Biological Interest Research Articles

High-throughput DNA sequence analysis elucidates novel insight into the genetic basis of adaptation in local sheep.

Understanding how evolutionary factors related to climate adaptation and human selection have influenced the genetic architecture of domesticated animals is of great interest in biology. In the current study, by using 304 whole genomes from different geographical regions (including Europe, north Africa, Southwest Asia, east Asia, west Africa, south Asia, east Africa, Australia and Turkey), We evaluate global sheep population dynamics in terms of genetic variation and population structure. We further conducted comparative population analysis to study the genetic underpinnings of climate adaption to local environments and also morphological traits. In order to identify genomic signals under selection, we applied fixation index (FST) and also nucleotide diversity (θπ) statistical measurements. Our results revealed several candidate genes on different chromosomes under selection for local climate adaptation (e.g. HOXC12, HOXC13, IRF1, FGD2 and GNAQ), body size (PDGFA, HMGA2, PDE3A) and also morphological related traits (RXFP2). The discovered candidate genes may offer newel insights into genetic underpinning of regional adaptation and commercially significant features in local sheep.

In defense of platinum: Amino acidic polydentate ligands as a shield against sulphur-donor nucleophilic attacks

The interactions of sulfur-containing peptides and proteins with platinum-based anticancer agents are of significant interest in the field of bioinorganic chemistry. We previously modified the lead compound potassium {trichlorido[η2-(but-3-en-1-yl)-2-acetoxybenzoate]platinate(II)} (Pt-butene-ASA) by exchanging two chlorido ligands for an amino acid chelating ligand to improve its stability in aqueous solutions. In the current study, we demonstrate how this amino acid ligand strengthens the inertness of this class of complexes against sulfur-containing compounds. We incubated four complexes, each bearing an amino acid chelating ligand, with various sulfur-containing compounds of biological interest, such as DMSO, methionine, glutathione, and substance P. The reactions were monitored using NMR spectroscopy and mass spectrometry, allowing the identification by combination with IR ion spectroscopy of exotic pentacoordinate platinum(II) complexes as reaction intermediates. The results indicated that the reactivity of complexes 1–4 ((ethene,N-trans)(l-alaninato-N,O)chlorido(η2-ethene)platinate(II), (ethene,O-trans)(β-alaninato-N,O)chlorido(η2-ethene)platinate(II), (l-histidinato-N,N)chlorido(η2-ethene)platinate(II), and (olefin,N-trans)(l-alaninato-N,O)chlorido(η2-(but-3-en-1-yl)-2-acetoxy benzoate)platinate(II), respectively) is determined by the inner coordination sphere, and the addition of an amino acid ligand significantly reduces the rate of nucleophilic substitutions by sulfur-containing nucleophiles. In particular, the N,ethylene-trans isomers reacted only to a low extent with the free thiol in glutathione, while the O,ethylene-trans isomer was completely consumed within 2 h. Complex 4, the new lead compound, showed low reactivity towards S-nucleophiles in general, which confirms the concept of using amino acids as biocompatible bidentate ligands to adjust the reactivity and stability of this kind of metallodrugs.

Listening to life: Sonification for enhancing discovery in biological research.

Sonification, or the practice of generating sound from data, is a promising alternative or complement to data visualization for exploring research questions in the life sciences. Expressing or communicating data in the form of sound rather than graphs, tables, or renderings can provide a secondary information source for multitasking or remote monitoring purposes or make data accessible when visualizations cannot be used. While popular in astronomy, neuroscience, and geophysics as a technique for data exploration and communication, its potential in the biological and biotechnological sciences has not been fully explored. In this review, we introduce sonification as a concept, some examples of how sonification has been used to address areas of interest in biology, and the history of the technique. We then highlight a selection of biology-related publications that involve sonifications of DNA datasets and protein datasets, sonifications for data collection and interpretation, and sonifications aimed to improve science communication and accessibility. Through this review, we aim to show how sonification has been used both as a discovery tool and a communication tool and to inspire more life-science researchers to incorporate sonification into their own studies.

Interferon-γ and infectious diseases: Lessons and prospects.

Infectious diseases continue to claim many lives. Prevention of morbidity and mortality from these diseases would benefit not just from new medicines and vaccines but also from a better understanding of what constitutes protective immunity. Among the major immune signals that mobilize host defense against infection is interferon-γ (IFN-γ), a protein secreted by lymphocytes. Forty years ago, IFN-γ was identified as a macrophage-activating factor, and, in recent years, there has been a resurgent interest in IFN-γ biology and its role in human defense. Here we assess the current understanding of IFN-γ, revisit its designation as an "interferon," and weigh its prospects as a therapeutic against globally pervasive microbial pathogens.

Antibody-Bridged DNAzyme Walker for Sensitive Detection of Small Molecules.

Sensitive detection of small molecules with biological and environmental interests is important for many applications, such as food safety, disease diagnosis, and environmental monitoring. Herein, we propose a highly selective antibody-bridged DNAzyme walker to sensitively detect small molecules. The antibody-bridged DNAzyme walker consists of a track, small-molecule-labeled DNAzyme walking strand, and antibody against small molecules. The track is built by co-modifying fluorophore-labeled substrates and small-molecule-labeled DNA linkers onto a gold nanoparticle (AuNP). In the absence of the target molecule, the antibody binds small molecule labels at the DNAzyme walking strand and the DNA linker, driving the DNAzyme walking strand on the surface of the AuNP. The attached DNAzyme walking strand moves along the track and cleaves substrates to generate high fluorescence signals to achieve signal amplification. As target molecules exist, they competitively bind with antibody to displace the small-molecule-labeled linker and DNAzyme walking strand, rendering the DNAzyme walker inactive in substrate cleavage and causing weak fluorescence. By using this antibody-bridged DNAzyme walker, we achieved sensitive detection of two biologically important small molecules, digoxin and folic acid. This work provides a new paradigm by combining the signal amplification strategy of a DNA walker and immunorecognition for sensitive and selective detection of small molecules.

Water‐Soluble μ‐oxo triruthenium Compound of Biological Interest: H‐Bonds Network and Interaction with HSA

AbstractThe water‐soluble compound [Ru3O(CH3COO)6(4‐ampy)3]Cl (1, 4‐ampy=4‐aminopyridine) was evaluated in terms of its biologically relevant properties. Compound 1 participates in a hydrogen bonding network which includes the NH2 substituents of the ancillary ligands, methanol molecules, the Cl− counter‐ion, and a non‐conventional hydrogen bond with the neighboring 4‐ampy molecules′ π‐cloud, as determined by X‐ray measurements. One protonation equilibrium was observed at pH values below 2.3. Additionally, the compound exhibited a partition coefficient value of −0.86 (±0.07), indicating that it is highly hydrophilic. At 37 0C and pH=7.4 (phosphate buffer), compound 1 shows moderate (Ksv=2.4 104 M−1) and spontaneous (ΔG=−26.4 kJ mol−1) binding to human serum albumin (HSA) through ground‐state association, which involves formation of hydrogen bonds (ΔH=−35.7 kJ mol−1 and, ΔS=−29.8 J mol−1 K−1). Molecular docking calculations support the formation of hydrogen bonds between 1 and HSA, and suggest subdomain IIA (site I), which contains the Trp‐214 residue, as the primary interactive pocket, in agreement with the experimental static fluorescence quenching mechanism. Furthermore, a preliminary assay reveals that 1 has low cytotoxicity towards human glioblastoma U87‐MG cells.

ENHANCING COGNITIVE ABILITIES OF SCHOOL STUDENTS IN BIOLOGY THROUGH MODERN PEDAGOGICAL TECHNOLOGIES

This article discusses the influence of modern pedagogical technologies on improving the cognitive abilities of students in the field of biology. Taking into account the rapid development of technology and the growing interest in biology, the authors review and consider the features of modern types of technology used in the educational process. The article analyzes the impact of modern technologies on educational indicators in the context of the formation of critical thinking and active interaction of students.

Zirconium-based hydrophobic-MOFs as innovative electrode modifiers for flibanserin determination: Exploring the electrooxidation mechanism using a comprehensive spectroelectrochemical study.

Threedifferent types of Zr-based MOFs derived from benzene dicarboxylic acid (BDC) and naphthalene dicarboxylic acid as organic linkers (ZrBDC, 2,6-ZrNDC, and 1,4-ZrNDC) were synthesized. They were characterized using X-ray diffraction analysis (XRD), X-ray photoelectron spectroscopy (XPS), Fourier-transform IR spectroscopy (FT-IR), and Transmission electron microscopy (TEM). Their hydrophilic/hydrophobic nature was investigated via contact angle measurements; ZrBDC MOF was hydrophilic and the other two (ZrNDC) MOFs were hydrophobic. The three MOFs were combined with MWCNTs as electrode modifiers for the determinationof a hydrophobic analyte, flibanserin (FLB), as a proof-of-concept analyte. Under the optimized experimental conditions, a significant enhancement in the oxidation peak current of FLB was observed when utilizing 2,6-ZrNDC and 1,4-ZrNDC, being the highest when using 1,4-ZrNDC. Furthermore, a thorough investigation of the complex oxidation pathway of FLB was performed by carrying out simultaneous spectroelectrochemical measurements. Based on the obtained results, it was verified that the piperazine moiety of FLB is the primary site for electrochemical oxidation. The fabricated sensor based on 1,4-ZrNDC/MW/CPE showed an oxidation peak of FLB at 0.8V vs Ag/AgCl. Moreover, it showed excellent linearity for the determinationof FLB in the range 0.05 to 0.80μmol L-1 with a correlation coefficient (r) = 0.9973 and limit of detection of 3.0nmol L-1. The applicability of the developed approach was demonstrated by determinationof FLB in pharmaceutical tablets and human urine samples with acceptable repeatability (% RSD values were below 1.9% and 2.1%, respectively) and reasonable recovery values (ranged between 97 and 103% for pharmaceutical tablets and between 96 and 102% for human urine samples). The outcomes of the suggested methodology can be utilized for the determinationof other hydrophobic compounds of pharmaceutical or biological interest with the aim of achieving low detection limits of these compounds in various matrices.

DEVELOPMENT OF WEB-BASED LEARNING MEDIA ON CLASS X VIRUS MATERIAL

Based on the results of the pre-survey that has been carried out at SMA Negeri 1 Kotagajah, a problem was found, namely the use of learning media that is lacking during teaching and learning activities on biological material including virus material. In teaching and learning activities, the educational media used are limited to Student Worksheets (LKPD) and Power Point. This resulted in some students having difficulty understanding the information and losing interest in biology. Scientists then developed a learning platform based on viral content available to Class X students via the Internet. The five stages of the ADDIE model are analysis, design, development, implementation, and evaluation. Percentage results of 80%, 87%, 94% and 85% were obtained from material expert, media expert, teacher and student validators. Students indicated that the use of web-based learning materials about viruses was "very feasible".

Long-Term Intracellular Tracking of Label-Free Nanoparticles in Live Cells and Tissues with Confocal Microscopy.

The label-free imaging of inorganic nanoparticles (NPs) using confocal laser scanning microscopy (CLSM) provides a powerful and versatile tool for studying interactions between NPs and biological systems. Without the need for exogenous labels or markers, it simply benefits from the differential scattering of visible photons between biomaterials and inorganic NPs. Validation experiments conducted on fixed and living cells in real-time, as well as mouse tissue sections following parenteral administration of NPs. Additionally, by incorporating reporter fluorophores and utilizing both reflectance and fluorescence imaging modalities, the method enables high-resolution multiplex imaging of cellular structures and NPs. Different sizes and concentrations of Au NPs are tested as for Ag, Fe3O4, and CeO2 NPs, all with biological interest. Overall, the comprehensive study of NP imaging by confocal microscopy in reflectance mode provides valuable insights and tools for researchers interested in monitoring the nano-bio interactions.

Flow similarity model predicts allometric size dependence, curvature, and covariation of 285 North American tree species

AbstractScaling patterns in plants have long interested biologists, particularly whether different species share similar patterns of growth, and whether differences in growth trajectories depend on plant size. Using 8,794,737 measurements for 285 species from the U.S. Forest Inventory and Analysis database, we test several predictions emerging from a recently published “flow similarity” model for plant growth and allometry. We show that the model's predicted curvature for intraspecific relationships between height, dbh, and biomass is found in 88.1% of examined cases, and empirical slopes fall as predicted between the elastic similarity and flow similarity predictions in 71.1% of cases. We also find a strong size dependence in observed intraspecific allometric exponents, with large species, particularly gymnosperms, converging near the expectation for elastic similarity and the central tendency among small species approaching the expectations for flow similarity in most cases. Our results support the idea that differences in growth patterns across plant species depend on plant size and their attendant hydraulic and/or biomechanical demands and helps to delineate the bounds of the theoretical morphospace in which they occur.

Asymmetric α-Fluoroalkyl-α-Amino Acids: Recent Advances in Their Synthesis and Applications.

Due to the specific properties provided by fluorine atoms to biomolecules, amino acids with fluorinated side chains are of great interest for medicinal chemistry and chemical biology. Among them, α-fluoroalkyl-α-amino acids constitute a unique class of compounds. In this review, we outline the strategies adopted for their syntheses in enantiopure or enantioenriched forms and their incorporation into peptides. We then describe the consequences of the introduction of fluorine atoms in these compounds for the modulation of their hydrophobicity and the control of their conformation. Emerging applications are presented in the areas of enzyme inhibition, medicinal chemistry, hydrolytic stability of peptides, antimicrobial peptides, PET, and 19F NMR probes.

Constrained Kripke structure for identifying parameters of biological models

When modelling a complex biological system, the bottleneck of the process is the determination of parameter values that lead to model dynamics that are compatible with observations. Even for discrete modelling frameworks, this step can be limiting. Here we introduce a representation of the whole family of discrete models that can be associated to a biological system, where states are shared by all models and transitions are labelled by constraints on dynamical parameters. A model checking procedure is defined to handle this new representation. This procedure extracts the conditions on parameter settings that are compatible with a given dynamical property expressed in a temporal logic. We prove the correctness of our model checking procedure and illustrate the advantage of such an approach on some different systems of biological interest.

Site-specific immobilization of the endosialidase reveals QSOX2 is a novel polysialylated protein.

Polysialic acid (polySia) is a linear polymer of α2,8-linked sialic acid residues that is of fundamental biological interest due to its pivotal roles in the regulation of the nervous, immune, and reproductive systems in healthy human adults. PolySia is also dysregulated in several chronic diseases, including cancers and mental health disorders. However, the mechanisms underpinning polySia biology in health and disease remain largely unknown. The polySia-specific hydrolase, endoneuraminidase NF (EndoN), and the catalytically inactive polySia lectin EndoNDM, have been extensively used for studying polySia. However, EndoN is heat stable and remains associated with cells after washing. When studying polySia in systems with multiple polysialylated species, the residual EndoN that cannot be removed confounds data interpretation. We developed a strategy for site-specific immobilization of EndoN on streptavidin-coated magnetic beads. We showed that immobilizing EndoN allows for effective removal of the enzyme from samples, while retaining hydrolase activity. We used the same strategy to immobilize the polySia lectin EndoNDM, which enabled the enrichment of polysialylated proteins from complex mixtures such as serum for their identification via mass spectrometry. We used this methodology to identify a novel polysialylated protein, QSOX2, which is secreted from the breast cancer cell line MCF-7. This method of site-specific immobilization can be utilized for other enzymes and lectins to yield insight into glycobiology.

Spatiotemporal Reaction Dynamics Control in Two‐Photon Polymerization for Enhancing Writing Characteristics

AbstractSince 2001, 3D microfabrication based on two‐photon polymerization (TPP) has drawn extensive attention and interest in biology, optics, photonics, material science, and high‐energy physics. The in‐volume fabrication capability due to the threshold behavior of two‐photon absorption enables TPP higher flexibility compared with other nanofabrication techniques. However, as determined by the in‐volume fabrication feature as well as various reaction dynamics, the writing characteristics of TPP, such as throughput, accuracy, surface quality, and fabrication capability, are still limited. Herein, a comprehensive study is performed on the spatiotemporal behavior of reaction dynamics during TPP fabrication, mainly focusing on spatiotemporal characteristics of radical diffusion, photothermal effect, microscale mechanics, and voxel stacking process. Based on the study, a nonsequential fabrication method is established to simultaneously improve key writing characteristics of TPP and realize sharp features, high speeds, large overhang structure, and smooth surfaces. The method established in this work can be applied to improve the performance of functional devices for various fields.

Vascular microforamina and endocranial surface: Normal variation and distribution in adult humans.

The term craniovascular traits refers to the imprints left by arteries and veins on the skull bones. These features can be used in biological anthropology and archaeology to investigate the morphology of the vascular network in extinct species and past populations. Generally, the term refers to macrovascular features of the endocranial cavity, like those associated with the middle meningeal artery, venous sinuses, emissary foramina, and diploic channels. However, small vascular passages (here called microforamina or microchannels) have been occasionally described on the endocranial surface. The larger ones (generally with a diameter between 0.5 and 2.0 mm) can be detected through medical scanners on osteological collections. In this study, we describe and quantify the number and distribution of these microforamina in adult humans (N = 45) and, preliminarily, in a small sample of children (N = 7). Adults display more microchannels than juvenile skulls. A higher frequency in females is also observed, although this result is not statistically significant and might be associated with allometric cranial variations. The distribution of the microforamina is particularly concentrated on the top of the vault, in particular along the sagittal, metopic, and coronal sutures, matching the course of major venous sinuses and parasagittal bridging veins. Nonetheless, the density is lower in the region posterior to bregma. Beyond oxygenation, these vessels are likely involved in endocranial thermal regulation, infection, inflammation, and immune responses, and their distribution and prevalence can hence be of interest in human biology, evolutionary anthropology, and medicine.

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatments. Focusing on gene expression, the transcriptomic market exploits the benefits of next-generation sequencing (NGS), leveraging RNA sequencing (RNA-seq) as standard for measuring genome-wide gene expression in biological samples. The cumbersome sample preparation, including RNA extraction, conversion to cDNA and amplification, prevents high-throughput translation of RNA-seq technologies. Bulk RNA barcoding and sequencing (BRB-seq) addresses this limitation by enabling sample preparation in multi-well plate format. Sample multiplexing combined with early pooling into a single tube reduces reagents consumption and manual steps. Enabling simultaneous pooling of all samples from the multi-well plate into one tube, our technology relies on smart labware: a pooling lid comprising fluidic features and small pins to transport the liquid, adapted to standard 96-well plates. Operated with standard fluidic tubes and pump, the system enables over 90% recovery of liquid in a single step in less than a minute. Large scale manufacturing of the lid is demonstrated with the transition from a milled polycarbonate/steel prototype into an injection molded polystyrene lid. The pooling lid demonstrated its value in supporting high-throughput barcode-based sequencing by pooling 96 different DNA barcodes directly from a standard 96-well plate, followed by processing within the single sample pool. This new pooling technology shows great potential to address medium throughput needs in the BRB-seq workflow, thereby addressing the challenge of large-scale and cost-efficient sample preparation for RNA-seq.Graphical abstract

Evolution of Impact Melt Pools on Titan

AbstractTitan is an ocean world with a dense atmosphere, where photochemistry produces complex organic molecules that fall to the surface. An important astrobiological question is whether this material can mix with water and form molecules of biological interest. Large impacts heat the moon's subsurface and create liquid water melt pools. A recent study investigated impacts into Titan's clathrate‐covered ice shell. Methane clathrates are stable at Titan's surface conditions and have low thermal conductivity, making them efficient insulators that can lead to steep thermal gradients and a thin stagnant lid. The authors showed that the clathrate layer thickness primarily influences the melt distribution, while its volume is governed by the impactor size. Here, we investigate the fate of melt formed during an impact into a clathrate‐covered ice shell. Our results show two different behaviors: in cases when less melt is produced, the subsurface melt pool remains close to the surface and freezes on timescales ≲25 kyr; in cases when larger volumes of melt are produced, a downward‐oriented transport of the molten material occurs. As it descends, part of the melt freezes but some may reach the ocean within a few kyr under certain conditions; vertical impacts, high surface porosity, low viscosity, and tidal heating all favor this surface‐to‐ocean exchange. While providing insights on parameters that allow a subsurface melt pool to remain liquid beneath a Selk‐sized crater for a few kyr, this study suggests that Dragonfly may be able to sample melt deposits where organics reacted with liquid water to produce biomolecules.

The role of MgO on physical and bioactive properties of borophosphate glasses for biomedical applications

In this work, a novel series of borophosphate glasses of the system 40B2O3–25P2O5–(20-x)Na2O–15CaF2–xMgO (x = 0, 2.5, 5, 7.5, and 10 mol%) were synthesized using the melt-quenching technique. The effect of replacing Na2O with MgO in the glasses was analyzed by the physical and bioactive properties. The glasses were characterized by density, molar volume, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Differential thermal analysis (DTA), bioactivity tests in simulated body fluid (SBF), pH measurements, mass loss, and verification of cellular compatibility in RAW 247 murine macrophages. XRD and FTIR analyses were performed before and after immersion in SBF to verify the bioactivity. Density, molar volume and FTIR results before SBF showed structural changes in the glasses due to the addition of MgO. The pH and mass loss measurements allowed to verify the degradation behavior of the glass series as a function of MgO concentration. The DTA data showed an increase in Tg, Tx, and thermal stability due to the increase in MgO addition. XRD and FTIR analyses after SBF soaking showed superficial formation of apatites and other calcium phosphates of biological interest in the samples, attesting the bioactivity. Cytotoxicity assessed by MTT assay on the cell line RAW 247 showed that at a concentration of 500 μg/mL all glasses were compatible (non-cytotoxic). The results suggest that the synthesized glasses are bioactive, with the sample containing 5 mol% MgO exhibiting the bioactivity and biocompatibility required for biomaterial applications.

In silico Design, Synthesis and Biological Evaluation of Novel Thieno[3,2-d]pyrimidine Derivatives for Cancer Therapy - A Preliminary Study on the Inhibitory Potential towards ATR Kinase Domain and PIKK Family.

Continuing our studies in the field of new heterocyclic compounds with biological interest, herein we report the synthesis and anticancer activity of new N- and S-substituted derivatives of tetracyclic pyrido[3',2' : 4,5]thieno[3,2-d]pyrimidines. In this regard, starting from the thieno[2,3-b]pyridine-2-carboxylates, the corresponding 8(9)-aminopyrido[3',2' : 4,5]thieno[3,2-d]pyrimidin-7(8)-ones, as well as chloro derivatives were obtained. Based on the latter, amino, hydrazino and S-alkyl derivatives of pyrido[3',2' : 4,5]thieno[3,2-d]pyrimidines were synthesized subsequently. The current study focuses on identifying the potential of thieno[3,2-d]pyrimidine derivatives primarily towards ATR kinase inhibition, through computational predictions, followed by synthesis and cancer cell viability studies, along with an aim to develop the core as PIKK inhibitors for cancer therapy.