Dynamics of karyotype evolution.

In the evolution of species, the karyotype changes with a timescale of tens to hundreds of thousand years. In the development of cancer, the karyotype often is modified in cancerous cells over the lifetime of an individual. Characterizing these changes and understanding the mechanisms leading to them has been of interest in a broad range of disciplines including evolution, cytogenetics, and cancer genetics.

Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring.

The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. Analysis of The Cancer Genome Atlas data shows recurrent deletion of chr4p in basal breast cancer.

Trans-regulatory variant network contributes to missing heritability.

In a recent Cell Genomics article, Tsouris et al. analyze the transcriptomes of a large diallel panel of hybrids from Saccharomyces cerevisiae natural isolates to study cis- and trans-regulatory changes underlying gene expression variation. Vanessa Pereira and Elena Kuzmin discuss the authors' findings and the wider context in missing heritability research in this preview.

Single-cell imaging of protein dynamics of paralogs reveals mechanisms of gene retention.

Gene duplication is common across the tree of life, including yeast and humans, and contributes to genomic robustness. In this study, we examined changes in the subcellular localization and abundance of proteins in response to the deletion of their paralogs originating from the whole-genome duplication event, which is a largely unexplored mechanism of functional divergence. We performed a systematic single-cell imaging analysis of protein dynamics and screened subcellular redistribution of proteins, capturing their localization and abundance changes, providing insight into forces determining paralog retention.

Closest horizons of Hsp70 engagement to manage neurodegeneration.

Our review seeks to elucidate the current state-of-the-art in studies of 70-kilodalton-weighed heat shock proteins (Hsp70) in neurodegenerative diseases (NDs). The family has already been shown to play a crucial role in pathological aggregation for a wide spectrum of brain pathologies. However, a slender boundary between a big body of fundamental data and its implementation has only recently been crossed.

Productivity of Concentration-Dependent Conversion of Substitutional Nitrogen Atoms into Nitrogen-Vacancy Quantum Emitters in Synthetic-Diamond by Ultrashort Laser Pulses.

Tightly focused 515-nm, 0.3-ps laser pulses modify in a laser filamentation regime the crystalline structure of an Ib-type high-pressure, high-temperature (HPHT) synthesized diamond in a thin-plate form. The modified microregions (micromarks) in the yellow and colorless crystal zones, possessing different concentrations of elementary substitutional nitrogen (N) impurity atoms (C-centers), exhibit their strongly diminished local IR absorption (upon correction to the thickness scaling factor).

Photoluminescent Microbit Inscripion Inside Dielectric Crystals by Ultrashort Laser Pulses for Archival Applications.

Inscription of embedded photoluminescent microbits inside micromechanically positioned bulk natural diamond, LiF and CaF crystals was performed in sub-filamentation (geometrical focusing) regime by 525 nm 0.2 ps laser pulses focused by 0.65 NA micro-objective as a function of pulse energy, exposure and inter-layer separation.

Hierarchical Surface Structures and Large-Area Nanoscale Gratings in AsS and AsSe Films Irradiated with Femtosecond Laser Pulses.

Chalcogenide vitreous semiconductors (ChVSs) find application in rewritable optical memory storage and optically switchable infrared photonic devices due to the possibility of fast and reversible phase transitions, as well as high refractive index and transmission in the near- and mid-infrared spectral range. Formed on such materials, laser-induced periodic surface structures (LIPSSs), open wide prospects for increasing information storage capacity and create polarization-sensitive optical elements of infrared photonics. In the present work, a possibility to produce LIPSSs under femtosecond laser irradiation (pulse duration 300 fs, wavelength 515 nm, repetition rate up to 2 kHz, pulse energy ranged 0.

Multi-Parametric Birefringence Control in Ultrashort-Pulse Laser-Inscribed Nanolattices in Fluorite.

An ultrashort-pulse laser inscription of embedded birefringent microelements was performed inside bulk fluorite in pre-filamentation (geometrical focusing) and filamentation regimes as a function of laser wavelength, pulsewidth and energy. The resulting elements composed of anisotropic nanolattices were characterized by retardance () and thickness () quantities, using polarimetric and 3D-scanning confocal photoluminescence microscopy, respectively. Both parameters exhibit a monotonous increase versus pulse energy, going over a maximum at 1-ps pulsewidth at 515 nm, but decrease versus laser pulsewidth at 1030 nm.

Nanoscale Vacancy-Mediated Aggregation, Dissociation, and Splitting of Nitrogen Centers in Natural Diamond Excited by Visible-Range Femtosecond Laser Pulses.

Natural IaA+B diamonds were exposed in their bulk by multiple 0.3 ps, 515 nm laser pulses focused by a 0.25 NA micro-objective, producing in the prefocal region (depth of 20-50 μm) a bulk array of photoluminescent nanostructured microtracks at variable laser exposures and pulse energies.

"Stealth Scripts": Ultrashort Pulse Laser Luminescent Microscale Encoding of Bulk Diamonds via Ultrafast Multi-Scale Atomistic Structural Transformations.

The ultrashort-laser photoexcitation and structural modification of buried atomistic optical impurity centers in crystalline diamonds are the key enabling processes in the fabrication of ultrasensitive robust spectroscopic probes of electrical, magnetic, stress, temperature fields, and single-photon nanophotonic devices, as well as in "stealth" luminescent nano/microscale encoding in natural diamonds for their commercial tracing. Despite recent remarkable advances in ultrashort-laser predetermined generation of primitive optical centers in diamonds even on the single-center level, the underlying multi-scale basic processes, rather similar to other semiconductors and dielectrics, are almost uncovered due to the multitude of the involved multi-scale ultrafast and spatially inhomogeneous optical, electronic, thermal, and structural elementary events. We enlighten non-linear wavelength-, polarization-, intensity-, pulsewidth-, and focusing-dependent photoexcitation and energy deposition mechanisms in diamonds, coupled to the propagation of ultrashort laser pulses and ultrafast off-focus energy transport by electron-hole plasma, transient plasma- and hot-phonon-induced stress generation and the resulting variety of diverse structural atomistic modifications in the diamond lattice.

Hierarchical Multi-Scale Coupled Periodical Photonic and Plasmonic Nanopatterns Inscribed by Femtosecond Laser Pulses in Lithium Niobate.

The ultrafast interaction of tightly focused femtosecond laser pulses with bulk dielectric media in direct laser writing (inscription) regimes is known to proceed via complex multi-scale light, plasma and material modification nanopatterns, which are challenging for exploration owing to their mesoscopic, transient and buried character. In this study, we report on the first experimental demonstration, analysis and modeling of hierarchical multi-period coupled longitudinal and transverse nanogratings in bulk lithium niobate inscribed in the focal region by 1030 nm, 300 fs laser pulses in the recently proposed sub-filamentary laser inscription regime. The longitudinal Bragg-like topography nanogratings, possessing the laser-intensity-dependent periods ≈ 400 nm, consist of transverse birefringent nanogratings, which are perpendicular to the laser polarization and exhibit much smaller periods ≈ 160 nm.

Up/Down-Scaling Photoluminescent Micromarks Written in Diamond by Ultrashort Laser Pulses: Optical Photoluminescent and Structural Raman Imaging.

Elongated photoluminescent micromarks were inscribed inside a IaAB-type natural diamond in laser filamentation regime by multiple 515 nm, 0.3 ps laser pulses tightly focused by a 0.25 NA micro-objective.

Correspondence between gene expression and neurotransmitter receptor and transporter density in the human brain.

Neurotransmitter receptors modulate signaling between neurons. Thus, neurotransmitter receptors and transporters play a key role in shaping brain function. Due to the lack of comprehensive neurotransmitter receptor/transporter density datasets, microarray gene expression measuring mRNA transcripts is often used as a proxy for receptor densities.

Structural changes of erythrocyte membrane revealed by 3D confocal optical profilometer.

We examined hematological changes influenced by the experimental hypervitaminosis A. The 3D confocal optical profilometer was applied for assessment of the erythrocytes' membrane structural changes influenced by an overdose of vitamin A. The blood smears were evaluated in terms of alterations of geometrical and optical parameters of erythrocytes for two groups of animals: oil base and retinol palmitate (n = 9 animals for each group).

Pulse-width-dependent critical power for self-focusing of ultrashort laser pulses in bulk dielectrics.

Microscale filamentation of 0.25 NA-focused, linearly and circularly polarized 1030 nm and 515 nm ultrashort laser pulses of variable pulse widths in fused silica, fluorite, and natural and synthetic diamonds demonstrates the Raman-Kerr effect in the form of critical pulse power magnitudes, proportional to squared wavelength and inversely proportional to laser pulse width of 0.3-10 ps.

Endosomal LC3C-pathway selectively targets plasma membrane cargo for autophagic degradation.

Autophagy selectively targets cargo for degradation, yet mechanistic understanding remains incomplete. The ATG8-family plays key roles in autophagic cargo recruitment. Here by mapping the proximal interactome of ATG8-paralogs, LC3B and LC3C, we uncover a LC3C-Endocytic-Associated-Pathway (LEAP) that selectively recruits plasma-membrane (PM) cargo to autophagosomes.

THE EVOLVING IDEA OF "HEALTH" IN THE LEGAL LANDSCAPE: AN ATTEMPT TO IDENTIFY CRITICAL ASPECTS.

Objective: The aim: The overall purpose of the research is to shed light on the evolving understanding of the concept of "health" in the legal field, attempting to identify its critical aspects.

Patients And Methods: Materials and methods: The study constitutes a comprehensive analysis of a large number of scholarly publications and international legal provisions through the prism of the principles of concreteness and objectivity, coupled with methodological pluralism, including both philosophical, general scientific, theoretical, general, and special legal research methods.

Conclusion: Conclusions: Considering the evolving idea of "health" in the legal landscape, it is noted that, in the current context, "health" should be perceived both as an individual and a collective feature, as well as the substance, legal right, and a state's obligation.

Biodiversity of a boreal mire, including its hydrographic network (Shichengskoe mire, north-western Russia).

Background: The paper is based on the dataset whose purpose was to deliver, in the form of GBIF-mediated data, diverse materials on the biodiversity of a large mire, Shichengskoe mire (Vologda Region, north-western Russia), including its various mire sites and intra-mire water bodies. The dataset was based on our materials collected for two decades (from 2000 to 2021) in different parts and biotopes of the Shichengskoe mire and complemented by scarce data obtained previously by other researchers. The data contain materials on the diversity of Animalia (2886 occurrences), Bacteria (22), Chromista (256), Fungi (111), Plantae (2463) and Protozoa (131).

Inferring Copy Number from Triple-Negative Breast Cancer Patient Derived Xenograft scRNAseq Data Using scCNA.

Cancer can develop from an accumulation of alterations, some of which cause a nonmalignant cell to transform to a malignant state exhibiting increased rate of cell growth and evasion of growth suppressive mechanisms, eventually leading to tissue invasion and metastatic disease. Triple-negative breast cancers (TNBC) are heterogeneous and are clinically characterized by the lack of expression of hormone receptors and human epidermal growth factor receptor 2 (HER2), which limits its treatment options. Since tumor evolution is driven by diverse cancer cell populations and their microenvironment, it is imperative to map TNBC at single-cell resolution.

Retention of duplicated genes in evolution.

Gene duplication is a prevalent phenomenon across the tree of life. The processes that lead to the retention of duplicated genes are not well understood. Functional genomics approaches in model organisms, such as yeast, provide useful tools to test the mechanisms underlying retention with functional redundancy and divergence of duplicated genes, including fates associated with neofunctionalization, subfunctionalization, back-up compensation, and dosage amplification.

Trigenic Synthetic Genetic Array (τ-SGA) Technique for Complex Interaction Analysis.

Complex genetic interactions occur when mutant alleles of multiple genes combine to elicit an unexpected phenotype, which could not be predicted given the expectation based on the combination of phenotypes associated with individual mutant alleles. Trigenic Synthetic Genetic Array (τ-SGA) methodology was developed for the systematic analysis of complex interactions involving combinations of three gene perturbations. With a series of replica pinning steps of the τ-SGA procedure, haploid triple mutants are constructed through automated mating and meiotic recombination.

τ-SGA: synthetic genetic array analysis for systematically screening and quantifying trigenic interactions in yeast.

Systematic complex genetic interaction studies have provided insight into high-order functional redundancies and genetic network wiring of the cell. Here, we describe a method for screening and quantifying trigenic interactions from ordered arrays of yeast strains grown on agar plates as individual colonies. The protocol instructs users on the trigenic synthetic genetic array analysis technique, τ-SGA, for high-throughput screens.

Exploring whole-genome duplicate gene retention with complex genetic interaction analysis.

Whole-genome duplication has played a central role in the genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated, and factors that influence the retention of persisting duplicates remain poorly understood. We describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event.