So-called 936-type phages are among the most frequently isolated phages in dairy facilities utilising Lactococcus lactis starter cultures. Despite extensive efforts to control phage proliferation and ...decades of research, these phages continue to negatively impact cheese production in terms of the final product quality and consequently, monetary return.
Whole genome sequencing and in silico analysis of three 936-type phage genomes identified several putative (orphan) methyltransferase (MTase)-encoding genes located within the packaging and replication regions of the genome. Utilising SMRT sequencing, methylome analysis was performed on all three phages, allowing the identification of adenine modifications consistent with N-6 methyladenine sequence methylation, which in some cases could be attributed to these phage-encoded MTases. Heterologous gene expression revealed that M.Phi145I/M.Phi93I and M.Phi93DAM, encoded by genes located within the packaging module, provide protection against the restriction enzymes HphI and DpnII, respectively, representing the first functional MTases identified in members of 936-type phages.
SMRT sequencing technology enabled the identification of the target motifs of MTases encoded by the genomes of three lytic 936-type phages and these MTases represent the first functional MTases identified in this species of phage. The presence of these MTase-encoding genes on 936-type phage genomes is assumed to represent an adaptive response to circumvent host encoded restriction-modification systems thereby increasing the fitness of the phages in a dynamic dairy environment.
Europa se posljednjih desetljeća hrva sa samom sobom. Kulturološke promjene koje su se dogodile bitno su uzdrmale njezin identitet, a poštovanje temeljnih načela i vrednota našlo se pred novim ...izazovom. Nove antropološke paradigme proizašle iz postmodernizma utjecale su na zaborav kršćanskih korijena i istina, koje su dobrim dijelom odredile smjer razvoja europske kulture. Posljedično, Europa kakvu poznajemo umire. Osnovna nakana ovog rada jest vidjeti u kakvom su odnosu umiranje
Europe i migracijska kriza. Ne govori se o smrti (i životu) kao biološkom procesu, nego o filozofsko-teološkom promatranju „umiranja“ i „oživljavanja“ svega europskoga, kršćanskoga, ljudskoga... Na temelju promatranja najvažnijih današnjih kulturoloških obilježja Europe te vjerskih istina kršćanstva i islama, posebno u poimanju života i smrti, odgovorit ćemo na pitanje jesu li migranti i izbjeglice nositelji života
ili smrti na europskom kontinentu. Čuvajući se idealiziranja imigranata
kao spasitelje Europe, ali i njihova demoniziranja kao jedinih krivaca propadanja Europe, pokušat ćemo vidjeti može li pozitivan stav prema njima pružiti bitan preduvjet za plodnu integraciju. Život ili smrt Europe ovisi o njoj samoj, a migranti i izbjeglice mogu doprinijeti jednoj i drugoj stvarnosti. Ipak, za kršćane jest obveza ljubavi, za koju ne smijemo zaboraviti da ima snagu oživljavati i mijenjati.
Europe has been wrestling with itself in recent decades. The cultural changes that have taken place have shaken its identity significantly, and adherence to fundamental principles and values has faced a new challenge. New anthropological paradigms arising from postmodernism have
influenced the oblivion of Christian roots and truths, which have largely determined the direction of the development of European culture.
Consequently, Europe as we know it is dying. The main purpose of this paper is to see the relationship between the dying of Europe and the migration crisis. It is not about death (and life) as a biological process, but more about a philosophical-theological observation of “dying “and “reviving “of all that is European, Christian, human ... On the basis of the observation of today's most important cultural features
of Europe and religious truths of Christianity and Islam, especially on
the understanding of life and death, we will answer the question of whether migrants and refugees are the bearers of life or death on the European continent. Being careful not to idealize immigrants as saviours
of Europe, but also not to demonize them as the only culprits of Europe's decline, we will try to see if a positive attitude towards them
can provide an essential precondition for fruitful integration. Europe's life or death depends on itself, and migrants and refugees can contribute to both realities. Yet for Christians there is an obligation of love, and we must not forget that it has the power to revive and change.
•Agarivorans gilvus WH0801T was a novel species within the genus Agarivorans.•This is the first report on complete genome sequence of Agarivorans gilvus.•The bacterium could produce various agarases ...and catalyze the hydrolysis of agar.•Complete genome sequence of a single 4,416,600bp chromosome with a GC content of 45.9%.•Including 4279 protein-coding sequences, 22 rRNAs, 91 tRNAs and 9 miscellaneous RNAs.
Agarivorans gilvus WH0801T, an agarase-producing bacterium, was isolated from the surface of seaweed. Here, we present the complete genome sequence, which consists of one circular chromosome of 4,416,600bp with a GC content of 45.9%. This genetic information will provide insight into biotechnological applications of producing agar for food and industry.
Morchella conica Pers. is a highly-prized mushroom for its edible and medical values. In this study, we determined the complete mitochondrial genome of M. conica combining both PacBio and Illumina ...sequencing technologies. The complete mitochondrial genome is 280,763 bp in length with a GC content of 39.88%. We identified a total of 14 core conserved protein-coding genes, 127 non-conserved open reading frames (ncORFs) and 30 tRNA genes in the M. conica mitogenome. However, no large or small rRNA subunits (rnl or rns) were identified in this mitogenome. In addition, we detected two mitochondrial RNase P (rnpB) genes and one ribosomal protein genes (rps3). Phylogenetic analysis was performed among M. conica and 18 other representative fungi from Ascomycota, Basidiomycota and Mucoromycota. Our results showed that M. conica was most closely related to M. importuna. The availability of the M. conica mitochondrial genome will form the basis of genetic breeding program and enhance our understanding of the evolution of this species.
The 2525 amino acid SMRT corepressor is an intrinsically disordered hub protein responsible for binding and coordinating the activities of multiple transcription factors and chromatin modifying ...enzymes. Here we have studied its interaction with HDAC7, a class IIa deacetylase that interacts with the corepressor complex together with the highly active class I deacetylase HDAC3. The binding site of class IIa deacetylases was previously mapped to an approximate 500 amino acid region of SMRT, with recent implication of short glycine-serine-isoleucine (GSI) containing motifs. In order to characterize the interaction in detail, we applied a random library screening approach within this region and obtained a range of stable, soluble SMRT fragments. In agreement with an absence of predicted structural domains, these were characterized as intrinsically disordered by NMR spectroscopy. We identified one of them, comprising residues 1255-1452, as interacting with HDAC7 with micromolar affinity. The binding site was mapped in detail by NMR and confirmed by truncation and alanine mutagenesis. Complementing this with mutational analysis of HDAC7, we show that HDAC7, via its surface zinc ion binding site, binds to a 28 residue stretch in SMRT comprising a GSI motif followed by an alpha helix.
The white-backed planthopper Sogatella furcifera is an economically important rice pest distributed throughout Asia. It damages rice crops by sucking phloem sap, resulting in stunted growth and plant ...virus transmission. We aimed to obtain the full-length transcriptome data of S. furcifera using PacBio single-molecule real-time (SMRT) sequencing. Total RNA extracted from S. furcifera at various developmental stages (egg, larval, and adult stages) was mixed and used to generate a full-length transcriptome for SMRT sequencing. Long non-coding RNA (lncRNA) identification, full-length coding sequence prediction, full-length non-chimeric (FLNC) read detection, simple sequence repeat (SSR) analysis, transcription factor detection, and transcript functional annotation were performed. A total of 12,514,449 subreads (15.64 Gbp, clean reads) were generated, including 630,447 circular consensus sequences and 388,348 FLNC reads. Transcript cluster analysis of the FLNC reads revealed 251,109 consensus reads including 29,700 high-quality reads. Additionally, 100,360 SSRs and 121,395 coding sequences were identified using SSR analysis and ANGEL software, respectively. Furthermore, 44,324 lncRNAs were annotated using four tools and 1,288 transcription factors were identified. In total, 95,495 transcripts were functionally annotated based on searches of seven different databases. To the best of our knowledge, this is the first study of the full-length transcriptome of the white-backed planthopper obtained using SMRT sequencing. The acquired transcriptome data can facilitate further studies on the ecological and viral-host interactions of this agricultural pest.
Histone deacetylases (HDACs) catalyze the hydrolysis of Ɛ-acetyl-lysine residues of histones. Removal of acetyl groups results in condensation of chromatin structure and repression of gene ...expression. Human class I, II, and IV HDACs are said to be zinc-dependent in that they require divalent zinc ions to catalyze the deacetylase reaction. HDACs are considered potential targets for the treatment of cancer due to their role in regulating transcription. They are also thought to play important roles in the development of organisms such as honey bees. The fatty acid, 10-hydroxy-2E-decenoic acid (10-HDA), which can account for up to 5% of royal jelly composition has been reported as an HDAC inhibitor. The crystal structure of the HDAC3:SMRT complex possesses two monovalent cations (MVCs) labeled as potassium with one MVC binding site near the active site Zn(II) and the second MVC binding site ≥20 Å from the active site Zn(II). We report here the inhibitory effects of excess Zn(II) on the catalytic activity of histone deacetylase 3 (HDAC3) bound to the deacetylase activating domain of nuclear receptor corepressor 2 (NCOR2). We also report the effects of varying concentrations of potassium ions where K+ up to 10 mM increase HDAC3 activity with a maximum kcat/KM of approximately 80,000 M-1s-1 while K+ above 10 mM inhibit HDAC3 activity. The inhibition constant (Ki) of 10-HDA was determined to be 5.32 mM. The regulatory effects of zinc, potassium, and 10-HDA concentration on HDAC3 activity suggest a strong correlation between these chemical species and epigenetic control over Apis mellifera caste differentiation among other control mechanisms.
DNA‐Forensik Kremer, Kerstin; Fritzsch, Sabrina; Stahl, Frank
Chemie in unserer Zeit,
December 2017, Letnik:
51, Številka:
6
Journal Article
Recenzirano
Zusammenfassung
Der Begriff Forensik fasst die wissenschaftlichen Arbeitsmethoden zusammen, mit denen Straftaten untersucht, analysiert und aufgeklärt werden können. Dienen der Aufklärung DNA‐Spuren, ...die am Tatort vorgefunden wurden, spricht man von DNA‐Forensik oder forensischer Genetik. Häufig liegt am Tatort nicht nur die DNA‐Spur des Täters vor, sondern es sind auch die DNA von Opfer, Zeugen und berechtigten Personen (Ersthelfer, Polizeikräfte, etc.) usw. aufzufinden. Dann wird die Analyse komplex und das Verhältnis der DNA‐Spuren zueinander bedeutsam. Seit einigen Jahren steht die DNA‐Forensik vor völlig neuen Möglichkeiten, die neu entwickelte, moderne Sequenzierungstechniken, die zusammengefasst als Next Generation Sequencing (NGS) oder inzwischen sogar als Third Generation Sequencing (SMRT) bezeichnet werden, bieten. Diese Techniken erlauben eine schnelle Sequenzierung des gesamten Genoms und damit Merkmale wie Augenfarbe und Haarfarbe einer Person zu bestimmen. So könnte aus dem abstrakten DNA‐Profil in den nächsten Jahren ein plastisches DNA‐Phantombild werden. Die Entwicklungen erfordern eine Anpassung der gesetzlichen Regelungen und öffentliche Akzeptanz. Im vorliegenden Artikel werden die aktuellen Praktiken der DNA‐Forensik am Tatort und in den Laboratorien beschrieben und ein Ausblick auf zukünftige Möglichkeiten der forensischen DNA‐Analyse gegeben werden.
Summary
Forensics deals with the scientific methods to gather information at a crime scene for solving criminal actions. DNA forensics uses genetic material for these purposes. DNA fingerprinting is established as an important method for police detective work since the end of the 1980s. Currently, DNA forensics faces completely new possibilities through the application of more efficient high‐throughput sequencing methods, summarized as Next Generation Sequencing (NGS). Using NGS it could be possible to predict numerous externally visible characteristics including the complete facial shape of an unknown perpetrator. This article aims at presenting practices of forensic DNA analyses used to date and extending the picture for future possibilities and challenges.
Die Ausstrahlung von Fernsehserien wie CSI: Miami, oder Navy CIS fördert ein öffentliches Interesse an den forensischen Wissenschaften und schafft Alltagsvorstellungen vom forensischen Arbeiten. Häufig wirken die in den Serien verwendeten analytischen Methoden jedoch im Vergleich zu den wirklich im Labor angewendeten Techniken wie Science Fiction. So führt in den Fernsehserien eine in wenigen Minuten durchgeführte DNA‐Analyse zur direkten Identifizierung des Täters mit komplettem Strafregister und aktueller Adresse. Diese Unterhaltungsserien bilden die Komplexität im kriminaltechnischen Labor und bei der Ermittlung jedoch nicht real ab, wodurch dem Zuschauer ein falscher Eindruck vermittelt wird. Hieraus kann sich eine Einstellung gegenüber der Forensik in der echten Kriminalistik ergeben, die nicht auf den tatsächlichen wissenschaftlichen Möglichkeiten beruht. Ziel dieses Beitrages ist es, aus wissenschaftlicher aber auch aus rechtlicher und bewertender Perspektive die aktuell realen Möglichkeiten und Grenzen der DNA‐Forensik aufzuzeigen.
Objective:
The aim of this project was to implement long-read sequencing for BCR-ABL1 TKI resistance mutation screening in a clinical setting for patients undergoing treatment for chronic myeloid ...leukemia.
Materials and Methods:
Processes were established for registering and transferring samples from the clinic to an academic sequencing facility for long-read sequencing. An automated analysis pipeline for detecting mutations was established, and an information system was implemented comprising features for data management, analysis and visualization. Clinical validation was performed by identifying BCR-ABL1 TKI resistance mutations by Sanger and long-read sequencing in parallel. The developed software is available as open source via GitHub at https://github.com/pharmbio/clamp
Results:
The information system enabled traceable transfer of samples from the clinic to the sequencing facility, robust and automated analysis of the long-read sequence data, and communication of results from sequence analysis in a reporting format that could be easily interpreted and acted upon by clinical experts. In a validation study, all 17 resistance mutations found by Sanger sequencing were also detected by long-read sequencing. An additional 16 mutations were found only by long-read sequencing, all of them with frequencies below the limit of detection for Sanger sequencing. The clonal distributions of co-existing mutations were automatically resolved through the long-read data analysis. After the implementation and validation, the clinical laboratory switched their routine protocol from using Sanger to long-read sequencing for this application.
Conclusions:
Long-read sequencing delivers results with higher sensitivity compared to Sanger sequencing and enables earlier detection of emerging TKI resistance mutations. The developed processes, analysis workflow, and software components lower barriers for adoption and could be extended to other applications.
Nuclear functions for IκB kinase (IKK), including phosphorylation of histone H3 and nuclear corepressors, have been recently described. Here, we show that IKK is activated in colorectal tumors ...concomitant with the presence of phosphorylated SMRT (silencing mediator of retinoic acid and thyroid hormone receptor) corepressor that is aberrantly localized in the cytoplasm. In these tumors, IKKα associates to the chromatin of specific Notch targets, leading to the release of SMRT. Abrogation of IKK activity by BAY11-7082 or by expressing dominant negative IKKα restores the association of SMRT with Notch target genes, resulting in specific gene repression. Finally, BAY11-7082 significantly reduces tumor size in colorectal cancer xenografts (CRC-Xs) implanted in nude mice.
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