Distinct Modes of Neuritic Growth in Purkinje Neurons at Different Developmental Stages: Axonal Morphogenesis and Cellular Regulatory Mechanisms

AbstractQuantitative real-time PCR (qRT-PCR) has been emerged as an effective method to explore the gene function and regulatory mechanisms. However, selecting appropriate reference gene (s) is a prerequisite for obtaining accurate qRT-PCR results. Peach is one of important fruit in Rosaceae and is widely cultivated worldwide. In this study, to explore reliable reference gene (s) in peach with different types during fruit ripening and softening (S1–S4), nine candidate reference genes (EF-1α, GAPDH, TBP, UBC, eIF-4α, TUB-A, TUB-B, ACTIN, and HIS) were selected from the whole-genome data. Then, the expression levels of the nine selected genes were detected using qRT-PCR in three peach types, including ‘Hakuho’ (melting type), ‘Xiacui’ (stony hard type), ‘Fantasia’ and ‘NJC108’ (non-melting type) cultivars were detected using qRT-PCR. Four software (geNorm, NormFinder, BestKeeper and RefFinder) were applied to evaluate the expression stability of these candidate reference genes. Gene expression was characterized in different peach types during fruit ripening and softening stages. The overall performance of each candidate in all samples was evaluated. The Actin gene (ACTIN) was a suitable reference gene and displayed excellent stability in ‘Total’ set, ‘Hakuho’ samples, S3 and S4 fruit developmental stages. Ubiquitin C gene (UBC) showed the best stability in most independent samples, including ‘Fantasia’, ‘NJC108’, S2 sets. Elongation factor-1α gene (EF-1α) was the most unstable gene across the set of all samples, ‘NJC108’ and S2 sets, while showed the highest stability in ‘Xiacui’ samples. The stability of candidate reference genes was further verified by analyzing the relative expression level of ethylene synthase gene of Prunus persica (PpACS1) in fruit ripening and softening periods of ‘Hakuho’. Taken together, the results from this study provide a basis for future research on the mining of important functional genes, expression patterns and regulatory mechanisms in peach.

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Genome-wide characterization of the Zn(II)2Cys6 zinc cluster-encoding gene family in Pleurotus ostreatus and expression analyses of this family during developmental stages and under heat stress

PeerJ ◽

10.7717/peerj.9336 ◽

2020 ◽

Vol 8 ◽

pp. e9336

Author(s):

Zhihao Hou ◽

Qiang Chen ◽

Mengran Zhao ◽

Chenyang Huang ◽

Xiangli Wu

Keyword(s):

Heat Stress ◽

Pleurotus Ostreatus ◽

Developmental Stages ◽

Expression Profiles ◽

Expression Patterns ◽

Regulatory Mechanisms ◽

Fruiting Body Formation ◽

Zinc Cluster ◽

Genome Wide ◽

A Genome

Pleurotus ostreatus is one of the most widely cultivated mushrooms in China. The regulatory mechanisms of fruiting body formation and the response to heat stress in P. ostreatus are main research focuses. The Zn(II)2Cys6 family is one of the largest families of transcriptional factors and plays important roles in multiple biological processes in fungi. In this study, we identified 66 zinc cluster proteins in P. ostreatus (PoZCPs) through a genome-wide search. The PoZCPs were classified into 15 types according to their zinc cluster domain. Physical and chemical property analyses showed a huge diversity among the PoZCPs. Phylogenetic analysis of PoZCPs classified these proteins into six groups and conserved motif combinations and similar gene structures were observed in each group. The expression profiles of these PoZCP genes during different developmental stages and under heat stress were further investigated by RNA-sequencing (RNA-seq), revealing diverse expression patterns. A total of 13 PoZCPs that may participate in development or the heat stress response were selected for validation of their expression levels through real-time quantitative PCR (RT-qPCR) analysis, and some developmental stage-specific and heat stress-responsive candidates were identified. The findings contribute to our understanding of the roles and regulatory mechanisms of ZCPs in P. ostreatus.

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Involvement of miR156 in the Regulation of Vegetative Phase Change in Plants

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.140.5.387 ◽

2015 ◽

Vol 140 (5) ◽

pp. 387-395 ◽

Cited By ~ 10

Author(s):

Lu Zhang ◽

You-biao Hu ◽

Hua-sen Wang ◽

Sheng-jun Feng ◽

Yu-ting Zhang

Keyword(s):

Phase Change ◽

Developmental Stages ◽

Developmental Process ◽

Regulatory Mechanisms ◽

Physiological Changes ◽

Plant Growth And Development ◽

Vegetative Phase ◽

Vegetative Phase Change ◽

Squamosa Promoter Binding Protein ◽

Adult Phase

Plant growth and development are determined by complex exogenous and endogenous cues. A plant follows several temporally distinct developmental stages, including embryonic, vegetative, and reproductive. The vegetative stage, which is usually the longest stage, can be subdivided into juvenile and adult phases. The transition from the juvenile to the adult phase, also called the vegetative phase change, is characterized by anatomical, morphological, and physiological changes in the vegetative parts of the shoot. Recent studies in several systems have identified the genetic temporal mechanisms of this process, which is regulated by an endogenous age cue (i.e., microRNA156/157) and its targeted genes (i.e., Squamosa promoter binding protein-box transcription factors). This review summarizes the recent advances in the study of the underlying regulatory mechanisms of vegetative phase change. This review also describes the modes of miRNA action and the functions of their targeted genes in this highly conserved developmental process.

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Genetic basis of orange spot formation in the guppy (Poecilia reticulata)

BMC Ecology and Evolution ◽

10.1186/s12862-021-01942-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Mayuko Kawamoto ◽

Yuu Ishii ◽

Masakado Kawata

Keyword(s):

Gene Expression ◽

Sexual Selection ◽

Genetic Basis ◽

Poecilia Reticulata ◽

Developmental Stages ◽

Female Mate Choice ◽

Regulatory Mechanisms ◽

Gene Expression Levels ◽

Spot Formation ◽

Orange Spot

Abstract Background To understand the evolutionary significance of female mate choice for colorful male ornamentation, the underlying regulatory mechanisms of such ornamentation must be understood for examining how the ornaments are associated with “male qualities” that increase the fitness or sexual attractiveness of offspring. In the guppy (Poecilia reticulata), an established model system for research on sexual selection, females prefer males possessing larger and more highly saturated orange spots as potential mates. Although previous studies have identified some chromosome regions and genes associated with orange spot formation, the regulation and involvement of these genetic elements in orange spot formation have not been elucidated. In this study, the expression patterns of genes specific to orange spots and certain color developmental stages were investigated using RNA-seq to reveal the genetic basis of orange spot formation. Results Comparing the gene expression levels of male guppy skin with orange spots (orange skin) with those without any color spots (dull skin) from the same individuals identified 1102 differentially expressed genes (DEGs), including 630 upregulated genes and 472 downregulated genes in the orange skin. Additionally, the gene expression levels of the whole trunk skin were compared among the three developmental stages and 2247 genes were identified as DEGs according to color development. These analyses indicated that secondary differentiation of xanthophores may affect orange spot formation. Conclusions The results suggested that orange spots might be formed by secondary differentiation, rather than de novo generation, of xanthophores, which is induced by Csf1 and thyroid hormone signaling pathways. Furthermore, we suggested candidate genes associated with the areas and saturation levels of orange spots, which are both believed to be important for female mate choice and independently regulated. This study provides insights into the genetic and cellular regulatory mechanisms underlying orange spot formation, which would help to elucidate how these processes are evolutionarily maintained as ornamental traits relevant to sexual selection.

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RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response

10.1101/166694 ◽

2017 ◽

Cited By ~ 2

Author(s):

Arjun Krishnan ◽

Chirag Gupta ◽

Madana M.R. Ambavaram ◽

Andy Pereira

Keyword(s):

Large Scale ◽

Developmental Stages ◽

Transcriptional Profiling ◽

Regulatory Mechanisms ◽

Specific Gene ◽

Abiotic Stress Response ◽

Web Resource ◽

Genomic Knowledge ◽

A Genome ◽

Differential Expression Profile

AbstractTranscriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g. response of rice to drought. However, functionally interpreting the resulting genome-wide gene expression changes is severely hampered by the large gaps in our genomic knowledge about which genes work together in cellular pathways/processes in rice. Here, we present a new web resource – RECoN – that relies on a network-based approach to go beyond currently limited annotations in delineating functional and regulatory perturbations in new rice stress transcriptome datasets generated by a researcher. To build RECoN, we first enumerated 1,744 stress-specific gene modules covering 28,421 rice genes (>72% of the genes in the genome). Each module contains a group of genes tightly coexpressed across a large number of environmental conditions and, thus, is likely to be functionally coherent. When a user provides a new differential expression profile, RECoN identifies modules substantially perturbed in their experiment and further suggests deregulated functional and regulatory mechanisms based on the enrichment of current annotations within the predefined modules. We demonstrate the utility of this resource by analyzing new drought transcriptomes of rice in three developmental stages, which revealed large-scale insights into the cellular processes and regulatory mechanisms involved in common and stage-specific drought responses. RECoN enables biologists to functionally explore new data from all abiotic stresses on a genome-scale and to uncover gene candidates, including those that are currently functionally uncharacterized, for engineering stress tolerance.

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Male germline stem cells in non-human primates

Primate Biology ◽

10.5194/pb-4-173-2017 ◽

2017 ◽

Vol 4 (2) ◽

pp. 173-184 ◽

Cited By ~ 3

Author(s):

Swati Sharma ◽

Joana M. D. Portela ◽

Daniel Langenstroth-Röwer ◽

Joachim Wistuba ◽

Nina Neuhaus ◽

...

Keyword(s):

Stem Cells ◽

Germ Cell ◽

Germ Cells ◽

Developmental Stages ◽

Expression Patterns ◽

Regulatory Mechanisms ◽

Primate Species ◽

Germline Stem Cells ◽

Germline Development ◽

Human Primate

Abstract. Over the past few decades, several studies have attempted to decipher the biology of mammalian germline stem cells (GSCs). These studies provide evidence that regulatory mechanisms for germ cell specification and migration are evolutionarily conserved across species. The characteristics and functions of primate GSCs are highly distinct from rodent species; therefore the findings from rodent models cannot be extrapolated to primates. Due to limited availability of human embryonic and testicular samples for research purposes, two non-human primate models (marmoset and macaque monkeys) are extensively employed to understand human germline development and differentiation. This review provides a broader introduction to the in vivo and in vitro germline stem cell terminology from primordial to differentiating germ cells. Primordial germ cells (PGCs) are the most immature germ cells colonizing the gonad prior to sex differentiation into testes or ovaries. PGC specification and migratory patterns among different primate species are compared in the review. It also reports the distinctions and similarities in expression patterns of pluripotency markers (OCT4A, NANOG, SALL4 and LIN28) during embryonic developmental stages, among marmosets, macaques and humans. This review presents a comparative summary with immunohistochemical and molecular evidence of germ cell marker expression patterns during postnatal developmental stages, among humans and non-human primates. Furthermore, it reports findings from the recent literature investigating the plasticity behavior of germ cells and stem cells in other organs of humans and monkeys. The use of non-human primate models would enable bridging the knowledge gap in primate GSC research and understanding the mechanisms involved in germline development. Reported similarities in regulatory mechanisms and germ cell expression profile in primates demonstrate the preclinical significance of monkey models for development of human fertility preservation strategies.

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MYB transcription factor CiMYB42 regulates limonoids biosynthesis in citrus

10.21203/rs.2.21480/v1 ◽

2020 ◽

Author(s):

pan zhang ◽

Xiaofeng Liu ◽

Xin Xu ◽

Fusheng Wang ◽

Junhong Long ◽

...

Keyword(s):

Transcription Factor ◽

Biosynthetic Pathway ◽

Developmental Stages ◽

Regulatory Mechanisms ◽

Myb Transcription Factor ◽

Transcription Activator ◽

Multiple Alignment Analysis ◽

Citrus Varieties ◽

Alignment Analysis

Abstract Backgrounds Limonoids, a major bioactive components, are produced by triterpenoids metabolic pathway. So far, the detailed biochemical reactions regarding to limonoid biosynthesis and their molecular regulation remain elusive. The identification of transcription factors that regulate limonoids biosynthetic pathways is not only necessary for understanding the regulatory mechanisms but also as a tool for manipulating biosynthetic genes for biotechnological applications.Results In this study, CiMYB42 transcription factor was isolated and identified. Multiple alignment analysis and phylogenetic analysis demonstrated that CiMYB42 is a typical R2R3MYB transcription factor and its amino acid is similar to that of AtMYB42 . The limonoids content was higher in the citrus sinensis and citrus grandis than other species. The diverse accumulation patterns also showed in different leaf developmental stages. Expression of CiMYB42 was significantly related to limonoids content and the expression of CiOSC in some of citrus varieties. CiMYB42 transgenic sweet orange resulted significantly change on limonoids contents. Noticeably, CiMYB42 -RNAi induced dwarf phenotype and mainly decreased nomilin accumulation. Overexpressing CiMYB42 mainly increased limonin content. Yeast one hybrid assay results indicated that CiMYB42 exclusively bind to the promoter of CiOSC. In brief, CiMYB42 involved in the limonoids biosynthesis through binding the promoter of CiOSC in citrus.Conclusions These results indicated that CiMYB42 is an important transcription activator involved in limonoids biosynthesis by regulating the expression of CiOSC . This is the first report elucidating the role of transcription factor in citrus limonoids biosynthesis. Our contributions will provide a reference to understanding regulatory mechanisms of R2R3MYB TFs in the triterpenoids biosynthetic pathway.

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Correlated Studies of Cellular Interactions Using TEM, Freeze Etching, and SEM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010005161x ◽

1974 ◽

Vol 32 ◽

pp. 320-321

Author(s):

J. P. Revel

Keyword(s):

Developmental Stages ◽

Three Dimensional ◽

Cell Movement ◽

Cellular Interactions ◽

Serial Sections ◽

Cell Sheets ◽

Freeze Etching ◽

Early Developmental

Movement of individual cells or of cell sheets and complex patterns of folding play a prominent role in the early developmental stages of the embryo. Our understanding of these processes is based on three- dimensional reconstructions laboriously prepared from serial sections, and from autoradiographic and other studies. Many concepts have also evolved from extrapolation of investigations of cell movement carried out in vitro. The scanning electron microscope now allows us to examine some of these events in situ. It is possible to prepare dissections of embryos and even of tissues of adult animals which reveal existing relationships between various structures more readily than used to be possible vithout an SEM.

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Electron investigations of rhabdovirus-like particles in mexican bean beetles and crickets

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100082753 ◽

1978 ◽

Vol 36 (2) ◽

pp. 378-379

Author(s):

J. R. Adams ◽

G. J Tompkins ◽

A. M. Heimpel ◽

E. Dougherty

Keyword(s):

Biological Control ◽

Integrated Pest Management ◽

Pest Management ◽

Developmental Stages ◽

Management Program ◽

Acheta Domesticus ◽

Epilachna Varivestis ◽

House Cricket ◽

Similar Morphology ◽

Bean Beetle

As part of a continual search for potential pathogens of insects for use in biological control or on an integrated pest management program, two bacilliform virus-like particles (VLP) of similar morphology have been found in the Mexican bean beetle Epilachna varivestis Mulsant and the house cricket, Acheta domesticus (L. ).Tissues of diseased larvae and adults of E. varivestis and all developmental stages of A. domesticus were fixed according to procedures previously described. While the bean beetles displayed no external symptoms, the diseased crickets displayed a twitching and shaking of the metathoracic legs and a lowered rate of activity.Examinations of larvae and adult Mexican bean beetles collected in the field in 1976 and 1977 in Maryland and field collected specimens brought into the lab in the fall and reared through several generations revealed that specimens from each collection contained vesicles in the cytoplasm of the midgut filled with hundreds of these VLP's which were enveloped and measured approximately 16-25 nm x 55-110 nm, the shorter VLP's generally having the greater width (Fig. 1).

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The Fine Structure of the Sheath of Volvox Carteri f. Weismannia

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100079231 ◽

1977 ◽

Vol 35 ◽

pp. 346-347

Author(s):

Regina Birchem

Keyword(s):

Developmental Stages ◽

Ruthenium Red ◽

Sulfated Polysaccharides ◽

Volvox Carteri ◽

High Voltage Electron Microscopy ◽

Ultrastructural Studies ◽

Voltage Electron ◽

Sheath Formation ◽

And Inversion ◽

Sheath Material

Spheroids of the green colonial alga Volvox consist of biflagellate Chlamydomonad-like cells embedded in a transparent sheath. The sheath, important as a substance through which metabolic materials, light, and the sexual inducer must pass to and from the cells, has been shown to have an ordered structure (1,2). It is composed of both protein and carbohydrate (3); studies of V. rousseletii indicate an outside layer of sulfated polysaccharides (4).Ultrastructural studies of the sheath material in developmental stages of V. carteri f. weismannia were undertaken employing variations in the standard fixation procedure, ruthenium red, diaminobenzidine, and high voltage electron microscopy. Sheath formation begins after the completion of cell division and inversion of the daughter spheroids. Golgi, rough ER, and plasma membrane are actively involved in phases of sheath synthesis (Fig. 1). Six layers of ultrastructurally differentiated sheath material have been identified.

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