BAC-browser: the tool for synthetic biology.

Background: Currently, synthetic genomics is a rapidly developing field. Its main tasks, such as the design of synthetic sequences and the assembly of DNA sequences from synthetic oligonucleotides, require specialized software. In this article, we present a program with a graphical interface that allows non-bioinformatics to perform the tasks needed in synthetic genomics.

High-pressure and low-temperature behaviour of organic ferroelectric (R)-3-quinuclidinol.

High-pressure and low-temperature structural changes in the ferroelectric phase of (R)-3-quinuclidinol are analysed. The changes in unit-cell volume and parameters are continuous both on cooling and under increasing pressure. The anisotropy of the structural strain, however, is found to be different.

Impact of Gene Knockout on Cell Aggregation in Suspension Culture.

The development of efficient producers of recombinant pharmaceuticals based on plant cell suspension cultures is a pressing challenge in modern applied science. A primary limitation of plant cell cultures is their relatively low yield of the target protein. One strategy to enhance culture productivity involves reducing cell aggregation.

Reducing the Formation of Toxic Byproducts During the Photochemical Release of Epinephrine.

Engineered light-sensitive molecules offer a sophisticated toolkit for the manipulation of biological systems with both spatial and temporal precision. Notably, artificial "caged" compounds can activate specific receptors solely in response to light exposure. However, the uncaging process can lead to the formation of potentially harmful byproducts.

Bimodal Patterns of Locomotor Activity and Sleep in : A Model for Their Simulation.

Purpose: Two previously proposed modelling approaches to explain the bimodal pattern of activity and/or sleep in are based on 1) the concept of morning and evening oscillators underlying the peaks of activity in the morning and evening, respectively, and 2) the concept of two cycles of buildup and decay of sleep pressure, gated only by the circadian oscillator. Previously, we simulated 24-h alertness-sleepiness curves in humans using a model postulating the circadian modulation of the buildup and decay phases of two (wake and sleep) homeostatic processes. Here, we tested whether a similar model could be applied to simulate the bimodal 24-h rhythm of fly locomotor activity and sleep.

Metabolomic and gene networks approaches reveal the role of mitochondrial membrane proteins in response of human melanoma cells to THz radiation.

Terahertz (THz) radiation has gained attention due to technological advancements, but its biological effects remain unclear. We investigated the impact of 2.3 THz radiation on SK-MEL-28 cells using metabolomic and gene network analysis.

Detection of cervical precancerous lesions and cancer by small-scale RT-qPCR analysis of oppositely deregulated mRNAs pairs in cytological smears.

Background: Cervical screening, aimed at detecting precancerous lesions and preventing cancer, is based on cytology and HPV testing. Both methods have limitations, the main ones being the variable diagnostic sensitivity of cytology and the moderate specificity of HPV testing. Various molecular biomarkers are proposed in recent years to improve cervical cancer management, including a number of mRNAs encoded by human genes involved in carcinogenesis.

The freeze-thaw cycle effect on blood serum autofluorescence, Raman spectroscopy and SERS: implications for sample classification and disease diagnostics.

The issue of variability introduced into blood plasma and serum analysis by preanalytical procedures is the major obstacle to obtaining accurate and reproducible results. While the question of how to overcome this issue has been discussed in biochemical detection of analytes and omics technologies, its relevance to the field of optical spectroscopy remains mostly unexplored. In this work, we evaluated the freeze-thaw cycle (FTC)-induced alternations in blood serum optical properties by means of autofluorescence and Raman spectroscopy, including surface-enhanced Raman spectroscopy (SERS).

Analyzing aptamer structure and interactions: in silico modelling and instrumental methods.

Aptamers are short oligonucleotides that bind specifically to various ligands and are characterized by their low immunogenicity, thermostability, and ease of labeling. Many biomedical applications of aptamers as biosensors and drug delivery agents are currently being actively researched. Selective affinity selection with exponential ligand enrichment (SELEX) allows to discover aptamers for a specific target, but it only provides information about the sequence of aptamers; hence other approaches are used for determining aptamer structure, aptamer-ligand interactions and the mechanism of action.

Morpho-physiological digestive features of genetically closely related sympatric lacustrine whitefish forms with different feeding habits.

The effect of different feeding habits on gut morphology and digestive function has been intensively studied during the last decades but sympatric closely related fishes are relatively rare objects of such studies. In the present study, we have identified both morphological and physiological changes in the digestive system of a sympatric pair of whitefish represented by "normal" Coregonus lavaretus pidschian (benthivorous) and "dwarf" C. l.

β-Diketonate Coordination: Vibrational Properties, Electronic Structure, Molecular Topology, and Intramolecular Interactions. Beryllium(II), Copper(II), and Lead(II) as Study Cases.

Nine metal complexes formed by three symmetric β-diketonates (, acetylacetonate (), 1,1,1,3,3,3-hexafluoro-acetylacetonate (), and 2,2,6,6-tetramethylheptane-3,5-dionate ()) and three metal ions (with three different coordination geometries, , Be - tetrahedral, Cu - square planar, and Pb - "swing" square pyramidal) were investigated. The study combines structural analyses, vibrational spectroscopic techniques, and quantum chemical calculations with the aim of bridging crystal structure, electronic structure, molecular topology, and far-infrared (FIR) spectroscopic characteristics. The effect of intramolecular interactions on the structural, electronic, and spectroscopic features is the center of this study.

Infrared photoresponse of GeSiSn p-i-n photodiodes based on quantum dots, quantum wells, pseudomorphic and relaxed layers.

Structural and photoelectric properties of p-i-n photodiodes based on GeSiSn/Si multiple quantum dots both on Si and silicon-on-insulator (SOI) substrates were investigated. Elastic strained state of grown films was demonstrated by x-ray diffractometry. Annealing of p-i-n structures before the mesa fabrication can improve the ideality factor of current-voltage characteristics.

GENA-LM: a family of open-source foundational DNA language models for long sequences.

Recent advancements in genomics, propelled by artificial intelligence, have unlocked unprecedented capabilities in interpreting genomic sequences, mitigating the need for exhaustive experimental analysis of complex, intertwined molecular processes inherent in DNA function. A significant challenge, however, resides in accurately decoding genomic sequences, which inherently involves comprehending rich contextual information dispersed across thousands of nucleotides. To address this need, we introduce GENA language model (GENA-LM), a suite of transformer-based foundational DNA language models capable of handling input lengths up to 36 000 base pairs.

Safety and Efficacy of Tranexamic Acid in General Surgery.

Importance: Perioperative bleeding is common in general surgery. The POISE-3 (Perioperative Ischemic Evaluation-3) trial demonstrated efficacy of prophylactic tranexamic acid (TXA) compared with placebo in preventing major bleeding without increasing vascular outcomes in noncardiac surgery.

Objective: To determine the safety and efficacy of prophylactic TXA, specifically in general surgery.

A comprehensive dataset and neural network approach for named entity recognition in the Uzbek language.

In this study, the authors presented a dataset for named entity recognition in the Uzbek language. The dataset consists of 2000 sentences and 25,865 words, and the sources were legal documents and hand-crafted sentences annotated using the BIOES scheme. The study is complemented by the fact that the authors demonstrated the applications of the created dataset by training a language model using the CNN + LSTM architecture, which achieves high accuracy in NER tasks, with an F1 score of 90.

Double kissing crush versus culotte for bifurcation percutaneous coronary interventions: insights from the PROGRESS-BIFURCATION registry.

Background: Upfront 2-stent techniques are often used in bifurcation percutaneous coronary interventions (PCI), but there is controversy about optimal strategy selection.

Methods: The authors examined the clinical and angiographic characteristics and long-term outcomes of 232 bifurcation PCIs that were performed using the double kissing (DK) crush or culotte technique in 216 patients between 2014 and 2023 using data from the Prospective Global Registry for the Study of Bifurcation Lesion Interventions (NCT05100992). The inverse probability of treatment weighted (IPTW) Cox proportional hazards model was used to assess long-term outcomes.

Infrared photoresponse of GeSiSn p-i-n photodiodes based on quantum dots, quantum wells, pseudomorphic and relaxed layers.

Structural and photoelectric properties of p-i-n photodiodes based on GeSiSn/Si multiple quantum dots both on Si and silicon-on-insulator (SOI) substrates were investigated. Elastic strained state of grown films was demonstrated by x-ray diffractometry. Annealing of p-i-n structures before the mesa fabrication can improve the ideality factor of current-voltage characteristics.

Laser-Induced Olfactory Bulbectomy in Adult Zebrafish as a Novel Putative Model for Affective Syndrome: A Research Tribute to Brian Leonard.

Inducing multiple neurobehavioural and neurochemical deficits, olfactory bulbectomy (OBX) has been developed as a rodent model of depression with potential for antidepressant drug screening. However, the generality of this model in other vertebrate taxa remains poorly understood. A small freshwater teleost fish, the zebrafish (Danio rerio), is rapidly becoming a common model species in neuroscience research.

Epidemiology of Mucopolysaccharidosis Type II According to the Register of the Russian Federation.

Objective: The study aimed to evaluate the epidemiological, clinical, and molecular data of mucopolysaccharidosis type II (MPS II) patients and their outcomes using the national registry of patients in the Russian Federation (RF). Materials and Methods: In the retrospective cohort study, the authors included data from the Russian national registry of MPS II. Results: The prevalence of MPS II in RF is 0.

Deregulation mechanisms and therapeutic opportunities of p53-responsive microRNAs in diffuse large B-cell lymphoma.

Here, we have discussed the molecular mechanisms of p53-responsive microRNAs dysregulation in response to genotoxic stress in diffuse large B-cell lymphoma (DLBCL) patients. The role of micro ribonucleic acids (microRNAs) in p53-signaling cellular stress has been studied. MicroRNAs are the small non-coding RNAs, which regulate genes expression at post-transcriptional level.

Design, synthesis, and evaluation of dehydroabietyl imidazolidine-2,4-diones, 2,4,5-triones, and 2-thioxoimidazolidine-4,5-diones as TDP1 inhibitors and dual TDP1/TDP2 inhibitors.

Tyrosyl DNA phosphodiesterases 1 and 2 (TDP1 and TDP2), which are enzymes involved in the repair of DNA, are regarded as promising targets for the development of new anticancer drugs. In this study, a series of imidazolidine-2,4-diones, 2,4,5-triones, and 2-thioxoimidazolidine-4,5-diones based on dehydroabietylamine (DHAAm) were synthesized. The inhibitory activity of the new compounds against TDP1 and TDP2, as well as their cytotoxic characteristics, were evaluated.

Variability of microbiomes in winter rye, wheat, and triticale affected by snow mold: predicting promising microorganisms for the disease control.

Background: Snow mold caused by different psychrophilic phytopathogenic fungi is a devastating disease of winter cereals. The variability of the snow mold pathocomplex (the quantitative composition of snow mold fungi) has not been evaluated across different crops or different agrocenoses, and no microbial taxa have been predicted at the whole-microbiome level as potential effective snow mold control agents. Our study aimed to assess the variability of the snow mold pathocomplex in different winter cereal crops (rye, wheat, and triticale) in different agrocenoses following the peak disease progression and to arrange a hierarchical list of microbial taxa predicted to be the main candidates to prevent or, conversely, stimulate the development of snow mold pathogens.

Phase transitions, Dirac and Weyl semimetal states in MnGeBiTe.

Using angle-resolved photoemission spectroscopy (ARPES) and density functional theory (DFT), an experimental and theoretical study of changes in the electronic structure (dispersion dependencies) and corresponding modification of the energy band gap at the Dirac point (DP) for topological insulator (TI) [Formula: see text] have been carried out with gradual replacement of magnetic Mn atoms by non-magnetic Ge atoms when concentration of the latter was varied from 10% to 75%. It was shown that when Ge concentration increases, the bulk band gap decreases and reaches zero plateau in the concentration range of 45-60% while trivial surface states (TrSS) are present and exhibit an energy splitting of 100 and 70 meV in different types of measurements. It was also shown that TSS disappear from the measured band dispersions at a Ge concentration of about 40%.

Synthesis and exploration of anticancer potential of spirocyclic 1,2,3-triazoline and aziridine derivatives of natural eudesmanolide isoalantolactone.

Eudesmane-type sesquiterpene lactone isoalantolactone 1 is of great interest due to its availability, biological activity and synthetic application. Respective series of original spirocyclic (11S,5') (1,2,3-triazoline-eudesma-4,15-enolides) and (11S)-aziridine-eudesma-4,15-enolides were efficiently synthesized via a chemoselective 1,3-dipolar cycloaddition reaction of organic azides to the exocyclic double bond of the lactone ring of isoalantolactone or 13E-(aryl)isoalantolactones by heating in DMF or toluene. The thermal reactions of isoalantolactone with benzyl azide, 2-azidoethanol, or n-butyl azide in 2-methoxyethanol afforded 13-(alkyamino)isoalantolactones formed as a mixture of (Z) and (E)-isomers.

The influence of the dry ashing procedure on the correctness of Pb determination in lichens and mosses.

Mosses and lichens are often used to assess atmospheric deposition of Pb. The most widely used method for determining this isotope is gamma spectrometric analysis. There is often a need to enhance the sensitivity of the method, which can be achieved by pre-concentrating Pb.