Cellular and gene expression patterns associated with root bifurcation in Selaginella

The roots of lycophytes branch through dichotomy or bifurcation, which means that the root apex splits into two daughter roots. This is morphologically distinct from lateral root (LR) branching in the extant euphyllophytes, where LRs develop along the root axis at different distances from the apex. The process of root bifurcation is poorly understood, while such knowledge can be important, as it may represent an evolutionarily ancient strategy that roots recruited to form new stem cells or meristems. In this study, we examined root bifurcation in the lycophyte Selaginella moellendorffii. We characterized an in vitro developmental time-frame based on repetitive apex bifurcations, allowing us to sample different stages of dichotomous root branching and analyze the root meristem and root branching in S. moellendorffii at the microscopical and transcriptional level. Our results show that, in contrast to previous assumptions, initial cells in the root meristem are mostly not tetrahedral but rather show an irregular shape. Tracking down the early stages during root branching argues for the occurrence of a symmetric division of the single initial cell resulting in two apical stem cells allowing for root meristem bifurcation. Moreover, we generated a S. moellendorffii root branching transcriptome, which resulted in the delineation of a subset of core meristem genes. The occurrence of multiple meristem-related orthologues in this dataset, including inversely correlated expression profiles of a SCARECROW (SCR) versus a RETINOBLASTOMA-RELATED1 (RBR1) homologue suggests the presence of conserved pathways in the control of meristem and root stem cell establishment or maintenance.

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Mesenchymal Stem Cell Differentiation Markers Shared with Soft Tissue Sarcomas

Blood ◽

10.1182/blood.v112.11.4755.4755 ◽

2008 ◽

Vol 112 (11) ◽

pp. 4755-4755

Author(s):

Stefan Wirths ◽

Hans-Joerg Buehring ◽

Lothar Kanz ◽

Joerg T Hartmann ◽

Hans-Georg Kopp

Keyword(s):

Stem Cells ◽

Soft Tissue ◽

Expression Pattern ◽

Cell Lines ◽

Expression Profiles ◽

Expression Patterns ◽

Soft Tissue Sarcomas ◽

Stem Cell Differentiation ◽

Antibody Panel

Abstract Malignant tumors are hypothesized to harbor small populations of self-renewing cancer stem cells. Targeting these cells may be the decisive step to overcome treatment resistance and achieve tumor eradication in cancer patients. Advanced soft tissue sarcomas (STS) are rare tumors with a dismal prognosis and a small number of systemic treatment options. STS may originate from mesenchymal stem cells (MSC); the latter have mainly been isolated from adult bone marrow (BM) as non-hematopoietic, self-renewing cells whose in vitro progeny comprises osteoblasts, chondroblasts, myocytes, and adipocytes. While in vitro expression profiles of MSC have been investigated extensively, the in vivo counterparts of MSC are still hypothetical. To target rare human cell BM populations including MSC, an exclusive antibody panel was developed. The target antigens include platelet-derived growth factor receptor-β (CD140b), HER-2/erbB2 (CD340), the recently described W8B2 antigen as well as several surface antigens identified by novel antibodies. To define the expression pattern of MSC-markers in STS, three STS cell lines were tested for expression of these antigens. In addition, snap-frozen primary STS sections were analyzed by immunohistochemistry using the same antibody panel. All cell lines revealed expression of selected markers including CD340, W8B2, and CD140b. Several MSC markers were restricted to a subpopulation of cells. In addition, leiomyosarcoma cells displayed a different expression pattern as compared to liposarcoma and Ewing’s sarcoma cells. Results of immunohistochemistry analysis of primary leiomyosarcoma tumor samples correlated strongly with expression patterns established by FACS analysis. However, important cytoarchitectural features regarding selected markers were revealed by immunohistochemistry: while primary leiomyosarcomas displayed uniform expression of W7C6, HEK3D6, CD10, and CD318, other markers such as CD34, W5C5, and 57D2 were expressed by tumor endothelia only. Moreover, a population of perivascular tumor cells was found to express the MSC-markers W4A5, W8B2, CD140b, W3D5, and W5C4. Novel MSC-markers are expressed by subpopulations in STS cell lines as well as in primary sarcoma tissue. Further studies on the functional significance of these phenotypical studies are underway and may help to identify novel specific targets recognizing the self-renewing STS-compartment.

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Developmental Transcriptional Model Describing Regulated Genes, Qtls And Pathways During The Primary And Secondary Cell Walls Of Pima Fibers

10.1101/056127 ◽

2016 ◽

Author(s):

Magdy S. Alabady ◽

Bulak A. Arpat

Keyword(s):

Gene Expression ◽

Developmental Stages ◽

Expression Profiles ◽

Fiber Quality ◽

Time Frame ◽

Developmental Time ◽

Transcriptional Level ◽

Specific Expression ◽

Time Points ◽

Cotton Genotypes

AbstractGossypium barbadense L. (Egyptian and Pima) produces single celled fiber trichomes that are the longest and richest in cellulosic contents in the plant kingdom. Developmental dissection of fiber at the transcriptional level is crucial to unveiling the genetic mechanisms underpinning fiber morphogenesis. We profiled the transcriptome of developing Pima fibers, as well as genes associated with consensus fiber quality QTLs, at seven developmental time points covering both primary (PCW) and secondary (SCW) cell wall stages. A total of 2,934 genes were differentially expressed at only one (45.19%) or at multiple (54.81%) developmental time points. Based on the coincidence between gene expression dynamics and the time frame of fiber developmental stages, five stage-specific expression profiles were identified. As a link between fiber QTLs and gene expression, 5 potential developmentally regulated QTLs (drQTLs) corresponding to different fiber developmental stages were identified. Genes in the ubiquitin proteolytic pathway, particularly QTL associated genes, appeared to be involved in regulating the transition stage between PCW and SCW; a stage that is crucial to both fiber length and strength in the extra-long staple cotton genotypes. In this respect, Yeast-two-hybrids identified interactions between UBC9 and genes involved in cell and organ elongation, polar cell expansion, microtubule cytoskeleton dynamics and organization, and basic amino acids transportation during the SCW/SCW transition. Altogether, these results were integrated into a proposed model linking fiber developmental stages with the Pima fiber traits.

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The Predominant microRNAs in β-cell Clusters for Insulin Regulation and Diabetic Control

Current Drug Targets ◽

10.2174/1389450121666191230145848 ◽

2020 ◽

Vol 21 (7) ◽

pp. 722-734

Author(s):

Adele Soltani ◽

Arefeh Jafarian ◽

Abdolamir Allameh

Keyword(s):

Mirna Expression ◽

Expression Profiles ◽

Expression Patterns ◽

Diabetic Control ◽

In Vitro Proliferation ◽

Cell Functions ◽

Mirna Expression Profiles ◽

Multiple Processes ◽

The Impact

micro (mi)-RNAs are vital regulators of multiple processes including insulin signaling pathways and glucose metabolism. Pancreatic β-cells function is dependent on some miRNAs and their target mRNA, which together form a complex regulative network. Several miRNAs are known to be directly involved in β-cells functions such as insulin expression and secretion. These small RNAs may also play significant roles in the fate of β-cells such as proliferation, differentiation, survival and apoptosis. Among the miRNAs, miR-7, miR-9, miR-375, miR-130 and miR-124 are of particular interest due to being highly expressed in these cells. Under diabetic conditions, although no specific miRNA profile has been noticed, the expression of some miRNAs and their target mRNAs are altered by posttranscriptional mechanisms, exerting diverse signs in the pathobiology of various diabetic complications. The aim of this review article is to discuss miRNAs involved in the process of stem cells differentiation into β-cells, resulting in enhanced β-cell functions with respect to diabetic disorders. This paper will also look into the impact of miRNA expression patterns on in vitro proliferation and differentiation of β-cells. The efficacy of the computational genomics and biochemical analysis to link the changes in miRNA expression profiles of stem cell-derived β-cells to therapeutically relevant outputs will be discussed as well.

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Differential expression and correlation analysis of miRNA–mRNA profiles in swine testicular cells infected with porcine epidemic diarrhea virus

Scientific Reports ◽

10.1038/s41598-021-81189-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xiaoqian Zhang ◽

Chang Li ◽

Bingzhou Zhang ◽

Zhonghua Li ◽

Wei Zeng ◽

...

Keyword(s):

Differential Expression ◽

Porcine Epidemic Diarrhea Virus ◽

Expression Profiles ◽

Expression Patterns ◽

Bacterial Invasion ◽

Sequencing Data ◽

Diarrhea Virus ◽

Comparison Groups ◽

Porcine Epidemic Diarrhea

AbstractThe variant virulent porcine epidemic diarrhea virus (PEDV) strain (YN15) can cause severe porcine epidemic diarrhea (PED); however, the attenuated vaccine-like PEDV strain (YN144) can induce immunity in piglets. To investigate the differences in pathogenesis and epigenetic mechanisms between the two strains, differential expression and correlation analyses of the microRNA (miRNA) and mRNA in swine testicular (ST) cells infected with YN15, YN144, and mock were performed on three comparison groups (YN15 vs Control, YN144 vs Control, and YN15 vs YN144). The mRNA and miRNA expression profiles were obtained using next-generation sequencing (NGS), and the differentially expressed (DE) (p-value < 0.05) mRNA and miRNA were obtained using DESeq R package. mRNAs targeted by DE miRNAs were predicted using the miRanda algortithm. 8039, 8631 and 3310 DE mRNAs, and 36, 36, and 22 DE miRNAs were identified in the three comparison groups, respectively. 14,140, 15,367 and 3771 DE miRNA–mRNA (targeted by DE miRNAs) interaction pairs with negatively correlated expression patterns were identified, and interaction networks were constructed using Cytoscape. Six DE miRNAs and six DE mRNAs were randomly selected to verify the sequencing data by real-time relative quantitative reverse transcription polymerase chain reaction (qRT-PCR). Based on bioinformatics analysis, we discovered the differences were mostly involved in host immune responses and viral pathogenicity, including NF-κB signaling pathway and bacterial invasion of epithelial cells, etc. This is the first comprehensive comparison of DE miRNA–mRNA pairs in YN15 and YN144 infection in vitro, which could provide novel strategies for the prevention and control of PED.

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Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis and Brassica rapa cultivars

10.1101/2020.08.26.266494 ◽

2020 ◽

Author(s):

Alexander Calderwood ◽

Jo Hepworth ◽

Shannon Woodhouse ◽

Lorelei Bilham ◽

D. Marc Jones ◽

...

Keyword(s):

Gene Expression ◽

Brassica Rapa ◽

Regulatory Networks ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Detailed Comparison ◽

Developmental Time ◽

Floral Transition ◽

Gene Regulatory

AbstractThe timing of the floral transition affects reproduction and yield, however its regulation in crops remains poorly understood. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. A direct comparison of gene expression over time between species shows little similarity, which could lead to the inference that different gene regulatory networks are at play. However, these differences can be largely resolved by synchronisation, through curve registration, of gene expression profiles. We find that different registration functions are required for different genes, indicating that there is no common ‘developmental time’ to which Arabidopsis and B. rapa can be mapped through gene expression. Instead, the expression patterns of different genes progress at different rates. We find that co-regulated genes show similar changes in synchronisation between species, suggesting that similar gene regulatory sub-network structures may be active with different wiring between them. A detailed comparison of the regulation of the floral transition between Arabidopsis and B. rapa, and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways, even when grown under the same environmental conditions. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa under long days and highlights the importance of registration methods for the comparison of developmental gene expression data.

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Is gene expression among women with rheumatoid arthritis dysregulated during a postpartum flare?

Arthritis Research & Therapy ◽

10.1186/s13075-021-02418-w ◽

2021 ◽

Vol 23 (1) ◽

Author(s):

Matthew Wright ◽

Mette K. Smed ◽

J. Lee Nelson ◽

Jørn Olsen ◽

Merete L. Hetland ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Gene Expression ◽

Disease Activity ◽

Activity Index ◽

Expression Profiles ◽

Expression Patterns ◽

Time Frame ◽

Differentially Expressed ◽

Healthy Women ◽

Immune Related Genes

Abstract Background To evaluate our hypotheses that, when rheumatoid arthritis (RA) flares postpartum, gene expression patterns are altered compared to (a) healthy women, (b) RA women whose disease activity is low or in remission postpartum, and (c) pre-pregnancy expression profiles. Methods Twelve women with RA and five healthy women were included in this pilot study. RA disease activity and postpartum flare were assessed using the Clinical Disease Activity Index (CDAI). Total RNA from frozen whole blood was used for RNA sequencing. Differential gene expression within the same women (within-group) over time, i.e., postpartum vs. third trimester (T3) or pre-pregnancy (T0), were examined, using a significance threshold of q < 0.05 and fold-change ≥ 2. Results Nine of the women with RA experienced a flare postpartum (RAFlare), while three had low disease activity or were in remission (RANoFlare) during that time frame. Numerous immune-related genes were differentially expressed postpartum (vs. T3) during a flare. Fold-changes in expression from T3 to postpartum were mostly comparable between the RAFlare and healthy groups. At 3 months postpartum, compared to healthy women, several genes were significantly differentially expressed only among the RAFlare women, and not among the RANoFlare women. Some of these genes were among those whose “normal” expression was significantly modulated postpartum, and the postpartum expression patterns were significantly altered during the RA flare. There were also some genes that were significantly differentially expressed in RAFlare compared to both healthy and RANoFlare women, even though their expression was not significantly modulated postpartum. Furthermore, while postpartum expression profiles were similar to those at pre-pregnancy among healthy women, significant differences were found between those time points among the RAFlare women. Conclusions The large majority of gene expression changes between T3 and 3 months postpartum among RA women who flared postpartum reflected normal postpartum changes also seen among healthy women. Nonetheless, during a postpartum flare, a set of immune-related genes showed dysregulated expression compared to healthy women and women with RA whose disease activity was low or in remission during the same time frame, while other genes demonstrated significant differences in expression compared to RA pre-pregnancy levels.

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Isolation of cDNA clones for genes exhibiting reduced expression after differentiation of murine teratocarcinoma stem cells.

Molecular and Cellular Biology ◽

10.1128/mcb.4.10.2142 ◽

1984 ◽

Vol 4 (10) ◽

pp. 2142-2150 ◽

Cited By ~ 26

Author(s):

R A Levine ◽

G J LaRosa ◽

L J Gudas

Keyword(s):

Stem Cells ◽

Retinoic Acid ◽

Cyclic Amp ◽

Cdna Library ◽

In Vitro Transcription ◽

In Vitro Translation ◽

Transcriptional Level ◽

Cdna Clones ◽

Dibutyryl Cyclic Amp

In the absence of retinoic acid, PSA-G teratocarcinoma stem cells spontaneously differentiate at a moderate frequency into fibroblast-like cells. In the presence of retinoic acid and dibutyryl cyclic AMP, PSA-G stem cells differentiate into parietal endoderm cells. We prepared a cDNA library from undifferentiated PSA-G teratocarcinoma stem cells; this cDNA library was then screened for gene sequences which exhibit a reduction in expression during the differentiation of these stem cells. From ca. 1,000 clones screened, eight independent sequences were isolated. The level of expression of these cloned genes decreases by 3.0-fold to more than 10-fold after differentiation of PSA-G cells into fibroblast-like cells. After treatment of either PSA-G or F9 teratocarcinoma cells with retinoic acid and dibutyryl cyclic AMP for 72 h, the expression of seven genes is inhibited by two- to fourfold. This decrease of clone-specific transcripts can be detected within 12 h after the addition of retinoic acid. Hybridization-selection and in vitro translation experiments identified the proteins encoded by three of the cloned genes: pST 6-23 codes for a 89,000-dalton protein, pST 7-105 codes for a 41,000-dalton protein, and pST 9-31 codes for a 34,000-dalton protein. The 89,000-dalton protein encoded by pST 6-23 is a heat shock protein. In vitro transcription experiments demonstrate that the retinoic acid-mediated decrease in pST 6-135- and pST 1-68-specific RNA occurs at the transcriptional level and that dibutyryl cyclic AMP acts posttranscriptionally to further depress the levels of these RNAs.

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Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽

10.1139/gen-2017-0163 ◽

2018 ◽

Vol 61 (2) ◽

pp. 121-130 ◽

Cited By ~ 4

Author(s):

Chenghao Zhang ◽

Wenqi Dong ◽

Zong-an Huang ◽

MyeongCheoul Cho ◽

Qingcang Yu ◽

...

Keyword(s):

Capsicum Annuum ◽

Abiotic Stresses ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Families ◽

Environmental Stresses ◽

Transcriptional Level ◽

Specific Expression ◽

Capsicum Annuum L ◽

Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

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Delineation of target expression profiles in CD34+/CD38− and CD34+/CD38+ stem and progenitor cells in AML and CML

Blood Advances ◽

10.1182/bloodadvances.2020001742 ◽

2020 ◽

Vol 4 (20) ◽

pp. 5118-5132 ◽

Cited By ~ 1

Author(s):

Harald Herrmann ◽

Irina Sadovnik ◽

Gregor Eisenwort ◽

Thomas Rülicke ◽

Katharina Blatt ◽

...

Keyword(s):

Stem Cells ◽

Messenger Rna ◽

Myeloid Leukemia ◽

Expression Profiles ◽

Quantitative Polymerase Chain Reaction ◽

Gene Array ◽

Nsg Mice ◽

Stem And Progenitor Cells ◽

Membrane Antigens

Abstract In an attempt to identify novel markers and immunological targets in leukemic stem cells (LSCs) in acute myeloid leukemia (AML) and chronic myeloid leukemia (CML), we screened bone marrow (BM) samples from patients with AML (n = 274) or CML (n = 97) and controls (n = 288) for expression of cell membrane antigens on CD34+/CD38− and CD34+/CD38+ cells by multicolor flow cytometry. In addition, we established messenger RNA expression profiles in purified sorted CD34+/CD38− and CD34+/CD38+ cells using gene array and quantitative polymerase chain reaction. Aberrantly expressed markers were identified in all cohorts. In CML, CD34+/CD38− LSCs exhibited an almost invariable aberration profile, defined as CD25+/CD26+/CD56+/CD93+/IL-1RAP+. By contrast, in patients with AML, CD34+/CD38− cells variably expressed “aberrant” membrane antigens, including CD25 (48%), CD96 (40%), CD371 (CLL-1; 68%), and IL-1RAP (65%). With the exception of a subgroup of FLT3 internal tandem duplication–mutated patients, AML LSCs did not exhibit CD26. All other surface markers and target antigens detected on AML and/or CML LSCs, including CD33, CD44, CD47, CD52, CD105, CD114, CD117, CD133, CD135, CD184, and roundabout-4, were also found on normal BM stem cells. However, several of these surface targets, including CD25, CD33, and CD123, were expressed at higher levels on CD34+/CD38− LSCs compared with normal BM stem cells. Moreover, antibody-mediated immunological targeting through CD33 or CD52 resulted in LSC depletion in vitro and a substantially reduced LSC engraftment in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice. Together, we have established surface marker and target expression profiles of AML LSCs and CML LSCs, which should facilitate LSC enrichment, diagnostic LSC phenotyping, and development of LSC-eradicating immunotherapies.

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187 INCREASED NUMBER OF EXPANDED BOVINE BLASTOCYSTS IN SOF AND CR1 RELATIVE TO KSOM

Reproduction Fertility and Development ◽

10.1071/rdv19n1ab187 ◽

2007 ◽

Vol 19 (1) ◽

pp. 210

Author(s):

D. M. Kohl ◽

R. L. Monson ◽

L. E. Enwall ◽

J. J. Rutledge

Keyword(s):

Gene Expression ◽

Culture Media ◽

Expression Profiles ◽

Expression Patterns ◽

Culture Conditions ◽

Pregnancy Rates ◽

Embryo Morphology ◽

Bovine Embryos ◽

Chi Square Analysis

Assessment of morphological stage grade is a subjective procedure. Stage grade is of vital importance to, among other things, recipient synchrony for the purpose of establishing successful pregnancies. Asynchronous embryo transfer has led to decreases in pregnancy rates (Farin et al. 1995 Biol. Reprod. 52, 676–682) and has been implicated in contributing to large offspring syndrome (Young et al. 1996 Theriogenology 45, 231). Differences in embryo kinetics based on culture conditions have been well documented (Mello et al. 2005 Reprod. Fert. Dev. 17, 221 abst). Whether such differences are the result of species, breed, metabolic stress, sire effects, or separation from an in vivo environment has yet to be determined. The correlation between oxygen respiration rates and embryo morphology as well as embryo diameter in bovine embryos produced in vitro has shown promise in the development of a more objective predictor of embryo quality and perhaps pregnancy initiation (Lopes et al. 2005 Reprod. Fert. Dev. 17, 151 abst). As well, recent examination of gene expression patterns of in vitro-derived bovine embryos seems to indicate that longer periods of in vitro culture are associated with lower rates of embryo survival (Lonergan et al. 2006 Theriogenology 65, 137–152). We hypothesize that differences do exist in the number, rate, and morphological appearance of blastocysts and that these parameters are in large part based on culture conditions in vitro. The objective of this experiment was to determine the timing and distribution of blastocyst formation of in vitro-produced bovine embryos cultured in SOF8, CR18AA, and KSOM8, under a standard incubation environment. Bovine ovaries from a local abattoir were aspirated and matured for 18-22. Oocytes were fertilized with frozen-thawed Percoll-separated semen from a Holstein bull. Presumptive zygotes were vortexed to remove cumulus cells and placed into 3 different culture media in a highly humidified atmosphere containing 20% oxygen, 5% carbon dioxide, and compressed air at 38.5�C. Embryos were evaluated specifically at 168 h post-insemination (Day 7) and assigned a morphological stage grade (IETS) to determine fixed time point differences. A total of 6 complete replicates were performed. Only embryos exhibiting the presence of a blastocoel at this time were documented (early blast, mid-blast, expanded blast). At 168 h post-insemination, there were no significant differences in the total number of embryos reaching early or mid-blast stage in any of the media. However, chi-square analysis revealed an increase in the number of expanded blastocysts in SOF (n = 813) and CR1 (n = 838) treatments compared to KSOM (n = 824; P < 0.0001). Expanded blastocysts in SOF were also greater in number than in CR1 (P < 0.05). Embryo selection based on development to the expanded blastocyst stage on Day 7 may prove useful in increasing pregnancy rates, and may validate qualitative correlations based on oxygen consumption and gene expression profiles for embryos produced in vitro.

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