Modern Biology Research Articles

Initiation, development and achievements of molecular-biological and molecular-genetic research in Ukraine (on the 50th anniversary of the Institute of Molecular Biology and Genetics of the NAS of Ukraine)

The paper is focused on the main events that initiated molecular biological and molecular genetic research in Ukraine. It examines the main directions and achievements of these sciences in the Sector of Molecular Biology and Genetics of the D. K. Zabolotny Institute of Microbiology and Virology of the Academy of Sciences of the Ukrainian SSR that was the forerunner of the IMBG. The scientific and organizational activities of the IMBG and the contribution of its employees to the development of modern biology are briefly analyzed over the 50 years of the institute’s existence.

Nucleation and Growth of Nanocrystals Investigated by In Situ Transmission Electron Microscopy.

Nanocrystals play a key role in the modern energy, catalysis, semiconductor, and biology industries due to their unique structures and performances. However, controllable fabrication of ideal nanocrystals with the desired structures and properties is still challenging, which needs a deep understanding of their nucleation and growth process. Here, the research on nucleation and growth of nanocrystals studied by in situ transmission electron microscopy (TEM) is reviewed, mainly focusing on the atomic migration dynamics, interface evolution, and structure transformation. In addition, the challenges in the study of nanocrystal growth by TEM are discussed and the perspective on the future development of advanced in situ TEM techniques is provided. It is hoped that the review can give a deep insight into the nanocrystal nucleation and growth process, and further contribute to the rational design and precise fabrication of high-performance functional nanocrystals.

Regulatory Effects of ABA and GA on the Expression of Conglutin Genes and LAFL Network Genes in Yellow Lupine (Lupinus luteus L.) Seeds.

The maturation of seeds is a process of particular importance both for the plant itself by assuring the survival of the species and for the human population for nutritional and economic reasons. Controlling this process requires a strict coordination of many factors at different levels of the functioning of genetic and hormonal changes as well as cellular organization. One of the most important examples is the transcriptional activity of the LAFL gene regulatory network, which includes LEAFY COTYLEDON1 (LEC1) and LEC1-LIKE (L1L) and ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 (LEAFY COTYLEDON2), as well as hormonal homeostasis-of abscisic acid (ABA) and gibberellins (GA) in particular. From the nutritional point of view, the key to seed development is the ability of seeds to accumulate large amounts of proteins with different structures and properties. The world's food deficit is mainly related to shortages of protein, and taking into consideration the environmental changes occurring on Earth, it is becoming necessary to search for a way to obtain large amounts of plant-derived protein while maintaining the diversity of its origin. Yellow lupin, whose storage proteins are conglutins, is one of the plant species native to Europe that accumulates large amounts of this nutrient in its seeds. In this article we have shown the key changes occurring in the developing seeds of the yellow-lupin cultivar Taper by means of modern molecular biology techniques, including RNA-seq, chromatographic techniques and quantitative PCR analysis. We identified regulatory genes fundamental to the seed-filling process, as well as genes encoding conglutins. We also investigated how exogenous application of ABA and GA3 affects the expression of LlLEC2, LlABI3, LlFUS3, and genes encoding β- and δ-conglutins and whether it results in the amount of accumulated seed storage proteins. The research shows that for each species, even related plants, very specific changes can be identified. Thus the analysis and possibility of using such an approach to improve and stabilize yields requires even more detailed and extended research.

The various meanings and uses of bone "remodeling" in biological anthropology: A review.

In modern bone biology, the term "remodeling" generally refers to internal bone turnover that creates secondary osteons. However, it is also widely used by skeletal biologists, including biological anthropologists as a catch-all term to refer to different skeletal changes. In this review, we investigated how "remodeling" is used across topics on skeletal biology in biological anthropology to demonstrate potential problems with such pervasive use of a generalized term. Using PubMed and Google Scholar, we selected and reviewed 205 articles that use the term remodeling to describe skeletal processes and have anthropological implications. Nine edited volumes were also reviewed as examples of collaborative work by different experts to demonstrate the diverse and extensive use of the term remodeling. Four general meanings of bone "remodeling" were identified, namely, internal turnover, functional adaptation, fracture repair, and growth remodeling. Additionally, remodeling is also used to refer to a broad array of pathological skeletal changes. Although we initially identified four general meanings of bone remodeling, they are not mutually exclusive and often occur in combination. The term "remodeling" has become an extensively used catch-all term to refer to different processes and outcomes of skeletal changes, which inevitably lead to misunderstanding and a loss of information. Such ambiguity and confusion are potentially problematic as the field of biological anthropology becomes increasingly multidisciplinary. Therefore, we advocate for precise, context-specific definitions and explanations of bone remodeling as it continues to be used across disciplines within and beyond biological anthropology.

Changing Natures: On Theory and Practice of Breeding in the European Middle Ages

While throughout modern history it has been shown how thoroughly biological discourses were shaped by conceptions originating in the theory and praxis of breeding, for the medieval period similar studies are mostly absent. This paper offers a symmetrical history of theory and praxis of breeding by asking to what extent they shaped medieval conceptions of human ‘race’ and ‘ancestry’ in Europe. For scholarly knowledge of breeding, the analysis relies on Albertus Magnus’ extensive Aristotelian work De animalibus. For the practical knowledge of the breeders, scattered indications from the secondary literature are compiled and promising primary sources are outlined for further research. The paper finds that various concepts and practices whose origins are commonly placed in the early modern period were already present in the Middle Ages, including the concept of reproductive heredity and the view that creation diversified over time through reproductive ancestry. Breeding practices, thus, existed before the rise of genetics in modern biology. The medieval conceptions of ‘race’ and ‘ancestry’ underwent conceptual transfers from the non-human into the human sphere, collapsing the qualitative distinction of the two spheres into one quantitively graded overarching image of nature.

Supramolecular Chirogenesis in a Sterically Hindered Porphyrin: A Critical Theoretical Analysis.

The determination of molecular stereochemistry and absolute configuration is an important part of modern chemistry, pharmacology, and biology. Electronic circular dichroism (ECD) spectroscopy is a widely used tool for chirality assignment, especially with porphyrin macrocycles employed as reporter chromophores. However, the mechanisms of induced ECD in porphyrin complexes are yet to be comprehensively rationalized. In this work, the ECD spectra of a sterically hindered hexa-cationic porphyrin with two camphorsulfonic acids in dichloromethane and chloroform were experimentally measured and computationally analyzed. The influence of geometric factors such as the position of chiral guest molecules, distortion of the porphyrin macrocycle, and orientation of aromatic and non-aromatic peripheral substituents on the ECD spectra was theoretically studied. Various potential pitfalls, such as a lack of significant conformations and accidental agreement of experimental and simulated spectra, are considered and discussed.

Real-time, deep-learning aided lensless microscope.

Traditional miniaturized fluorescence microscopes are critical tools for modern biology. Invariably, they struggle to simultaneously image with a high spatial resolution and a large field of view (FOV). Lensless microscopes offer a solution to this limitation. However, real-time visualization of samples is not possible with lensless imaging, as image reconstruction can take minutes to complete. This poses a challenge for usability, as real-time visualization is a crucial feature that assists users in identifying and locating the imaging target. The issue is particularly pronounced in lensless microscopes that operate at close imaging distances. Imaging at close distances requires shift-varying deconvolution to account for the variation of the point spread function (PSF) across the FOV. Here, we present a lensless microscope that achieves real-time image reconstruction by eliminating the use of an iterative reconstruction algorithm. The neural network-based reconstruction method we show here, achieves more than 10000 times increase in reconstruction speed compared to iterative reconstruction. The increased reconstruction speed allows us to visualize the results of our lensless microscope at more than 25 frames per second (fps), while achieving better than 7 µm resolution over a FOV of 10 mm2. This ability to reconstruct and visualize samples in real-time empowers a more user-friendly interaction with lensless microscopes. The users are able to use these microscopes much like they currently do with conventional microscopes.

Current progress of immunotherapy based on NK cell in cancer therapy

Cancer generally refers to malignant tumor, including carcinoma, sarcoma and carcinosarcoma. This disease is caused by malignant cell hyperplasia. It is invasive and metastable. It is manifested by the continuous growth of a local mass of the body that destroys the normal tissue structure and can be transferred to other sites. It has been reported that there will be about 20 million new cases of cancer in 2020 and half of all cancer patients will die. Surgery, chemotherapy and radiotherapy, as the three standard treatment methods for cancer, plays an vital role in improving the survival rate and prolonging the survival time of cancer patients. In recent years, researchers have focused on the immune mechanism of tumors to explore the treatment of malignant tumors. Driven by the rapid development of modern molecular biology and gene engineering technology, immunotherapy has been paid more and more attention, showing good effect and application prospects, has become the world's recognized malignancy of the fourth treatment mode. Among these, natural killer cells (NK) fight cancer through their cytolytic function and the production of IFN-γ. One of the primary clinical objectives is to use their abilities for tumour immunotherapy. This article looks at advances in NK cell-based tumor therapy.

Cyanotoxins, biosynthetic gene clusters, and factors modulating cyanotoxin biosynthesis.

Cyanobacterial harmful algal blooms (CHABs) are a global environmental concern that encompasses public health issues, water availability, and water quality owing to the production of various secondary metabolites (SMs), including cyanotoxins in freshwater, brackish water, and marine ecosystems. The frequency, extent, magnitude, and duration of CHABs are increasing globally. Cyanobacterial species traits and changing environmental conditions, including anthropogenic pressure, eutrophication, and global climate change, together allow cyanobacteria to thrive. The cyanotoxins include a diverse range of low molecular weight compounds with varying biochemical properties and modes of action. With the application of modern molecular biology techniques, many important aspects of cyanobacteria are being elucidated, including aspects of their diversity, gene-environment interactions, and genes that express cyanotoxins. The toxicological, environmental, and economic impacts of CHABs strongly advocate the need for continuing, extensive efforts to monitor cyanobacterial growth and to understand the mechanisms regulating species composition and cyanotoxin biosynthesis. In this review, we critically examined the genomic organization of some cyanobacterial species that lead to the production of cyanotoxins and their characteristic properties discovered to date.

Dil Biliş İlişkileri ve Dilin Evrimi Üzerine

One can understand the importance of language with its relation to mental activities such as memory and thinking. Language, a crucial human ability, has long attracted the attention of various theorists and philosophers. Language, by its nature, interacts with many biological, cultural and psychological factors. This article has drawn a general framework by bringing together the views from disciplines such as linguistics, psychology, anthropology, biology and neuroscience. On the one hand, while the theoretical opinions about language are included, on the other hand, language is discussed in the context of the changes we went through by separating from our common ancestor in the evolution process. When dealing with language, it is possible to talk about our differences from animals, the interaction of language with our cognitive processes and its organization in the brain. The views put forward by philosophers such as Plato and Descartes about the relationship between language and cognitions have expanded by Chomsky, Pinker, Dunbar and others on the evolution of language. In this article, evolutionary psychology, which strives to understand language and its relationship with cognitions, is emphasized by combining the data of modern evolutionary biology and cognitive psychology. Language is acquired quickly and without the intense need for learning experiences, thanks to innate schemas, suggests that evolution formed these schemas. According to another view, the influence of the environment and culture gains importance instead of innatism. In addition, different opinions on the evolution of language are briefly discussed. Discussion topics include triggers of language development in evolution. These are related to biological and cultural influences, influences of vocalization and hand gestures on language. When thinking about language and its evolution, it is inevitable to observe and examine cognitive processes and thought. Multidisciplinary studies can also provide important information about the evolution of language while trying to understand the complex relationship between language and cognition.

Dispersed differential hunger games search for high dimensional gene data feature selection

The realms of modern medicine and biology have provided substantial data sets of genetic roots that exhibit a high dimensionality. Clinical practice and associated processes are primarily dependent on data-driven decision-making. However, the high dimensionality of the data in these domains increases the complexity and size of processing. It can be challenging to determine representative genes while reducing the data's dimensionality. A successful gene selection will serve to mitigate the computing costs and refine the accuracy of the classification by eliminating superfluous or duplicative features. To address this concern, this research suggests a wrapper gene selection approach based on the HGS, combined with a dispersed foraging strategy and a differential evolution strategy, to form a new algorithm named DDHGS. Introducing the DDHGS algorithm to the global optimization field and its binary derivative bDDHGS to the feature selection problem is anticipated to refine the existing search balance between explorative and exploitative cores. We assess and confirm the efficacy of our proposed method, DDHGS, by comparing it with DE and HGS combined with a single strategy, seven classic algorithms, and ten advanced algorithms on the IEEE CEC 2017 test suite. Furthermore, to further evaluate DDHGS' performance, we compare it with several CEC winners and DE-based techniques of great efficiency on 23 popular optimization functions and the IEEE CEC 2014 benchmark test suite. The experimentation asserted that the bDDHGS approach was able to surpass bHGS and a variety of existing methods when applied to fourteen feature selection datasets from the UCI repository. The metrics measured--classification accuracy, the number of selected features, fitness scores, and execution time--all showed marked improvements with the use of bDDHGS. Considering all results, it can be concluded that bDDHGS is an optimal optimizer and an effective feature selection tool in the wrapper mode.

Deciphering molecular mechanisms of phase separation in RNA biology by single-molecule biophysical technologies.

Ribonucleic acid (RNA) biology has emerged as one of the most important areas in modern biology and biomedicine. RNA and RNA-binding proteins (RBPs) are involved in forming biomolecular condensates, which are crucial for RNA metabolism. To quantitively decipher the molecular mechanisms of RNP granules, researchers have turned to single-molecule biophysical techniques, such as single-molecule Förster resonance energy transfer (smFRET), in vivo single-molecule imaging technique with single particle tracking (SPT), DNA Curtains, optical tweezers, and atomic force microscopy (AFM). These methods are used to investigate the molecular biophysical properties within RNP granules, as well as the molecular interactions between RNA and RBPs and RBPs themselves, which are challenging to study using traditional experimental methods of the liquid-liquid phase separation (LLPS) field, such as fluorescence recovery after photobleaching (FRAP). In this work, we summarize the applications of single-molecule biophysical techniques in RNP granule studies and highlight how these methods can be used to reveal the molecular mechanisms of RNP granules.

Lacanyen Bilinçdışı ve Yeni Medya Estetiği

Contemporary biotechnologies provide an entryway into thinking about bodies and organisms not as natural and biological entities but as informational media, technological apparatuses, instrumental mediums, symbolic systems and coded means of communication, replacing the theories and practices concerning mimetic imitation of life and mechanical reproduction of nature with the semiotic, linguistic, and bioinformatic reproduction of bodies and organisms. This article examines postbiological articulation of bodies, desires, and sexualities at the site of the convergence between Lacanian psychoanalysis and new media aesthetics. It is at the interstices of the connections between information and communication technologies, modern biology, and structural linguistics that Jacques Lacan locates his psychoanalytic conception of the unconscious and desire. The notion of the unconscious as it is mapped by Lacan over structural linguistics’ intrinsic kinship with information and communication technologies enables him to examine desire and sexuality at the site of the convergence between linguistic-informational, biological, and psychoanalytic discourses. This bioinformatic revolution transforms the aesthetic stakes of everyday life by suggesting new ways of thinking about bodies, desires, and sexualities. By drawing on acoustic and visual remappings of the body, fragmented and hybrid bodies, digital desires and sexualities in new media artworks, I analyze the body in contemporary art as a biotechnological apparatus, symbolic system, and discursive and non-discursive mode of communication flowing among various media networks and systems.

Ribozyme activity modulates the physical properties of RNA-peptide coacervates.

Condensed coacervate phases are now understood to be important features of modern cell biology, as well as valuable protocellular models in origin-of-life studies and synthetic biology. In each of these fields, the development of model systems with varied and tuneable material properties is of great importance for replicating properties of life. Here, we develop a ligase ribozyme system capable of concatenating short RNA fragments into long chains. Our results show that the formation of coacervate microdroplets with the ligase ribozyme and poly(L-lysine) enhances ribozyme rate and yield, which in turn increases the length of the anionic polymer component of the system and imparts specific physical properties to the droplets. Droplets containing active ribozyme sequences resist growth, do not wet or spread on unpassivated surfaces, and exhibit reduced transfer of RNA between droplets when compared to controls containing inactive sequences. These altered behaviours, which stem from RNA sequence and catalytic activity, constitute a specific phenotype and potential fitness advantage, opening the door to selection and evolution experiments based on a genotype-phenotype linkage.

Conventional and contemporary approaches for drought tolerance rice breeding: Progress and prospects

AbstractDrought is becoming a major threat to rice farming across the globe owing to the depletion of water tables in rice‐growing belts. Drought affects rice plants at multiple stages, causing damage at morphological and physio‐biochemical levels, leading to severe losses that exceed losses from all other stresses. The amalgamation of conventional breeding methods with modern molecular biology tools and biometrical methods could help accelerate the genetic gain for drought tolerance in rice. Many drought‐tolerance traits with genetic determinants have been identified and exploited for tolerance rice variety breeding. The integration of genome‐wide association study and genomic selection tools with speed breeding shortened the breeding cycle and aided in rapid improvement of genetic gain. In this review, we emphasized the progress made through classical breeding as well as the limitations and usefulness of current genomic methods in improving drought tolerance. We briefly addressed methods for identifying genetic determinants for drought tolerance and deploying them through genomics‐assisted breeding programmes to develop high‐yielding drought‐tolerant rice cultivars.

Solution Structure Ensembles of the Open and Closed Forms of the ∼130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and NMR.

Large-scale interdomain rearrangements are essential to protein function, governing the activity of large enzymes and molecular machineries. Yet, obtaining an atomic-resolution understanding of how the relative domain positioning is affected by external stimuli is a hard task in modern structural biology. Here, we show that combining structural modeling by AlphaFold2 with coarse-grained molecular dynamics simulations and NMR residual dipolar coupling data is sufficient to characterize the spatial domain organization of bacterial enzyme I (EI), a ∼130 kDa multidomain oligomeric protein that undergoes large-scale conformational changes during its catalytic cycle. In particular, we solve conformational ensembles for EI at two different experimental temperatures and demonstrate that a lower temperature favors sampling of the catalytically competent closed state of the enzyme. These results suggest a role for conformational entropy in the activation of EI and demonstrate the ability of our protocol to detect and characterize the effect of external stimuli (such as mutations, ligand binding, and post-translational modifications) on the interdomain organization of multidomain proteins. We expect the ensemble refinement protocol described here to be easily transferrable to the investigation of the structure and dynamics of other uncharted multidomain systems and have assembled a Google Colab page (https://potoyangroup.github.io/Seq2Ensemble/) to facilitate implementation of the presented methodology elsewhere.

Yijung-tang improves thermogenesis and reduces inflammation associated with gut microbiota in hypothyroid rats

Currently, considerable attention is focused on exploring the potential relationship between herbal medicine (HM) and the gut microbiome in terms of thermoregulation, which is an important aspect of human health, in modern system biology. However, our knowledge of the mechanisms of HM in thermoregulation is inadequate. Here, we demonstrate that the canonical herbal formula, Yijung-tang (YJT), protects against hypothermia, hyperinflammation, and intestinal microbiota dysbiosis in PTU-induced hypothyroid rats. Notably, these properties were associated with alterations in the gut microbiota and signaling crosstalk between the thermoregulatory and inflammatory mediators in the small intestine and brown adipose tissue (BAT). In contrast to the conventional drug L-thyroxine for curing hypothyroidism, YJT has an efficacy for attenuating systematic inflammatory responses, related with depression in intestinal TLR4 and Nod2/Pglyrp1 signaling pathways. Our findings suggest that YJT could promote BAT thermogenesis and prevent systemic inflammation in PTU-induced hypothyroid rats, which was associated with its prebiotic effect on modulating of the gut microbiota and gene expression with relevance in the enteroendocrine function and innate immune systems. These findings may strengthen the rationale of the microbiota–gut–BAT axis for a paradigm shift to enable holobiont-centric medicine.

Correlating cryo-super resolution radial fluctuations and dual-axis cryo-scanning transmission electron tomography to bridge the light-electron resolution gap

Visualization of organelles and their interactions with other features in the native cell remains a challenge in modern biology. We have introduced cryo-scanning transmission electron tomography (CSTET), which can access 3D volumes on the scale of 1 micron with a resolution of nanometers, making it ideal for this task. Here we introduce two relevant advances: (a) we demonstrate the utility of multi-color super-resolution radial fluctuation light microscopy under cryogenic conditions (cryo-SRRF), and (b) we extend the use of deconvolution processing for dual-axis CSTET data. We show that cryo-SRRF nanoscopy is able to reach resolutions in the range of 100 nm, using commonly available fluorophores and a conventional widefield microscope for cryo-correlative light-electron microscopy. Such resolution aids in precisely identifying regions of interest before tomographic acquisition and enhances precision in localizing features of interest within the 3D reconstruction. Dual-axis CSTET tilt series data and application of entropy regularized deconvolution during post-processing results in close-to-isotropic resolution in the reconstruction without averaging. The integration of cryo-SRRF with deconvolved dual-axis CSTET provides a versatile workflow for studying unique objects in a cell.

Guest Editorial Special Feature on Quantum Biology

Quantum biology is not a new field of study: as the physicists’ work on foundations of quantum theory matured, the question of linking it with the secrets of living organisms drew more and more attention. It was posed as a natural philosophy question as well, exploring the link of quantum randomness with the competing perceptions of the world, idealist and materialist. It also posed a question to what will later become known as systems theory: is reductionism ever warranted in complex systems? These first thoughts on quantum effects as underlying mechanisms of living organisms predate the modern molecular biology revolution.

Infrastructure and resources for advancing modern biology and biotechnology (NSF)

Federal Grants & ContractsVolume 47, Issue 13 p. 3-3 Grants Alerts Infrastructure and resources for advancing modern biology and biotechnology (NSF) First published: 30 May 2023 https://doi.org/10.1002/fgc.33056Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL No abstract is available for this article. Volume47, Issue131 June 2023Pages 3-3 RelatedInformation