Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing

Herpesvirus gene expression is co-ordinately regulated and sequentially ordered during productive infection. The viral genes can be classified into three distinct kinetic groups: immediate-early, early, and late classes. In this study, a massively parallel sequencing technique that is based on PacBio Single Molecule Real-time sequencing platform, was used for quantifying the poly(A) fraction of the lytic transcriptome of pseudorabies virus (PRV) throughout a 12- hour interval of productive infection on PK-15 cells. Other approaches, including microarray, real-time RT-PCR and Illumina sequencing are capable of detecting only the aggregate transcriptional activity of particular genomic regions, but not individual herpesvirus transcripts. However, SMRT sequencing allows for a distinction between transcript isoforms, including length- and splice variants, as well as between overlapping polycistronic RNA molecules. The non-amplified Isoform Sequencing (Iso-Seq) method was used to analyse the kinetic properties of the lytic PRV transcripts and to then classify them accordingly. Additionally, the present study demonstrates the general utility of long-read sequencing for the time-course analysis of global gene expression in practically any organism

Third-generation Sequencing Reveals Extensive Polycistronism and Transcriptional Overlapping in a Baculovirus

The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is an insect-pathogen baculovirus. In this study, we applied the Oxford Nanopore Technologies platform for the analysis of the polyadenylated fraction of the viral transcriptome using both cDNA and direct RNA sequencing methods. We identified and annotated altogether 132 novel transcripts and transcript isoforms, including 4 coding and 4 non-coding RNA molecules, 47 length variants, 5 splice isoforms, as well as 23 polycistronic and 49 complex transcripts. All of the identified novel protein-coding genes were 5'-truncated forms of longer host genes. In this work, we demonstrated that in the case of transcript start site isoforms, the promoters and the initiator sequence of the longer and shorter variants belong to the same kinetic class. Long-read sequencing also revealed a complex meshwork of transcriptional overlaps, the function of which needs to be clarified. Additionally, we developed bioinformatics methods to improve the transcript annotation and to eliminate the non-specific transcription reads generated by template switching and false priming

Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus

Third-generation sequencing is an emerging technology that is capable of solving several problems that earlier approaches were not able to, including the identification of transcripts isoforms and overlapping transcripts. In this study, we used long-read sequencing for the analysis of pseudorabies virus (PRV) transcriptome, including Oxford Nanopore Technologies MinION, PacBio RS-II, and Illumina HiScanSQ platforms. We also used data from our previous short-read and long-read sequencing studies for the comparison of the results and in order to confirm the obtained data. Our investigations identified 19 formerly unknown putative protein-coding genes, all of which are 5′ truncated forms of earlier annotated longer PRV genes. Additionally, we detected 19 non-coding RNAs, including 5′ and 3′ truncated transcripts without in-frame ORFs, antisense RNAs, as well as RNA molecules encoded by those parts of the viral genome where no transcription had been detected before. This study has also led to the identification of three complex transcripts and 50 distinct length isoforms, including transcription start and end variants. We also detected 121 novel transcript overlaps, and two transcripts that overlap the replication origins of PRV. Furthermore, in silico analysis revealed 145 upstream ORFs, many of which are located on the longer 5′ isoforms of the transcripts

Fotometriai vöröseltolódások és az SDSS adatbázis = Photometric redshifts and the SDSS Science Archive

A kitűzött célokat messzemenően teljesítettük. Az általunk folyamatosan fejlesztett fotometrikus vöröseltolódás becslésének technika az SDSS hivatalos módszerévé vált, ennek segítségével készítettük el a publikus adatkibocsátások katalógusait. A fotometrikus vöröseltolódás becslés felhasználásával MgII abszorberek távolságát határoztuk meg spektroszkópiai észlelések nélkül, LRG-MgII korrelációs függvényeket, és halo tömeget becsültünk. Kimutattuk, hogy az MgII felhők nem virializálódnak, melyből sejtéseket lehet felállítani keletkezésük körülményeire. Az adatbázis indexelési technológiákat fejlesztve kialakítottunk egy több-dimenziós (pl. fotometriai) térben hatékonyan kereső keretrendszert, melyet integráltuk az SDSS adatbázis architektúrájába, újfajta kereséseket lehetővé téve. Elkészültek prototípusok, amelyek az adatok 2 és 3 dimenziós, az adatbázissal közvetlenül kölcsönható vizualizációját szolgálják. Bekapcsolódtunk a nemzetközi Virtuális Obszervatórium munkájába, és büszkén mondhatjuk, hogy a valójában működő eszközök (Spectrum and Filter Services, Footprint Services, SkyServer, CasJobs, SDSS WorldWind) jelentős hányada elsősorban a pályázatban résztvevő kollégák munkájának eredménye. A pályázat lehetővé tette számos diák bekapcsolódását a nemzetközi kutatásokba, mely több diploma- és PhD munka alapját képezte, hozzájárult a témavezető MTA doktori disszertációjának elkészítéséhez valamint új alapkutatási és kutatás-fejlesztési pályázatok elnyeréséhez. | The goals of the proposal have been fulfilled. Our photometric estimation technique became the official method to estimate galaxy redshifts for the SDSS. With our algorithm we have created the public catalogs for the yearly data releases. With the help of the estimated photometric redshifts we were able to measure the distance of MgII absorbers without spectroscopic observations, and estimated the LRG-MgII correlation function and the mass of halos. We have shown, that the MgII clouds are not virialized, which fact contributes to the understanding of their formation. The development of new database indexing techniques resulted in a new multidimensional search method, which has been integrated into the SDSS archive to search the magnitude space. We have created prototypes for interactive data visualization in 2 and 3 dimensions. We have joined the International Virtual Observatory Alliance, and most of the flagship tools (Spectrum and Filter Services, Footprint Services, SkyServer, CasJobs, SDSS WorldWind) are results of mostly colleagues participating in this project. The support of the project made possible for several students to join the international astronomical research community, several theses were based on this research, and it was a solid base for further grant proposals, where the work can be continued

Adatok a Körös-Maros Nemzeti Park illetékességi területének vízibogár-faunájához (Coleoptera: Haliplidae, Dytiscidae, Noteridae, Gyrinidae, Hydrochidae, Helophoridae, Hydrophilidae) = Data to the water beetle fauna of Körös–Maros Nati onal Park (Coleoptera: Haliplidae, Dytiscidae, Noteridae, Gyrinidae, Hydro chidae, Helophoridae, Hydrophilidae)

Data to the water beetle fauna of Körös–Maros Nati onal Park (Coleoptera: Haliplidae, Dytiscidae, Noteridae, Gyrinidae, Hydro chidae, Helophoridae, Hydrophilidae): Collecting data of 83 water beetle species [Haliplid ae (9), Dytiscidae (39), Noteridae (2), Gyrinidae (4), Hydrochidae (1), Helophoridae (6) and Hydrophi lidae (22)] are given from 35 localities in the operational area of Körös–Maros National Park. Results summarized in a table

Könyvszemle

Buda Béla: A lélek egészsége. A mentálhigiéné alapkérdései; Pikó Bettina: Kultúra, társadalom és lélektan; Gyöngyösi Zoltán: Az élet és test feletti rendelkezések joga; Desmond Morris: Bensőséges kötelékek; Em Griffin: Együtt-lét. Mitől jó egy csoport?; David Lewis: Hogyan értessük meg magunkat? A hatékony kommunikáció gyakorlati útmutatója; Horányi Özséb (szerk.): A sokarcú kép. Válogatott tanulmányok a képek logikájáról; Nyíri Kristóf - Kovács Gábor (szerk.): Virtuális egyetem Magyarországon