Herpesvirus-Associated Proliferative Skin Disease in Frogs and Toads: Proposed Pathogenesis

A comparative study was carried out on common and agile frogs ( Rana temporaria and R. dalmatina) naturally infected with ranid herpesvirus 3 (RaHV3) and common toads ( Bufo bufo) naturally infected with bufonid herpesvirus 1 (BfHV1) to investigate common pathogenetic pathways and molecular mechanisms based on macroscopic, microscopic, and ultrastructural pathology as well as evaluation of gene expression. Careful examination of the tissue changes, supported by in situ hybridization, at different stages of development in 6 frogs and 14 toads revealed that the skin lesions are likely transient, and part of a tissue cycle necessary for viral replication in the infected hosts. Transcriptomic analysis, carried out on 2 naturally infected and 2 naïve common frogs ( Rana temporaria) and 2 naturally infected and 2 naïve common toads ( Bufo bufo), revealed altered expression of genes involved in signaling and cell remodeling in diseased animals. Finally, virus transcriptomics revealed that both RaHV3 and BfHV1 had relatively high expression of a putative immunomodulating gene predicted to encode a decoy receptor for tumor necrosis factor in the skin of the infected hosts. Thus, the comparable lesions in infected frogs and toads appear to reflect a concerted epidermal and viral cycle, with presumptive involvement of signaling and gene remodeling host and immunomodulatory viral genes.

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Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels

Scientific Reports ◽

10.1038/s41598-020-65638-1 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Saket Choudhary ◽

Suzanne C. Burns ◽

Hoda Mirsafian ◽

Wenzheng Li ◽

Dat T. Vo ◽

...

Keyword(s):

Molecular Mechanisms ◽

Early Response ◽

Radiation Sensitivity ◽

Integrated Analysis ◽

High Dose ◽

Transcriptional Level ◽

Altered Expression ◽

Expression Of Genes ◽

Post Radiation ◽

Main Component

Abstract High-dose radiation is the main component of glioblastoma therapy. Unfortunately, radio-resistance is a common problem and a major contributor to tumor relapse. Understanding the molecular mechanisms driving response to radiation is critical for identifying regulatory routes that could be targeted to improve treatment response. We conducted an integrated analysis in the U251 and U343 glioblastoma cell lines to map early alterations in the expression of genes at three levels: transcription, splicing, and translation in response to ionizing radiation. Changes at the transcriptional level were the most prevalent response. Downregulated genes are strongly associated with cell cycle and DNA replication and linked to a coordinated module of expression. Alterations in this group are likely driven by decreased expression of the transcription factor FOXM1 and members of the E2F family. Genes involved in RNA regulatory mechanisms were affected at the mRNA, splicing, and translation levels, highlighting their importance in radiation-response. We identified a number of oncogenic factors, with an increased expression upon radiation exposure, including BCL6, RRM2B, IDO1, FTH1, APIP, and LRIG2 and lncRNAs NEAT1 and FTX. Several of these targets have been previously implicated in radio-resistance. Therefore, antagonizing their effects post-radiation could increase therapeutic efficacy. Our integrated analysis provides a comprehensive view of early response to radiation in glioblastoma. We identify new biological processes involved in altered expression of various oncogenic factors and suggest new target options to increase radiation sensitivity and prevent relapse.

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Endometritis and pyometra in bitches: a review

Veterinární Medicína ◽

10.17221/6864-vetmed ◽

2013 ◽

Vol 58 (No. 6) ◽

pp. 289-297 ◽

Cited By ~ 6

Author(s):

B. Kempisty ◽

D. Bukowska ◽

M. Wozna ◽

H. Piotrowska ◽

M. Jackowska ◽

...

Keyword(s):

Molecular Basis ◽

Molecular Mechanisms ◽

Reproductive Tract ◽

Molecular Level ◽

Altered Expression ◽

Expression Of Genes ◽

Clinical Stages ◽

Compound Process ◽

Immunological Changes

Endometritis-pyometra is the most frequent and complex pathology in domestic bitches. This process involves several immunological changes as well as molecular mechanisms responsible for inflammation in the female uterus. The various clinical stages of pyometra are associated with various symptoms. In this review, several aspects are described, including physiological and pathological mechanisms as well as molecular changes which take place during induction of endometritis-pyometra. The authors also highlight the important role of growth factors and their receptors in this process. It is well known that pyometra is a compound process which mainly involves immunological changes during inflammation. However, this review presents a new overview of this process, which includes changes at the molecular level, e.g., the altered expression of genes crucial for the development of this disease. Although pyometra is the most frequent disease of the reproductive tract in bitches, the molecular basis of this process is still not entirely understood.  

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Intracorneal Hematoma Showing Clinical and Dermoscopic Features of Acral Lentiginous Melanoma

Case Reports in Dermatological Medicine ◽

10.1155/2017/3509146 ◽

2017 ◽

Vol 2017 ◽

pp. 1-3

Author(s):

Ugur Uslu ◽

Franz Heppt ◽

Michael Erdmann

Keyword(s):

Correct Diagnosis ◽

Surgical Excision ◽

Skin Lesions ◽

Melanocytic Nevus ◽

Careful Examination ◽

Acral Lentiginous Melanoma ◽

Melanoma In Situ ◽

Malignant Skin ◽

Rule Out

Intra- and subcorneal hematoma, a skin alteration seen palmar and plantar after trauma or physical exercise, can be challenging to distinguish from in situ or invasive acral lentiginous melanoma. Thus, careful examination including dermoscopic and histologic assessment may be necessary to make the correct diagnosis. We here present a case of a 67-year-old healthy female patient who presented with a pigmented plantar skin alteration. Differential diagnoses included benign skin lesions, for example, hematoma or melanocytic nevus, and also acral lentiginous melanoma or melanoma in situ. Since clinical and dermoscopic examinations did not rule out a malignant skin lesion, surgical excision was performed and confirmed an intracorneal hematoma. In summary, without adequate physical trigger, it may be clinically and dermoscopically challenging to make the correct diagnosis in pigmented palmar and plantar skin alterations. Thus, biopsy or surgical excision of the skin alteration may be necessary to rule out melanoma.

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Integrated analyses of early responses to radiation in glioblastoma identify new alterations in RNA processing and candidate targets to improve treatment outcomes

10.21203/rs.2.20465/v1 ◽

2020 ◽

Author(s):

Saket Choudhary ◽

Suzanne Burns ◽

Hoda Mirsafian ◽

Whenzheng LI ◽

Dat Vo ◽

...

Keyword(s):

Molecular Mechanisms ◽

Early Response ◽

Radiation Sensitivity ◽

Integrated Analysis ◽

High Dose ◽

Transcriptional Level ◽

Altered Expression ◽

Improve Treatment ◽

Expression Of Genes ◽

Main Component

Abstract BackgroundHigh-dose radiation is the main component of glioblastoma therapy. Unfortunately, radio-resistance is a common problem and a major contributor to tumor relapse. Understanding the molecular mechanisms driving response to radiation is critical for identifying regulatory routes that could be targeted to improve treatment response. Methods: We conducted an integrated analysis in the U251 and U343 glioblastoma cell lines to map early alterations in the expression of genes at three levels: transcription, splicing, and translation in response to ionizing radiation. ResultsChanges at the transcriptional level were the most prevalent response. Downregulated genes are strongly associated with cell cycle and DNA replication and linked to a coordinated module of expression. Alterations in this group are likely driven by decreased expression of the transcription factor FOXM1 and members of the E2F family. Genes involved in RNA regulatory mechanisms were affected at the mRNA, splicing, and translation levels, highlighting their importance in radiation-response. We identified a number of oncogenic factors, with an increased expression upon radiation exposure, including BCL6, RRM2B, IDO1, FTH1, APIP, and LRIG2 and lncRNAs NEAT1 and FTX. Several of these targets have been previously implicated in radio- resistance. Therefore, antagonizing their effects post-radiation could increase therapeutic efficacy. ConclusionsOur integrated analysis provides a comprehensive view of early response to radiation in glioblastoma. We identify new biological processes involved in altered expression of various oncogenic factors and suggest new target options to increase radiation sensitivity and prevent relapse.

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Expression profiles of multiple genes in single neurons of Alzheimer’s disease

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.95.16.9620 ◽

1998 ◽

Vol 95 (16) ◽

pp. 9620-9625 ◽

Cited By ~ 56

Author(s):

Nienwen Chow ◽

Chris Cox ◽

Linda M. Callahan ◽

Jill M. Weimer ◽

LiRong Guo ◽

...

Keyword(s):

Single Cell ◽

Northern Blot ◽

Antisense Rna ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Single Neurons ◽

Altered Expression ◽

Rna Profiling ◽

Multiple Messages

Many changes have been described in the brains of Alzheimer’s disease (AD) patients, including loss of neurons and formation of senile plaques and neurofibrillary tangles. The molecular mechanisms underlying these pathologies are unclear. Northern blot, dot-blot, and reverse transcription-coupled PCR analyses have demonstrated altered expression levels of multiple messages in AD brain. Because not all cells are equally affected by the disease, these methods obviously cannot study the changes in relation to disease states of individual cells. We address this problem by using antisense RNA profiling of single cells. We present expression profiles of single neurons at early and late stages of AD and describe statistical tools for data analysis. With multivariate canonical analysis, we were able to distinguish the disease state on the basis of altered expression of multiple messages. To validate this approach, we compared results obtained by this approach with results obtained by in situ hybridization analysis. When the neurofilament medium subunit was used as a marker, our results from an antisense RNA profiling revealed no change in neurofilament medium subunit expression between early- and late-stage AD, consistent with findings obtained with in situ hybridization. However, our results obtained by either analysis at the single-cell level differed from the reported decrease in AD neocortex obtained by Northern blot analysis [Kittur, S., Hoh, J., Endo, H., Tourtellotte, W., Weeks, B. S., Markesbery, W. & Adler, W. (1994) J. Geriatr. Psychiatry Neurol. 7, 153–158]. Thus, the strategy of using the single-cell antisense RNA approach to identify altered gene expression in postmortem AD brain, followed by detailed in situ hybridization studies for genes of interest, is valuable in the study of the molecular mechanisms underlying AD neuropathology.

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Pasteurella multocida Gene Expression in Response to Iron Limitation

Infection and Immunity ◽

10.1128/iai.69.6.4109-4115.2001 ◽

2001 ◽

Vol 69 (6) ◽

pp. 4109-4115 ◽

Cited By ~ 67

Author(s):

Michael L. Paustian ◽

Barbara J. May ◽

Vivek Kapur

Keyword(s):

Gene Expression ◽

Pasteurella Multocida ◽

Molecular Mechanisms ◽

Iron Acquisition ◽

Expression Profiles ◽

Growth Conditions ◽

Whole Genome ◽

Altered Expression ◽

Expression Of Genes ◽

Wide Range

ABSTRACT Pasteurella multocida is the causative agent of a wide range of diseases in avian and mammalian hosts. Gene expression in response to low iron conditions was analyzed in P. multocida using whole-genome microarrays. The analysis shows that the expression of genes involved in energy metabolism and electron transport generally decreased 2.1- to 6-fold while that of genes used for iron binding and transport increased 2.1- to 7.7-fold in P. multocida during the first 2 h of growth under iron-limiting conditions compared with controls. Notably, 27% of the genes with significantly altered expression had no known function, illustrating the limitations of using publicly available databases to identify genes involved in microbial metabolism and pathogenesis. Taken together, the results of our investigations demonstrate the utility of whole-genome microarray analyses for the identification of genes with altered expression profiles during varying growth conditions and provide a framework for the detailed analysis of the molecular mechanisms of iron acquisition and metabolism in P. multocida and other gram-negative bacteria.

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FoxO6 affects Plxna4-mediated neuronal migration during mouse cortical development

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1609111113 ◽

2016 ◽

Vol 113 (45) ◽

pp. E7087-E7096 ◽

Cited By ~ 9

Author(s):

Ricardo H. Paap ◽

Saskia Oosterbroek ◽

Cindy M. R. J. Wagemans ◽

Lars von Oerthel ◽

Raymond D. Schellevis ◽

...

Keyword(s):

Axon Guidance ◽

Neuronal Migration ◽

Molecular Mechanisms ◽

Cortical Development ◽

Forkhead Transcription Factor ◽

Altered Expression ◽

Radial Migration ◽

Expression Of Genes ◽

Genome Wide ◽

Developing Neocortex

The forkhead transcription factor FoxO6 is prominently expressed during development of the murine neocortex. However, its function in cortical development is as yet unknown. We now demonstrate that cortical development is altered in FoxO6+/− and FoxO6−/− mice, showing migrating neurons halted in the intermediate zone. Using a FoxO6-directed siRNA approach, we substantiate the requirement of FoxO6 for a correct radial migration in the developing neocortex. Subsequent genome-wide transcriptome analysis reveals altered expression of genes involved in cell adhesion, axon guidance, and gliogenesis upon silencing of FoxO6. We then show that FoxO6 binds to DAF-16–binding elements in the Plexin A4 (Plxna4) promoter region and affects Plxna4 expression. Finally, ectopic Plxna4 expression restores radial migration in FoxO6+/− and siRNA-mediated knockdown models. In conclusion, the presented data provide insights into the molecular mechanisms whereby transcriptional programs drive cortical development.

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Live cell monitoring for factors affecting genome variation

10.1101/508150 ◽

2018 ◽

Cited By ~ 1

Author(s):

Yuntao Xia ◽

Kuangzheng Zhu ◽

Jerome Irianto ◽

Jason C Andrechak ◽

Lawrence J Dooling ◽

...

Keyword(s):

Single Cell ◽

Molecular Mechanisms ◽

Spindle Assembly Checkpoint ◽

Ips Cells ◽

Live Cell ◽

Chromosome 5 ◽

Altered Expression ◽

Factors Affecting ◽

Expression Of Genes ◽

Cancer Line

Cancer cells and pluripotent stem cells frequently exhibit gains or losses of entire chromosomes and chromosome segments, and the typical terminal analyses of genomes suggest this aneuploidy is ongoing and particularly variable in solid tumors. Here, we quantify aneuploidy-inducing perturbations by live cell fluorescence monitoring for changes in chromosome-5 in a lung cancer line and in normal diploid iPS cells. Inhibition of the spindle assembly checkpoint (SAC) and knockdown of DNA repair factors cause chromosome mis-segregation to increase several-fold above a low baseline level, and both perturbations also generate several-fold more rare fluorescent-null cells. Loss of chromosome-5 is confirmed by single cell karyotyping, SNP arrays on stable isolated clones, and downregulated expression of genes on chromosome-5 in single cell transcriptomics. The iPS cells also show loss of fluorescence in infrequent cells after SAC inhibition and upon growth as teratomas in mice. Viability, selection, and altered expression can thus be tracked to reveal molecular mechanisms in aneuploidy.

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HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽

10.1038/s41586-021-03460-z ◽

2021 ◽

Author(s):

Fides Zenk ◽

Yinxiu Zhan ◽

Pavel Kos ◽

Eva Löser ◽

Nazerke Atinbayeva ◽

...

Keyword(s):

Genome Organization ◽

Molecular Mechanisms ◽

High Throughput Sequencing ◽

De Novo ◽

Early Embryo ◽

Heterochromatin Protein ◽

Chromosome Conformation ◽

3D Genome ◽

Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

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Transcriptomic Analysis of Short-Term Salt-Stress Response in Mega Hybrid Rice Seedlings

Agronomy ◽

10.3390/agronomy11071328 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1328

Author(s):

Noushin Jahan ◽

Yang Lv ◽

Mengqiu Song ◽

Yu Zhang ◽

Liangguang Shang ◽

...

Keyword(s):

Salt Stress ◽

Molecular Mechanisms ◽

Oryza Sativa L ◽

Transcriptome Profiling ◽

Bhlh Transcription Factor ◽

F1 Hybrid ◽

Salt Stress Response ◽

Productivity Losses ◽

Expression Of Genes ◽

Trait Locus

Salinity is a major abiotic stressor that leads to productivity losses in rice (Oryza sativa L.). In this study, transcriptome profiling and heterosis-related genes were analyzed by ribonucleic acid sequencing (RNA-Seq) in seedlings of a mega rice hybrid, Liang-You-Pei-Jiu (LYP9), and its two parents 93–11 and Pei-ai64s (PA64s), under control and two different salinity levels, where we found 8292, 8037, and 631 salt-induced differentially expressed genes (DEGs), respectively. Heterosis-related DEGs were obtained higher after 14 days of salt treatment than after 7 days. There were 631 and 4237 salt-induced DEGs related to heterosis under 7-day and 14-day salt stresses, respectively. Gene functional classification showed the expression of genes involved in photosynthesis activity after 7-day stress treatment, and in metabolic and catabolic activity after 14 days. In addition, we correlated the concurrence of an expression of DEGs for the bHLH transcription factor and a shoot length/salinity-related quantitative trait locus qSL7 that we fine-mapped previously, providing a confirmed case of heterosis-related genes. This experiment reveals the transcriptomic divergence of the rice F1 hybrid and its parental lines under control and salt stress state, and enlightens about the significant molecular mechanisms developed over time in response to salt stress.

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