Long-read genome assembly of the insect model organism reveals spread of satellite DNA in gene-rich regions by recurrent burst events.

Eukaryotic genomes are replete with satellite DNAs (satDNAs), large stretches of tandemly repeated sequences that are mostly underrepresented in genome assemblies. Here we combined nanopore long-read sequencing with a reference-guided assembly approach to generate an improved, high-quality genome assembly, TcasONT, of the model beetle Enriched by 45 Mb in repetitive regions, the new assembly comprises almost the entire genome sequence. We use the enhanced assembly to conduct global and in-depth analyses of abundant euchromatic satDNAs.

Novel amino acid distance matrices based on conductance measure.

Ancestral relationships among biological species are often represented and analyzed by means of phylogenetic trees. Substitution and distance matrices are two main types of matrices that are used in phylogeny analyses. Substitution matrices describe a frequency change of amino acids in nucleotide or protein sequence over time, while distance matrices estimate phylogeny using a matrix of pairwise distances based on a particular code or analytical concept.

Quantifying the effects of the mitochondrial genome on milk production traits in dairy cows: Empirical results and modeling challenges.

Substantial advances in livestock traits have been achieved primarily through selection strategies targeting variation in the nuclear genome, with little attention given to mitogenome variation. We analyzed the influence of the mitogenome on milk production traits of Holstein cattle in Croatia based on strategically generated next-generation sequencing data for 109 cows pedigree-linked to 7,115 milk production records (milk, fat, and protein yield) from 3,006 cows (first 5 lactations). Because little is known about the biology of the relationship between mitogenome variation and production traits, our quantitative genetic modeling was complex.

Histochemical Analysis and Distribution of Digestive Enzymes in the Gastrointestinal System of the European Barracuda (Linnaeus, 1758).

In this study, we examined the gastrointestinal tract of the European barracuda () living in the Adriatic Sea near Dubrovnik, Croatia. The study aimed to identify the presence and distribution of four digestive enzymes: alkaline phosphatase, aminopeptidase, acid phosphatase, and non-specific esterase. We found that alkaline phosphatase activity was present in the brush border of the enterocytes in all the investigated intestinal segments.

Metal-Free C-X Functionalization in Solid-State via Photochemistry in Ball Mills.

We report the first metal- and catalyst-free protocol for the facile cross-coupling of aryl halides towards C-B, C-P and C-S bonds under solid-state ball milling conditions via UV light irradiation. The reactions can be performed in the absence of bulk solvents at room temperature in a mixer mill, yielding up to 99 % and being tolerant towards various functionalized aryl halides (X=I or Br). Furthermore, we developed a novel photoreactor design increasing the light intensity.

Cyclin C promotes development and progression of B-cell acute lymphoblastic leukemia by counteracting p53-mediated stress responses.

Despite major therapeutic advances in the treatment of acute lymphoblastic leukemia (ALL), resistances and long-term toxicities still pose significant challenges. Cyclins and their associated cyclin-dependent kinases are one focus of cancer research when looking for targeted therapies. We discovered cyclin C as a key factor for B-ALL development and maintenance.

Fundamental data for modeling electron-induced processes in plasma remediation of perfluoroalkyl substances.

Plasma treatment of per- and polyfluoroalkyl substances (PFAS) contaminated water is a potentially energy efficient remediation method. In this treatment, an atmospheric pressure plasma interacts with surface-resident PFAS molecules. Developing a reaction mechanism and modeling of plasma-PFAS interactions requires fundamental data for electron-molecule reactions.

Beach wracks microbiome and its putative function in plastic polluted Mediterranean marine ecosystem.

The coasts of the world's oceans and seas accumulate various types of floating debris, commonly known as beach wracks, including organic seaweeds, seagrass, and ubiquitous anthropogenic waste, mainly plastic. Beach wrack microbiome (MB), surviving in the form of a biofilm, ensures decomposition and remineralization of wracks, but can also serve as a vector of potential pathogens in the environment. Through the interdisciplinary approach and comprehensive sampling design that includes geological analysis of the sediment, plastic debris composition analysis (ATR-FTIR) and application of 16S rRNA gene metabarcoding of beach wrack MBs, this study aims to describe MB in relation to beach exposure, sediment type and plastic pollution.

A Strategy for Modeling Nonstatistical Reactivity Effects: Combining Chemical Activation Estimates with a Vibrational Relaxation Model.

The kinetics of many chemical reactions can be readily explained with a statistical approach, for example, using a form of transition state theory and comparing calculated Gibbs energies along the reaction coordinate(s). However, there are cases where this approach fails, notably when the vibrational relaxation of the molecule to its statistical equilibrium occurs on the same time scale as the reaction dynamics, whether it is caused by slow relaxation, a fast reaction, or both. These nonstatistical phenomena are then often explored computationally using (quasi)classical ab initio molecular dynamics by calculating a large number of trajectories while being prone to issues such as zero-point energy leakage.

Longer Telomere Length in Patients with Balkan Endemic Nephropathy Undergoing Chronic Hemodialysis Is Associated with Lower Cardiovascular Mortality.

Key Points: Longer telomeres are associated with less cardiovascular mortality in patients undergoing chronic hemodialysis. In patients with Balkan endemic nephropathy, telomere length was negatively associated with arterial stiffness and positively associated with survival. The association of Balkan endemic nephropathy with slower vascular aging and longer telomere length may partially explain this phenomenon.

Characterization of Anticancer Drug Protomers Using Electrospray Ionization and Ion Mobility Spectrometry-Mass Spectrometry.

We used electrospray ionization and ion mobility spectrometry-mass spectrometry to detect and characterize the three anticancer drugs palbociclib, copanlisib, and olaparib. Ion mobility-mass spectrometry and density functional theory revealed that these compounds generate isomers during ionization (protomers) due to the presence of multiple protonation sites within their chemical structures. Our work has implications for understanding the solution- and gas-phase chemistry of these molecules during spray-based ionization processes.

Virulence Factors and Susceptibility to Ciprofloxacin, Vancomycin, Triclosan, and Chlorhexidine among Enterococci from Clinical Specimens, Food, and Wastewater.

and are opportunistic pathogens commonly found in the microbiota of humans and other animals as well as in the environment. This article presents the results of antimicrobial susceptibility testing using phenotypic methods (broth microdilution and standardized disk diffusion) on selected clinical, food, and wastewater isolates of and The isolates were divided into subgroups based on their sensitivity to the following antibiotics: vancomycin (VAN) and ciprofloxacin (CIP), and biocides triclosan (TCL) and chlorhexidine (CHX). The study also investigated in vitro virulence factors, including biofilm formation ability, cell surface hydrophobicity (CSH) and β-hemolysis, to explore aspects of pathogenesis.

Editorial for the Special Issue "Satellite DNA Genomics".

A significant portion of eukaryotic genomes consists of non-coding repetitive DNA sequences arranged in tandem arrays, known as satellite DNA (satDNA) [...

Inhibition of Oxidative Stress and Related Signaling Pathways in Neuroprotection.

Oxidative stress, characterized by increased production of reactive oxygen species (ROS) and disturbed redox homeostasis, is one of the key mechanisms underlying synaptic loss and neuronal death in various neurodegenerative diseases [...

Nationwide evaluation of treatment outcomes and survival of patients with non-tuberculous mycobacterial pulmonary disease.

Treatment outcomes and long-term survival of non-tuberculous mycobacterial pulmonary disease (NTM-PD) in a real-world setting are difficult to assess, especially for species other than complex (MAC).This was a retrospective cohort study on all Croatian residents with respiratory NTM isolates from 2006 to 2015, with follow-up to 2020.Therapy was started in 98/137 (71.