ChannelsDB: database of biomacromolecular tunnels and pores

ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

The centromere is a functional chromosome domain that is essential for faithful chromosome segregation during cell division and that can be reliably identified by the presence of the centromere-specific histone H3 variant CenH3. In monocentric chromosomes, the centromere is characterized by a single CenH3-containing region within a morphologically distinct primary constriction. This region usually spans up to a few Mbp composed mainly of centromere-specific satellite DNA common to all chromosomes of a given species. In holocentric chromosomes, there is no primary constriction; the centromere is composed of many CenH3 loci distributed along the entire length of a chromosome. Using correlative fluorescence light microscopy and high-resolution electron microscopy, we show that pea (Pisum sativum) chromosomes exhibit remarkably long primary constrictions that contain 3-5 explicit CenH3-containing regions, a novelty in centromere organization. In addition, we estimate that the size of the chromosome segment delimited by two outermost domains varies between 69 Mbp and 107 Mbp, several factors larger than any known centromere length. These domains are almost entirely composed of repetitive DNA sequences belonging to 13 distinct families of satellite DNA and one family of centromeric retrotransposons, all of which are unevenly distributed among pea chromosomes. We present the centromeres of Pisum as novel ``meta-polycentric'' functional domains. Our results demonstrate that the organization and DNA composition of functional centromere domains can be far more complex than previously thought, do not require single repetitive elements, and do not require single centromere domains in order to segregate properly. Based on these findings, we propose Pisum as a useful model for investigation of centromere architecture and the still poorly understood role of repetitive DNA in centromere evolution, determination, and function

Symposium Report The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function

ABSTRACT This symposium summary, sponsored by the ASPET, was held at Experimental Biology 2015 on March 29, 2015, in Boston, Massachusetts. The symposium focused on: 1) the interactions of cytochrome P450s (P450s) with their redox partners; and 2) the role of the lipid membrane in their orientation and stabilization. Two presentations discussed the interactions of P450s with NADPH-P450 reductase (CPR) and cytochrome b 5 . First, solution nuclear magnetic resonance was used to compare the protein interactions that facilitated either the hydroxylase or lyase activities of CYP17A1. The lyase interaction was stimulated by the presence of b 5 and 17a-hydroxypregnenolone, whereas the hydroxylase reaction was predominant in the absence of b 5 . The role of b 5 was also shown in vivo by selective hepatic knockout of b 5 from mice expressing CYP3A4 and CYP2D6; the lack of b 5 caused a decrease in the clearance of several substrates. The role of the membrane on P450 orientation was examined using computational methods, showing that the proximal region of the P450 molecule faced the aqueous phase. The distal region, containing the substrate-access channel, was associated with the membrane. The interaction of NADPH-P450 reductase (CPR) with the membrane was also described, showing the ability of CPR to "helicopter" above the membrane. Finally, the endoplasmic reticulum (ER) was shown to be heterogeneous, having ordered membrane regions containing cholesterol and more disordered regions. Interestingly, two closely related P450s, CYP1A1 and CYP1A2, resided in different regions of the ER. The structural characteristics of their localization were examined. These studies emphasize the importance of P450 protein organization to their function

<scp>ReSurveyEurope</scp>: A database of resurveyed vegetation plots in Europe

AbstractAimsWe introduce ReSurveyEurope — a new data source of resurveyed vegetation plots in Europe, compiled by a collaborative network of vegetation scientists. We describe the scope of this initiative, provide an overview of currently available data, governance, data contribution rules, and accessibility. In addition, we outline further steps, including potential research questions.ResultsReSurveyEurope includes resurveyed vegetation plots from all habitats. Version 1.0 of ReSurveyEurope contains 283,135 observations (i.e., individual surveys of each plot) from 79,190 plots sampled in 449 independent resurvey projects. Of these, 62,139 (78%) are permanent plots, that is, marked in situ, or located with GPS, which allow for high spatial accuracy in resurvey. The remaining 17,051 (22%) plots are from studies in which plots from the initial survey could not be exactly relocated. Four data sets, which together account for 28,470 (36%) plots, provide only presence/absence information on plant species, while the remaining 50,720 (64%) plots contain abundance information (e.g., percentage cover or cover–abundance classes such as variants of the Braun‐Blanquet scale). The oldest plots were sampled in 1911 in the Swiss Alps, while most plots were sampled between 1950 and 2020.ConclusionsReSurveyEurope is a new resource to address a wide range of research questions on fine‐scale changes in European vegetation. The initiative is devoted to an inclusive and transparent governance and data usage approach, based on slightly adapted rules of the well‐established European Vegetation Archive (EVA). ReSurveyEurope data are ready for use, and proposals for analyses of the data set can be submitted at any time to the coordinators. Still, further data contributions are highly welcome.</jats:sec

Czech mortgage market: The analysis of the products used for housing finance

Cílem této diplomové práce je podat podrobný a ucelený přehled o českém hypotečním trhu a analyzovat nákladovost vybraných hypotečních produktů. První dvě kapitoly práce jsou ryze teoretické. Cílem těchto kapitol je poskytnout základní vymezení hypotečního úvěru, stručně popsat historii českého hypotečního trhu a konečně podrobněji přiblížit základní charakteristiky hypotečního úvěru, jako je úroková sazba, splácení apod. Poslední dvě kapitoly práce obsahují analýzu českého hypotečního trhu a dále analýzu vybraných produktů dvou českých bank.The aim of this thesis is to give a detailed and complete description of the Czech mortgage market and to analyse the costs of the selected mortgage products. The first two chapters are rather theoretical. The aim of the chapters is to provide the reader with the basic definition of the mortgage, briefly describe the history of the Czech mortgage market and finally to provide the detailed description of basic characteristics of the mortgages such as interest rate, repayments etc. The last two chapters analyse the Czech mortgage market an also the selected products of two Czech banks

Zpracování studie pro projektovou žádost v rámci programu POVEZ II

The aim of this bachelor thesis is to elaborate a study concerning the project application in program called Support of professional education for employees (POVEZ II). The theoretical part describes fundamental principles of subsidy including detailed explanation of POVEZ II and rudiments of project management. The analytical part is focused on evaluating the situation of a company using SWOT analysis, Porter`s five forces analysis and principle of key factors. The outcome of the analytical work is to establish an educational plan covering the areas of education and the reasons leading to this need, which is crucial for the applicatio

Accounting result as a base for setting income tax

Tato diplomová práce se zabývá problematikou výsledku hospodaření a specifiky, která výsledek hospodaření ovlivňují. Práce je rozdělena do dvou hlavních částí. Teoretická část je zaměřena na základní pojmy související s výsledkem hospodaření, které je nutné definovat. Jedná se především o definici nákladů, výnosů, příjmů a výdajů. Diplomová práce rozebírá zjišťování výsledku hospodaření, odložené a akruální položky, popisuje účetní závěrku a problematiku daně z příjmů. Praktická část charakterizuje stavebnictví a specifika společností podnikajících v této oblasti. Diplomová práce aplikuje teoretické poznatky na vybranou společnost, zabývá se organizací práce v závislosti na sezónnosti a řeší výkonnost podniku. Dále práce rozebírá výsledek hospodaření v konkrétním podniku, porovnává ho mezi jednotlivými lety a nabízí možnosti daňové optimalizace.This diploma thesis deals with the problematics of the accounting result and the specifics, which influence it. This work is divided into two main parts. The theoretical part is focused on basic concepts related to the accounting result, which need to be defined. This is primarily about the definition of costs, returns, incomes and expenses. Diploma thesis analyses the calculation of the accounting result and deferred entries, describes the financial statement and the issue of income tax. The practical part characterizes the construction industry and specifics of companies operating in the such industry. This diploma thesis also applies the theoretical findings on a chosen company, deals with the organization of work depending on seasonality and solves the company performance. Furthermore, this thesis analyzes the accounting result in chosen company, compares it between individual years and offers possible tax optimizations