scholarly journals European Population of Pectobacterium punjabense: Genomic Diversity, Tuber Maceration Capacity and a Detection Tool for This Rarely Occurring Potato Pathogen

2021 ◽  
Vol 9 (4) ◽  
pp. 781
Author(s):  
Jérémy Cigna ◽  
Angélique Laurent ◽  
Malgorzata Waleron ◽  
Krzysztof Waleron ◽  
Pauline Dewaegeneire ◽  
...  
Keyword(s):  
Soft Rot ◽  
European Population ◽  
Genomic Diversity ◽  
Taqman Assay ◽  
Culture Collections ◽  
Strain Characterization ◽  
Detection Tool ◽  
European Culture ◽  
Specific Strain ◽  
Long Time

Enterobacteria belonging to the Pectobacterium and Dickeya genera are responsible for soft rot and blackleg diseases occurring in many crops around the world. Since 2016, the number of described species has more than doubled. However, some new species, such as Pectobacterium punjabense, are often poorly characterized, and little is known about their genomic and phenotypic variation. Here, we explored several European culture collections and identified seven strains of P. punjabense. All were collected from potato blackleg symptoms, sometimes from a long time ago, i.e., the IFB5596 strain isolated almost 25 years ago. We showed that this species remains rare, with less than 0.24% of P. punjabense strains identified among pectinolytic bacteria present in the surveyed collections. The analysis of the genomic diversity revealed the non-clonal character of P. punjabense species. Furthermore, the strains showed aggressiveness differences. Finally, a qPCR Taqman assay was developed for rapid and specific strain characterization and for use in diagnostic programs.

scholarly journals Neolithic and medieval virus genomes reveal complex evolution of hepatitis B

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Ben Krause-Kyora ◽  
Julian Susat ◽  
Felix M Key ◽  
Denise Kühnert ◽  
Esther Bosse ◽  
...  
Keyword(s):  
Hepatitis B ◽  
De Novo ◽  
Phylogenetic Network ◽  
European Population ◽  
Human Pathogens ◽  
Sequencing Data ◽  
B Virus ◽  
Long Time ◽  
Close Relatives ◽  
Virus Genomes

The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genome by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results demonstrated that HBV has circulated in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. The ancient viruses appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses.

scholarly journals Interoperability of CABRI Services and Biochemical Pathways Databases

2004 ◽  
Vol 5 (2) ◽  
pp. 169-172 ◽  
Author(s):  
Paolo Romano ◽  
Ottavia Aresu ◽  
Maria Assunta Manniello ◽  
Barbara Parodi
Keyword(s):  
Culture Collections ◽  
Biochemical Pathways ◽  
Related Information ◽  
Biological Resource Centres ◽  
Quality Guidelines ◽  
European Culture ◽  
One Stop ◽  
Set Up ◽  
Search Facility ◽  
Simple Search

Common Access to Biological Resources and Information (CABRI) service is a ‘one-stop-shop’ for materials that are collected by a number of European culture collections that engage themselves in a quality service for the scientific community by adhering to Quality Guidelines for the management of resources and related information. It includes collections' catalogues that can be searched in an SRS implementation. A simple search facility, including a synonym search and a shopping cart, is also available. Within the European Biological Resource Centres Network (EBRCN) project, an extension and improvement of the catalogues' information is under way. This includes adding links to bibliographic databanks and sequence databases. Revision of ‘in-house’ controlled vocabularies used by data annotators is under way, in order to improve the setting up of external links, and new links to biochemical pathways databases are being set up for some of the catalogues.

scholarly journals Interwar Ukrainian Political Emigrants in Yugoslavia: Relations with the Authorities

2019 ◽  
pp. 132-140
Author(s):  
Valerii Vlasenko
Keyword(s):  
World War Ii ◽  
Central Government ◽  
Positive Impact ◽  
Local Authorities ◽  
The Balkans ◽  
European Culture ◽  
State Commission ◽  
Long Time ◽  
The One ◽  
Head Of Government

This article is devoted to the relationship between interwar Ukrainian political emigrants and local authorities in the Kingdom of Serbs, Croats and Slovenes (Yugoslavia). A comparative analysis of the attitude of the Yugoslav authorities towards Russian and Ukrainian emigrants was conducted. The Russophilia of Yugoslav authorities, who viewed the Ukrainian question through the lense of the Russian emigrants, was described. The idea of Pan-Slavism had been spreading in the Balkans for a long time, which facilitated the legitimization of friendly relations between the southern Slavs (primarily Serbs) and Russians, whom Serbs considered as protectors from the Ottoman and Austro-Hungarian Empires. Yugoslavia sided with the anti-Bolshevik White Movement, an ally of the Entente, which had a positive impact on the situation of Russian emigrants. The young state was in need of professionals with a good command of foreign languages and European culture. Many emigrants met those requirements. Therefore, in the early 1920s, several thousands of emigrants worked in the public service. The reigning Karadjordjević dynasty had marital ties with the Romanov dynasty. A former Russian diplomat was among advisers to the king and the head of government. The immigration from the former Russian Empire was addressed by the Royal Court as well as several ministries and central government institutions. Direct support to the immigrants was provided by the State Commission for Assistance to Russian Refugees. Yugoslavia was a center of political and religious immigration for Russians and a provincial center for Ukrainian emigration. It is concluded that the Yugoslav authorities did not distinguish Ukrainians from Russian emigrants, therefore, any specific policy towards them was not carried out. The degree of interaction of Ukrainian emigrants with local authorities in Yugoslavia varied geographically (Slovenia and Croatia, on the one hand, and Serbia and Macedonia, on the other) and in time (in the first half of the 1920s and from the mid-1920s until the beginning of World War II). Keywords: authorities, emigration, Kingdom of Serbs, Croats and Slovenes, Yugoslavia.

scholarly journals Isolation of SAR11 Marine Bacteria from Cryopreserved Seawater

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
pp. e00954-20
Author(s):  
Elizabeth A. Monaghan ◽  
Kelle C. Freel ◽  
Michael S. Rappé
Keyword(s):  
High Throughput ◽  
Marine Bacteria ◽  
Mixed Cultures ◽  
Rrna Gene ◽  
Marine Microorganisms ◽  
Culture Collections ◽  
Natural Systems ◽  
Wide Range ◽  
Long Time ◽  
Cultivation Experiment

ABSTRACTWhile marine microorganisms are frequently studied in their natural environment, isolated strains are invaluable resources that can be used in controlled experiments to expand upon direct observations from natural systems. Here, we sought a means to enhance culture collections of SAR11 marine bacteria by testing the use of seawater cryopreserved with glycerol as an inoculum. Using a raw seawater sample collected from the tropical Pacific Ocean, a subsample was diluted in seawater growth medium to create 576 2-ml dilution cultures containing 5 cells each and incubated for a high-throughput culturing (HTC) experiment, while another portion was cryopreserved in 10% glycerol. After 10 months, a cryopreserved aliquot was thawed and used to create a second cultivation experiment of 480 2-ml cultures containing 5 cells each and 470 cultures containing 105 cells each. The raw seawater cultivation experiment resulted in the successful isolation of 54 monocultures and 29 mixed cultures, while cryopreserved seawater resulted in 59 monocultures and 29 mixed cultures. Combined, the cultures included 51 SAR11 isolates spanning 11 unique 16S rRNA gene amplicon sequence variants (ASVs) from the raw seawater inoculum and 74 SAR11 isolates spanning 13 unique ASVs from cryopreserved seawater. A vast majority (92%) of SAR11 isolates from the two HTC experiments were members of SAR11 subclade Ia, though subclades IIIa and Va were also recovered from cryopreserved seawater and subclade Ib was recovered from both. The four most abundant SAR11 subclade Ia ASVs found in the initial seawater environmental sample were isolated by both approaches.IMPORTANCE High-throughput dilution culture has proved to be a successful approach to bring some difficult-to-isolate planktonic microorganisms into culture, including the highly abundant SAR11 lineage of marine bacteria. While the long-term preservation of bacterial isolates by freezing them in the presence of cryoprotectants, such as glycerol, has been shown to be an effective method of storing viable cells over long time periods (i.e., years), to our knowledge it had not previously been tested for its efficacy in preserving raw seawater for later use as an inoculum for high-throughput cultivation experiments. We found that SAR11 and other abundant marine bacteria could be isolated from seawater that was previously cryopreserved for nearly 10 months at a rate of culturability similar to that of the same seawater used fresh, immediately after collection. Our findings (i) expand the potential of high-throughput cultivation experiments to include testing when immediate isolation experiments are impractical, (ii) allow for targeted isolation experiments from specific samples based on analyses such as microbial community structure, and (iii) enable cultivation experiments across a wide range of other conditions that would benefit from having source inocula available over extended periods of time.

scholarly journals Uncommon disorders and decay in near-isogenic lines of melon and reference cultivars

2009 ◽  
Vol 27 (4) ◽  
pp. 505-514
Author(s):  
Juan Antonio Martínez ◽  
Mohammad-Madi Jowkar ◽  
Javier Mauricio Obando-Ulloa ◽  
Plácido Varó ◽  
Eduard Moreno ◽  
...  
Keyword(s):  
Placental Tissue ◽  
Grey Mould ◽  
Soft Rot ◽  
Economic Losses ◽  
Near Isogenic Lines ◽  
Physiological Basis ◽  
Isogenic Lines ◽  
Fruit Cracking ◽  
Long Time ◽  
Cucumis Melo L

Postharvest disorders and rots can produce important economic losses in fruits stored for long time for exportation. The genetic and physiological basis of some disorders in melon (Cucumis melo L.) are unknown and particularly the possible relation with climacteric behavior. A collection of melon near-isogenic lines (NILs) (SC3-5 and seven more showing climacteric and two non-climacteric ripening pattern) were analyzed to study genetic and physiological aspects of fruit disorders and rots. Two non-climacteric (Nicolás; Inodorus Group; and Shongwan Charmi PI161375, Conomon Group) and two climacteric cultivars (Fado, Reticulatus Group; Védrantais, Cantaloupensis Group) were used as reference. The field was divided in eight blocks containing one three-plant replication for each NIL, two for the parental cultivar Piel de Sapo and one or two for the reference cultivars. Replications evaluated were more than six in the cultivars studied. Plant problems included aphids, powdery mildew, and leaf wind injury. Preharvest fruit disorders included whole fruit cracking in cultivar Védrantais and NIL 5M2, and stylar-end cracking in cultivar Fado. Climacteric NILs with yellow skin were particularly affected by over-ripening, stylar-end cracking, and sunburn during cultivation. At harvest, two NILs showed slight placental tissue necrosis which was inherited from SC and were also detected after storage. Other uncommon disorders seen at harvest or 30 days after storage at 8ºC included warted skin (scarring), flesh discoloration (light brown or translucent areas), hollow flesh disorder, and deep furrow netting inherited from SC. Less common rots included grey mould, bacterial soft rot, Penicillium rot, cottony leak and internal Cladosporium rot. Stylar-end hardness below 20 N·mm-1 was associated with cracking and softening. The incidence of the disorders and rots was too low to confirm that the genetic component played a role in their development.

Improving survival and storage stability of bacteria recalcitrant to freeze-drying: a coordinated study by European culture collections

2015 ◽  
Vol 99 (8) ◽  
pp. 3559-3571 ◽  
Author(s):  
Jindrich Peiren ◽  
Joke Buyse ◽  
Paul De Vos ◽  
Elke Lang ◽  
Dominique Clermont ◽  
...  
Keyword(s):  
Freeze Drying ◽  
Storage Stability ◽  
Culture Collections ◽  
European Culture ◽  
And Storage

MICROMORPHOLOGICAL CHARACTERISTICS OF WOOD BIODEGRADATION IN WET ENVIRONMENTS: A REVIEW

IAWA Journal ◽  
2000 ◽  
Vol 21 (2) ◽  
pp. 135-155 ◽  
Author(s):  
Yoon Soo Kim ◽  
Adya P. Singh
Keyword(s):  
Service Life ◽  
Wood Decay ◽  
Brown Rot ◽  
Soft Rot ◽  
High Moisture ◽  
Brown Rot Fungi ◽  
Wood Biodegradation ◽  
Oxygen Conditions ◽  
Long Time ◽  
Basidiomycete Fungi

Wood in wet environments is attacked and degraded by soft rot fungi and erosion and tunnelling bacteria, which are more tolerant to high moisture and reduced oxygen conditions than basidiomycetes, such as white and brown rot fungi. Since wood decaying basidiomycete fungi are normally more aggressive and can degrade wood faster than soft rot fungi and bacteria, wood in wet environments can survive for a relatively long time. Archaeological investigations show that wood buried deep in ocean sediments can survive for hundreds and even thousands of years. In this review degradation patterns of various types of microbial wood decay are briefly described, and examples of decay type(s) in wood exposed in various wet environments presented. It is important to understand biological wood decay in wet environments in order to find appropriate ways to prolong woodʼs service life and properly restore wooden artefacts.

scholarly journals RANCANG BANGUN ALAT PENDETEKSI KONDISI TELUR AYAM BERBASIS MIKROKONTROLER ATMEGA 32 DENGAN SENSOR CAHAYA

Foristek ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Afdal Tahir ◽  
Mery Subito ◽  
Agustinus Kali
Keyword(s):  
Storage Time ◽  
Time Efficiency ◽  
Chicken Egg ◽  
Detection Tool ◽  
Light Sensor ◽  
Long Time ◽  
Egg Storage ◽  
Speed Up ◽  
Chicken Eggs

When consumers buy eggs, consumers should be more careful choosing the egg because there are some eggs that the quality has been decreased or the eggs are damaged and cannot be consumed anymore. This is caused by the length of egg storage time and didn’t have a tool that capable to detect the condition of the egg. People or egg breeders / entrepreneurs habit on looking the quality of eggs still use manual way, as a result it takes a long time because it must select the eggs condition one by one. The purpose of this research is to design and make the detection tool of chicken egg condition with ATmega 32 microcontroller using light sensor, so that the time efficiency and the result of egg selection becomes faster. . The use of tools is very easy and simple so that consumers or breeders / entrepreneurs can use it. Then to simplify and speed up the selection time of chicken eggs breeder or entrepreneur to distinguish good and damaged egg condition.

scholarly journals Genomic diversity and meiotic recombination among isolates of the biotech yeast Komagataella phaffii (Pichia pastoris)

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Stephanie Braun-Galleani ◽  
Julie A. Dias ◽  
Aisling Y. Coughlan ◽  
Adam P. Ryan ◽  
Kevin P. Byrne ◽  
...  
Keyword(s):  
Pichia Pastoris ◽  
Meiotic Recombination ◽  
Genomic Diversity ◽  
Yeast Culture ◽  
Culture Collections ◽  
Komagataella Phaffii ◽  
Rich Media ◽  
Natural Isolates ◽  
Trait Locus ◽  
Almost All

Abstract Background Komagataella phaffii is a yeast widely used in the pharmaceutical and biotechnology industries, and is one of the two species that were previously called Pichia pastoris. However, almost all laboratory work on K. phaffii has utilized strains derived from a single natural isolate, CBS7435. There is little information about the sequence diversity of K. phaffii or the genetic properties of this species. Results We sequenced the genomes of all the known isolates of K. phaffii. We made a genetic cross between derivatives of two isolates that differ at 44,000 single nucleotide polymorphism sites, and used this cross to analyze the rate and landscape of meiotic recombination. We conducted tetrad analysis by making use of the property that K. phaffii haploids do not mate in rich media, which enabled us to isolate and sequence the four types of haploid cell that are present in the colony that forms when a tetra-type ascus germinates. Conclusions We found that only four distinct natural isolates of K. phaffii exist in public yeast culture collections. The meiotic recombination rate in K. phaffii is approximately 3.5 times lower than in Saccharomyces cerevisiae, with an average of 25 crossovers per meiosis. Recombination is suppressed, and genetic diversity among natural isolates is low, in a region around centromeres that is much larger than the centromeres themselves. Our work lays a foundation for future quantitative trait locus analysis in K. phaffii.

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