AFLP fingerprinting reveals pattern differences between template DNA extracted from different plant organs

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 521-526 ◽  
Author(s):  
P. Donini ◽  
R. M. D. Koebner ◽  
M. L. Elias ◽  
S. M. Bougourd
Keyword(s):  
Genome Mapping ◽  
Organ Specificity ◽  
Aegilops Speltoides ◽  
Phylogenetic Studies ◽  
Efficient Detection ◽  
Large Numbers ◽  
Organ Specific ◽  
Genotypic Mixtures ◽  
Dna Template ◽  
Template Dna

AFLP (amplified fragment length polymorphism) fingerprinting of cultivars of bread wheat (Triticum aestivum) and some of its wild relatives has allowed the efficient detection of large numbers of polymorphic amplified fragments. While the reproducibility of fingerprints in repeated experiments is high, pattern differences were observed between fingerprints obtained from seed and leaf DNA template from the same wheat accession. These distinct organ specific amplified DNA fragments were shown to be due neither to genotypic mixtures nor to pathogen contamination. They are likely a result of differences in DNA methylation between organs. Even greater numbers of organ specific amplified fragments were observed when fingerprints obtained from the root and shoot of individual seedlings of the wheat relatives Aegilops mutica and Aegilops speltoides were compared. This phenomenon underlines the importance of ensuring that DNA is extracted from physiologically uniform tissue in phylogenetic studies based on AFLP fingerprints. For this purpose, mature seed is a convenient source.Key words: AFLPs, fingerprinting, genome mapping, organ specificity.

Potentiation to vasodilators by nitric oxide synthase blockade in superior mesenteric but not hepatic artery

1997 ◽  
Vol 272 (3) ◽  
pp. G507-G514 ◽  
Author(s):  
M. P. Macedo ◽  
W. W. Lautt
Keyword(s):  
Nitric Oxide ◽  
Hepatic Artery ◽  
Organ Specificity ◽  
No Production ◽  
Compensatory Mechanism ◽  
Basal Tone ◽  
Before And After ◽  
Organ Specific ◽  
Pentobarbital Sodium Anesthesia ◽  
Oxide Synthase

Our objective was to determine the vasodilator effect of adenosine and isoproterenol on the hepatic artery (HA) and superior mesenteric artery (SMA) before and after blockade of nitric oxide (NO) production to evaluate the possibility of organ specificity. Vascular circuits supplied blood flow to the liver or intestine in cats under pentobarbital sodium anesthesia. The NO synthase (NOS) antagonist N(G)-nitro-L-arginine methyl ester (L-NAME; 2.5 mg/kg iv) increased arterial pressure from 106.4 +/- 7.6 to 141.4 +/- 8.1 mmHg and raised basal vascular tone in the SMA but not in the HA. The NOS substrate L-arginine (75 mg/kg) reversed these effects. The decrease in perfusion pressure in response to adenosine was 51.7 +/- 2.9, 135.2 +/- 6.1, and 16.7 +/- 2.4 mmHg, respectively, for control and after L-NAME and L-arginine. Isoproterenol was also potentiated in the SMA. Adenosine and isoproterenol were not potentiated in the HA by L-NAME. Potentiation did not occur when HA or SMA basal tone was elevated by norepinephrine. In conclusion, L-NAME increased basal tone for the SMA and potentiated the dilation induced by adenosine and isoproterenol in the SMA but not in the HA. This study provides evidence that there is a highly organ-specific compensatory mechanism in which the absence of NO promotes potentiation of other vasodilators.

scholarly journals Open microfluidic coculture reveals paracrine signaling from human kidney epithelial cells promotes kidney specificity of endothelial cells

2020 ◽  
Vol 319 (1) ◽  
pp. F41-F51
Author(s):  
Tianzi Zhang ◽  
Daniel Lih ◽  
Ryan J. Nagao ◽  
Jun Xue ◽  
Erwin Berthier ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Epithelial Cells ◽  
Matrix Metalloproteinase ◽  
Culture Media ◽  
Human Kidney ◽  
Organ Specificity ◽  
Paracrine Signaling ◽  
Human Organ ◽  
Extrinsic Cues ◽  
Organ Specific

Endothelial cells (ECs) from different human organs possess organ-specific characteristics that support specific tissue regeneration and organ development. EC specificity is identified by both intrinsic and extrinsic cues, among which the parenchyma and organ-specific microenvironment are critical contributors. These extrinsic cues are, however, largely lost during ex vivo cultures. Outstanding challenges remain to understand and reestablish EC organ specificity for in vitro studies to recapitulate human organ-specific physiology. Here, we designed an open microfluidic platform to study the role of human kidney tubular epithelial cells in supporting EC specificity. The platform consists of two independent cell culture regions segregated with a half wall; culture media are added to connect the two culture regions at a desired time point, and signaling molecules can travel across the half wall (paracrine signaling). Specifically, we report that in the microscale coculture device, primary human kidney proximal tubule epithelial cells (HPTECs) rescued primary human kidney peritubular microvascular EC (HKMEC) monolayer integrity and fenestra formation and that HPTECs upregulated key HKMEC kidney-specific genes (hepatocyte nuclear factor 1 homeobox B, adherens junctions-associated protein 1, and potassium voltage-gated channel subfamily J member 16) and endothelial activation genes (vascular cell adhesion molecule-1, matrix metalloproteinase-7, and matrix metalloproteinase-10) in coculture. Coculturing with HPTECs also promoted kidney-specific genotype expression in human umbilical vein ECs and human pluripotent stem cell-derived ECs. Compared with culture in HPTEC conditioned media, coculture of ECs with HPTECs showed increased upregulation of kidney-specific genes, suggesting potential bidirectional paracrine signaling. Importantly, our device is compatible with standard pipettes, incubators, and imaging readouts and could also be easily adapted to study cell signaling between other rare or sensitive cells.

Comprehensive Analysis of Circulating microRNA Specific to the Liver, Heart, and Skeletal Muscle of Cynomolgus Monkeys

2017 ◽  
Vol 36 (3) ◽  
pp. 220-228 ◽  
Author(s):  
Takuma Iguchi ◽  
Noriyo Niino ◽  
Satoshi Tamai ◽  
Ken Sakurai ◽  
Kazuhiko Mori
Keyword(s):  
Skeletal Muscle ◽  
Expression Patterns ◽  
Interindividual Variation ◽  
Organ Specificity ◽  
Circulating Microrna ◽  
Circulating Mirnas ◽  
Male And Female ◽  
Cynomolgus Monkeys ◽  
Toxicological Studies ◽  
Organ Specific

Circulating microRNAs (miRNAs) could represent sensitive and specific biomarkers for tissue injury. However, their utility as biomarkers in nonclinical toxicological studies using nonhuman primates is limited by a lack of information on their organ specificity and circulating levels under resting condition of the animals. Herein, liver, heart, and skeletal muscle-specific expression patterns of miRNAs were determined in 27 tissues/organs from male and female monkeys (n =2/sex) by next-generation sequencing (NGS) analysis. This analysis revealed organ-specific miRNAs in the liver (miR-122), heart (miR-208a and miR-499a), and skeletal muscle (miR-206). Next, plasma was collected from conscious-naive male and female cynomolgus monkeys (n = 25/sex) to better understand the expressions of organ-specific circulating miRNAs. The absolute values of circulating miRNAs were quantified using a Taqman microRNA assay. MiR-1, miR-133a, and miR-208b showed preferential expression in the heart and skeletal muscles, whereas miR-192 was abundant in the liver, stomach, small intestine, and kidney. These miRNAs had identical sequences to their human counterparts. Six organ-specific miRNAs (miR-1, miR-122, miR-133a, miR-192, miR-206, and miR-499a) could be evaluated quantitatively by quantitative real-time reverse transcription polymerase chain reaction with or without preamplification. No significant sex differences were noted for these circulating miRNAs. For their circulation levels, miR-133a showed more than 900-fold interindividual variation, whereas miR-122 showed only a 20-fold variation. In conclusion, we profiled circulating organ-specific miRNAs for the liver, heart, and skeletal muscle of cynomolgus monkeys.

scholarly journals Cryptococcus neoformans Capsule Structure Evolution In Vitro and during Murine Infection

2004 ◽  
Vol 72 (6) ◽  
pp. 3359-3365 ◽  
Author(s):  
Dea Garcia-Hermoso ◽  
Françoise Dromer ◽  
Guilhem Janbon
Keyword(s):  
Cryptococcus Neoformans ◽  
Organ Specificity ◽  
Structure Evolution ◽  
Specific Monoclonal Antibody ◽  
Organ Specific ◽  
The Brain ◽  
Over Time ◽  
Selection Of

ABSTRACT Cryptococcus neoformans capsule structure modifications after prolonged in vitro growth or in vivo passaging have been reported previously. However, nothing is known about the dynamics of these modifications or about their environmental specificities. In this study, capsule structure modifications after mouse passaging and prolonged in vitro culturing were analyzed by flow cytometry using the glucuronoxylomannan-specific monoclonal antibody E1. The capsule structures of strains recovered after 0, 1, 8, and 35 days were compared by using the level of E1-specific epitope expression and its cell-to-cell heterogeneity within a given cell population. In vitro, according to these parameters, the diversity of the strains was higher on day 35 than it was initially, suggesting the absence of selection during in vitro culturing. In contrast, the diversity of the strains recovered from the brain tended to decrease over time, suggesting that selection of more adapted strains had occurred. The strains recovered on day 35 from the spleen and the lungs had different phenotypes than the strains isolated from the brain of the same mouse on the same day, thus strongly suggesting that there is organ specificity for C. neoformans strain selection. Fingerprinting of the strains recovered in vitro and in vivo over time confirmed that genotypes evolved very differently in vitro and in vivo, depending on the environment. Overall, our results suggest that organ-specific selection can occur during cryptococcosis.

scholarly journals Assessment of the Genetic Diversity among Arcobacters Isolated from Poultry Products by Using Two PCR-Based Typing Methods

2002 ◽  
Vol 68 (5) ◽  
pp. 2172-2178 ◽  
Author(s):  
Kurt Houf ◽  
Lieven De Zutter ◽  
Jan Van Hoof ◽  
Peter Vandamme
Keyword(s):  
Genotypic Diversity ◽  
Epidemiological Studies ◽  
Dna Templates ◽  
Poultry Products ◽  
Large Numbers ◽  
Rapd Pcr ◽  
Arcobacter Butzleri ◽  
Typing Methods ◽  
Dna Template

ABSTRACT In this study, enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) and randomly amplified polymorphic DNA PCR (RAPD-PCR) were optimized for characterization of Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii. In addition, a simple and rapid DNA extraction method was tested for use in both typing procedures. Both methods had satisfactory typeability and discriminatory power, but the fingerprints generated with ERIC-PCR were more reproducible and complex than those obtained with RAPD-PCR. The use of nondiluted boiled cell suspensions as DNA templates was found to be very useful in ERIC-PCR. Characterization of large numbers of Arcobacter isolates is therefore preferably performed by the ERIC-PCR procedure. Isolates for which almost identical ERIC fingerprints are generated may subsequently be characterized by RAPD-PCR, although adjustment and standardization of the amount of the DNA template are necessary. In the second part of this study, the genotypic diversity of arcobacters present on broiler carcasses was assessed by using both typing methods. A total of 228 cultures from 24 samples were examined after direct isolation and enrichment. The isolates were identified by using a multiplex PCR as A. butzleri (n = 182) and A. cryaerophilus (n = 46). A total of 131 types (91 A. butzleri types and 40 A. cryaerophilus types) were discerned without discordance between the two typing techniques. The analysis of the poultry isolates showed that poultry products may harbor not only more than one species but also multiple genotypes. All genotypes were confined to one poultry sample, and only three genotypes were found after simultaneous enrichment and direct isolation. These results demonstrate that different outcomes can be obtained in epidemiological studies depending on the isolation procedure used and the number of isolates characterized.

scholarly journals Targeted capture of complete coding regions across divergent species

2017 ◽  
Author(s):  
Ryan K Schott ◽  
Bhawandeep Panesar ◽  
Daren C Card ◽  
Matthew Preston ◽  
Todd A Castoe ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Large Scale ◽  
Functional Studies ◽  
Coding Regions ◽  
Sequencing Technologies ◽  
Phylogenetic Studies ◽  
Large Numbers ◽  
Capture Method ◽  
Targeted Capture ◽  
And Function

AbstractDespite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still being developed and generally focus on the capture of conserved regions, rather than complete coding regions from specific genes of interest. The resulting data is thus useful for phylogenetic studies, but the wealth of comparative data that could be used for evolutionary and functional studies is lost. Here we design and implement a targeted capture method that enables recovery of complete coding regions across broad taxonomic scales. Capture probes were designed from multiple reference species and extensively tiled in order to facilitate cross-species capture. Using novel bioinformatics pipelines we were able to recover nearly all of the targeted genes with high completeness from species that were up to 200 myr divergent. Increased probe diversity and tiling for a subset of genes had a large positive effect on both recovery and completeness. The resulting data produced an accurate species tree, but importantly this same data can also be applied to studies of molecular evolution and function that will allow researchers to ask larger questions in broader phylogenetic contexts. Our method demonstrates the utility of cross-species approaches for the capture of full length coding sequences, and will substantially improve the ability for researchers to conduct large-scale comparative studies of molecular evolution and function.

scholarly journals Mouse Organ Specific Proteins and Functions

2021 ◽  
Author(s):  
Bingyun Sun ◽  
Cynthia Lorang ◽  
Yijuan Zhang ◽  
Ken Liu ◽  
Zhi Sun ◽  
...  
Keyword(s):  
Human Population ◽  
Molecular Diversity ◽  
Alanine Transaminase ◽  
Organ Specificity ◽  
Mouse Strains ◽  
Biological Functions ◽  
Organ Specific ◽  
Specific Proteins ◽  
Mouse Organ

Organ specific proteins (OSPs) possess great medical potentials both in clinics and in biomedical research. Applications of them - such as alanine transaminase, aspartate transaminase, and troponins - in clinics have raised certain concerns of their organ specificity. The dynamics and diversity of protein expression in heterogeneous human population are well known, yet their effects on OSPs are less addressed. Here we use mouse as a model and implemented a scheme of breadth study to examine the pan-organ proteome for potential variations of organ specificity in different genetic backgrounds. Using reasonable resources, we generated pan-organ proteomes of four in-bred mouse strains. The results revealed a large diversity that is more profound among OSPs than the overall proteomes. We defined a robustness score to quantify such variation and derived three sets of OSPs with different stringencies. In the meantime, we found that the enriched biological functions of OSPs are also organ specific that are sensitive and useful to assess the quality of OSPs. We hope our breadth study can open doors to explore the molecular diversity and dynamics of organ specificity at the protein level.

scholarly journals Organ-specific exposure and response to sulforaphane, a key chemopreventive ingredient in broccoli: implications for cancer prevention

2012 ◽  
Vol 109 (1) ◽  
pp. 25-32 ◽  
Author(s):  
Omkara L. Veeranki ◽  
Arup Bhattacharya ◽  
James R. Marshall ◽  
Yuesheng Zhang
Keyword(s):  
Cancer Prevention ◽  
Tissue Response ◽  
Organ Specificity ◽  
Tissue Uptake ◽  
Once Daily ◽  
Naturally Occurring ◽  
Biochemical Assays ◽  
Organ Specific ◽  
Gastro Intestinal Tract ◽  
Further Development

Naturally occurring sulforaphane (SF) has been extensively studied for cancer prevention. However, little is known as to which organs may be most affected by this agent, which impedes its further development. In the present study, SF was administered to rats orally either in a single dose or once daily for 7 d. Tissue distribution of SF was measured by a HPLC-based method. Glutathione S-transferase (GST) and NAD(P)H:quinone oxidoreductase 1 (NQO1), two well-known cytoprotective phase 2 enzymes, were measured using biochemical assays to assess tissue response to SF. SF was delivered to different organs in vastly different concentrations. Tissue uptake of SF was the greatest in the stomach, declining rapidly in the descending gastro-intestinal tract. SF was rapidly eliminated through urinary excretion, and urinary concentrations of SF equivalents were 2–4 orders of magnitude higher than those of plasma. Indeed, tissue uptake level of SF in the bladder was second only to that in the stomach. Tissue levels of SF in the colon, prostate and several other organs were very low, compared to those in the bladder and stomach. Moreover, induction levels of GST and NQO1 varied by 3- to 6-fold among the organs of SF-treated rats, though not strictly correlated with tissue exposure to SF. Thus, there is profound organ specificity in tissue exposure and response to dietary SF, suggesting that the potential chemopreventive benefit of dietary SF may differ significantly among organs. These findings may provide a basis for prioritising organs for further chemopreventive study of SF.

scholarly journals A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

2021 ◽  
Author(s):  
Graeme T Lloyd ◽  
Graham J Slater
Keyword(s):  
Phylogenetic Trees ◽  
Species Level ◽  
Total Group ◽  
Phylogenetic Studies ◽  
Large Numbers ◽  
Extant Species ◽  
Molecular Phylogenies ◽  
Phylogenetic Hypotheses ◽  
Fossil Data ◽  
Rapid Radiations

Abstract Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the ∼ 90 extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa, and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.

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