scholarly journals Bioinformatic identification of Ty1/Copia-like transposable elements in Deschampsia antarctica E. Desv.

2019 ◽  
Vol 24 ◽  
pp. 317-320
Author(s):  
I. O. Andreev ◽  
I. I. Konvalyuk ◽  
V. A. Kunakh
Keyword(s):  
Transposable Elements ◽  
In Silico ◽  
Transcriptional Activity ◽  
Background Level ◽  
Bioinformatic Analysis ◽  
Reference Sequence ◽  
Deschampsia Antarctica ◽  
The Family ◽  
High Level ◽  
Copia Retrotransposons

Aim. Identification of Ty1/Copia-like transposable elements in Deschampsia antarctica E Desv. in silico. Methods. Bioinformatic analysis of sequence read archives of D. antarctica genome and transcriptome contained in the GenBank database was conducted. The search was carried out using the rice Ty1/Copia TE Tos 17 as a reference sequence. Results. The search revealed the sequences of Ty1/Copia retrotransposons in the D. antarctica genome to show a high level of identity (up to 75% in the homologous regions) to Tos 17. The uneven distribution of the found reads along the reference sequence indicates the existence of a group of the sequences in the genome to contain elements typical of the family and have varying degrees of identity to Tos 17, with more conservative ones being represented in correspondingly greater numbers among the found reads. The presence of the reads identical to Tos 17 in transcriptome indicates that the TE sequences identified in genome have a certain background level of transcriptional activity. Conclusions. Transcriptionally active Ty1/Copia-like transposable elements were identified in silico in D. antarctica genome using methods of bioinformatics. The sequences found can be used to construct primers for PCR and to analyze the activity of the TE of this family in D. antarctica in further studies. Keywords: bioinformatic analysis, Deschampsia antarctica E Desv., transposable elements, Ty1/Copia.

scholarly journals Truncated Non-Nuclear Transposable Elements in Grapevine: A Mini Review

2019 ◽  
Vol 50 (4) ◽  
pp. 219-227
Author(s):  
A.V. Milovanov ◽  
J. Tello ◽  
U.C.M. Anhalt ◽  
A. Forneck
Keyword(s):  
Gene Transfer ◽  
Mitochondrial Genome ◽  
Transposable Elements ◽  
Vitis Vinifera ◽  
In Silico ◽  
Gene Evolution ◽  
High Rate ◽  
Miniature Inverted Transposable Elements ◽  
High Level ◽  
Inner Region

Abstract In this mini-review we present insight to the non-nuclear transposable elements and in silico analysis of miniature inverted transposable elements (MITEs) in the grapevine mitochondrial genome. Here we report the identification of 17 truncated sequences in grapevine (Vitis vinifera L.) mitochondrial genome which expectedly belongs to the four ancient transposon families (hAT, Tc1Mariner, Mutator and PIF/Harbinger). Some sequences with a high rate of homology in chloroplast and nuclear genomes were also identified. Thus, it suggests the intercellular gene transfer between these three organelles. These partial sequences showed a high level of similitude with full MITE sequences, and they were found in their inner region, supporting their MITE origin. Further analysis revealed these sequences in other life kingdoms (including eubacteria and archaea), which indicates their ancient origin. Further research showed that 13 out of the 17 sequences are conserved domains of the genes where they are located, suggesting their contribution to gene evolution. Therefore, we suppose that more studies of nature, origin and functional meaning of these sequences and their fusion with genes are necessary. In the light of our observations it will be useful for further studies of V. vinifera genome organizing and systematics, as well as for other species.

In the Quest for a Stable Triplet State in Small Polyaromatic Hydrocarbons : An In-Silico Tool for Rational Design and Prediction

2019 ◽  
Author(s):  
Madhumita Rano ◽  
Sumanta K Ghosh ◽  
Debashree Ghosh
Keyword(s):  
Triplet State ◽  
Small Molecules ◽  
In Silico ◽  
Qualitative Agreement ◽  
Rational Design ◽  
Polyaromatic Hydrocarbons ◽  
Spin Hamiltonian ◽  
Spin Frustration ◽  
Computationally Efficient ◽  
High Level

<div>Combining the roles of spin frustration and geometry of odd and even numbered rings in polyaromatic hydrocarbons (PAHs), we design small molecules that show exceedingly small singlet-triplet gaps and stable triplet ground states. Furthermore, a computationally efficient protocol with a model spin Hamiltonian is shown to be capable of qualitative agreement with respect to high level multireference calculations and therefore, can be used for fast molecular discovery and screening.</div>

scholarly journals The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jung-Hyun Kim ◽  
Vladimir N. Noskov ◽  
Aleksey Y. Ogurtsov ◽  
Ramaiah Nagaraja ◽  
Nikolai Petrov ◽  
...  
Keyword(s):  
Genomic Structure ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Chromosome 21 ◽  
Reference Sequence ◽  
Chromosome 22 ◽  
Rdna Variation ◽  
High Level ◽  
Tar Cloning

AbstractThe rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.

scholarly journals Implementation of the Family HELP Protocol: A Feasibility Project for a West Texas ICU

Healthcare ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 146
Author(s):  
Rebecca McClay
Keyword(s):  
Strong Support ◽  
Family Intervention ◽  
Successful Implementation ◽  
Positive Perception ◽  
Family Presence ◽  
West Texas ◽  
The Family ◽  
Control And Prevention ◽  
High Level ◽  
Near Future

The purpose of this project was to determine if bedside intensive care unit (ICU) nurse buy-in to the Family Hospital Elder Life Program (HELP) protocol was sufficient to make implementation feasible at one county hospital in West Texas. Surveys were anonymous with ballot box collection being available to the bedside ICU nurses for one week each. Questions were based on literature findings of expected outcomes, identified barriers and facilitators, Calgary Family Intervention Method framework domains, and the Centers for Disease Control and Prevention Framework for program evaluation. Outcome measures were taken from the stated aims of the project and evaluated from paired baseline and summative survey questions. Survey participation was approximately half of nurses employed in the studied ICU. Analysis of the surveys showed a positive perception of family presence decreasing patient delirium symptoms, and a positive perception of the Family HELP protocol. The results described a high perception of family members as partners in care and high intention to implement the Family HELP protocol, indicating strong support of a full implementation of the protocol. The high level of bedside nurse buy-in present in this study has large implications for successful implementation of the Family HELP protocol in the near future, with sustainability and continued use supported by potential inclusion of the task in the electronic health record charting.

scholarly journals In silico Phylogenetic Analysis of hAT Transposable Elements in Plants

Genes ◽  
2018 ◽  
Vol 9 (6) ◽  
pp. 284 ◽  
Author(s):  
Gökhan Karakülah ◽  
Athanasia Pavlopoulou
Keyword(s):  
Phylogenetic Analysis ◽  
Transposable Elements ◽  
In Silico

Academic Achievement of Female Students at College Level In Relation to Their Family Environment And Locale

2021 ◽  
pp. 51-65
Author(s):  
Nishta Rana ◽  
Shivani Kapoor
Keyword(s):  
Academic Achievement ◽  
Academic Success ◽  
Family Environment ◽  
Sampling Technique ◽  
Female Students ◽  
College Level ◽  
Family Environment Scale ◽  
Environment Scale ◽  
The Family ◽  
High Level

Academic achievement is often considered as a key criterion to judge one's total potentialities and capabilities. Academic achievement has become a prime interest for the teachers, educationists, psychologists and parents to predict children's academic success which is considered to be an outcome of the learning environment and the family. The present study aimed at seeking the level of academic achievement of female students at the college level with respect to their family environment and locale. Random Sampling Technique was applied to draw the sample of 200 female students studying in the five-degree colleges of Jammu City (J&K) in the year 2015. Family Environment Scale (FES-BC) by Bhatia and Chadha (2012) was used for data collection. This tool has eight dimensions-Cohesion, Expressiveness, Conflict, Acceptance and Caring, Independence, Active-Recreational Orientation, Organisation and Control. The findings revealed that most of the female students were having an average level of academic achievement. Very few female students were found to have a high level of academic achievement. No significant differences in the level of academic achievement were found among female students in relation to their residential background, whereas significant differences were found in the family environment of female students with respect to the locality at the sub-scale “Acceptance and Caring” and “Active Recreational Orientation”. The value of the coefficient of correlation was found to be low, positive but significant at the 0.01 level of significance at the sub-scale “Cohesion” of Family Environment Scale. It shows that academic achievement and cohesion in the family are positively related with each other, however, the correlation is low.

scholarly journals Quality of life of elderly with alzheimer’s disease: a comparative study between the patient’s and the caregiver’s report

2010 ◽  
Vol 18 (1) ◽  
pp. 26-32 ◽  
Author(s):  
Keika Inouye ◽  
Elisete Silva Pedrazzani ◽  
Sofia Cristina Iost Pavarini ◽  
Cristina Yoshie Toyoda
Keyword(s):  
Quality Of Life ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Life Assessment ◽  
Quality Of Life Assessment ◽  
Patient Reports ◽  
The Family ◽  
Final Score ◽  
High Level

This paper aimed to compare the reports of patients and caregivers about how they perceive quality of life (QoL) in general and each of its dimensions in elderly with Alzheimer’s Disease (AD). The participants were elderly diagnosed with AD (n=53) attended by the Exceptional Medication Program in a city in the interior of Sao Paulo; and their respective family caregivers. The QoL measures were obtained through the Quality of Life Assessment Scale on Alzheimer’s Disease. The results showed statistically significant differences in the “memory” (p<0.05) and “you in general” (p<0.005) dimensions. Regarding the final score, the average in the patient’s version was 29.32 points (sd=6.27), against 28.33 points (sd=5.58) in the family version, p>0.100. Although the relative and patient reports were not identical, the results pointed to a high level of consistency among information.

scholarly journals Preliminary study of the enzyme ubiquitin carboxylterminal hydrolase 14 (UBP6) in Giardia intestinalis: structural bioinformatic analysis and transcriptional profile during encystation

2015 ◽  
Vol 43 (2) ◽  
pp. 32-40
Author(s):  
Magda E Alvarado ◽  
Camila A González ◽  
Moisés Wasserman ◽  
Claudia C Rubiano
Keyword(s):  
Protein Turnover ◽  
Bioinformatic Analysis ◽  
Giardia Intestinalis ◽  
Deubiquitinating Enzyme ◽  
Combined Approach ◽  
Protein Coding ◽  
Starting Point ◽  
The Family ◽  
Preliminary Study ◽  
Carboxyl Terminal

This paper presents a combined approach<br />with two aims. The first is to analyze the<br />reported sequence of the enzyme ubiquitin<br />carboxyl-terminal hydrolase 14 of Giardia<br />intestinalis (UBP6) through computational<br />methods to find components related with<br />its hypothetical function. The second is<br />to determine if the protein-coding gene is<br />expressed in G. intestinalis and, if such is<br />the case, also determine its transcription<br />pattern along the life cycle of the parasite. It<br />was established that the protein belongs to<br />the family of Cys-dependent deubiquitinases<br />and more specifically to ubiquitin specific<br />proteases (USPs). Moreover, the catalytic<br />center with the complete triad as well as<br />typical features of the USP motif were also<br />identified. Since the computational findings<br />suggest that the enzyme could be functional,<br />reverse transcription coupled to PCR was<br />used as a first approach to establish if in fact<br />the coding gene is expressed in the parasite.<br />Interestingly, it was found not only that<br />the gene is expressed, but also that there<br />is a transcription variation along the life<br />cycle of the parasite. These two findings are<br />the starting point for further studies since<br />they tentatively suggest that this enzyme<br />could be involved in the protein turnover<br />that occurs during parasite encystation.<br />Although preliminary, this study is the first<br />report concerning the study of a specific<br />deubiquitinating enzyme in the parasite G.<br />intestinalis.

scholarly journals Halomicrococcus hydrotolerans gen. nov., sp. nov., an extremely halophilic archaeon isolated from a subterranean salt deposit

2020 ◽  
Vol 70 (8) ◽  
pp. 4425-4431 ◽  
Author(s):  
Shaoxing Chen ◽  
Yao Xu ◽  
Siqi Sun ◽  
Jingwen Liu ◽  
Feilong Chen
Keyword(s):  
16S Rrna ◽  
In Silico ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Genes ◽  
Salt Deposit ◽  
Halophilic Archaeon ◽  
Content Type ◽  
Link Type ◽  
The Family

A halophilic archaeon, strain H22T, was isolated from a subterranean salt deposit sampled at Yunnan salt mine, PR China. Colonies of strain H22T were light pink-pigmented. Cells were coccus, non-motile, Gram-stain-negative, and did not lyse in distilled water. The strain was aerobic and grew at 20–55 °C (optimum, 37 °C), in the presence of 10–30 % (w/v) NaCl (20 %) and at pH 6.5–9.0 (pH 7.0). Mg2+ was required for growth (optimum, 0.005 M). Major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and sulfated mannosyl-glucosyl-glycerol diether-1. Sequence similarity search based on the multiple 16S rRNA genes (rrnA, rrnB and rrnC) of strain H22T revealed that it was most closely related to species of the genera Haloarchaeobius , Haladaptatus , Halorussus and Halorubellus with relative low sequence similarities (91.9–93.7 %). The strain, however, shared highest rpoB′ gene sequence identities with Halorussus rarus TBN4T (90.8 % rpoB′ gene sequence similarity). Phylogenetic trees based on 16S rRNA and rpoB′ gene sequences revealed a robust lineage of the strain H22T with members of related genera of the family Halobacteriaceae . The DNA G+C content of strain H22T was 62.9 mol%. Genome-based analysis of average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) between strains H22T and its closest relative were equal or lower than 77.7 and 22.4 %, respectively, which were far below the threshold for delineation of a new species. Based on ANI values, in silico DDH, and distinct morphological and physiological differences from the previously described taxa, we suggest that strain H22T represents a novel species of a new genus within the family Halobacteriaceae , for which the name Halomicrococcus hydrotolerans gen. nov., sp. nov. is proposed. The type strain is H22T (=CGMCC 1.16291T=NBRC 113231T).

scholarly journals INDIVIDUAL-TYPOLOGICAL CHARACTERISTICS OF PERSONALITY OF CANDIDATES TO PARENTS IN SUBSTITUTE FAMILIES

2020 ◽  
Vol 11 (87) ◽  
Author(s):  
Elena Vishtalenko ◽  
◽  
Emma Andreasyan ◽  
Keyword(s):  
Social Services ◽  
Family Relationships ◽  
Foster Parents ◽  
Foster Families ◽  
The Family ◽  
Role Of Parents ◽  
Life Path ◽  
The Individual ◽  
High Level

Most researchers of socialization processes agree that the primary socialization carried out in the family is crucial. The phenomenon of the family was considered in terms of psychological, sociological, anthropological, philosophical, biological and cultural approaches. Now the question of surrogacy is being studied in terms of the psychology of the life path of the individual; as manifestations of the meaning of life, will, responsibility; as a world of the subjective, where is always something more. Many scientists pay attention to the methodology, organization, functioning of foster families; the problems of lifestyle of orphan children in general, and in particular – in a professionally foster family. Scientists have considered the motivation of the adopted child into the family and some socio-psychological characteristics of parents. However, there are almost no studies of some individual-typological features that dysfunctionally affect family relationships, although these features may be the reason for the denial of the family's ability to be a substitute. The relevance of the study is due to the need of supplement the structural and semantic components of the psychological diagnosis of potential parents in foster families. The empirical study was conducted on the basis of the Odessa Regional Center for Social Services for Families, Children and Youth, a territorial division of the Odessa Regional State Administration. In testing took a part about 30 applicants for foster parents. With the help of Individual-typological questionnaire LM Sobchyk (ITO) there was created an average statistical portrait of candidates for the role of parents in foster families. They are characterized by a high level of extraversion (48.6%); average level of rigidity (82.9%), aggression (54.3%), anxiety (82.9%), introversion (71.5%), lability (74.3%), sensitivity (62.9%), spontaneity (60%). All these qualities positively characterize all members of the sample and confirm their reliability as potential parents in foster families. These conclusions can be used by psychologists in the selection of candidates for the role of foster parents in foster families, as well as in psychological counseling.

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