Field Of Biology Research Articles

Orthogonal Control of Nucleic Acid Function via Chemical Caging-Decaging Strategies.

The ability to precisely control the function of nucleic acids plays an important role in biosensing and biomedicine. In recent years, novel strategies employing biological, physical, and chemical triggers have been developed to modulate the function of nucleic acids spatiotemporally. These approaches commonly involve the incorporation of stimuli-responsive groups onto nucleic acids to block their functions until triggers-induced decaging restore activity. These inventive strategies deepen our comprehension of nucleic acid molecules' dynamic behavior and provide new techniques for precise disease diagnosis and treatment. Focusing on the spatiotemporal regulation of nucleic acid molecules through the chemical caging-decaging strategy, we here present an overview of the innovative triggered control mechanisms and accentuate their implications across the fields of chemical biology, biomedicine, and biosensing.

Autologous platelet concentrates in root coverage procedures.

Gingival recessions are vastly prevalent among the general population. With regards to their treatment, recent advancements in periodontal and microsurgical procedures, focusing on minimal invasiveness and patient-centered therapies, have propelled a shift in their contemporary treatment, highlighting the field of biologics and bioactive mediators. Among different classes and types of biologics, autologous platelet concentrates (APCs), also referred to as autologous blood-derived products, are commonly used and preferred among many clinicians. These are essentially obtained via venipuncture (intravenous access) followed by centrifugation, for which numerous protocols and preparation methods have been used, leading to varieties of blood-derived products. In this review, via a systematic search, we explored the efficacy of the different utilized preparation methods and centrifugation protocols of APCs (e.g., platelet-rich plasma (PRP), platelet-rich fibrin (PRF), leucocyte-PRF, advanced-PRF, concentrated growth factor (CGF), etc.) for the treatment of type 1 gingival recessions (RT1, without interproximal attachment loss or noticeable tooth displacement), as well as their effectiveness relative to a common control (treatment with flap advancement alone without any additional material). Based on the available literature from randomized trials found in our systematic search, we observed that utilization of PRF can significantly enhance treatment outcomes when performing a coronally advanced flap, in terms of the amount of root coverage. The improvement in root coverage was further enhanced in the presence of baseline keratinized tissue width, and with an increasing relative magnitude (the more the baseline keratinized tissue width, the better the root coverage outcomes when using PRF). The efficacy of these products needs to be further explored with different graft substitutes and matrices, as well as relative to other commonly applied biologics, through well-conducted and adequately-powered randomized clinical trials.

Using active learning methodologies to teach sequence analysis and molecular phylogeny.

The great development of high-throughput molecular biology techniques and the consequent generation of massive data have made Bioinformatics essential for undergraduate Bioscience students. The importance of this scientific discipline is evidenced by the huge number of specialized publications, tools, and databases available. Training in Bioinformatics equips undergraduates with transferable skills that can be applied in all fields of Biology, such as programming abilities, data analysis, database management, biological knowledge, statistics, problem solving, and interdisciplinary collaboration. Over the past decade, there has been a notable increase in the number of higher education institutions worldwide that have adopted a competency-based curricula. This approach places a significant emphasis on the actions and skills that students are expected to develop, rather than merely focusing on the information, they are required to memorize. In this educational context, the use of active learning strategies has been demonstrated to enhance student comprehension and competency development. This paper describes the implementation of an active learning approach in a hands-on lesson performed by undergraduate students of Biology at the University of Malaga (Spain). Its main objective is to introduce students to molecular databases and information search systems on genes, proteins, and phylogeny. This is achieved within the framework of a smart campus, which integrates technological and sustainable resources to promote a positive and productive learning environment for the university community. This work presents the content and procedure of this practical activity, as well as the evaluation method and the results of a student survey to assess their opinions.

Controlling Directional Liquid Transfer over a Ratchet-like Surface with Oriented Open-Wedges

Directed transfer of liquids is widely used as an important mass transfer strategy in the nature biology, industry, agriculture, and medical fields. Based on the bionic concept, researchers have constructed various forms of surface structures to realize controlled transport of liquids. However, current methods for preparing surfaces with directional liquid transport often suffer from cumbersome preparation processes, complexity of the prepared structures, and high costs. In this paper, we prepared a topological structure surface capable of precisely controlling liquid transport by a facile method. By utilizing 3D printing technology, we designed and fabricated a wedge-shaped surface with a periodic tilting scale arrangement. We accomplished the precise regulation of liquid transport on the surface of the structure, which not only realized the bi-directional transport of liquid anisotropically to the uni-directional transport on the surface but also achieved the precise regulation of the distance and speed of liquid transport through adjusting the opening angle formed by the open-wedges. We expect that the as-prepared wedge-shaped surface will provide a facile and efficient strategy for directional liquid transport.

Insights into Crystallization of Neuronal Nicotinic α4β2 Receptor in Polarized Lipid Matrices

Obtaining high-resolution 3D structures of membrane proteins through X-ray crystallography remains a longstanding bottleneck in the field of structural biology. This challenge has led to the optimization of purification methods to acquire high-yielding, pure proteins suitable for crystallization. In this study, we performed crystallization screenings of purified human α4β2 nAChR using a polarized in meso method. After reconstituting the detergent-solubilized α4β2 nAChR into the LCP matrix, the samples were incubated in a polarized lipid matrix using the RMP@LMx device developed in our laboratory. The results showed that under these conditions, the α4β2-nAChR-LFC 16 complex gave a mobile fraction >0.8, suggesting that its diffusion in the polarized lipid matrix is favorable for crystal nucleation. Voltages above 70 mV restricted crystal formation due to sample dehydration. Furthermore, a lipid analysis using UPLC-ESI MS/MS revealed a profile necessary for preserving protein integrity and promoting diffusion across the LCP. We harvested a single crystal and subjected it to X-ray diffraction, resulting in reflections comparable to previous studies of the muscle-type nAChR from Torpedo californica. X-ray diffraction of a single crystal gave distinct low-resolution diffractions of protein nature. These findings lay the groundwork for further optimization of membrane protein crystallization in polarized in meso phases.

Electrically Conductive Nanomaterials: Transformative Applications in Biomedical Engineering - A Review.

In recent years, significant advancements in nanotechnology have improved the various disciplines of scientific fields. Nanomaterials, like, carbon-based (carbon nanotubes, graphene), metallic, metal oxides, conductive polymers, and 2D materials (MXenes) exhibit exceptional electrical conductivity, mechanical strength, flexibility, thermal property and chemical stability. These materials hold significant capability in transforming material science and biomedical engineering by enabling the creation of more efficient, miniaturized, and versatile devices. The indulgence of nanotechnology with conductive materials in biological fields promises a transformative innovation across various industries, from bioelectronics to environmental regulations. The conductivity of nanomaterials with a suitable size and shape exhibits unique characteristics, which provides a platform for realization in bioelectronics as biosensors, tissue engineering, wound healing, and drug delivery systems. It can be explored for state-of-the-art cardiac, skeletal, nerve, and bone scaffold fabrication while highlighting their proof-of-concept in the development of biosensing probes and medical imaging. This review paper highlights the significance and application of the conductive nanomaterials associated with conductivity and their contribution towards a new perspective in improving the healthcare system globally.&#xD.

Optical investigation of degradation of graphene oxide in alkaline environment: Evidence of two distinct photon-emitting phases in visible region.

In this work we show a procedure of treating of the graphene oxide in alkaline environment as a function of the treatment time in order to obtain novel structures with strong luminescence properties, water-stable, useful as potential replacement for critical raw materials employed as example in optical and optoelectronic devices or for diagnostic and therapeutic technology. These structures have distinct blue and green-luminescence properties which derived most likely from different structural conformations, one associable with that of carbon quantum dots (or as an alternative to that of the Oxidative Debris), the other, lighter and more similar to organic compounds, reported in literature as fulvic-like molecules, but whose nature has to be further investigated. We show that the lighter fraction has a dual mechanism of photoemission: the excitation-independent PL for excitation wavelength within 350 nm and the excitation-dependent component for excitation wavelength ranging in the visible spectrum. The PL dual behaviour could depend on fluorescent nanoclusters composed by specific organic fluorophores with a carbonaceous core. FTIR analysis shows reasonably the same functional groups unless of some difference discussed in the text, meanwhile UV–Vis and PL analysis clearly highlight two distinct emissions (450 nm and 530 nm) in the visible region of the electromagnetic spectrum. Excitation-dependent photoluminescence, water stability and organic fluorescent nanostructures are issues particularly required for application in the biological field but also in materials science.

Advanced Laser Techniques for the Development of Nature-Inspired Biomimetic Surfaces Applied in the Medical Field

This review focuses on the innovative use of laser techniques in developing and functionalizing biomimetic surfaces, emphasizing their potential applications in the medical and biological fields. Drawing inspiration from the remarkable properties of various natural systems, such as the water-repellent lotus leaf, the adhesive gecko foot, the strong yet lightweight spider silk, and the unique optical structures of insect wings, we explore the potential for replicating these features through advanced laser surface modifications. Depending on the nature and architecture of the surface, particular techniques have been designed and developed. We present an in-depth analysis of various methodologies, including laser ablation/evaporation techniques, such as Pulsed Laser Deposition and Matrix-Assisted Pulsed Laser Evaporation, and approaches for laser surface structuring, including two-photon lithography, direct laser interference patterning, laser-induced periodic surface structures, direct laser writing, laser-induced forward transfer, and femtosecond laser ablation of metals in organic solvents. Additionally, specific applications are highlighted with the aim of synthesizing this knowledge and outlining future directions for research that further explore the intersection of laser techniques and biomimetic surfaces, paving the way for advancements in biomedical applications.

Microscopic Phage Adsorption Assay: High-throughput quantification of virus particle attachment to host bacterial cells.

Phages, viruses of bacteria, play a pivotal role in Earth's biosphere and hold great promise as therapeutic and diagnostic tools in combating infectious diseases. Attachment of phages to bacterial cells is a crucial initial step of the interaction. The classic assay to quantify the dynamics of phage attachment involves co-culturing and enumeration of bacteria and phages, which is laborious, lengthy, hence low-throughput, and only provides ensemble estimates of model-based adsorption rate constants. Here, we utilized fluorescence microscopy and particle tracking to obtain trajectories of individual virus particles interacting with cells. The trajectory durations quantified the heterogeneity in dwell time, the time that each phage spends interacting with a bacterium. The average dwell time strongly correlated with the classically-measured adsorption rate constant. We successfully applied this technique to quantify host-attachment dynamics of several phages including those targeting key bacterial pathogens. This approach should benefit the field of phage biology by providing highly quantitative, model-free readouts at single-virus resolution, helping to uncover single-virus phenomena missed by traditional measurements. Owing to significant reduction in manual effort, our method should enable rapid, high-throughput screening of a phage library against a target bacterial strain for applications such as therapy or diagnosis.

Modulating Immune Responses: The Double-Edged Sword of Platelet CD40L.

The CD40-CD40L receptor ligand pair plays a fundamental role in the modulation of the innate as well as the adaptive immune response, regulating monocyte, T and B cell activation, and antibody isotype switching. Although the expression and function of the CD40-CD40L dyad is mainly attributed to the classical immune cells, the majority of CD40L is expressed by activated platelets, either in a membrane-bound form or shed as soluble molecules in the circulation. Platelet-derived CD40L is involved in the communication with different immune cell subpopulations and regulates their functions effectively. Thus, platelet CD40L contributes to the containment and clearance of bacterial and viral infections, and additionally guides leukocytes to sites of infection. However, platelet CD40L promotes inflammatory cellular responses also in a pathophysiological context. For example, in HIV infections, platelet CD40L is supportive of neuronal inflammation, damage, and finally HIV-related dementia. In sepsis, platelet CD40L can induce extensive endothelial and epithelial damage resulting in barrier dysfunction of the gut, whereby the translocation of microbiota into the circulation further aggravates the uncontrolled systemic inflammation. Nevertheless, a distinct platelet subpopulation expressing CD40L under septic conditions can attenuate systemic inflammation and reduce mortality in mice. This review focuses on recent findings in the field of platelet CD40L biology and its physiological and pathophysiological implications, and thereby highlights platelets as vital immune cells that are essential for a proper immune surveillance. In this context, platelet CD40L proves to be an interesting target for various inflammatory diseases. However, either an agonism or a blockade of CD40L needs to be well balanced since both the approaches can cause severe adverse events, ranging from hyperinflammation to immune deficiency. Thus, an interference in CD40L activities should be likely done in a context-dependent and timely restricted manner.

The O-GlcNAc database: introducing new features and tools developed from community feedback.

O-GlcNAc is a reversible post-translational modification found on serine and threonine residues of nucleocytoplasmic proteins. Four years ago, we released the O-GlcNAc Database( oglcnac.mcw.edu ), a comprehensive catalog of O-GlcNAcylated proteins that has become one of the most cited resources in the field, with hundreds of unique users per month. We are now presenting an updated O-GlcNAc Database, which includes nearly 20,000 O-GlcNAcylated proteins and 48 species, marking substantial growth in data volume and scope. This paper presents the most noteworthy features implemented over the last year, often originating from feedback from the O-GlcNAc community. Among these features, we provide a brief overview of the database content, introduce our new protein viewer mode, and discuss the implementation of subcellular localization information and its applications in the O-GlcNAc score. We also provide an interface to use CytOVS, a tool designed to evaluate and sort O-GlcNAcome datasets derived from MS experiments. In conclusion, this new and improved O-GlcNAc Database represents a significant advancement in providing a comprehensive and expanded resource for researchers in the field of O-GlcNAc biology.

From Knallgas Bacterium to Promising Biomanufacturing Host: The Evolution of Cupriavidus necator.

The expanding field of synthetic biology requires diversification of microbial chassis to expedite the transition from a fossil fuel-dependent economy to a sustainable bioeconomy. Relying exclusively on established model organisms such as Escherichia coli and Saccharomyces cerevisiae may not suffice to drive the profound advancements needed in biotechnology. In this context, Cupriavidus necator, an extraordinarily versatile microorganism, has emerged as a potential catalyst for transformative breakthroughs in industrial biomanufacturing. This comprehensive book chapter offers an in-depth review of the remarkable technological progress achieved by C. necator in the past decade, with a specific focus on the fields of molecular biology tools, metabolic engineering, and innovative fermentation strategies. Through this exploration, we aim to shed light on the pivotal role of C. necator in shaping the future of sustainable bioprocessing and bioproduct development.

Design, fabrication, and calibration of a micromachined thermocouple for biological applications in temperature monitoring

This paper presents a microneedle thermocouple probe designed for temperature measurements in biological samples, addressing a critical need in the field of biology. Fabricated on a Silicon-On-Insulator (SOI) wafer, the probe features a doped silicon (Si)/chrome (Cr)/gold (Au) junction, providing a high Seebeck coefficient, rapid response times, and excellent temperature resolution. The microfabrication process produces a microneedle with a triangular sensing junction. Finite Element Analysis (FEA) was employed to evaluate the thermal time constant and structural integrity in tissue, supporting the probe's suitability for biological applications. Experimental validation included temperature measurements in ex-vivo tissue and live Xenopus laevis oocytes. Notably, intracellular thermogenesis was detected by increasing extracellular potassium concentration to depolarize the oocyte membrane, resulting in a measurable temperature rise. These findings highlight the probe's potential as a robust tool for monitoring temperature variations in biological systems.

Blue Laser for Production of Carbon Dots.

The synthesis of carbon dots (CDs) is gaining wide-ranging interest due to their broad applicability, owing to their small size and luminescence. CDs were prepared from charcoal via a one-step process using laser ablation in liquid without the use of reagents. The adopted method was based on the use of a commercially available continuous wave (CW) laser diode emitting a 450 nm wavelength and, for the liquid, a phosphate-buffered saline (PBS) solution, routinely used in the biological field. Photoluminescence analysis revealed fluorescence, at 480 nm, increasing with laser irradiation time. The atomic force microscopy (AFM) of the CDs revealed an average sphere shape with a size of about 10 nm. Biodegradable polycaprolactone (PCL), typically adopted in biomedicine applications, was used as a matrix to show the preserved luminescence, ideal for the non-invasive monitoring of implanted scaffolds in tissue engineering.

Roles of ZEB1 and ZEB2 in E-cadherin expression and cell aggressiveness in head and neck cancer.

Zinc finger E-box binding homeobox 1 (ZEB1) has been identified as a key factor in cancer cell differentiation and metastasis, and has been well studied in the field of cancer cell biology. ZEB2 has a highly similar conformation to ZEB1, but its role in head and neck squamous cell carcinoma (HNSCC) cells is not fully understood. Here, we separately overexpressed ZEB1 and ZEB2 in C57BL/6 mouse oral cancer (MOC) cells and investigated their cellular characteristics, including E-cadherin levels, motile properties, chemoresistance, and metastatic ability in immunocompetent mice. Both ZEB1 and ZEB2 overexpression reduced epithelial traits and converted cells to an aggressive phenotype. Surprisingly, ZEB1 overexpression increased the endogenous level of ZEB2 in MOC cells, and vice versa. The molecular mechanisms underlying these findings remain unclear. However, the in vitro anchorage-independent growth of MOC cells overexpressing ZEB2 was considerably greater than that of MOC cells overexpressing ZEB1. These findings suggest that ZEB2, like ZEB1, has the ability to induce the differentiation of cancer cells into those with highly aggressive traits.

Conserved allomorphs of MR1 drive the specificity of MR1-restricted TCRs.

Major histocompatibility complex class-1-related protein (MR1), unlike human leukocyte antigen (HLA) class-1, was until recently considered to be monomorphic. MR1 presents metabolites in the context of host responses to bacterial infection. MR1-restricted TCRs specific to tumor cells have been described, raising interest in their potential therapeutic application for cancer treatment. The diversity of MR1-ligand biology has broadened with the observation that single nucleotide variants (SNVs) exist within MR1 and that allelic variants can impact host immunity. The TCR from a MR1-restricted T-cell clone, MC.7.G5, with reported cancer specificity and pan-cancer activity, was cloned and expressed in Jurkat E6.1 TCRαβ- β2M- CD8+ NF-κB:CFP NFAT:eGFP AP-1:mCherry cells or in human donor T cells. Functional activity of 7G5.TCR-T was demonstrated using cytotoxicity assays and by measuring cytokine release after co-culture with cancer cell lines with or without loading of previously described MR1 ligands. MR1 allele sequencing was undertaken after the amplification of the MR1 gene region by PCR. In vivo studies were undertaken at Labcorp Drug Development (Ann Arbor, MI, USA) or Epistem Ltd (Manchester, UK). The TCR cloned from MC.7.G5 retained MR1-restricted functional cytotoxicity as 7G5.TCR-T. However, activity was not pan-cancer, as initially reported with the clone MC.7.G5. Recognition was restricted to cells expressing a SNV of MR1 (MR1*04) and was not cancer-specific. 7G5.TCR-T and 7G5-like TCR-T cells reacted to both cancer and healthy cells endogenously expressing MR1*04 SNVs, which encode R9H and H17R substitutions. This allelic specificity could be overcome by expressing supraphysiological levels of the wild-type MR1 (MR1*01) in cell lines. Healthy individuals harbor T cells reactive to MR1 variants displaying self-ligands expressed in cancer and benign tissues. Described "cancer-specific" MR1-restricted TCRs need further validation, covering conserved allomorphs of MR1. Ligands require identification to ensure targeting MR1 is restricted to those specific to cancer and not normal tissues. For the wider field of immunology and transplant biology, the observation that MR1*04 may behave as an alloantigen warrants further study. .

Extraction and characterization of essential oils from fresh and dry leaves of Pinus elliottii

Essential oils are secondary metabolites whose properties have been studied mainly with emphasis on antimicrobial, biological and pharmaceutical fields, such as antibacterial, antifungal, antiviral, pest control and insect repellents. Essential oils from fresh and dry leaves of Pinus elliottii were extracted by hydrodistillation, chemically characterized and quantified by gas chromatography coupled to a mass spectrometer. The plant leaves were collected in a reforested area in the south of the state of Minas Gerais, Brazil. The two main components in both characterized essential oils were Germacrene D and β-Pinene. In the essential oil from fresh foliage, Germacrene D (47.71%) was the majority component, while in the essential oil from dry foliage, β-Pinene (30.06%) was the majority component. Literature data point that essential oils with large amount of Germacrene D may act as antibacterial and repellent agents. Additionally, literature data also support that essential oils with large amount of β-Pinene exhibit several biological properties, similar to the Germacrene D, in addition with a wide range of medicinal and pharmacological activities. Thus, from our results and with literature data, it is possible to elucidate new potential applications to essential oils from fresh and dry leaves of Pinus elliottii.

Influence of slip conditions and applied magnetic field on peristaltic propulsion of ellis fluid flow in a homogeneous conduit: a parametric analysis

The peristaltic mechanism has recently garnered significant attention in biological and biomedical engineering fields. This study investigates the magnetohydrodynamic (MHD) peristaltic propulsion of an Ellis fluid through a uniform channel, incorporating slip boundary conditions. Both magnetic field presence and slip effects modulate the peristaltic motion, with various factors influencing the sinusoidal waves along the channel walls. Through appropriate assumptions and simplifications, we derive governing equations for the flow and magnetic field. The resulting nonlinear system of differential equations is solved using a perturbation technique. We thoroughly examine three key metrics: velocity, pressure gradient, and streamlines. Findings indicate that magnetic field presence and slip conditions significantly impact flow behaviour. Slip coefficients positively influence velocity and pressure difference, while the magnetic field tends to decelerate the velocity profile. A comparative analysis between Newtonian and non-Newtonian models reveals notable differences in velocity profiles. These insights have potential applications across a wide spectrum of industrial and biological contexts. This study contributes to the understanding of complex fluid dynamics in peristaltic systems, offering valuable perspectives for both theoretical advancement and practical applications in biomedical and industrial fields.

A Comprehensive Spatially Resolved Metabolomics Dataset for Lampreys

As one of the two most ancient groups of extant vertebrates, lamprey has become an important model organism in various fields of biology. In this paper, we present a comprehensive tissue-wide spatial metabolomics dataset for lampreys, where 14 distinct tissues were analyzed using liquid chromatography-mass spectrometry (LC-MS) in both positive and negative ion modes. The dataset has been fully validated using internal standard and pooled quality control samples and is readily accessible at the UCSD Metabolomics Workbench. This dataset serves as a valuable resource for researchers using lampreys as a model organism. Additionally, it acts as a benchmark metabolomics dataset for evaluating new algorithms and software tools and comparing them with previously published results. A lamprey spatial metabolomics database is also provided to support studies utilizing lampreys as an animal model, and to complement and validate other spatial metabolomics studies on lampreys conducted with mass spectrometry imaging or other techniques.

The Structures, Functions, and Roles of Class III HDACs (Sirtuins) in Neuropsychiatric Diseases.

Over the past two decades, epigenetic regulation has become a rapidly growing and influential field in biology and medicine. One key mechanism involves the acetylation and deacetylation of lysine residues on histone core proteins and other critical proteins that regulate gene expression and cellular signaling. Although histone deacetylases (HDACs) have received significant attention, the roles of individual HDAC isoforms in the pathogenesis of psychiatric diseases still require further research. This is particularly true with regard to the sirtuins, class III HDACs. Sirtuins have unique functional activity and significant roles in normal neurophysiology, as well as in the mechanisms of addiction, mood disorders, and other neuropsychiatric abnormalities. This review aims to elucidate the differences in catalytic structure and function of the seven sirtuins as they relate to psychiatry.