Infrared Spectroscopy of Human Cells and Tissue. Part VII: FT-IR Microspectroscopy of DNase- and RNase-Treated Normal, Cirrhotic, and Neoplastic Liver Tissue

In our efforts to understand the infrared spectral features of cells and tissues, and the spectral changes occurring between normal and disease states, we reported previously a detailed correlation between histochemical/immunohistochemical and spectral results. These results suggested an increase of nucleic acid spectral contributions in neoplastic, as compared to normal, tissue samples. In the present paper, these studies are extended to report the spectral features of DNA and RNA separately in these tissue samples. This was accomplished by selectively digesting either DNA or RNA from tissue sections, leaving behind the protein matrix with nuclear/cytoplasmic RNA or the protein matrix with nuclear DNA, respectively. These results demonstrate that the spectral changes between normal and neoplastic tissue are mostly due to an enhanced signature of DNA in neoplastic tissue. This enhancement is sufficiently large to suggest that it is most likely due to an increased detectability of DNA, rather than an increase in concentration.

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Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa

Scientific Reports ◽

10.1038/s41598-021-99127-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

T. Goolam Mahomed ◽

R. P. H. Peters ◽

M. Allam ◽

A. Ismail ◽

S. Mtshali ◽

...

Keyword(s):

Beta Diversity ◽

Small Sample ◽

Chronic Obstructive ◽

Shotgun Metagenomics ◽

Alpha And Beta Diversity ◽

Microbiome Composition ◽

Disease States ◽

Dna And Rna ◽

Lung Microbiome ◽

Copd Patients

AbstractChronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.

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DNA-RNA complexes that might represent transient attachment sites of nuclear DNA to the matrix

Journal of Cell Science ◽

10.1242/jcs.95.4.667 ◽

1990 ◽

Vol 95 (4) ◽

pp. 667-674

Author(s):

C. Patriotis ◽

M. Andreeva ◽

M. Pascaleva ◽

V. Ivanov ◽

L. Djondjurov

Keyword(s):

Dna Sequences ◽

Nuclear Dna ◽

Rna Polymerase Iii ◽

Erythroid Differentiation ◽

Rnase H ◽

Dna And Rna ◽

Attachment Sites ◽

The Matrix ◽

Exo Iii ◽

Rna Complexes

In this study we describe DNA-RNA complexes in matrix DNA of Friend cells. The presence of such unusual structures is confirmed by the following evidence. When a preparation of matrix DNA is electrophoresed in agarose an RNA component always migrates together with DNA. There should be a close interaction between DNA and RNA in such a preparation because the presence of the RNA component causes resistance of DNA to DNase I and Exo III. An intimate, hybrid-type association of part of the RNA component with DNA is indicated also by the fact that about 20% of this RNA is sensitive to RNase H. By specific inhibition of the RNA synthesis with alpha-amanitin and actinomycin D it was shown that the bulk of associated RNA is transcribed by RNA polymerase III. Hybridization experiments showed similarity between the DNA sequences isolated from the complexes and those from the base of dehistonized DNA loops obtained by high-salt extraction of nuclei. This observation suggests that the complexes might represent attachment sites of nuclear DNA to the matrix: possibly, the attachment is mediated via the RNA component. Experiments with induction of erythroid differentiation indicated that a profound reorganization of the nucleus, accompanying terminal differentiation, leads to a striking reduction in the number of complexes and thus in the number of attachment sites. This suggests that the complexes should function as transient attachment sites.

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Abstract 438: Hydrogen Sulfide Promotes Mitochondrial Biogenesis Through the Regulation of AMP-activated Protein Kinase

Circulation Research ◽

10.1161/res.119.suppl_1.438 ◽

2016 ◽

Vol 119 (suppl_1) ◽

Author(s):

Yuuki Shimizu ◽

Rohini Polavarapu ◽

John Calvert

Keyword(s):

Hydrogen Sulfide ◽

Mitochondrial Biogenesis ◽

Target Genes ◽

Nuclear Dna ◽

Citrate Synthase ◽

Serine Phosphorylation ◽

Signaling Cascade ◽

Disease States ◽

Upstream Kinase ◽

High Concentrations

Background: Hydrogen sulfide (H 2 S) possesses numerous cellular actions that account for its cardioprotective effects. A mechanism of particular interest is its effects on the mitochondria. At low concentrations, H 2 S donates electrons to the electron transport chain, whereas at high concentrations it inhibits mitochondrial respiration. H 2 S therapy improves mitochondrial function and prevents the loss of mitochondria following the onset of myocardial ischemia. However, it is not known if these improvements are associated with simply a reduction in injury or if mitochondrial biogenesis is involved. Therefore, the purpose of this study was to determine if H 2 S regulates/induces mitochondrial biogenesis in the heart. Methods and Results: C57BL/6J mice (8 weeks of age) were given an orally active H 2 S donor (SG-1002; 20 mg/kg/day) in their chow for 4 weeks. For these studies we focused our analysis on an AMPK-PGC1α signaling cascade. SG-1002 significantly increased the phosphorylation of AMPK, the serine phosphorylation of PGC1α, and increased the nuclear localization of PGC1α. This was associated with an increase in the gene expression of PGC1α target genes associated with mitochondrial biogenesis, an increase in mitochondrial to nuclear DNA ratios and an increase in citrate synthase activity. SG-1002 failed to elicit these changes in AMPK deficient mice. Therefore, we sought to determine how SG-1002 activated AMPK. SG-1002 did not alter the phosphorylation of LKB1, an upstream kinase of AMPK, and did not alter the levels of AMP (activator of AMPK). SG-1002 did not alter the expression of protein phosphatase 2A (PP2A; dephosphorylates AMPK), but it did significantly decrease the activity of PP2A). This decrease was accompanied by an increase in the sulfhydration of PP2A, suggesting that this modification is inhibitory. Conclusion: These data suggest that H 2 S augments mitochondrial biogenesis in the heart via an AMPK-PGC1α signaling cascade. This is important because mitochondrial abnormalities are associated with a number of disease states (diabetes and heart failure) where H 2 S levels are decreased. Therefore, strategies aimed at increasing H 2 S levels could potentially induce the generation of new, healthy mitochondria.

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A Microdissection and Molecular Genotyping Assay to Confirm the Identity of Tissue Floaters in Paraffin-Embedded Tissue Blocks

Archives of Pathology & Laboratory Medicine ◽

10.5858/2003-127-213-mamgat ◽

2003 ◽

Vol 127 (2) ◽

pp. 213-217 ◽

Cited By ~ 11

Author(s):

Jennifer L. Hunt ◽

Patricia Swalsky ◽

E. Sasatomi ◽

Laura Niehouse ◽

Anke Bakker ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Tissue Sample ◽

Small Samples ◽

Allelic Loss ◽

Chain Reaction ◽

Neoplastic Tissue ◽

Tissue Samples ◽

Genotyping Assay ◽

Tissue Identification ◽

Polymerase Chain

Abstract Context.—A recurring problem in surgical pathology practice is specimen mix-up and floater contamination. While many cases can be resolved histologically, a significant number remain unclear and may have serious clinical and medicolegal implications. Objectives.—To design a microdissection and genotyping assay to identify contaminating floater tissues in paraffin-embedded tissues that is optimized for small samples, and to use the assay to resolve a series of clinical cases with floater tissues. Materials and Methods.—Twenty-one cases of possible tissue floater contamination in paraffin-embedded tissue blocks were included. Using 4 unstained, 4-μm-thick histologic sections, multiple sites were microdissected under direct visualization either by hand or by laser capture microdissection. Nonneoplastic and neoplastic tissues were sampled. Polymerase chain reaction was performed for a panel of 10 polymorphic microsatellite markers at 1p34, 3p26, 5q21, 9p21, 10q23, and 17p13. Allele size and content were analyzed semiquantitatively by fluorescent capillary electrophoresis, and the genotypes for the tissues in the paraffin-embedded tissue blocks were compared for identity. Results.—Tissue identification was successful in all cases, despite small tissue sample size and fixation effects. Comparative analysis of neoplastic tissue floaters and the presumptive source tumor was performed when possible to control for possible allelic loss or microsatellite instability. Conclusions.—Microdissection and genotyping are effective and reliable means to objectively resolve problems of possible floater contamination. Even minute tissue samples provide sufficient DNA template for polymerase chain reaction microsatellite analysis. Because of the potential clinical implications of floaters, we recommend that all suspected floaters that would change a diagnosis from benign to malignant be subjected to genotyping assay to confirm the identity of the floater tissue.

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Prevalence, Geographic Distribution, Risk Factors and Co-Infections of Feline Gammaherpesvirus Infections in Domestic Cats in Switzerland

Viruses ◽

10.3390/v11080721 ◽

2019 ◽

Vol 11 (8) ◽

pp. 721 ◽

Cited By ~ 2

Author(s):

Novacco ◽

Kohan ◽

Stirn ◽

Meli ◽

Díaz-Sánchez ◽

...

Keyword(s):

Risk Factors ◽

Feline Leukemia Virus ◽

Domestic Cats ◽

Neoplastic Tissue ◽

Pathogenic Potential ◽

Tissue Samples ◽

Blood Samples ◽

Stray Cats ◽

Swiss Cantons ◽

Pcr Targeting

Recently, a gammaherpesvirus was described in domestic cats (FcaGHV1). The goal of the present study was to investigate the presence of FcaGHV1 in Swiss domestic cats and analyze potential risk factors. Blood samples from 881 cats presented to veterinarians in all Swiss cantons and from 91 stray cats and neoplastic tissue samples from 17 cats with lymphoma were evaluated. FcaGHV1 was detected by real-time PCR targeting the glycoprotein B gene, followed by sequencing. Blood samples were also tested for feline hemoplasmas, feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV). The molecular prevalence of FcaGHV1 was 6.0% (95% confidence interval (CI), 4.5–7.8%) in cats presented to veterinarians and 5.5% (95% CI, 1.8–12.4%) in stray cats. FcaGHV1 PCR-positive cats originated from 19/26 Swiss cantons. Factors significantly associated with FcaGHV1 detection included male sex, age >3 years, nonpedigree status and co-infection with FIV and hemoplasmas. Moreover, FeLV viremia tended to be associated with FcaGHV1 detection. High FcaGHV1 blood loads were found more frequently in FeLV-viremic cats and less frequently in hemoplasma-infected cats than in uninfected cats. Clinical information was unavailable for most of the 881 cats, but leukemia, carcinoma and cardiomyopathy were reported in FcaGHV1-positive cats. None of the tissue samples from the 17 cats with lymphoma tested positive for FcaGHV1. Sequence analyses revealed homogeneity among the Swiss isolates and >99.7% identity to published FcaGHV1 sequences. In conclusion, FcaGHV1 is present in Switzerland with a similar prevalence in cats presented to veterinarians and in stray cats. The pathogenic potential of FcaGHV1 needs further evaluation.

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High Throughput Screening of Normal and Neoplastic Tissue Samples

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/138620710790980540 ◽

2010 ◽

Vol 13 (3) ◽

pp. 253-267 ◽

Cited By ~ 2

Author(s):

Heidi Erickson ◽

Gallya Gannot ◽

Michael Tangrea ◽

Rodrigo Chuaqui ◽

John Gillespie ◽

...

Keyword(s):

High Throughput ◽

High Throughput Screening ◽

Neoplastic Tissue ◽

Tissue Samples

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The transforming protein of the MC29-related virus CMII is a nuclear DNA-binding protein whereas MH2 codes for a cytoplasmic RNA-DNA binding polyprotein.

The EMBO Journal ◽

10.1002/j.1460-2075.1983.tb01550.x ◽

1983 ◽

Vol 2 (7) ◽

pp. 1087-1092 ◽

Cited By ~ 34

Author(s):

T. Bunte ◽

I. Greiser-Wilke ◽

K. Moelling

Keyword(s):

Dna Binding ◽

Nuclear Dna ◽

Binding Protein ◽

Dna Binding Protein ◽

Related Virus ◽

Cytoplasmic Rna

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Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations

Bioinformatics ◽

10.1093/bioinformatics/btaa436 ◽

2020 ◽

Vol 36 (Supplement_1) ◽

pp. i300-i308 ◽

Cited By ~ 1

Author(s):

Dan Guo ◽

Melanie Christine Föll ◽

Veronika Volkmann ◽

Kathrin Enderle-Ammour ◽

Peter Bronsert ◽

...

Keyword(s):

Mass Spectrometry ◽

Supervised Classification ◽

Mass Spectrometry Imaging ◽

Ground Truth ◽

Tissue Level ◽

Multiple Instance Learning ◽

Spectral Features ◽

Weak Supervision ◽

Disease States ◽

Class Labels

Abstract Motivation Mass spectrometry imaging (MSI) characterizes the molecular composition of tissues at spatial resolution, and has a strong potential for distinguishing tissue types, or disease states. This can be achieved by supervised classification, which takes as input MSI spectra, and assigns class labels to subtissue locations. Unfortunately, developing such classifiers is hindered by the limited availability of training sets with subtissue labels as the ground truth. Subtissue labeling is prohibitively expensive, and only rough annotations of the entire tissues are typically available. Classifiers trained on data with approximate labels have sub-optimal performance. Results To alleviate this challenge, we contribute a semi-supervised approach mi-CNN. mi-CNN implements multiple instance learning with a convolutional neural network (CNN). The multiple instance aspect enables weak supervision from tissue-level annotations when classifying subtissue locations. The convolutional architecture of the CNN captures contextual dependencies between the spectral features. Evaluations on simulated and experimental datasets demonstrated that mi-CNN improved the subtissue classification as compared to traditional classifiers. We propose mi-CNN as an important step toward accurate subtissue classification in MSI, enabling rapid distinction between tissue types and disease states. Availability and implementation The data and code are available at https://github.com/Vitek-Lab/mi-CNN_MSI.

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