scholarly journals Evaluation of DNA degradation and establishment of a degradation analysis model for Lepidoptera specimens

BioTechniques ◽  
2020 ◽  
Vol 68 (3) ◽  
pp. 138-147
Author(s):  
Yao Xu ◽  
XueYu Ren ◽  
HongBin Wang ◽  
Mei Wang ◽  
GuoHong Li
Keyword(s):  
Dna Sequences ◽  
Dna Degradation ◽  
Museum Specimens ◽  
Analysis Model ◽  
Preservation Method ◽  
Degradation Analysis ◽  
Fragment Distribution ◽  
Dna Fragment ◽  
Formalin Fixed ◽  
Over Time

Millions of museum specimens are integral to biodiversity studies; however, DNA degradation may limit the ability to obtain DNA sequences. In this study, a degradation analysis model for Lepidoptera specimens was established. Based on this model, we revealed the characteristics of DNA fragment distribution caused by external DNA damage factors during specimen preservation. We found that the degree of DNA degradation increased over time; DNA degradation of spread and dried adult specimens was significantly higher than that in the folded and formalin-fixed larval specimens. However, the effects of folding wings on DNA degradation and the effects of the preservation method/stage (formalin-fixed larval vs air-dried adult specimens) were different for different species.

Highly repeated DNA sequences in birds: The structure and evolution of an abundant, tandemly repeated 190-bp DNA fragment in parrots

Genomics ◽  
1992 ◽  
Vol 14 (2) ◽  
pp. 462-469 ◽  
Author(s):  
Cort S. Madsen ◽  
Dineke H. de Kloet ◽  
Jean E. Brooks ◽  
Siwo R. de Kloet
Keyword(s):  
Dna Sequences ◽  
Repeated Dna ◽  
Repeated Dna Sequences ◽  
Highly Repeated Dna ◽  
Dna Fragment

scholarly journals ЦАХИЛДАГНЫ ТӨРЛИЙН УРГАМЛЫН ФИЛОГЕНЕТИК ХОЛБОО

2016 ◽  
pp. 25-31
Author(s):  
Х Алтанзул ◽  
Ю Оюунбилэг
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Relationship ◽  
Dna Sequences ◽  
Fragment Size ◽  
Dna Fragment ◽  
Relationship Of

The phylogenetic relationship of eight Iris species (I.flavisimma, I.ventricosa, I.bungei,I.kaempferi, I.tenuifolia, I.lactea, I.tigrida, I.dichotoma) were studied by PCR using six specificprimers (S-523, Z1204R, trnL, trnF and ITS1, ITS4). All species except I.ventricosa wereidentified when using S-523, Z1204R and trnL, trnF primers and the DNA fragment size rangedbetween 500 to 600 bp and 800 bp, respectively. Primers ITS1 and ITS4 produced double bandsin about 500 and 1500 bp to I.bungei, I.kaempferi, and I.lactea species. On the phylogenetic tree, some iris species have close relations based on chloroplastic DNA sequences. The closest relationships showed between I.sanguinea and I.sibirica, I.rutenica and I.uniflora. Also I.tenuifolia, I.ventricosa and I.halophila located on one branch of phylogenetic tree.

scholarly journals Identification of Extracytoplasmic Proteins in Bradyrhizobium japonicum Using Phage Display

2003 ◽  
Vol 16 (8) ◽  
pp. 727-737 ◽  
Author(s):  
Anna Rosander ◽  
Lars Frykberg ◽  
Nora Ausmees ◽  
Peter Müller
Keyword(s):  
Signal Peptide ◽  
Dna Sequences ◽  
Bradyrhizobium Japonicum ◽  
Expression Library ◽  
Recombinant Fusion Proteins ◽  
Small Proteins ◽  
Phage Protein ◽  
Powerful Means ◽  
Genes Encoding ◽  
Dna Fragment

A novel gene bank of Bradyrhizobium japonicum USDA110spc4 was constructed using pG3DSS, a phagemid vector designed for detecting genes encoding secreted proteins. In this phagemid, the phage protein III lacks its indigenous signal peptide required for protein secretion, thus recombinant fusion proteins are displayed on the phage surface only if a functional signal peptide is provided by an inserted DNA fragment. In addition, the N-terminal half of protein III has been replaced by a short linker region (the E-tag) that is recognized by a monoclonal antibody, which enables isolation of phages displaying a fusion protein. The expression library described here, therefore, provides a powerful means to affinity select for B. japonicum genes encoding extracytoplasmic proteins. In total, 182 DNA sequences were analyzed, among which 132 different putative extracytoplasmic proteins could be identified. The function of most proteins could be predicted and support an extracytoplasmic localization. In addition, genes encoding novel extracytoplasmic proteins were found. In particular, a novel family of small proteins has been identified that is characterized by a conserved pattern of four cysteine residues.

Measurements of T1 and T2 over Time in Formalin-Fixed Human Whole-Brain Specimens

1992 ◽  
Vol 33 (5) ◽  
pp. 400-404 ◽  
Author(s):  
M. Tovi ◽  
A. Ericsson
Keyword(s):  
White Matter ◽  
Gray Matter ◽  
Relaxation Times ◽  
Fixation Procedure ◽  
Whole Brain ◽  
T1 And T2 ◽  
Phospholipid Structure ◽  
Formalin Fixed ◽  
Over Time

Abstract T1 and T2 were measured in 5 formalin-fixed human whole-brain specimens as a function of time. Gray matter/white matter contrast reversal was observed around the 4th day and was considered to be due to the greater decrease in T1 in gray than in white matter. A possible explanation for this is that the decomposition of the myelin phospholipid structure by formalin somewhat counteracts the general reductive effect of the fixation procedure on relaxation times.

scholarly journals BDS Satellite Clock Prediction Considering Periodic Variations

2021 ◽  
Vol 13 (20) ◽  
pp. 4058
Author(s):  
Lin Zhao ◽  
Nan Li ◽  
Hui Li ◽  
Renlong Wang ◽  
Menghao Li
Keyword(s):  
Fourier Transform ◽  
Prediction Model ◽  
Prediction Accuracy ◽  
Analysis Model ◽  
Satellite Clock ◽  
Periodic Term ◽  
Periodic Noise ◽  
Clock Prediction ◽  
The Impact ◽  
Over Time

The periodic noise exists in BeiDou navigation satellite system (BDS) clock offsets. As a commonly used satellite clock prediction model, the spectral analysis model (SAM) typically detects and identifies the periodic terms by the Fast Fourier transform (FFT) according to long-term clock offset series. The FFT makes an aggregate assessment in frequency domain but cannot characterize the periodic noise in a time domain. Due to space environment changes, temperature variations, and various disturbances, the periodic noise is time-varying, and the spectral peaks vary over time, which will affect the prediction accuracy of the SAM. In this paper, we investigate the periodic noise and its variations present in BDS clock offsets, and improve the clock prediction model by considering the periodic variations. The periodic noise and its variations over time are analyzed and quantified by short time Fourier transform (STFT). The results show that both the amplitude and frequency of the main periodic term in BDS clock offsets vary with time. To minimize the impact of periodic variations on clock prediction, a time frequency analysis model (TFAM) based on STFT is constructed, in which the periodic term can be quantified and compensated accurately. The experiment results show that both the fitting and prediction accuracy of TFAM are better than SAM. Compared with SAM, the average improvement of the prediction accuracy using TFAM of the 6 h, 12 h, 18 h and 24 h is in the range of 6.4% to 10% for the GNSS Research Center of Wuhan University (WHU) clock offsets, and 11.1% to 14.4% for the Geo Forschungs Zentrum (GFZ) clock offsets. For the satellites C06, C14, and C32 with marked periodic variations, the prediction accuracy is improved by 26.7%, 16.2%, and 16.3% for WHU clock offsets, and 29.8%, 16.0%, 21.0%, and 9.0% of C06, C14, C28, and C32 for GFZ clock offsets.

scholarly journals Transformation of Saccharomyces cerevisiae with nonhomologous DNA: illegitimate integration of transforming DNA into yeast chromosomes and in vivo ligation of transforming DNA to mitochondrial DNA sequences

1993 ◽  
Vol 13 (5) ◽  
pp. 2697-2705
Author(s):  
R H Schiestl ◽  
M Dominska ◽  
T D Petes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Topoisomerase I ◽  
Target Sequence ◽  
Base Pairing ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
Dna Fragment

When the yeast Saccharomyces cerevisiae was transformed with DNA that shares no homology to the genome, three classes of transformants were obtained. In the most common class, the DNA was inserted as the result of a reaction that appears to require base pairing between the target sequence and the terminal few base pairs of the transforming DNA fragment. In the second class, no such homology was detected, and the transforming DNA was integrated next to a CTT or GTT in the target; it is likely that these integration events were mediated by topoisomerase I. The final class involved the in vivo ligation of transforming DNA with nucleus-localized linear fragments of mitochondrial DNA.

scholarly journals A longitudinal study of the stress of poor glucose control and diabetes distress

2019 ◽  
pp. 135910531989300
Author(s):  
Christina M Marengo ◽  
Benjamin D Aronson ◽  
Kelley J Sittner ◽  
Melissa L Walls
Keyword(s):  
Longitudinal Study ◽  
Indirect Effects ◽  
Glucose Control ◽  
Perceived Control ◽  
Blood Glucose Control ◽  
Diabetes Distress ◽  
Analysis Model ◽  
The Relationship ◽  
Over Time ◽  
Path Analysis Model

Poor glucose control can be viewed as a stressor, possibly promulgating diabetes distress. We examined the relationship between perceived blood glucose control and diabetes distress over time using a partially controlled cross-lagged path analysis model. After controlling for demographics, control at 6 months was directly related to change in distress at 12 months. Subsequently, distress at 12 months was directly related to change in control at 18 months. Both 6-month control and distress had significant indirect effects on 18-month control and distress. This demonstrates the nuanced bi-directional relationship between the stress of poor perceived control and diabetes distress.

Isolation and subcloning analysis of functional centromere DNA (CEN11) from Saccharomyces cerevisiae chromosome XI

1982 ◽  
Vol 2 (1) ◽  
pp. 82-87
Author(s):  
M Fitzgerald-Hayes ◽  
J M Buhler ◽  
T G Cooper ◽  
J Carbon
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Sequences ◽  
Plasmid Dna ◽  
Genomic Library ◽  
Genetic Evidence ◽  
Hybrid Plasmid ◽  
Meiotic Behavior ◽  
Base Pairs ◽  
Dna Fragment

We have cloned segments of yeast DNA containing the centromere XI-linked MET14 gene. This was done by selecting directly in Saccharomyces cerevisiae for complementation of a met14 mutation after transformation with a hybrid plasmid DNA genomic library. Genetic evidence indicates that functional centromere DNA (CEN11) from chromosome XI is also contained on the segment of S. cerevisiae DNA cloned in pYe(MET14)2. This plasmid is maintained stably in budding S. cerevisiae cultures and segregates predominantly 2+:20- through meiosis. The CEN11 element has been subcloned in vector YRp7' on an S. cerevisiae DNA fragment 900 base pairs in length [pYe(CEN11)10]. The mitotic and meiotic behavior of plasmids containing CEN11 plus a DNA replicator (ars) indicates that the centromere DNA sequences enable these plasmids to function as true minichromosomes in S. cerevisiae.

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