modulation of C=O groups concentration in carbon-based materials to enhance peroxymonosulfate activation towards degradation of organic contaminant: mechanism of the non-radical oxidation pathway.

O-GlcNAcylation in Gli1+ Mesenchymal Stem Cells Is Indispensable for Bone Formation and Fracture Healing.

Adult mesenchymal stem cells (MSCs) play a crucial role in maintaining bone health and promoting regeneration. In our previous research, we identified Gli1+ MSCs as key contributors to the formation of most trabecular bone in adulthood and as essential for healing bicortical fractures. However, the mechanisms behind the maintenance and differentiation of Gli1+ MSCs are still not fully understood. O-linked N-acetylglucosamine modification (O-GlcNAcylation), mediated by O-GlcNAc glycosyltransferase (OGT), is involved in various biological processes and diseases. Our earlier work also demonstrated that O-GlcNAcylation is necessary for Wnt-stimulated bone formation. Nonetheless, the specific functions of O-GlcNAcylation in MSCs have not been completely elucidated. In this study, we found that the absence of OGT in Gli1+ MSCs led to a decrease in O-GlcNAcylation, which impaired both the bone formation and regeneration following fractures. Mechanistically, the Hedgehog signaling pathway induced O-GlcNAcylation through the insulin-like growth factor (Igf)-mTORC2 axis. This process stabilized the Gli2 protein at a specific site Ser355 and promoted osteogenesis in MSCs in vitro. Our findings reveal a significant mechanism by which O-GlcNAcylation regulates bone development and repair in mammals.

A Polymeric mRNA Vaccine Featuring Enhanced Site-Specific mRNA Delivery and Inherent STING-Stimulating Performance for Tumor Immunotherapy.

The development of mRNA delivery carriers with innate immune stimulation functions has emerged as a focal point in the field of mRNA vaccines. Nonetheless, the expression of mRNA in specific sites and innate immune stimulation at specific sites are prerequisites for ensuring the safety of mRNA vaccines. Based on the synthetic PEIRs carriers library, this study identifies an innovative mRNA delivery carrier named POctS with the following characteristics: 1) simultaneously possessing high mRNA delivery efficiency and stimulator of interferon genes (STING) stimulation function. 2) Leveraging the distinctive site-specific delivery capabilities of POctS, the expression of mRNA at specific sites and the activation of innate immune responses at designated sites are achieved, minimizing formulation toxicity and maximizing the vaccine performance. 3) Tailoring two types of mRNA vaccines based on POctS according to the immune infiltration status of different types of tumors. Briefly, POctS-loading ovalbumin (OVA) mRNA as a tumor antigen vaccine achieves the prevention and treatment of melanoma in mice. Further, POctS-loading mixed lineage kinase domain-like protein (MLKL) mRNA as an in situ tumor vaccine effectively treats orthotopic pancreatic cancer in mice. This delivery carrier offers a feasible mRNA vaccine-based immunotherapy strategy for various types of tumors.

High performance carbon matrix and aqueous zinc ion hybrid capacitors were prepared from waste biomass cotton fiber.

High performance carbon matrix and aqueous zinc ion hybrid capacitors were prepared from waste biomass cotton fiber.

The SLC26A4-AS1/NTRK2 axis in breast cancer: insights into the ceRNA network and implications for prognosis and immune microenvironment

Breast cancer is a leading malignancy in women, with mortality disparities between developed and underdeveloped regions. Accumulating evidence suggests that the competitive endogenous RNA (ceRNA) regulatory networks play paramount roles in various human cancers. However, the complexity and behavior characteristics of the ceRNA network in breast cancer progression have not been fully elucidated. The expression profiles of three RNAs (long non-coding RNAs [lncRNAs], microRNAs [miRNAs], and mRNAs) were extracted from breast cancer and adjacent samples were sourced from the TCGA database. The SLC26A4-AS1- hsa-miR-19a-3p-NTRK2 ceRNA network related to the prognosis of breast cancer was obtained by performing bioinformatics analysis. Importantly, we identified the SLC26A4-AS1/NTRK2 axis within the ceRNA network through correlation analysis and found it to be a potential prognostic model in clinical outcomes based on Cox regression analysis. Moreover, methylation analysis suggests that the aberrant downregulation of the SLC26A4-AS1/NTRK2 axis might be attributed to hypermethylation at specific sites. Immune infiltration analysis indicates that the SLC26A4-AS1/NTRK2 axis may have implications for the alteration of the tumor immune microenvironment and the emergence and progression of immune evasion in breast cancer. Finally, we validated the expression of SLC26A4-AS1-hsa-miR-19a-3p-NTRK2 in breast cancer cell lines. In summary, the present study posits that the SLC26A4-AS1/NTRK2 axis, based on the ceRNA network, could be a novel and significant prognostic factor associated with breast cancer diagnosis and outcomes.

Mitogenome of Neolissochilus pnar, the largest cavernicolous species of Mahseer

The study of the mitogenome of Neolissochilus pnar, the world’s largest cave fish, uncovered its structural features, gene content and evolutionary dynamics within mahseer. Its mitogenome is of 16,440 base pairs, resembling those of the teleost species and exhibits a high degree of conservation in genes arrangement. It comprises 37 mitochondrial genes, including 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs) and a control region. Notably, the distribution of genes on the L- and H-strands is consistent with that of the typical teleost. The study reveals the lengths and variations in PCGs in mahseer species, displaying a range from 164 to 11,404 bp. The tRNA and rRNA genes and the control region also demonstrate conservation among the species. A robust phylogenetic analysis, employing Bayesian and ASAP methods, supports the classification of N. pnar within the Neolissochilus genus and validates the taxonomic status of this species. Selection pressure analyses indicate positive selection in seven genes: COII , COIII, Cytb, ND1, ND2, ND5 and ND6. These findings suggest the dynamic nature of mitochondrial evolution in mahseer species. The purifying selection preserve essential mitochondrial functions, and additionally, the specific sites in ND5 and ND6 genes undergo episodic positive or diversifying selection, likely in response to environmental changes or selective pressures. In conclusion, this research enriches our understanding of N. pnar visa-vis other mahseers’ mitogenomes, pointing to its possible mitogenome evolution to adaptation to cave environment.

Microplastic contaminant adsorption by graphene oxide layer.

The increasing prevalence of microplastics in water sources poses significant threats to both human health and environmental sustainability. Bisphenol A (BPA) and polyethylene terephthalate (PET), two hazardous microplastic contaminants, are known to cause endocrine disruption and other health risks. This study investigates the potential of graphene oxide (GO) as an efficient adsorbent for the removal of these contaminants through detailed molecular interaction analysis. The adsorption efficiencies of GO were quantitatively assessed, demonstrating strong binding affinities of ∆G = - 9.50kcal/mol for BPA and ∆G = - 6.90kcal/mol for PET. The adsorption process is primarily governed by π-π stacking interactions between the aromatic structure of the microplastics and the polycyclic surface of GO, with additional contributions from hydrogen bonding and van der Waals forces. Computational simulations revealed consistent binding across specific active sites on the GO surface, indicating minimal variation in adsorption performance. These findings highlight the potential of GO-based filtration systems for large-scale water treatment applications, offering a promising approach to mitigating microplastic contamination and ensuring safer water supplies. These findings highlight the potential of GO-based filtration systems for large-scale water treatment applications, offering a promising approach to mitigating microplastic contamination and ensuring safer water supplies. Future research should focus on optimizing GO-based filtration techniques and exploring their long-term environmental impact.

Integrating PLOR and SPAAC Click Chemistry for Efficient Site-Specific Fluorescent Labeling of RNA.

Precisely fluorescently labeling specific nucleotide sites of RNA is critical for gaining insights into the structure and function of RNA through multiple fluorescence detection techniques. The position-selective labeling of RNA (PLOR) method provides a promising strategy to achieve this, wherein the fluorophore-modified NTPs can be co-transcriptionally introduced to specific sites of nascent RNA by using T7 RNA polymerase (T7 RNAP). However, due to steric hindrance limitations, the efficiency of T7 RNAP in recognizing and incorporating large fluorophore-modified NTPs into RNA is far from satisfactory. To overcome this challenge, in this work, we developed an efficient PLOR variant (ePLOR) for the site-specific fluorescent labeling of RNA by integrating PLOR with a post-transcriptional SPAAC (strain-promoted azido-alkyne cycloaddition) click chemistry reaction. The efficiency of the SPAAC reaction occurring on RNA is nearly 100%. Consequently, ePLOR enables the precise fluorescent labeling of designated sites across various structural regions of SAM-VI riboswitch and adenine riboswitch RNA, with labeling and synthesis efficiencies that are 2-2.5 times higher than those of PLOR. The strategy developed in this work can be used for the efficient synthesis of a broader spectrum of long-strand RNAs with site-specific fluorescent labeling and greatly facilitate the detection of the structure and function of these RNAs.

Water quality and diarrhoeagenic Escherichia coli detection in surface Pampean aquatic systems.

Many surface water systems are impacted by point source pollution from sewage discharges and industrial wastes, as well as diffuse pollution from agriculture and livestock farming, inducing a potential biohazard to human, animal, and environmental health. This study aimed to determine the presence of diarrhoeagenic Escherichia coli (DEC) pathotypes and their antibiotic resistance, as well as the bacteriological, physical, and chemical water quality conditions in two Pampean peri-urban rivers (Rojas and Salado rivers, Buenos Aires, Argentina) used for recreation. Additionally, we explored the impact of the surrounding land use on the water quality. In the Rojas (R) and Salado (S) rivers, wastewater discharges from treatment plants increased nutrient content and coliform abundances at specific sampling sites (R2 and S3) and downstream (R3 and S4, respectively). Coliform abundances correlated with ammoniacal nitrogen concentrations, both exceeding recreational use guidelines. Out of 36 samples positive for DEC virulence factors, 11 DEC strains were isolated (5 enteroaggregative, 3 enteropathogenic, 1 shigatoxigenic-stx1/stx2, 1 shigatoxigenic-stx2, 1 hybrid enteroaggregative-enterotoxigenic). Six strains were resistant to one or more antibiotics. Our results suggest that differences in E. coli pathotypes between the two rivers and the water quality of each sampling site are linked to the surrounding land use, evidencing both diffuse and point source pollution.

A combination of top-down and bottom-up approaches in addressing major challenges of long-term socio-ecological research—the Taiwan experience

Abstract Long-term socio-ecological research (LTSER) has been suggested to have high potential in providing insights and knowledge necessary for a sustainability transition. However, long-term and transdisciplinary, the core value of LTSER, remain major challenges. We describe how Taiwan LTSER addressed the two challenges through an approach that combines bottom up and top down processes. From the top-down, the funding agency categorized LTSER as a core facility like research vessels that monitors fundamental ecological and social drivers and indicators of the dynamics of the inter-linked and entangled social and ecological systems. From the top down, the funding agency established a LTSER program office which set criteria, highlighting that transdisciplinary is a pre-requisite for LTSER site selection. From the bottom up, scientists proposed potential LTSER sites based on their interest and each potential site formed a team that includes both natural scientists and social scientists. Thus, transdisciplinary research is a common understanding among scientists that propose a specific site. Because Taiwan LTSER is not a re-start or shift from the previous Long-term Ecological Research (LTER) in Taiwan, the potential conflict due to the lack of consensus on extending the research to include social dimension is avoided. Taiwan LTSER was initiated in 2021 and has established six sites by 2024. Based on the known challenges, Taiwan LTSER innovated the development and governance of LTSER to address the challenges. Thus, although it is still developing, sharing Taiwan LTSER experience to the academia is important and it would be informative to check the progress of Taiwan LTSER in the decades to come.