Hasil untuk "Biotechnology"

Ayal Hendel, R. Bak, Joseph Clark et al.

R. Harun, Manjinder Singh, G. Forde et al.

S. Lee, J. Park, S. Jang et al.

D. Luo, W. Saltzman

Waqas Waqas, Ye Yuan, Yongyi Chen et al.

Heavy metal(loid)s (HMs) represent significant environmental and health threats due to their persistence, bioaccumulation, and ability to induce oxidative stress and lipid peroxidation (LPO) in aquatic organisms. Here, we present the first lipidome analysis of the mud crab Scylla paramamosain to examine associations between lipid profiles and 12 HMs across three contaminated estuaries in Guangdong Province. We observed pronounced sex-specific differences in both HMs concentrations and lipid composition (P < 0.05). The lipidome showed marked dysregulation of membrane lipids, with glycerophospholipids (52.33%) and sphingolipids (11.9%) predominating, alongside elevated energy-storage lipids such as triacylglycerols (24.35%). Major glycerophospholipid classes included phosphatidylcholines (7.7%), phosphatidylethanolamine (7.49%), phosphatidylserine (6.98%), and phosphatidylglycerol (5.31%), while within the sphingolipid fraction, carnitines (4.43%) and ceramides (>2.26%) were abundant, and saccharolipids such as MGDG were present at low levels (0.07%). Female crabs exhibited significantly higher HMs concentrations and lipid levels than males, with copper (Cu), iron (Fe), and zinc (Zn) being the most abundant. Notably, Cu, Fe, and lead (Pb) showed strong positive correlations with all lipid groups. The associated lipid alterations are consistent with mitochondrial dysfunction and oxidative stress-related pathways commonly linked to HMs exposure. Although sex- and site-specific differences cannot be attributed exclusively to HMs under field conditions. These findings demonstrate the sensitivity of lipidomic profiles to environmental contamination and highlight lipidomics as a powerful tool for assessing ecological risks in HM-contaminated estuarine systems.

Paul Van Liedekerke, Jiří Pešek, Kevin Alessandri et al.

The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to decipher emergent multi-cellular behaviors. In particular agent-based (or cell-based) models that consider the individual cell as basic modeling unit tracked in space and time enjoy increasing interest across scientific communities. In this article we explore a particular class of cell-based models, so-called Deformable Cell Models (DCMs), that allow to simulate the biophysics of the cell with high realism. After situating this model among other model types, We give an overview of past and recent DCM developments and discuss new simulation results of several applications covering in-vitro and in-vivo systems. Our goal is to demonstrate how such models can generate quantitative added value in biological and biotechnological problems.

Dmitriy Serkin, Kirill Buzaverov, Aleksandr Baburin et al.

Extremely low-loss silicon nitride integrated circuits is a potential platform for a growing number of frontier applications in quantum technologies, high-performance and analog computing, nonlinear optics, light detection and ranging (LiDAR), and biotechnologies. However, efficient optical modulation with a wide frequency response, high contrast, low power and scalable manufacturing remains one of the key challenges for silicon nitride integrated photonics. Here, we propose an integrated thermo-optic phase shifter with isolation trenches operating in the C-band. The fabricated thermo-optic modulator capable to achieve a $π$-phase shift shift at a power consumption of 65 mW, bandwidth of 12 kHz, and extinction ratio (ER) over 80 dB. Moreover, we systematically demonstrate its compatibility with low-loss silicon nitride photonic integrated circuits with microring resonators exibiting an average quality factor more than $5.9 \times 10^{6}$, which correspond to propagation loss of 0.058 dB/cm.

Arben Ristemi

The process of decentralization in the Republic of North Macedonia is an important step towards strengthening local government and distributing political, economic, and social resources across the country. The decentralization period began in 2005 with amendments to the Constitution of the Republic of Macedonia and other legal provisions that created a framework for redistributing powers, resources, and responsibilities from the central government to local governments. The goal of the decentralization process is to ensure greater autonomy for local authorities, enable more efficient resource management, and increase the effectiveness of public services. However, as practice shows, this process also brings numerous challenges, such as a lack of financial resources, insufficiently trained personnel, and inadequate coordination between different levels of government. This paper aims to examine the decentralization process in the Republic of North Macedonia, with a particular focus on its impact on local government, the problems and challenges faced by municipalities, and the changes in legal and institutional frameworks.

Paula Momo Cabrera, Nicholas A. Bokulich, Petra Zimmermann

ABSTRACT The gut microbiome is crucial for host health. Early childhood is a critical period for the development of a healthy gut microbiome, but it is particularly sensitive to external influences. Recent research has focused on using advanced techniques like shotgun metagenome sequencing to identify key microbial signatures and disruptions linked to disease. For accurate microbiome analysis, samples need to be collected and stored under specific conditions to preserve microbial integrity and composition, with −80°C storage considered the gold standard for stabilization. This study investigates the effect of domestic freezer storage on the microbial composition of stool samples obtained from 20 children under 4 years of age with the use of shotgun metagenome sequencing. Fresh stool samples were aliquoted into sterile tubes, with one aliquot stored at 4°C and analyzed within 24 hours, while others were frozen in domestic freezers (below −18°C) and analyzed after 1 week, 2 months, and 6 months. Assessments of contig assembly quality, microbial diversity, and antimicrobial resistance genes revealed no significant degradation or variation in microbial composition.IMPORTANCEMost prior studies on sample storage have relied on amplicon sequencing, which is less applicable to metagenome sequencing—given considerations of contig quality and functional gene detection—and less reliable in representing microbial composition. Moreover, the effects of domestic freezer storage for at-home stool collection on microbiome profiles, contig quality, and antimicrobial resistance gene profiles have not been previously investigated. Our findings suggest that stool samples stored in domestic freezers for up to 6 months maintain the integrity of metagenomic data. These findings indicate that domestic freezer storage does not compromise the integrity or reproducibility of metagenomic data, offering a reliable and accessible alternative for temporary sample storage. This approach enhances the feasibility of large-scale at-home stool collection and citizen science projects, even those focused on the more easily perturbed early life microbiome. This advancement enables more inclusive research into the gut microbiome, enhancing our understanding of its role in human health.

Elena V. Komarova

This study examines how digital learning environments shape biology students' bioethical reasoning, focusing particularly on perceptions of biotechnological human enhancement. As technological advances in gene editing coincided with the global pandemic, both events catalyzed significant changes in biological education and highlighted the importance of bioethical understanding. Through a survey of 80 students at different educational levels, we explored how exposure to bioethical content in digital educational settings influenced students' ethical reasoning about emerging biotechnologies. Our findings reveal that students who experienced interactive and dialogic digital learning formats demonstrated more nuanced ethical positions, with greater recognition of social implications and potential risks of biotechnological enhancements. The research provides insights into how technological mediation of bioethics education shapes value formation in biology students and suggests strategies for effective digital pedagogical approaches when teaching complex bioethical topics. These findings have significant implications for technology-enhanced biology education during and beyond crisis periods, particularly for preparing future biologists to navigate complex ethical landscapes in their professional practice.

Dana Rubin, Allan dos Santos Costa, Manvitha Ponnapati et al.

Ribonucleic acid (RNA) plays fundamental roles in biological systems, from carrying genetic information to performing enzymatic function. Understanding and designing RNA can enable novel therapeutic application and biotechnological innovation. To enhance RNA design, in this paper we introduce RiboGen, the first deep learning model to simultaneously generate RNA sequence and all-atom 3D structure. RiboGen leverages the standard Flow Matching with Discrete Flow Matching in a multimodal data representation. RiboGen is based on Euclidean Equivariant neural networks for efficiently processing and learning three-dimensional geometry. Our experiments show that RiboGen can efficiently generate chemically plausible and self-consistent RNA samples, suggesting that co-generation of sequence and structure is a competitive approach for modeling RNA.

Priyanka Ghosh, Kjiersten Fagnan, Ryan Connor et al.

The volume of biological data being generated by the scientific community is growing exponentially, reflecting technological advances and research activities. The National Institutes of Health's (NIH) Sequence Read Archive (SRA), which is maintained by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), is a rapidly growing public database that researchers use to drive scientific discovery across all domains of life. This increase in available data has great promise for pushing scientific discovery but also introduces new challenges that scientific communities need to address. As genomic datasets have grown in scale and diversity, a parade of new methods and associated software have been developed to address the challenges posed by this growth. These methodological advances are vital for maximally leveraging the power of next-generation sequencing (NGS) technologies. With the goal of laying a foundation for evaluation of methods for petabyte-scale sequence search, the Department of Energy (DOE) Office of Biological and Environmental Research (BER), the NIH Office of Data Science Strategy (ODSS), and NCBI held a virtual codeathon 'Petabyte Scale Sequence Search: Metagenomics Benchmarking Codeathon' on September 27 - Oct 1 2021, to evaluate emerging solutions in petabyte scale sequence search. The codeathon attracted experts from national laboratories, research institutions, and universities across the world to (a) develop benchmarking approaches to address challenges in conducting large-scale analyses of metagenomic data (which comprises approximately 20% of SRA), (b) identify potential applications that benefit from SRA-wide searches and the tools required to execute the search, and (c) produce community resources i.e. a public facing repository with information to rebuild and reproduce the problems addressed by each team challenge.

Katherine Vilinski-Mazur, Bogdan Kirillov, Oleg Rogozin et al.

A three-dimensional cell culture called a spheroid serves as a foundational entity in a wide variety of modern tissue engineering applications, including 3D-bioprinting and preclinical drug testing. Lack of oxygen within tissue spheroids hinders metabolism of cells and eventually leads to cell death. Prevention of necrosis is crucial to success of tissue engineering methods and such prevention requires estimation of cell viability in the spheroid. We propose a novel approach for numerical modeling of diffusion in tissue spheroids during their fusion. The approach is based on numerical solutions of partial differential equations and the application of Functional Representations (FRep) framework for geometric modeling. We present modeling of oxygen diffusion based on meshes derived from the geometry of fusing spheroids, a method for selecting optimal spheroid size, and several statistics for estimating cellular viability. Our findings provide insights into oxygen diffusion in three-dimensional cell cultures thus improving the robustness of biotechnological methods that employ tissue spheroids.

Sara Maria Brancato, Davide Salzano, Davide Fiore et al.

Microbial consortia offer significant biotechnological advantages over monocultures for bioproduction. However, industrial deployment is hampered by the lack of scalable architectures to ensure stable coexistence between populations. Existing strategies rely on genetic modifications, which impose metabolic load, or environmental changes, which can reduce production. We present a versatile control architecture to regulate density and composition of a two-strain consortium without genetic engineering or drastic environmental changes. Our bioreactor-based control architecture comprises a mixing chamber where both strains are co-cultured and a reservoir sustaining the slower-growing strain. For both chambers we develop model-based and sim-to-real learning controllers. The control architecture is then validated in vivo on a two-strain Escherichia coli consortium, achieving precise and robust regulation of consortium density and composition, including tracking of time-varying references and recovery from perturbations.

Marius Bargo, Yacouba Simpore

We propose and analyze a nonlinear age-structured multi-species model that serves as a unifying framework for ecological and biotechnological systems in complex environments (microbial communities, bioreactors, and others). The formulation incorporates nonlocal intra- and interspecific interactions modulated by environmental covariates. Under general assumptions on mortality, reproduction rates, and interaction kernels, we establish existence, uniqueness, and positivity of solutions. We illustrate the model's practical relevance along two lines. First, multi-species examples, notably a non-transitive (cyclic) competition model, for which we show that, under the model assumptions, a control applied to a single species can achieve global stabilization of the system. Second, the population dynamics of malaria-vector mosquitoes, for which we develop two control strategies (biological and genetic). In the biological-control scenario, we prove global asymptotic stability of the aquatic compartment by constructing an explicit Lyapunov function. Numerical simulations validate the theoretical results and compare the effectiveness of the proposed strategies in reducing vector density and malaria transmission.

María Domínguez-Ruiz, Silvia Murillo-Cuesta, Julio Contreras et al.

Abstract Inherited hearing impairment is a remarkably heterogeneous monogenic condition, involving hundreds of genes, most of them with very small (< 1%) epidemiological contributions. The exception is GJB2, the gene encoding connexin-26 and underlying DFNB1, which is the most frequent type of autosomal recessive non-syndromic hearing impairment (ARNSHI) in most populations (up to 40% of ARNSHI cases). DFNB1 is caused by different types of pathogenic variants in GJB2, but also by large deletions that keep the gene intact but remove an upstream regulatory element that is essential for its expression. Such large deletions, found in most populations, behave as complete loss-of-function variants, usually associated with a profound hearing impairment. By using CRISPR-Cas9 genetic edition, we have generated a murine model (Dfnb1 em274 ) that reproduces the most frequent of those deletions, del(GJB6-D13S1830). Dfnb1 em274 homozygous mice are viable, bypassing the embryonic lethality of the Gjb2 knockout, and present a phenotype of profound hearing loss (> 90 dB SPL) that correlates with specific structural abnormalities in the cochlea. We show that Gjb2 expression is nearly abolished and its protein product, Cx26, is nearly absent all throughout the cochlea, unlike previous conditional knockouts in which Gjb2 ablation was not obtained in all cell types. The Dfnb1 em274 model recapitulates the clinical presentation of patients harbouring the del(GJB6-D13S1830) variant and thus it is a valuable tool to study the pathological mechanisms of DFNB1 and to assay therapies for this most frequent type of human ARNSHI.

Sérgio da Costa Dias, Andressa Lima de Brida, Maguintontz Cedney Jean-Baptiste et al.

The spotted-wing drosophila, <i>Drosophila suzukii</i> (Matsumura) (Diptera: Drosophilidae), is a pest that reduces the productivity of small fruits. Entomopathogenic nematodes (EPNs) and chemical insecticides can suppress this pest, but the compatibility of the two approaches together requires further examination. This laboratory study evaluated the compatibility of <i>Steinernema brazilense</i> IBCBn 06, <i>S. carpocapsae</i> IBCBn 02, <i>Heterorhabditis amazonensis</i> IBCBn 24, and <i>H. bacteriophora</i> HB with ten chemical insecticides registered for managing <i>D. suzukii</i> pupae. In the first study, most insecticides at the recommended rate did not reduce the viability (% of living infective juveniles (IJs)) of <i>S. braziliense</i> and both <i>Heterorhabditis</i> species. The viability of <i>S. carpocapsae</i> was lowered by exposure to spinetoram, malathion, abamectin, azadirachtin, deltamethrin, lambda-cyhalothrin, malathion, and spinetoram after 48 h. During infectivity bioassays, phosmet was compatible with all the EPNs, causing minimal changes in infectivity (% pupal mortality) and efficiency relative to EPN-only controls, whereas lambda-cyhalothrin generally reduced infectivity of EPNs on <i>D. suzukii</i> pupae the most, with a 53, 75, 57, and 13% reduction in infectivity efficiency among <i>H. bacteriophora, H. amazonensis, S. carpocapsae</i>, and <i>S. brazilense</i>, respectively. The second study compared pupal mortality caused by the two most compatible nematode species and five insecticides in various combinations. Both <i>Heterorhabditis</i> species caused 78–79% mortality among <i>D. suzukii</i> pupae when used alone, and were tested in combination with spinetoram, malathion, azadirachtin, phosmet, or novaluron at a one-quarter rate. Notably, <i>H. bacteriophora</i> caused 79% mortality on <i>D. suzukii</i> pupae when used alone, and 89% mortality when combined with spinetoram, showing an additive effect. Novaluron drastically reduced the number of progeny IJs when combined with <i>H. amazonensis</i> by 270 IJs and <i>H. bacteriophora</i> by 218. Any adult flies that emerged from EPN–insecticide-treated pupae had a shorter lifespan than from untreated pupae. The combined use of <i>Heterorhabditis</i> and compatible chemical insecticides was promising, except for novaluron.

Xin Zhang, Ge Wang, Xiaoru Li et al.

Background. Gastric cancer (GC) is the most common malignant tumor and ranks third in the world. LncRNA H19 (H19), one of the members of lncRNA, is overexpressed in various tumors. However, many undetermined molecular mechanisms by which H19 promotes GC progression still need to be further investigated. Methodology. A series of experiments was used to confirm the undetermined molecular mechanism including wound healing and transwell assays. Key Results. In this study, a significant upregulation of H19 expression was detected in GC cells and tissues. The poor overall survival was observed in GC patient with high H19 expression. Overexpression of H19 promoted the migration of GC cells, while knockdown of H19 significantly inhibited cell migration. Moreover, miR-148a-3p had a certain negative correlation with H19. Luciferase reporter assay confirmed that H19 could directly bind to miR-148a-3p. As expected, miR-148a mimics inhibited cell migration and invasion induced by H19 overexpression. The above findings proved that H19 functions as a miRNA sponge and verified that miR-148a-3p is the H19-associated miRNA in GC. We also confirmed that SOX-12 expression was upregulated in GC patient’s samples. SOX-12 expression was positively correlated with expression of H19 and was able to directly bind to miR-148a-3p. Importantly, in vitro wound healing assay showed that knockout of SOX-12 could reverse the promoting effect of H19 overexpression on cell migration. Conclusion. In conclusion, H19 has certain application value in the diagnosis and prognosis of GC. Specifically, H19 accelerates GCs to migration and metastasis by miR-138a-3p/SOX-12 axis.

Yi-Wei Zhao, Li-Li Du, Bing Hu et al.

Nitrous oxide (N2O) emissions from the wastewater treatment sector are a significant contributor to global greenhouse gas levels. This investigation delves into the mechanisms of N2O generation and uptake, correlating microbial processes with variables such as influent characteristics and operational parameters. The nature of carbon substrates in the influent profoundly influences microbial consortia and N2O output. Elevating the carbon-to-nitrogen (C/N) ratio has been shown to curtail N2O emissions by alleviating the competitive dynamics among denitrifying enzymes. Optimal activity of N2O reductase is achieved by maintaining a neutral to mildly alkaline pH and stable ambient temperatures. It is imperative to circumvent extreme aeration rates and prolonged aeration periods to reduce N2O release. The study underscores the importance of an effective carbon feed strategy and advocates for prolonged hydraulic retention times (HRT) and sludge retention times (SRT) in activated sludge suspension systems to inhibit N2O escape. Notably, excessive internal recycling, coupled with heightened dissolved oxygen (DO) levels in aerobic zones, intensifies N2O emission risks. Moreover, the presence of hazardous contaminants, such as heavy metals and antibiotics, interferes with nitrogen elimination processes, warranting a comprehensive assessment of consequent N2O emission hazards. This research provides a scientific basis as well as practical management approaches to diminish N2O emissions.

Kathleen R. Mullen, Imke Tammen, Nicolas A. Matentzoglu et al.

Background: Limited universally-adopted data standards in veterinary medicine hinder data interoperability and therefore integration and comparison; this ultimately impedes the application of existing information-based tools to support advancement in diagnostics, treatments, and precision medicine. Objectives: A single, coherent, logic-based standard for documenting breed names in health, production, and research-related records will improve data use capabilities in veterinary and comparative medicine. Methods: The Vertebrate Breed Ontology (VBO) was created from breed names and related information compiled from the Food and Agriculture Organization of the United Nations, breed registries, communities, and experts, using manual and computational approaches. Each breed is represented by a VBO term that includes breed information and provenance as metadata. VBO terms are classified using description logic to allow computational applications and Artificial Intelligence-readiness. Results: VBO is an open, community-driven ontology representing over 19,500 livestock and companion animal breed concepts covering 49 species. Breeds are classified based on community and expert conventions (e.g., cattle breed) and supported by relations to the breed's genus and species indicated by National Center for Biotechnology Information (NCBI) Taxonomy terms. Relationships between VBO terms (e.g., relating breeds to their foundation stock) provide additional context to support advanced data analytics. VBO term metadata includes synonyms, breed identifiers/codes, and attributed cross-references to other databases. Conclusion and clinical importance: The adoption of VBO as a source of standard breed names in databases and veterinary electronic health records can enhance veterinary data interoperability and computability.