High Resolution Mapping of Enhancer-Promoter Interactions

RNA Polymerase II ChIA-PET data has revealed enhancers that are active in a profiled cell type and the genes that the enhancers regulate through chromatin interactions. The most commonly used computational method for analyzing ChIA-PET data, the ChIA-PET Tool, discovers interaction anchors at a spatial resolution that is insufficient to accurately identify individual enhancers. We introduce Germ, a computational method that estimates the likelihood that any two narrowly defined genomic locations are jointly occupied by RNA Polymerase II. Germ takes a blind deconvolution approach to simultaneously estimate the likelihood of RNA Polymerase II occupation as well as a model of the arrangement of read alignments relative to locations occupied by RNA Polymerase II. Both types of information are utilized to estimate the likelihood that RNA Polymerase II jointly occupies any two genomic locations. We apply Germ to RNA Polymerase II ChIA-PET data from embryonic stem cells to identify the genomic locations that are jointly occupied along with transcription start sites. We show that these genomic locations align more closely with features of active enhancers measured by ChIP-Seq than the locations identified using the ChIA-PET Tool. We also apply Germ to RNA Polymerase II ChIA-PET data from motor neuron progenitors. Based on the Germ results, we observe that a combination of cell type specific and cell type independent regulatory interactions are utilized by cells to regulate gene expression.National Institutes of Health (U.S.) (Grant 1U01HG007037

Using CdTe/ZnSe core/shell quantum dots to detect DNA and damage to DNA

CdTe/ZnSe core/shell quantum dot (QD), one of the strongest and most highly luminescent nanoparticles, was directly synthesized in an aqueous medium to study its individual interactions with important nucleobases (adenine, guanine, cytosine, and thymine) in detail. The results obtained from the optical analyses indicated that the interactions of the QDs with different nucleobases were different, which reflected in different fluorescent emission maxima and intensities. The difference in the interaction was found due to the different chemical behavior and different sizes of the formed nanoconjugates. An electrochemical study also confirmed that the purines and pyrimidines show different interactions with the core/shell QDs. Based on these phenomena, a novel QD-based method is developed to detect the presence of the DNA, damage to DNA, and mutation. The QDs were successfully applied very easily to detect any change in the sequence (mutation) of DNA. The QDs also showed their ability to detect DNAs directly from the extracts of human cancer (PC3) and normal (PNT1A) cells (detection limit of 500 pM of DNA), which indicates the possibilities to use this easy assay technique to confirm the presence of living organisms in extreme environments

Status crvene lunje Milvus milvus u Hrvatskoj na temelju satelitskog praćenja: prostorno i vremensko pojavljivanje te ponovno gniježđenje

Until 2018 the Red Kite was considered a regionally extinct breeding species in Croatia and a rare winter visitor in Eastern Slavonia. This paper provides an overview of the results of a satellite telemetry study of Red Kites tagged in Austria, Slovakia and the Czech Republic. This is the first comprehensive study on the phenology of the species in Croatia. Between September 2014 and October 2018, a total of 39 tagged individuals have been recorded in Croatia and spent a collective total of 1484 days here. Red Kites mainly occurred in Croatia from September to March, while few birds remained here during the summer. Birds nesting in central Europe migrate through Croatia in broad front, appearing in all parts of the country, moving SW to wintering grounds in Italy, while fewer individuals follow the SE direction to Greece. Furthermore, the wintering behaviour of four tagged Red Kites were recorded using communal roosts in the continental part of Croatia. During the early spring of 2018, a female Red Kite tagged in the Czech Republic was suspected of breeding in Eastern Slavonia and later in the season the nesting was confirmed south of the town of Đakovo, even though it was unsuccessful.Crvena lunja nastanjuje otvorena mozaična staništa zapadnog palearktika s najvažnijim gnijezdećim populacijama u Njemačkoj, Švicarskoj, Francuskoj i Španjolskoj. Prema istoku Europe brojnost parova postaje sve manja. U Hrvatskoj se sve do 2018. godine smatrala regionalno izumrlom gnjezdaricom te rijetkom zimovalicom istočne Slavonije i Baranje. Ranije se gnijezdila na istoku Hrvatske, a posljednje gniježđenje je zabilježeno 1968. godine kod Migalovaca. Nakon što je 2014. godine u Austriji, Slovačkoj i Češkoj pokrenut projekt praćenja crvenih lunja pomoću GPS/GSM i GPS/GSM/UHF uređaja, pokazalo se da mnoge od njih zalaze i u Hrvatsku. Ovaj rad daje kratak pregled rezultata dobivenih analizom podataka sa satelitske telemetrije. U razdoblju od rujna 2014. do listopada 2018.g. u Hrvatskoj je zabilježeno 39 različitih crvenih lunja označenih uređajima za praćenje te su ovdje provele sveukupno 1484 dana. Glavni period pojavljivanja crvenih lunja u Hrvatskoj je od rujna do ožujka (s vrhuncem selidbe u listopadu odnosno ožujku), dok se malobrojne ptice ovdje zadržavaju i tijekom ljetnog lutanja. Ptice koje gnijezde u srednjoj Europi kroz Hrvatsku sele u širokom pojasu, pojavljujući se u svim dijelovima zemlje pa čak i na nekim pučinskim otocima, prateći osnovni smjer JJZ do zimovališta u Italiji, dok manji broj jedinki seli u smjeru JI i zimuje u Grčkoj. Između 2014. i 2018. zabilježeno je zimovanje četiri označene crvene lunje u Hrvatskoj (po jedna ptica u Baranji, istočnoj Slavoniji, srednjoj Posavini i Pokupskom bazenu), s dolaskom na zimovališta većinom ulistopadu i odlaskom oko sredine ožujka. Terenski obilasci su pokazali da se tijekom zime crvene lunje u manjim skupinama (3-13 jed.) okupljaju na redovito korištenim noćilištima (šumarci, drvoredi i sl.) te je na dva mjesta utvrđeno zajedničko noćenje s crnim lunjama Milvus migrans. Tijekom ranog proljeća 2018. godine jedna od crvenih lunja zadržavala se u istočnoj Slavoniji južno od Đakova te se sumnjalo na mogući pokušaj gniježđenja. Radilo se o mladoj ženki s uređajem AUKI49 označenoj kao ptić prstenom C144030 tijekom 2016. godine u okolici Břeclava u Češkoj, nakon čega je u dva navrata zimovala u Italiji i redovito selila preko Hrvatske. Obilaskom terena u travnju opaženo je svadbeno ponašanje ženke i mužjaka crvene lunje bez oznake, dok je u svibnju na istom mjestu na rubu šume hrasta i graba pronađeno gnijezdo na hrastu lužnjaku i ženka koja je sjedila u njemu. Početkom lipnja tijekom provjere gnijezda nisu pronađeni mladi, već samo nekoliko pera i jedno napuklo jaje crvene lunje. Mužjak je uočen iznad šume dok je ženka netom prije napustila područje i uputila se prema Češkoj. Na temelju analize uzorka kretanja ženke tijekom proljeća odnosno činjenica utvrđenih terenskim obilascima, pretpostavlja se da se u gnijezdu najmanje jedan ptić uspješno izlegao te da je vjerojatno postao žrtvom predacije. Iako tijekom 2018.godine par crvenih lunja nije othranio nijednog ptića, nedvojbeno je dokazano ponovno gniježđenje vrste nakon 50 godina izostanka. Tijekom zimovanja i gniježđenja u Hrvatskoj crvene lunje su koristile mozaična nizinska poljoprivredna područja s manjim njivama, livadama, drvoredima i šumarcima. Noviji podaci prikupljeni tijekom zimskog prebrojavanja ptica odnosno satelitskim praćenjem ptica iz sjevernijih populacija, pokazali su da je crvena lunja redovita preletnica u čitavoj Hrvatskoj te redovita zimovalica, prvenstveno u istočnoj Slavoniji i Baranji. Gnijezdeća populacija crvene lunje u srednjoj Europi pokazuje blago rastući trend te se u narednim godinama može očekivati eventualni pronalazak novih gnijezdećih parova i u Hrvatskoj

Nationwide increases in anti-SARS-CoV-2 IgG antibodies between October 2020 and March 2021 in the unvaccinated Czech population

Background: The aim of the nationwide prospective seroconversion (PROSECO) study was to investigate the dynamics of anti-SARS-CoV-2 IgG antibodies in the Czech population. Here we report on baseline prevalence from that study. Methods: The study included the first 30,054 persons who provided a blood sample between October 2020 and March 2021. Seroprevalence was compared between calendar periods, previous RT-PCR results and other factors. Results: The data show a large increase in seropositivity over time, from 28% in October/November 2020 to 43% in December 2020/January 2021 to 51% in February/March 2021. These trends were consistent with government data on cumulative viral antigenic prevalence in the population captured by PCR testing – although the seroprevalence rates established in this study were considerably higher. There were only minor differences in seropositivity between sexes, age groups and BMI categories, and results were similar between test providing laboratories. Seropositivity was substantially higher among persons with history of symptoms (76% vs. 34%). At least one third of all seropositive participants had no history of symptoms, and 28% of participants with antibodies against SARS-CoV-2 never underwent PCR testing. Conclusions: Our data confirm the rapidly increasing prevalence in the Czech population during the rising pandemic wave prior to the beginning of vaccination. The difference between our results on seroprevalence and PCR testing suggests that antibody response provides a better marker of past infection than the routine testing program

The electrochemical and statistical evaluation of isolation of mellitin and apamin from honey bee (Apis Mellifera) venom.

We present in this manuscript for the first time the electrochemical and statistical evaluation of FPLC isolation of mellitin and apamin from honey bee (Apis mellifera) venom. Venoms are extremely complex blends of diverse substances that target a myriad of receptors or ion channels. Therefore, toxins, isolated from venomous organisms can be a valuable tool with diverse biological applications. In this study we decided to optimize the purification of honey bee venom by using fast protein liquid chromatography, to obtain biologically active peptide - melittin (2846.46 Da). Due to a presence of other compounds with similar molecular weight (apamin 2027.34 Da), we optimized a differential pulse voltammetry method with adsorptive transfer technique (AdT DPV), utilizing Brdicka supporting electrolyte for measurements. Typical voltammograms - fingerprints for each substance were obtained and numerical projections of voltammograms were employed to propose an artificial neural network. Our suggested neural network can simply predict the content of each peptide in fraction with following performance: 100 % for training and 100 % for testing