scholarly journals Characterization of strawberry (Fragaria vesca) sequence genome

2018 ◽  
Author(s):  
Ao Li ◽  
Lide Chen ◽  
Zhongjie Liu ◽  
Mengjie Cui ◽  
Lingfei Shangguan ◽  
...  
Keyword(s):  
Function Analysis ◽  
Average Length ◽  
Statistical Characteristics ◽  
Intronless Gene ◽  
Individual Gene ◽  
Expression Of Genes ◽  
Number Of Genes ◽  
General Statistical ◽  
The Individual ◽  
Different Parts

AbstractBackgroundIn order to understand strawberry genes’ structure and evolution in this era of genomics, it is important to know the general statistical characteristics of the gene, intron and exon structures of strawberry and the expression of genes on different parts of strawberry genome. In the present study, about 32,422 genes on strawberry chromosomes were evaluated, and a number of bioinformatic softwares were used to analyze the characteristics of genes, exons and introns, expression of genes in different regions on the chromosomes. Also, the positions of strawberry centromeres were predicted.ResultsOur results showed that, there are differences in the various features of different chromosomes and also vary in different parts of the same chromosome. The longer the number of genes, the longer the length of chromosome. The average length of genes is about 2809bp and the length of the individual gene is 0–2000bp with 5.3 exons and 4.3 introns per gene. The average length of the exon was 229bp and the intron was 413bp. Among the evaluated genes, ehe intronless gene accounted for 20.05%. Consistently a same trend with the expression levels of the same parts of the gene on a chromosome in different organizations was observed. Finally, the number of genes was positively correlated with the number of intronless, and there was a negative correlation of the length of the gene. The length of the gene depends primarily on the length of the intron, and the length of the exon has little effect on it. The number of exons was negatively correlated with the length of the exons, and the intron was also true.ConclusionThe results of this investigation could definitely provide a significant foundation for further research on function analysis of gene family in Strawberry.

Study on Pramana Shareera in relation to Prakriti

2016 ◽  
Vol 2 (3) ◽  
Author(s):  
Rajendra Pai N. ◽  
U. Govindaraju
Keyword(s):  
Observational Study ◽  
Upper Limb ◽  
Lower Limb ◽  
Characteristic Property ◽  
The Body ◽  
Artificial Limbs ◽  
Body Parts ◽  
Unit Of Measurement ◽  
The Individual ◽  
Different Parts

Ayurveda in its principle has given importance to individualistic approach rather than generalize. Application of this examination can be clearly seem like even though two patients suffering from same disease, the treatment modality may change depending upon the results of Dashvidha Pariksha. Prakruti and Pramana both used in Dashvidha Pariksha. Both determine the health of the individual and Bala (strength) of Rogi (Patient). Ayurveda followed Swa-angula Pramana as the unit of measurement for measuring the different parts of the body which is prime step assessing patient before treatment. Sushruta and Charaka had stated different Angula Pramana of each Pratyanga (body parts). Specificity is the characteristic property of Swa-angula Pramana. This can be applicable in present era for example artificial limbs. A scientific research includes collection, compilation, analysis and lastly scrutiny of entire findings to arrive at a conclusion. Study of Pramana and its relation with Prakruti was conducted in 1000 volunteers using Prakruti Parkishan proforma with an objective of evaluation of Anguli Pramana in various Prakriti. It was observed co-relating Pramana in each Prakruti and Granthokta Pramana that there is no vast difference in measurement of head, upper limb and lower limb. The observational study shows closer relation of features with classical texts.

scholarly journals A Synergistic Anti-Diabetic Effect by Ginsenosides Rb1 and Rg3 through Adipogenic and Insulin Signaling Pathways in 3T3-L1 Cells

2021 ◽  
Vol 11 (4) ◽  
pp. 1725
Author(s):  
Hee-Do Hong ◽  
Sun-Il Choi ◽  
Ok-Hwan Lee ◽  
Young-Cheul Kim
Keyword(s):  
Transcription Factors ◽  
Insulin Signaling ◽  
Adipocyte Differentiation ◽  
Red Ginseng ◽  
Inhibitory Effects ◽  
Rt Pcr ◽  
High Concentration ◽  
Expression Of Genes ◽  
The Individual ◽  
Maximal Expression

Although ginsenosides Rb1 and Rg3 have been identified as the significant ginsenosides found in red ginseng that confer anti-diabetic actions, it is unclear whether insulin-sensitizing effects are mediated by the individual compounds or by their combination. To determine the effect of ginsenosides Rb1 and Rg3 on adipocyte differentiation, 3T3-L1 preadipocytes were induced to differentiate the standard hormonal inducers in the absence or presence of ginsenosides Rb1 or Rg3. Additionally, we determined the effects of Rb1, Rg3, or their combination on the expression of genes related to adipocyte differentiation, adipogenic transcription factors, and the insulin signaling pathway in 3T3-L1 cells using semi-quantitative RT-PCR. Rb1 significantly increased the expression of CEBPα, PPARγ, and aP2 mRNAs. However, Rg3 exerted its maximal stimulatory effect on these genes at 1 μM concentration, while a high concentration (50 μM) showed inhibitory effects. Similarly, treatment with Rb1 and Rg3 (1 μM) increased the expression of IRS-1, Akt, PI3K, GLUT4, and adiponectin. Importantly, co-treatment of Rb1 and Rg3 (9:1) induced the maximal expression levels of these mRNAs. Our data indicate that the anti-diabetic activity of red ginseng is, in part, mediated by synergistic actions of Rb1 and Rg3, further supporting the significance of minor Rg3.

scholarly journals Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Bing He ◽  
Ping Chen ◽  
Sonia Zambrano ◽  
Dina Dabaghie ◽  
Yizhou Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Human Kidney ◽  
Cell Types ◽  
Model Organisms ◽  
Mural Cell ◽  
Glomerular Cell ◽  
Individual Gene ◽  
The Individual

AbstractMolecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, however, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), are missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we use Smart-seq2 to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. The analysis reveals genetic programs for all four glomerular cell types (podocytes, glomerular endothelial cells, MCs and PECs) as well as rare glomerulus-associated macula densa cells. Importantly, we detect heterogeneity in glomerulus-associated Pdgfrb-expressing cells, including bona fide intraglomerular MCs with the functionally active phagocytic molecular machinery, as well as a unique mural cell type located in the central stalk region of the glomerulus tuft. Furthermore, we observe remarkable species differences in the individual gene expression profiles of defined glomerular cell types that highlight translational challenges in the field and provide a guide to design translational studies.

Craniometric data of Apodemus sylvaticus in Slovakia

Biologia ◽  
2015 ◽  
Vol 70 (7) ◽  
Author(s):  
Alexander Čanády ◽  
Ladislav Mošanský
Keyword(s):  
Discriminant Analysis ◽  
Genetic Interaction ◽  
Function Analysis ◽  
Geographic Distance ◽  
Wood Mouse ◽  
Apodemus Sylvaticus ◽  
Small Scale ◽  
Craniometric Analysis ◽  
North Western ◽  
Different Parts

AbstractA craniometric analysis of skulls of the wood mouse (Apodemus sylvaticus) from three different parts of Slovakia (north-western, northern and south-eastern) was conducted. Twenty-nine skull and dental variables were measured and evaluated on a sample of 56 adult individuals. The overlap of the values of the measured traits was high. Moreover, the differences among the populations were different for each trait. The non-parametric Kruskal-Wallis test and Discriminant function analysis showed variations in the cranial variables among the different parts of country. We have identified six morphometric variables suitable for the differentiation of populations on the basis of discriminant analysis. Significant differences were confirmed in the characteristics between the analyzed regions; thus, we can speak about small-scale craniometric differentiation. In addition, the results could indicate the influence of altitude, even over a shorter geographic distance between 48-49º N. Moreover, restriction of genetic interaction between the populations may in the future lead to even greater differences between the populations in Slovakia.

scholarly journals Assessment of the Mate Retention Inventory-Short Form Using Item Response Theory

2021 ◽  
Vol 19 (4) ◽  
pp. 147470492110441
Author(s):  
Patrick J. Nebl ◽  
Mark G. McCoy ◽  
Garett C. Foster ◽  
Michael J. Zickar
Keyword(s):  
Item Response Theory ◽  
Evolutionary Psychology ◽  
Item Response ◽  
Function Analysis ◽  
Short Form ◽  
Response Theory ◽  
Female Behavior ◽  
Mate Retention ◽  
Good Scale ◽  
The Individual

The mate retention inventory (MRI) has been a valuable tool in the field of evolutionary psychology for the past 30 years. The goal of the current research is to subject the MRI to rigorous psychometric analysis using item response theory to answer three broad questions. Do the individual items of the MRI fit the scale well? Does the overall function of the MRI match what is predicted? Finally, do men and women respond similarly to the MRI? Using a graded response model, it was found that all but two of the items fit acceptable model patterns. Test information function analysis found that the scale acceptably captures individual differences for participants with a high degree of mate retention but the scale is lacking in capturing information from participants with a low degree of mate retention. Finally, discriminate item function analysis reveals that the MRI is better at assessing male than female participants, indicating that the scale may not be the best indicator of female behavior in a relationship. Overall, we conclude that the MRI is a good scale, especially for assessing male behavior, but it could be improved for assessing female behavior and individuals lower on overall mate retention behavior. It is suggested that this paper be used as a framework for how the newest psychometrics techniques can be applied in order to create more robust and valid measures in the field of evolutionary psychology.

Structure–function analysis of full-length midkine reveals novel residues important for heparin binding and zebrafish embryogenesis

2013 ◽  
Vol 451 (3) ◽  
pp. 407-415 ◽  
Author(s):  
Jackwee Lim ◽  
Sheng Yao ◽  
Martin Graf ◽  
Christoph Winkler ◽  
Daiwen Yang
Keyword(s):  
Function Analysis ◽  
Structural Features ◽  
Full Length ◽  
Domain Growth ◽  
Heparin Binding ◽  
Cellular Mechanisms ◽  
The Individual ◽  
Zebrafish Embryogenesis

Midkine is a heparin-binding di-domain growth factor, implicated in many biological processes as diverse as angiogenesis, neurogenesis and tumorigenesis. Elevated midkine levels reflect poor prognosis for many carcinomas, yet the molecular and cellular mechanisms orchestrating its activity remain unclear. At the present time, the individual structures of isolated half domains of human midkine are known and its functionally active C-terminal half domain remains a popular therapeutic target. In the present study, we determined the structure of full-length zebrafish midkine and show that it interacts with fondaparinux (a synthetic highly sulfated pentasaccharide) and natural heparin through a previously uncharacterized, but highly conserved, hinge region. Mutating six consecutive residues in the conserved hinge to glycine strongly abates heparin binding and midkine embryogenic activity. In contrast with previous in vitro studies, we found that the isolated C-terminal half domain is not active in vivo in embryos. Instead, we have demonstrated that the N-terminal half domain is needed to enhance heparin binding and mediate midkine embryogenic activity surprisingly in both heparin-dependent and -independent manners. Our findings provide new insights into the structural features of full-length midkine relevant for embryogenesis, and unravel additional therapeutic routes targeting the N-terminal half domain and conserved hinge.

scholarly journals Parallel Comparison of Major Sudden Stratospheric Warming Events in CESM1-WACCM and CESM2-WACCM

Atmosphere ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 679 ◽  
Author(s):  
Si-Ming Liu ◽  
Yuan-Hao Chen ◽  
Jian Rao ◽  
Can Cao ◽  
Si-Yu Li ◽  
...  
Keyword(s):  
North America ◽  
Climate Model ◽  
Polar Vortex ◽  
Statistical Characteristics ◽  
Stratospheric Warming ◽  
Sudden Stratospheric Warming ◽  
Near Surface ◽  
Eddy Heat Flux ◽  
General Statistical ◽  
Vortex Split

After the recent release of the historical runs by community Earth system model version 2–the whole atmosphere community climate model (CESM2-WACCM), the major sudden stratospheric warming (SSW) events in this model and in its previous version (CESM1-WACCM) are compared based on a modern reanalysis (JRA55). Using the World Meteorological Organization (WMO) definition of SSWs and a threshold-based classification method that can describe the polar vortex morphology, SSWs in models and the reanalysis are further classified into two types, vortex displacement SSWs and vortex split SSWs. The general statistical characteristics of the two types of SSW events in the two model versions are evaluated. Both CESM1-WACCM and CESM2-WACCM models are shown to reproduce the SSW frequency successfully, although the circulations differences between vortex displacement SSWs and vortex split SSWs in CESM2-WACCM are smaller than in CESM1-WACCM. Composite polar temperature, geopotential height, wind, and eddy heat flux anomalies in both the two models and the reanalysis show similar evolutions. In addition, positive Pacific–North America and negative Western Pacific patterns in the troposphere preceding vortex displacement and split SSWs are observed in both observations and the models. The strong negative North Atlantic oscillation-like pattern, especially after vortex split SSW onset, is also identified in models. The near-surface cold Eurasia–warm North America pattern before both types of SSW onset, the warm Eurasia–cold North America pattern after displacement SSW onset, and the cold Eurasia–cold North America pattern after split SSW onset are consistently identified in JRA55, CESM1-WACCM, and CESM2-WACCM, although the temperature anomalies after the split SSW onset in CESM2-WACCM are somewhat underestimated.

scholarly journals Technical considerations when designing a gene expression panel for renal transplant diagnosis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
F. Toulza ◽  
K. Dominy ◽  
T. Cook ◽  
J. Galliford ◽  
J. Beadle ◽  
...  
Keyword(s):  
Gene Expression ◽  
Renal Transplant ◽  
Biological Significance ◽  
Tissue Sampling ◽  
Individual Gene ◽  
Antibody Mediated Rejection ◽  
Gene Level ◽  
Diagnostic Panel ◽  
The Individual ◽  
Gene Panels

Abstract Gene expression analysis is emerging as a new diagnostic tool in transplant pathology, in particular for the diagnosis of antibody-mediated rejection. Diagnostic gene expression panels are defined on the basis of their pathophysiological relevance, but also need to be tested for their robustness across different preservatives and analysis platforms. The aim of this study is the investigate the effect of tissue sampling and preservation on candidate genes included in a renal transplant diagnostic panel. Using the NanoString platform, we compared the expression of 219 genes in 51 samples, split for formalin-fixation and paraffin-embedding (FFPE) and RNAlater preservation (RNAlater). We found that overall, gene expression significantly correlated between FFPE and RNAlater samples. However, at the individual gene level, 46 of the 219 genes did not correlate across the 51 matched FFPE and RNAlater samples. Comparing gene expression results using NanoString and qRT-PCR for 18 genes in the same pool of RNA (RNAlater), we found a significant correlation in 17/18 genes. Our study indicates that, in samples from the same routine diagnostic renal transplant biopsy procedure split for FFPE and RNAlater, 21% of 219 genes of potential biological significance do not correlate in expression. Whether this is due to fixatives or tissue sampling, selection of gene panels for routine diagnosis should take this information into consideration.

scholarly journals Dispersion and topological characteristics of permutative polyatomic phononic crystals

2019 ◽  
Vol 475 (2226) ◽  
pp. 20190022 ◽  
Author(s):  
H. Al Ba'ba'a ◽  
M. Nouh ◽  
T. Singh
Keyword(s):  
Function Analysis ◽  
Finite Lattice ◽  
Wave Dispersion ◽  
Phononic Crystals ◽  
Mathematical Treatment ◽  
Plot Analysis ◽  
Local Arrangement ◽  
Transfer Function Analysis ◽  
Unit Cells ◽  
The Individual

This work presents a comprehensive mathematical treatment of phononic crystals (PCs) which comprise a finite lattice of repeated polyatomic unit cells. Wave dispersion in polyatomic lattices is susceptible to changes in the local arrangement of the monatoms (subcells) constituting the individual unit cell. We derive and interpret conditions leading to identical and contrasting band structures as well as the possibility of distinct eigenmodes as a result of cyclic and non-cyclic cellular permutations. Different modes associated with cyclic permutations yield topological invariance, which is assessed via the winding number of the complex eigenmode. Wave topology variations in the polyatomic PCs are quantified and conditions required to support edge modes in such lattices are established. Next, a transfer function analysis of finite polyatomic PCs is used to explain the formation of multiple Bragg band gaps as well as the emergence of truncation resonances within them. Anomalies arising from the truncation of the infinite lattice are further exploited to design mirror symmetrical edge modes in an extended lattice. We conclude with a generalized explanation of the band gap evolution mechanism based on the Bode plot analysis.

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