Functional Specificity Research Articles

Design of a structural insulating panel based on wood-based corrugated panels as an alternative to light-frame construction

The performance of building envelopes is one of the cores of environmental issues related to the construction sector. Lightweight wood framing, widely used in North America, appears to be a solution to be favored in this context. However, since structural thermal bridges are now considered in the thermal resistance of an opaque wall by the Canadian National Building Code, its thermal performance remains limited if it is to be maintained. Structural insulated panels (SIPs) are becoming increasingly popular in the scientific literature on construction. These systems have advantages over conventional systems, such as light-frame construction. This study focuses on the design of new envelope compositions based on wood-based corrugated panels. The design was carried out by reverse engineering conventional light-frame envelope systems. A functional specification was established based on the performance of traditional envelopes. These performances were evaluated according to thermal resistance, mold growth index, assembly time, environmental impact, cost, dimensions, etc. To calculate the mold growth index and thermal resistance, a model was built according to ASHRAE 160. It was run over a four-year period on COMSOL software. The results showed that one of the prototypes designed outperformed lightweight wood framing in terms of the specifications.

Tubulin glutamylation regulates axon guidance via the selective tuning of microtubule-severing enzymes.

The microtubule cytoskeleton is a major driving force of neuronal circuit development. Fine-tuned remodelling of this network by selective activation of microtubule-regulating proteins, including microtubule-severing enzymes, has emerged as a central process in neuronal wiring. Tubulin posttranslational modifications control both microtubule properties and the activities of their interacting proteins. However, whether and how tubulin posttranslational modifications may contribute to neuronal connectivity has not yet been addressed. Here we show that the microtubule-severing proteins p60-katanin and spastin play specific roles in axon guidance during zebrafish embryogenesis and identify a key role for tubulin polyglutamylation in their functional specificity. Furthermore, our work reveals that polyglutamylases with undistinguishable activities in vitro, TTLL6 and TTLL11, play exclusive roles in motor circuit wiring by selectively tuning p60-katanin- and spastin-driven motor axon guidance. We confirm the selectivity of TTLL11 towards spastin regulation in mouse cortical neurons and establish its relevance in preventing axonal degeneration triggered by spastin haploinsufficiency. Our work thus provides mechanistic insight into the control of microtubule-driven neuronal development and homeostasis and opens new avenues for developing therapeutic strategies in spastin-associated hereditary spastic paraplegia.

Functional specificity of liquid-liquid phase separation at the synapse

The mechanisms that enable synapses to achieve temporally and spatially precise signaling at nano-scale while being fluid with the cytosol are poorly understood. Liquid-liquid phase separation (LLPS) is emerging as a key principle governing subcellular organization; however, the impact of synaptic LLPS on neurotransmission is unclear. Here, using rat primary hippocampal cultures, we show that robust disruption of neuronal LLPS with aliphatic alcohols severely dysregulates action potential-dependent neurotransmission, while spontaneous neurotransmission persists. Synaptic LLPS maintains synaptic vesicle pool clustering and recycling as well as the precise organization of active zone RIM1/2 and Munc13 nanoclusters, thus supporting fast evoked Ca2+-dependent release. These results indicate although LLPS is necessary within the nanodomain of the synapse, the disruption of this nano-organization largely spares spontaneous neurotransmission. Therefore, properties of in vitro micron sized liquid condensates translate to the nano-structure of the synapse in a functionally specific manner regulating action potential-evoked release.

PEak: A Single Source of Truth for Hardware Design and Verification

Domain-specific languages for hardware can significantly enhance designer productivity, but sometimes at the cost of ease of verification. On the other hand, ISA specification languages are too static to be used during early stage design space exploration. We present PEak, an open-source hardware design and specification language, which aims to improve both design productivity and verification capability. PEak does this by providing a single source of truth for functional models, formal specifications, and RTL. PEak has been used in several academic projects, and PEak-generated RTL has been included in three fabricated hardware accelerators. In these projects, the formal capabilities of PEak were crucial for enabling both novel design space exploration techniques and automated compiler synthesis.

Научно-академический дискурс в образовательном пространстве неязыкового вуза

The article deals with the phenomenon of scientific academic discourse. A nomenclature of discourse typological characteristics is analysed. The concept of scientific academic discourse is defined as a specialized type of institutional discourse. In our research we consider the scientific academic discourse as an integrative concept combining the features of scientific and academic types of discourse due to the interpenetration and intersection of their components. Cognitive and communicative aspects of scientific discourse are examined specific attributes of scientific texts such as harmony, consistency, objectivity and others are determined. The article focuses on the analysis of scientific discourse genre varieties. The authors describe the specifics of functioning of a research paper and a scientific report as main genres of scientific academic discourse, reveal their peculiarities in realizing English language oral and written discourse. From the theoretical and practical points of view both a research aper and a scientific report represent oral/ written communication aimed at scientific informing. The scientific polylexemic templates suggested in the article prove to be useful in academic writing.

Assembly of functional microbial ecosystems: from molecular circuits to communities.

Microbes compete and cooperate with each other via a variety of chemicals and circuits. Recently, to decipher, simulate or reconstruct microbial communities, many researches have been engaged in engineering microbiomes with bottom-up synthetic biology approaches for diverse applications. However, they have been separately focused on individual perspectives including genetic circuits, communications tools, microbiome engineering, or promising applications. The strategies for coordinating microbial ecosystems based on different regulation circuits have not been systematically summarized, which calls for a more comprehensive framework for the assembly of microbial communities. In this review, we summarize diverse cross-talk and orthogonal regulation modules for de novo bottom-up assembling functional microbial ecosystems, thus promoting further consortia-based applications. Firstly, we review the cross-talk communication-based regulations among various microbial communities from intra-species and inter-species aspects. Then, orthogonal regulations are summarized at metabolites, transcription, translation, and post-translation levels, respectively. Furthermore, to give more details for better design and optimize various microbial ecosystems, we propose a more comprehensive design-build-test-learn (cDBTL) procedure including function specification, chassis selection, interaction design, system build, performance test, modelling analysis, and global optimization. Finally, current challenges and opportunities are discussed for the further development and application of microbial ecosystems.

The autophagy protein, ATG14 safeguards against unscheduled pyroptosis activation to enable embryo transport during early pregnancy.

Recurrent pregnancy loss (RPL), characterized by two or more failed clinical pregnancies, poses a significant challenge to reproductive health. In addition to embryo quality and endometrial function, proper oviduct function is also essential for successful pregnancy establishment. Therefore, structural abnormalities or inflammation resulting from infection in the oviduct may impede the transport of embryos to the endometrium, thereby increasing the risk of miscarriage. However, our understanding of the biological processes that preserve the oviductal cellular structure and functional integrity is limited. Here, we report that Atg14-dependent autophagy plays a crucial role in maintaining the cellular integrity of the oviduct by controlling inflammatory responses, thereby supporting efficient embryo transport. Specifically, the conditional depletion of the autophagy-related gene, Atg14 in the oviduct causes severe structural abnormalities compromising its cellular integrity leading to the abnormal retention of embryos. Interestingly, the selective loss of Atg14 in oviduct ciliary epithelial cells did not impact female fertility, highlighting the specificity of ATG14 function in distinct cell types within the oviduct. Mechanistically, loss of Atg14 triggered unscheduled pyroptosis via altering the mitochondrial integrity leading to inappropriate embryo retention and impeded embryo transport in the oviduct. Finally, pharmacological activation of pyroptosis in pregnant mice phenocopied the genetically induced defect and caused impairment in embryo transport. Together, we found that ATG14 safeguards against unscheduled pyroptosis activation to enable embryo transport from the oviduct to uterus for the successful implantation. Of clinical significance, these findings provide possible insights into the underlying mechanism(s) of early pregnancy loss and might aid in developing novel prevention strategies using autophagy modulators.

Atp13a5 Marker Reveals Pericyte Specification in the Mouse Central Nervous System.

Perivascular mural cells including vascular smooth cells (VSMCs) and pericytes are integral components of the vascular system. In the central nervous system (CNS), pericytes are also indispensable for the blood-brain barrier (BBB), blood-spinal cord barrier, and blood-retinal barrier and play key roles in maintaining cerebrovascular and neuronal functions. However, the functional specifications of pericytes between CNS and peripheral organs have not been resolved at the genetic and molecular levels. Hence, the generation of reliable CNS pericyte-specific models and genetic tools remains very challenging. Here, we report a new CNS pericyte marker in mice. This putative cation-transporting ATPase 13A5 (Atp13a5) marker was identified through single-cell transcriptomics, based on its specificity to brain pericytes. We further generated a knock-in model with both tdTomato reporter and Cre recombinase. Using this model to trace the distribution of Atp13a5-positive pericytes in mice, we found that the tdTomato reporter reliably labels the CNS pericytes, including the ones in spinal cord and retina but not peripheral organs. Interestingly, brain pericytes are likely shaped by the developing neural environment, as Atp13a5-positive pericytes start to appear around murine embryonic day 15 (E15) and expand along the cerebrovasculature. Thus, Atp13a5 is a specific marker of CNS pericyte lineage, and this Atp13a5-based model is a reliable tool to explore the heterogeneity of pericytes and BBB functions in health and diseases.

DDX RNA helicases: key players in cellular homeostasis and innate antiviral immunity.

RNA helicases are integral in RNA metabolism, performing important roles in cellular homeostasis and stress responses. In particular, the DExD/H-box (DDX) helicase family possesses a conserved catalytic core that binds structural features rather than specific sequences in RNA targets. DDXs have critical roles in all aspects of RNA metabolism including ribosome biogenesis, translation, RNA export, and RNA stability. Importantly, functional specialization within this family arises from divergent N and C termini and is driven at least in part by gene duplications with 18 of the 42 human helicases having paralogs. In addition to their key roles in the homeostatic control of cellular RNA, these factors have critical roles in RNA virus infection. The canonical RIG-I-like receptors (RLRs) play pivotal roles in cytoplasmic sensing of viral RNA structures, inducing antiviral gene expression. Additional RNA helicases function as viral sensors or regulators, further diversifying the innate immune defense arsenal. Moreover, some of these helicases have been coopted by viruses to facilitate their replication. Altogether, DDX helicases exhibit functional specificity, playing intricate roles in RNA metabolism and host defense. This review will discuss the mechanisms by which these RNA helicases recognize diverse RNA structures in cellular and viral RNAs, and how this impacts RNA processing and innate immune responses.

Specificity determinants of pathogens in forest

Abstract Host‐specific pathogens have long been suggested to act as a major driver of species diversity in tropical forests. However, determining the degree of host specificity of potential pathogens coupled to key cellular characteristics of infection is difficult and time‐consuming. These challenges have delayed progress in relating the functional specificity of pathogenic fungi to ecological consequences. We tested the pathogenicity of 27 (of 215) fungi that were isolated from surface sterilized roots of seedlings from four common tree species in a diverse subtropical forest. Inoculation experiments showed that six fungi exhibited strong pathogenicity on the host seedlings. Five of these only infected their specific hosts (i.e. host‐specific pathogen species). Green fluorescent protein labelling revealed that in three host‐specific pathogens fungal hyphae were able to grow into the vascular tissues only in their specific host plant, in contrast to other fungal‐host combinations that exhibit non‐pathogenic interactions. This fluorescent labelling technique allows direct tracking of the progress of fungal infection in different host tissues. Synthesis. By coupling the green fluorescent protein technique with standard host inoculation experiments, we determined the developmental differences between infections by pathogenic and non‐pathogenic fungi in a relatively simple and straightforward way. Our work provides a useful tool for rapidly screening and categorizing host–fungal interactions, reflecting the functional basis of host specificity of pathogenic fungi. More broadly, this technique can contribute to understanding the roles of pathogens in species coexistence and biodiversity maintenance in forest communities.

Functional specificity in biomolecular condensates revealed by genetic complementation.

Biomolecular condensates are thought to create subcellular microenvironments that regulate specific biochemical activities. Extensive in vitro work has helped link condensate formation to a wide range of cellular processes, including gene expression, nuclear transport, signalling and stress responses. However, testing therelationship between condensateformation and function in cellsis more challenging.In particular, the extent to which the cellular functions of condensates depend on the nature of the molecular interactions through which the condensatesform is a major outstanding question. Here, we review results from recent genetic complementation experiments in cells, and highlight how genetic complementation provides important insights into cellular functions and functional specificity of biomolecular condensates. Combined with observations from human genetic disease, these experiments suggest that diverse condensate-promoting regions within cellular proteins confer different condensate compositions, biophysical properties and functions.

Design and Testing of a Web-Based Student Information Management System

Politeknik Piksi Ganesha is an institution of higher learning located in Bandung, Indonesia, specializing in engineering and technological curricula. The research's general objective is to describe the design and implementation of the web-based Student Information Management System (SIMS) to manage student data at Politeknik Piksi Ganesha Bandung. The functional and non-functional specifications are represented using Unified Modeling Language (UML) based on broad data collection through observation, interviews, and a literature review. It also entails black-box testing, which measures the system's performance against set criteria, focusing on the output without the details of its internal workings. The significant findings indicate that SIMS enhances highly administrative processes, accuracy in data, and good communication among stakeholders by applying clear UML diagrams of the system. This successful system development meets the institution's requirements and adds to the bar for other developments within the educational technology sector. The result has also emphasized the need for practical design methodologies and testing frameworks to develop reliable information systems to improve decision-making in academic institutions. The research has contributed significantly to the discipline because it has shown how different technological innovations can alleviate the problems surrounding managing student information at higher education levels.

Translation of Mutant Repetitive Genomic Sequences in Hirsutella sinensis and Changes in the Secondary Structures and Functional Specifications of the Encoded Proteins.

Multiple repetitive sequences of authentic genes commonly exist in fungal genomes. AT-biased genotypes of Ophiocordyceps sinensis have been hypothesized as repetitive pseudogenes in the genome of Hirsutella sinensis (GC-biased Genotype #1 of O. sinensis) and are generated through repeat-induced point mutation (RIP), which is charactered by cytosine-to-thymine and guanine-to-adenine transitions, concurrent epigenetic methylation, and dysfunctionality. This multilocus study examined repetitive sequences in the H. sinensis genome and transcriptome using a bioinformatic approach and revealed that 8.2% of the authentic genes had repetitive copies, including various allelic insertions/deletions, transversions, and transitions. The transcripts for the repetitive sequences, regardless of the decreases, increases, or bidirectional changes in the AT content, were identified in the H. sinensis transcriptome, resulting in changes in the secondary protein structure and functional specification. Multiple repetitive internal transcribed spacer (ITS) copies containing multiple insertion/deletion and transversion alleles in the genome of H. sinensis were GC-biased and were theoretically not generated through RIP mutagenesis. The repetitive ITS copies were genetically and phylogenetically distinct from the AT-biased O. sinensis genotypes that possess multiple transition alleles. The sequences of Genotypes #2-17 of O. sinensis, both GC- and AT-biased, were absent from the H. sinensis genome, belong to the interindividual fungi, and differentially occur in different compartments of the natural Cordyceps sinensis insect-fungi complex, which contains >90 fungal species from >37 genera. Metatranscriptomic analyses of natural C. sinensis revealed the transcriptional silencing of 5.8S genes in all C. sinensis-colonizing fungi in natural settings, including H. sinensis and other genotypes of O. sinensis. Thus, AT-biased genotypes of O. sinensis might have evolved through advanced evolutionary mechanisms, not through RIP mutagenesis, in parallel with GC-biased Genotype #1 of H. sinensis from a common genetic ancestor over the long course of evolution.

Antigen specificity of clonally-enriched CD8+ T cells in multiple sclerosis.

CD8+ T cells are the dominant lymphocyte population in multiple sclerosis (MS) lesions where they are highly clonally expanded. The clonal identity, function, and antigen specificity of CD8+ T cells in MS are not well understood. Here we report a comprehensive single-cell RNA-seq and T cell receptor (TCR)-seq analysis of the cerebrospinal fluid (CSF) and blood from a cohort of treatment-naïve MS patients and control participants. A small subset of highly expanded and activated CD8+ T cells were enriched in the CSF in MS that displayed high activation, cytotoxicity and tissue-homing transcriptional profiles. Using a combination of unbiased and targeted antigen discovery approaches, MS-derived CD8+ T cell clonotypes recognizing Epstein-Barr virus (EBV) antigens and multiple novel mimotopes were identified. These findings shed vital insight into the role of CD8+ T cells in MS and pave the way towards disease biomarkers and therapeutic targets.

Targeted metagenomics – Enrichment for enzymes active on sulfated polysaccharides from seaweeds

Seaweeds (macroalgae) are an attractive resource for diverse microbial- and enzymatic production processes. They are abundant, underutilized, cheap, and rich in carbohydrates, and therefore have the potential to be used as a source of mono- or oligosaccharides, and as substrates for industrial fermentation processes. Many seaweed polysaccharides, including the sulfated polysaccharides ulvan and fucoidan, are however complex and heterogenous in structure, and there are currently few enzymes available to modify them, and understanding of their enzymatic depolymerization remains limited. The present study aimed to identify and characterize robust fucoidanases and ulvan lyases. Metagenomes were obtained from microbial enrichments from an intertidal hot-spring, genes identified that expressed putative fucoidanases and ulvan lyases, and following gene cloning and expression, the respective enzymes were screened for enzymatic activity. Consistent with their origin, the identified protein sequences were considerably divergent from previously characterized enzymes, with a 44 % average maximal sequence identity. In total, the study resulted in the characterization of 10 new fucoidanases (GH107 and GH168 families) and 8 new ulvan lyases (PL24, PL25 and PL40 families). Notably, the new fucoidanases appeared to have functional specificity towards fucoidan containing α-1,3 linked L-fucosyl and several functioned at high temperature. The study contributes a metagenomics-based approach to identify new seaweed polysaccharide degrading enzymes and an increased understanding of the diversity of such enzymes, which may have implications for the realization of biotechnology based valorization of seaweed biomass.

Development of Tertiary Structure of Laccase from Geobacillus uzenensis using Homology Modelling

Laccases are a versatile enzyme with immense potential in various biotechnological applications. In this study, the protein structure prediction of laccase from Geobacillus uzenensis, a bacteria known for its robust enzymatic activity is focused. The protein structural elucidation of this laccase is crucial to understand its substrate binding and overall functionality. Protein structure can be determined by computational prediction, which is commonly known as homology modelling. The three-dimensional (3D) model was built based on the available crystal structures of related laccase enzymes and aligned with the primary sequence of the target protein. The resulting model exhibited a high degree of structural similarity and conservation of key catalytic residues, supporting its reliability for further analyses. Firstly, the suitable template was identified with 85.61% of sequence identity determined by sequence alignment. Then, MODELLER program was used to predict the model using the method of satisfaction of spatial restraints. The model was then analyzed for its quality by computational analysis tools such as Ramachandran's Plot. Finally, the binding site of the protein was identified using the GRaSP computational tool. These findings provide significant insight on comprehensive analysis of the laccase from G. uzenensis, by providing a structural framework to unravel its functional properties and substrate specificity.

Dietary titanium dioxide nanoparticles impair intestinal epithelial regeneration by perturbating the function of intestinal stem cells

Intestinal health is closely linked to intestinal stem cells (ISCs), which are highly sensitive to the harmful substances in the lumen. However, there is limited knowledge regarding the effects of food additives on ISCs. This study aims to investigate the impact of dietary titanium dioxide nanoparticles (TiO2 NPs) compared with titanium dioxide microparticles (TiO2 MPs) on intestinal health associated with ISCs in response to dextran sodium sulfate (DSS)-induced enteritis in mice, as well as the related mechanism. We found that exposure to 1% (w/w) TiO2 NPs aggravated DSS-induced enteritis in mice, while this effect could not be observed under exposure to TiO2 MPs. Additionally, 1% (w/w) TiO2 NPs exposure under DSS-induced enteritis worsened the ISC-mediated regeneration of intestinal epithelium by decreasing the epithelial cell proliferation and epithelial turnover rate while increasing epithelial cell death. Meanwhile, using a 3D intestinal organoid model, we discovered that 20 μg/mL TiO2 NPs impaired ISC function and disrupted ISC fate specification both ex vivo and in vitro. Furthermore, TiO2 NPs hindered the nuclear translocation of β-catenin, reducing the overall output of Wnt signaling. Together, TiO2 NPs deteriorated the intestinal epithelial regeneration of mice with DSS-induced enteritis by perturbating ISC function and fate specification through a mechanism involving Wnt signaling. These findings highlight the adverse effect of dietary TiO2 NPs on ISCs and shed light on the particle size optimization of TiO2 food additive.

Evaluation of the functional activity and specificity of the <i>hSLPI</i> gene promoter

BACKGROUND: One of the main problems of modern oncotherapy is the lack of selectivity of the antitumor drugs, leading to their systemic toxicity on the body. Targeted expression of therapeutic genes represents a new approach in cancer gene therapy. One of the ways to achieve the selectivity of action of the therapeutic genes towards tumor cells is the use of promoters that are active only in tumor cells, but not in normal cells. AIM: To evaluate the functional activity and specificity of the promoter of the human secretory leukocyte protease inhibitor hSLPI. MATERIALS AND METHODS: The promoter of the hSLPI gene was cloned into the promotorless vector pTurboGFP-PRL. The functional activity and specificity of the promoter were assessed by the expression of the mRNA of the TurboGFP reporter gene and the intensity of its luminescence in A549, MCF-7, HeLa tumor cells and WI-38 normal cells using real-time polymerase chain reaction with reverse transcription and fluorescence analysis, respectively. RESULTS: Despite the literature data, the promoter of the hSLPIa gene demonstrated high transcriptional activity only against HeLa cervical cancer tumor cells. At the same time, in the cells of lung adenocarcinoma A549 and breast cancer MCF-7, as in normal WI-38 cells, a reduced level of promoter activity was observed. CONCLUSION: The data obtained confirm the need for a preliminary assessment of the functional activity of tumor-specific promoters in relation to tumor and normal cells.

Cognitive aspects of interaction in the “Human — Artificial Intelligence” system

Abstract The article, based on empirical and theoretical research, reveals the phenomenology of transformations of the human cognitive sphere when interacting with artificial intelligence. The analysis of the indicated changes in the cognitive sphere is carried out on the basis of the “Concept of cognitive multi-channel Human-Computer interaction” developed by us. The essence of this concept is that the interaction of the cognitive sphere of human and artificial intelligence is implemented on the basis of the actualization and formation of typical cognitive phenomena. These phenomena are considered systemically and multifunctionally, namely as relatively independent cognitive: types of interactions, stages, strategies, channels, ontologies. Within the conceptual and substantive framework of this concept, we distinguish the following types of cognition (channels, strategies, etc.): I – orientational-cognitive; II – subject-cognitive; III – communicative and cognitive; IV – cognitive and analytical; V – cognitive and hermeneutic; VI-cognitive-ontological; VII – cognitive and creative. The identification of the indicated types of cognitive interactions is aimed at its representation as a complex, dynamic, multidimensional, multichannel intellectual system, the features of which are significant for educational and sociocultural practices, as well as for further development of artificial intelligence technologies, including its functional orientation and specificity, ergonomics, architecture, design and features of the interface. A study was conducted among students of higher education institutions aimed at determining the cognitive specificity (structure) of interaction in the “Human – Artificial Intelligence” system. Based on the analysis of the results of the distribution of answers for each of the test questions and the interpretation of the results of the cluster analysis (the Canopy algorithm was used), the dominance of the “I – orientational-cognitive” type of interactions was determined, which indicates a rather significant but initial interest in artificial intelligence technologies. There is also a relatively even distribution of all other types of cognitive interactions. The above reveals the novelty and innovation of artificial intelligence technology. This correlates with the respondents having developed different types of cognition, namely: orientational, analytical-synthetic, conceptual, interpretive, ontological, creative thinking, and corresponding intellectual intentions and motivation to use artificial intelligence tools in various spheres of activity.

Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways.

Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be predicted. Here, we developed a knowledge-guided bioinformatic pipeline to solve these issues. We analyzed 1928 genomes of Pseudomonas bacteria and focused on iron-scavenging pyoverdines as model metabolites. Our pipeline predicted 188 chemically different pyoverdines with nearly 100% structural accuracy and the presence of 94 distinct receptor groups required for the uptake of iron-loaded pyoverdines. Our pipeline unveils an enormous yet overlooked diversity of siderophores (151 new structures) and receptors (91 new groups). Our approach, combining feature sequence with phylogenetic approaches, is extendable to other metabolites and microbial genera, and thus emerges as powerful tool to reconstruct bacterial secondary metabolism pathways based on sequence data.