scholarly journals Measurement of Chromosomal Arms and FISH Reveal Complex Genome Architecture and Standardized Karyotype of Model Fish, Genus Carassius

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2343
Author(s):  
Martin Knytl ◽  
Nicola Reinaldo Fornaini
Keyword(s):  
Research Field ◽  
Biological Characteristics ◽  
Evolutionary Relationships ◽  
Fish Analysis ◽  
Fish Model ◽  
Interspecies Hybridization ◽  
Short Period ◽  
Chromosomal Architecture ◽  
Karyotype Formula ◽  
Measured Length

The widely distributed ray-finned fish genus Carassius is very well known due to its unique biological characteristics such as polyploidy, clonality, and/or interspecies hybridization. These biological characteristics have enabled Carassius species to be successfully widespread over relatively short period of evolutionary time. Therefore, this fish model deserves to be the center of attention in the research field. Some studies have already described the Carassius karyotype, but results are inconsistent in the number of morphological categories for individual chromosomes. We investigated three focal species: Carassius auratus, C. carassius and C. gibelio with the aim to describe their standardized diploid karyotypes, and to study their evolutionary relationships using cytogenetic tools. We measured length (q+plength) of each chromosome and calculated centromeric index (i value). We found: (i) The relationship between q+plength and i value showed higher similarity of C. auratus and C. carassius. (ii) The variability of i value within each chromosome expressed by means of the first quartile (Q1) up to the third quartile (Q3) showed higher similarity of C. carassius and C. gibelio. (iii) The fluorescent in situ hybridization (FISH) analysis revealed higher similarity of C. auratus and C. gibelio. (iv) Standardized karyotype formula described using median value (Q2) showed differentiation among all investigated species: C. auratus had 24 metacentric (m), 40 submetacentric (sm), 2 subtelocentric (st), 2 acrocentric (a) and 32 telocentric (T) chromosomes (24m+40sm+2st+2a+32T) ; C. carassius: 16m+34sm+8st+42T; and C. gibelio: 16m+22sm+10st+2a+50T. (v) We developed R scripts applicable for the description of standardized karyotype for any other species. The diverse results indicated unprecedented complex genomic and chromosomal architecture in the genus Carassius probably influenced by its unique biological characteristics which make the study of evolutionary relationships more difficult than it has been originally postulated.

scholarly journals An optimized LC-HRMS untargeted metabolomics workflow for multi-matrices investigations in the three-spined stickleback

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260354
Author(s):  
Emmanuelle Lebeau-Roche ◽  
Gaëlle Daniele ◽  
Aurélie Fildier ◽  
Cyril Turies ◽  
Odile Dedourge-Geffard ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Gasterosteus Aculeatus ◽  
High Resolution Mass Spectrometry ◽  
Reversed Phase ◽  
Research Field ◽  
Untargeted Metabolomics ◽  
Whole Body ◽  
Systematic Analysis ◽  
Fish Model ◽  
Ionization Mode

Environmental metabolomics has become a growing research field to understand biological and biochemical perturbations of organisms in response to various abiotic or biotic stresses. It focuses on the comprehensive and systematic analysis of a biologic system’s metabolome. This allows the recognition of biochemical pathways impacted by a stressor, and the identification of some metabolites as biomarkers of potential perturbations occurring in a body. In this work, we describe the development and optimization of a complete reliable methodology based on liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS) for untargeted metabolomics studies within a fish model species, the three-spined stickleback (Gasterosteus aculeatus). We evaluated the differences and also the complementarities between four different matrices (brain, gills, liver and whole fish) to obtain metabolome information. To this end, we optimized and compared sample preparation and the analytical method, since the type and number of metabolites detected in any matrix are closely related to these latter. For the sample preparation, a solid-liquid extraction was performed on a low quantity of whole fish, liver, brain, or gills tissues using combinations of methanol/water/heptane. Based on the numbers of features observed in LC-HRMS and on the responses of analytical standards representative of different metabolites groups (amino acids, sugars…), we discuss the influence of the nature, volume, and ratio of extraction solvents, the sample weight, and the reconstitution solvent. Moreover, the analytical conditions (LC columns, pH and additive of mobile phases and ionization modes) were also optimized so as to ensure the maximum metabolome coverages. Thus, two complementary chromatographic procedures were combined in order to cover a broader range of metabolites: a reversed phase separation (RPLC) on a C18 column followed by detection with positive ionization mode (ESI+) and a hydrophilic interaction chromatography (HILIC) on a zwitterionic column followed by detection with negative ionization mode (ESI-). This work provides information on brain, gills, liver, vs the whole body contribution to the stickleback metabolome. These information would help to guide ecotoxicological and biomonitoring studies.

scholarly journals Scientometric analysis of COVID-19 studies: how the velocity of science leads to discoveries and new technology

2021 ◽  
Author(s):  
Mario Coccia
Keyword(s):  
Science Studies ◽  
Critical Role ◽  
Scientific Progress ◽  
Research Field ◽  
Scientometric Analysis ◽  
Origin And Evolution ◽  
Research Fields ◽  
Short Period ◽  
New Research ◽  
Dynamics Of Science

Abstract Scholars argue that the ‘‘science of science’’ studies have to investigate the critical role of exogenous events in the emergence of new research fields. The goal of this study is to analyze and explain the birth and growth of new research fields driven by exogenous event to science, such as COVID-19 (Coronavirus disease 2019) global pandemic crisis. This study here analyzes how the novel research field of COVID-19 emerges, in a comparative analysis with other scientific fields concerning respiratory illnesses (e.g., Chronic Obstructive Pulmonary Disease, COPD and Lung Cancer), to explain factors determining the unique dynamics of science that is generating scientific breakthroughs in a short period of time. The origin and evolution of the research field of COVID-19 reveal that has an acceleration of scientific production equal to a growth of 1.71% daily in 2020, laying the foundations for science advances and a likely paradigm shift in the treatment of infectious diseases with novel mRNA vaccines. Main results are generalized in properties that clarify the dynamics of science and explain the characteristics that generate the origin and evolution of new research fields driven by unforeseen crises with critical implications for technological and social change directed scientific progress of human societies.

Establishment and Characterization of a New Human Ph+ Erythroleukemic Cell Line, VES.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4558-4558
Author(s):  
Mirna Golemovic ◽  
Lana Rnjak ◽  
Klara Dubravcic ◽  
Sanja Davidovic-Mrsic ◽  
Ivana Franic ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Cell Line ◽  
Multiparameter Flow Cytometry ◽  
Fish Analysis ◽  
Suitable Model ◽  
Short Period ◽  
Erythroleukemia Cell ◽  
Erythroleukemic Cell ◽  
Erythroleukemic Cell Line

Abstract Continuous human malignant hematopoietic cell lines are invaluable tool for hematological research. Here we report on a new erythroleukemic cell line termed VES that was established from the bone marrow mononuclear cells (BMNC) of a 22-year-old woman with Ph+ CML during her second post-transplant period. Actually, after unsuccessful allo-transplantation, the patient received auto-transplant that also failed to engraft. At the time of initiation of BMNC into culture for the analysis of stromal cell capacity, her bone marrow was tested Ph-negative by both FISH and PCR. Instead of establishment of an adherent stromal layer in vitro, blast-like cells appeared in the supernatant on day 27. These blast cells expressed highly amplified bcr/abl locus as shown by FISH, whereas the patient’s bone marrow was still Ph-negative at the time. Following a very short period, the cultured cells started to express stable features of erythroleukemia cell line. Optimal growth was obtained by suspending the cells at concentration of 0.3x106 cells/ml in IMDM containing 10% FBS, 1% penicillin-streptomycin and 1% L-glutamine solution. After 3 days of culture, cell concentration varied between 1.3 and 1.8x106 cells/ml. VES cells were tested negative for the presence of EBV virus. For analysis of clonogenicity, VES cells at concentration of 103/ml were grown in a serum-free methylcellulose medium without cytokines (H4236; StemCell Tech., Canada). Following 7-day culture, 103 VES cells produced 251 ±42 and after 14 days 431 ±30 GF-independent colonies. Furthermore, on day 14 of the cell culture it was possible to observe reddish color of the colonies indicating the presence of hemoglobin. Cytological examination of cytospin preparations indicated homogenous population of leukemia blasts (>80%) the majority of them (>90%) being glycophorinA positive and MPO negative. Imunophenotyping and multiparameter flow cytometry revealed proerythroblastic lineage-associated profile: GlyA/CD235a+, CD11b+, CD15+, CD29+, CD33+, and CD117+. Conventional cytogenetics revealed complex karyotype with multiple numerical/structural abnormalities (MAKA), while metaphase FISH revealed the following aberrations: t(9;22), 5q31, 7q31, +8, +6. Since FISH analysis detected highly amplified bcr/abl locus, we tested VES cells’ sensitivity to imatinib (Gleevec). Treatment with imatinib for 3 days (MTS assay) inhibited proliferation of VES cells with IC50 value of 0.2mM. Following 14 days of culture in methylcellulose medium with addition of 0.2mM imatinib, the clonogenic potential of VES cells was reduced by 55% in relation to untreated control. We demonstrated that imatinib induced apoptosis in VES cells in time- and dose-dependant manner, assessed with AnnexinV and PI staining, while there were no significant changes observed in the cell cycle except for a mild increase in cells in G0/G1 phase. Although further analyses are required, we believe that VES cells represent a new Ph+ erythroleukemia cell line and a suitable model for studying Ph+ malignant hematopoiesis in vitro.

scholarly journals Research Trends with Cross Tabulation Search Engine

2013 ◽  
Vol 11 (1) ◽  
pp. 31-44 ◽  
Author(s):  
Chengjiu Yin ◽  
Sachio Hirokawa ◽  
Jane Yin-Kim Yau ◽  
Kiyota Hashimoto ◽  
Yoshiyuki Tabata ◽  
...  
Keyword(s):  
Search Engine ◽  
Learning Strategy ◽  
Research Field ◽  
Research Trends ◽  
Research Trend ◽  
Processing Technologies ◽  
Research Survey ◽  
Short Period ◽  
Cross Tabulation ◽  
Conducting Research

To help researchers in building a knowledge foundation of their research fields which could be a time-consuming process, the authors have developed a Cross Tabulation Search Engine (CTSE). Its purpose is to assist researchers in 1) conducting research surveys, 2) efficiently and effectively retrieving information (such as important researchers, research groups, keywords), and also 3) providing analytical information relating to past and current research trends in a particular field. Their CTSE system employs data-processing technologies and emphasizes the use of a “Learn by Searching” learning strategy to support students to analyze such research trends. To show the effectiveness of CTSE, a pilot experiment has been conducted, where participants were assigned to do research survey tasks and then answer a questionnaire regarding the effectiveness and usability of the system. The results showed that the system has been helpful to students in conducting research surveys, and the research trend transitions that our system presented were effective for producing research trend surveys. Moreover, the results showed that most students had favorable attitudes toward the usage and usability of the system, and those students were satisfied in gaining more know ledge in a particular research field in a short period.

Commercial high-throughput sequencing and its applications in DNA analysis

Biologia ◽  
2009 ◽  
Vol 64 (1) ◽  
Author(s):  
Hai Peng ◽  
Jing Zhang
Keyword(s):  
High Throughput ◽  
Protein Interactions ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Dna Analysis ◽  
Research Field ◽  
The Past ◽  
Sequencing Method ◽  
Short Period ◽  
Sequencing Platforms

AbstractDNA sequences can be used for the analysis of genetic variation and gene function. The high-throughput sequencing techniques that have been developed over the past three years can read as many as one billion bases per run, and are far less expensive than the traditional Sanger sequencing method. Therefore, the high-throughput sequencing has been applied extensively to genomic analyses, such as screening for mutations, construction of genomic methylation maps, and the study of DNA-protein interactions. Although they have only been available for a short period, high-throughput sequencing techniques are profoundly affecting many of the life sciences, and are opening out new potential avenues of research. With the highly-developed commercial high-throughput sequencing platforms, each laboratory has the opportunity to explore this research field. Therefore, in this paper, we have focused on commercially-popular high-throughput sequencing techniques and the ways in which they have been applied over the past three years.

The Origin of the Moon and its Relationship to the Origin of the Solar System

1962 ◽  
Vol 14 ◽  
pp. 133-148 ◽  
Author(s):  
Harold C. Urey
Keyword(s):  
Solar System ◽  
The Moon ◽  
The Past ◽  
The Earth ◽  
Short Period ◽  
Origin Of The Moon

During the last 10 years, the writer has presented evidence indicating that the Moon was captured by the Earth and that the large collisions with its surface occurred within a surprisingly short period of time. These observations have been a continuous preoccupation during the past years and some explanation that seemed physically possible and reasonably probable has been sought.

the effects of resonance with Jupiter in the system of short-period comets

1974 ◽  
Vol 22 ◽  
pp. 193-203
Author(s):  
L̆ubor Kresák
Keyword(s):  
Structural Effects ◽  
Order Resonance ◽  
Mean Motion ◽  
Short Period ◽  
The Mean ◽  
Compound Effect ◽  
Low Order

AbstractStructural effects of the resonance with the mean motion of Jupiter on the system of short-period comets are discussed. The distribution of mean motions, determined from sets of consecutive perihelion passages of all known periodic comets, reveals a number of gaps associated with low-order resonance; most pronounced are those corresponding to the simplest commensurabilities of 5/2, 2/1, 5/3, 3/2, 1/1 and 1/2. The formation of the gaps is explained by a compound effect of five possible types of behaviour of the comets set into an approximate resonance, ranging from quick passages through the gap to temporary librations avoiding closer approaches to Jupiter. In addition to the comets of almost asteroidal appearance, librating with small amplitudes around the lower resonance ratios (Marsden, 1970b), there is an interesting group of faint diffuse comets librating in characteristic periods of about 200 years, with large amplitudes of about±8% in μ and almost±180° in σ, around the 2/1 resonance gap. This transient type of motion appears to be nearly as frequent as a circulating motion with period of revolution of less than one half that of Jupiter. The temporary members of this group are characteristic not only by their appearance but also by rather peculiar discovery conditions.

Models of comets with strongly variable nongravitational effects

1999 ◽  
Vol 173 ◽  
pp. 381-387
Author(s):  
M. Królikowska ◽  
G. Sitarski ◽  
S. Szutowicz
Keyword(s):  
Cometary Nucleus ◽  
Spin Axis ◽  
Reactive Force ◽  
Orbital Elements ◽  
Cometary Nuclei ◽  
Short Period ◽  
Basic Parameters ◽  
Polar Radius ◽  
Cometary Activity ◽  
Nongravitational Effects

AbstractThe nongravitational motion of five “erratic” short-period comets is studied on the basis of published astrometric observations. We present the precession models which successfully link all the observed apparitions of the comets: 21P/Giacobini-Zinner, 31P/Schwassmann-Wachmann 2, 32P/Comas Solá, 37P/Forbes, and 43P/Wolf-Harrington. We used the Sekanina's forced precession model of the rotating cometary nucleus to include the nongravitational terms into equations of the comet's motion. Values of six basic parameters (four connected with the rotating comet nucleus and two describing the precession of spin-axis of the nucleus) have been determined along the orbital elements from positional observations of the comets. The solutions were derived with additional assumptions which introduce instantaneous changes of modulus of reactive force,Aand of maximum of cometary activity with respect to perihelion time. The present precession models impose some contraints on sizes and rotational periods of cometary nuclei. According to our solutions the nucleus of 21P/Giacobini-Zinner with oblateness along the spin-axis of about 0.32 (equatorial to polar radius of 1.46) is the most oblate among five investigated comets.

Covering of cometary nucleus by refractory crust and its evolution into asteroid-like body

1999 ◽  
Vol 173 ◽  
pp. 365-370
Author(s):  
Kh.I. Ibadinov
Keyword(s):  
Laboratory Experiments ◽  
Cometary Nucleus ◽  
Sublimation Rate ◽  
Cometary Nuclei ◽  
Short Period Comet ◽  
Short Period ◽  
Brightness Decrease ◽  
Crust Thickness ◽  
Ice Sublimation ◽  
Period Comet

AbstractFrom the established dependence of the brightness decrease of a short-period comet dependence on the perihelion distance of its orbit it follows that part of the surface of these cometary nuclei gradually covers by a refractory crust. The results of cometary nucleus simulation show that at constant insolation energy the crust thickness is proportional to the square root of the insolation time and the ice sublimation rate is inversely proportional to the crust thickness. From laboratory experiments resulted the thermal regime, the gas productivity of the nucleus, covering of the nucleus by the crust, and the tempo of evolution of a short-period comet into the asteroid-like body studied.

From the Oort cloud to Halley-type comets

1999 ◽  
Vol 173 ◽  
pp. 327-338 ◽  
Author(s):  
J.A. Fernández ◽  
T. Gallardo
Keyword(s):  
Total Population ◽  
Complex Function ◽  
Dynamical Evolution ◽  
Oort Cloud ◽  
Capture Process ◽  
Influx Rate ◽  
Short Period ◽  
Dynamical Properties ◽  
Orbital Periods ◽  
Probability Of Capture

AbstractThe Oort cloud probably is the source of Halley-type (HT) comets and perhaps of some Jupiter-family (JF) comets. The process of capture of Oort cloud comets into HT comets by planetary perturbations and its efficiency are very important problems in comet ary dynamics. A small fraction of comets coming from the Oort cloud − of about 10−2− are found to become HT comets (orbital periods < 200 yr). The steady-state population of HT comets is a complex function of the influx rate of new comets, the probability of capture and their physical lifetimes. From the discovery rate of active HT comets, their total population can be estimated to be of a few hundreds for perihelion distancesq <2 AU. Randomly-oriented LP comets captured into short-period orbits (orbital periods < 20 yr) show dynamical properties that do not match the observed properties of JF comets, in particular the distribution of their orbital inclinations, so Oort cloud comets can be ruled out as a suitable source for most JF comets. The scope of this presentation is to review the capture process of new comets into HT and short-period orbits, including the possibility that some of them may become sungrazers during their dynamical evolution.

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