ARTICLE | doi:10.20944/preprints202207.0376.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: information theory; embryogenesis; regeneration; cell biology; morphogenesis; calcium
Online: 25 July 2022 (12:35:28 CEST)
There is a growing appreciation in the fields of Cell and Developmental Biology that cells collectively process information in time and space. While many powerful molecular tools exist to observe biophysical dynamics biologists must find ways to quantitatively understand these phenomena at the systems level. Here, we present a guide for application of well-established information theory metrics to biological datasets and explain these metrics using examples from cell, developmental and regenerative biology. We introduce a novel computational tool (CAIM) for simple, rigorous application of these metrics to timeseries datasets. Finally, we use CAIM to study calcium and cytoskeletal Actin information flow patterns between Xenopus laevis embryonic animal cap stem cells. The tools that we present here will enable biologists to apply information theory to develop systems level understanding of a diverse array of experimental systems.
ARTICLE | doi:10.20944/preprints202103.0087.v1
Subject: Life Sciences, Biochemistry Keywords: Cranial neural crest cells; embryogenesis; development; cell migration
Online: 2 March 2021 (12:28:49 CET)
A recent study from our lab revealed that inhibition of cyclooxygenase-2 exclusively reduces the level of PGE2 amongst the prostanoids and hamper the normal development of several structures, strikingly the cranial vault, in chick embryos. In order to unearth the mechanism behind the deviant development of cranial features, the expression pattern of various factors that are known to influence the cranial neural crest cell (CNCC) migration were checked in chick embryo after inhibiting the COX-2 activity using etoricoxib. The compromised level of cell adhesion molecules and their upstream regulators, namely CDH1, CDH2, MSX1, and TGF-β, observed in the etoricoxib treated embryos indicate that COX-2, through its downstream effector PGE2, regulates the expression of these factors perhaps to aid the migration of CNCC. The histological features and levels of FoxD3 as well as PCNA further consolidates the role of COX-2 in migration and survival of CNCC in developing embryo. The results of the current study indicate that the COX-2 plays a pivotal role in orchestrating the proliferation and migration of CNCC during embryonic development of chick.
REVIEW | doi:10.20944/preprints202103.0209.v1
Subject: Life Sciences, Biochemistry Keywords: Genetic Mapping; Vascular system; Embryogenesis; Vascular disorder; PIk3CA gene
Online: 8 March 2021 (10:43:40 CET)
Term vascular dysfunctional refers to a wide spectrum of vascular abnormalities including pathogenesis of tumors, their proliferation and leading to malfunctioned conditions. The treatment of most of the vascular anomalies including peripheral arterial disease and cardiac disease is multi factor procedure which include the embolic therapy, laser-based treatments and coagulation are all plating important role in managing the disease associated with vascular breakdown. The research proposal defines the treatment and diagnosis procedures involved in treatment of vascular abnormalities with a deep emphasis on techniques, efficiency and complications resulted from various other procedure and use of mapping and sequencing techniques based on genetics of variants of selected genes PIk3CA which will ultimately be more effective.
ARTICLE | doi:10.20944/preprints202101.0513.v1
Subject: Life Sciences, Biochemistry Keywords: Aleppo pine; conifers; phytosulfokine; plant growth regulators; somatic embryogenesis
Online: 26 January 2021 (14:21:31 CET)
Organogenesis and somatic embryogenesis have been widely applied as the two main regeneration pathways in plant tissue culture. However, recalcitrance is still a main restriction in the clonal propagation of many woody species, especially in conifers. They undergo a “phase change” that leads to significant loss of organogenic and embryogenic capacity, thus reducing the responsive tissues or organs to juvenile material, and narrowing the competence window. In this sense, in vitro regeneration of mature conifer trees has been a long-cherished goal in many laboratories worldwide. In this work, apical shoot buds were used as explants for both organogenesis and somatic embryogenesis in order to cloning mature trees of Aleppo pine. Reinvigorated axillary shoots were submitted to somatic embryogenesis induction through the manipulation of culture media, including the use of auxins such as 2,4-D and NAA, cytokinins (BA and kinetin) and phytosulfokine (50, 100 and 200 nM). Although somatic embryos could not be obtained, embryogenic-like tissue was produced followed by the appearance of actively proliferating non-embryogenic calli and differences between treatments were found, especially when phytosulfokine was added to the induction media. Organogenic system produced reinvigorated shoots from both BA treatments tested (22 and 44 µM), from juvenile somatic trees and adult trees, and ex-vitro acclimatized plants were developed.
ARTICLE | doi:10.20944/preprints201608.0108.v1
Subject: Biology, Anatomy & Morphology Keywords: developmental biology; computational biology; lineage trees; embryogenesis; biological complexity
Online: 10 August 2016 (11:36:39 CEST)
Embryonic development proceeds through a series of differentiation events. The mosaic version of this process (binary cell divisions) can be analyzed by comparing early development of Ciona intestinalis and Caenorhabditis elegans. To do this, we reorganize lineage trees into differentiation trees using the graph theory ordering of relative cell volume. Lineage and differentiation trees provide us with means to classify each cell using binary codes. Extracting data characterizing lineage tree position, cell volume, and nucleus position for each cell during early embryogenesis, we conduct several statistical analyses, both within and between taxa. We compare both cell volume distributions and cell volume across developmental time within and between single species and assess differences between lineage tree and differentiation tree orderings. This enhances our understanding of the differentiation events in a model of pure mosaic embryogenesis and its relationship to evolutionary conservation. We also contribute several new techniques for assessing both differences between lineage trees and differentiation trees, and differences between differentiation trees of different species. The results suggest that at the level of differentiation trees, there are broad similarities between distantly related mosaic embryos that might be essential to understanding evolutionary change and phylogeny reconstruction. Differentiation trees may therefore provide a basis for an Evo-Devo Postmodern Synthesis.
ARTICLE | doi:10.20944/preprints202112.0408.v1
Subject: Life Sciences, Biotechnology Keywords: Embryogenesis; Cobalt-60 radiation-induced mutagenesis; Temporary immersion systems (TIS).
Online: 24 December 2021 (14:47:29 CET)
The development of gamma rays mutant rice lines would be a solution for introducing variability in already farmer using varieties. In vitro gamma (60Co) mutagenesis reduces chimeras and allows a faster selection of desired traits but requires laboratory process optimization. The objective of the present work was the in vitro establishment of a recalcitrant rice embryogenic calli, the determination of its sensitivity to gamma radiation (Co-60), sequencing MATK and Rubisco for identification purposes, as well as generation optimization. The radiosensitivity of embryogenic calli resulted in an LD50 of 110Gy, while the 20% lethal dose was 64Gy. All sequenced genes matched perfectly with already reported MATK and Rubisco O. sativa genes with a clear SNP that identifies the local variety related to the southeast Asia Region. Callus induction improves with an MS with 2mg/L 2,4D, and the regeneration was achieved with an MS medium with 3mg/L BAP and 0,5mg/L NAA. The optimized radiation condition was 60Gy with an 83% regeneration in a semisolid medium, allowing a balance between mutation and regeneration. When increased to 80Gy, the regeneration rate falls to 29%. An immersion system (RITA®) of either 60 or 120 seconds every 8hours allowed a systematic and homogeneous total regeneration of the recalcitrant line, in contrast with the semisolid medium that resulted in positive but irregular regeneration. Other well-known recalcitrant cultivars, CR1821, CR1113 also had an improving regeneration in the immersion system, demonstrating its potential use for recalcitrant materials. To our knowledge, this is the first report on using an immersion system to allow regeneration of gamma-ray mutants from recalcitrant rice materials.
Subject: Biology, Plant Sciences Keywords: callus; genotype-specific recalcitrance; reprogramming; somatic embryogenesis; transcriptomics; upland cotton
Online: 20 July 2021 (15:30:47 CEST)
Somatic embryogenesis-mediated plant regeneration is essential for genetic manipulation of agronomically important traits in upland cotton. Genotype specific recalcitrance to regeneration is a primary challenge in deploying genome editing and incorporating useful transgenes into elite cotton germplasm. In this study, transcriptomes of a semi-recalcitrant cotton (Gossypium hirsutum L.) genotype ‘Coker312’ were analyzed at two critical stages of Somatic Embryogenesis that includes non-embryogenic callus (NEC) and embryogenic callus (EC) cells, and the results compared to a non-recalcitrant genotype ‘Jin668’. We discovered of 305 differentially expressed genes in Coker312, whereas, in Jin668, about 6-fold more genes (2,155) were differentially expressed. A total of 154 differentially expressed genes were common between the two genotypes. Gene enrichment analysis of upregulated genes identified functional categories such as lipid transport, embryo development, regulation of transcription, sugar transport, vitamin biosynthesis, among others. In Coker312 EC cells, five major transcription factors were highly upregulated: LEAFY COTYLEDON 1 (LEC1), WUS-related homeobox 5 (WOX5), ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and WRKY2. In Jin668, LEC1, BABY BOOM (BBM), FUS3, and AGAMOUS-LIKE15 (AGL15) were highly expressed in EC cells. We also found that gene expression of these embryogenesis genes was typically higher in Jin668 when compared to Coker312. We conclude that significant differences in expression of the above genes between Coker312 and Jin668 may be a critical factor affecting the regenerative ability of these genotypes.
Subject: Biology, Other Keywords: embryogenesis; blastocyst; trophoblast; stem cell; differentiation; placenta; Ovo-like 2
Online: 8 March 2020 (04:11:35 CET)
Trophoblasts are the first cell-type to be specified during embryogenesis, and they are essential for placental morphogenesis and function. Trophoblast stem (TS) cells are the progenitor cells for all trophoblast lineages; control of TS cell differentiation into distinct trophoblast subtypes is not well understood. Mice lacking the transcription factor OVO-like 2 (OVOL2) fail to produce a functioning placenta, and die around embryonic day 10.5, suggesting that OVOL2 may be critical for trophoblast development. Therefore, our objective was to determine the role of OVOL2 in mouse TS cell fate. We found that OVOL2 was highly expressed in mouse placenta and differentiating TS cells. Placentas and TS cells lacking OVOL2 showed poor trophoblast differentiation potential, including increased expression of stem-state associated genes (Eomes, Esrrb, Id2) and decreased levels of differentiation-associated transcripts (Gcm1, Tpbpa, Prl3b1, Syna). Ectopic OVOL2 expression in TS cells elicited precocious differentiation. OVOL2 bound proximate to the gene encoding inhibitor of differentiation 2 (ID2), a dominant negative helix-loop-helix protein, and directly repressed its activity. Overexpression of ID2 was sufficient to reinforce the TS cell stem state. Our findings reveal a critical role of OVOL2 as a regulator of TS cell differentiation and placental development, in-part by coordinating repression of ID2.
ARTICLE | doi:10.20944/preprints202201.0113.v1
Subject: Biology, Plant Sciences Keywords: Group II; Intron; Splicing; PPR; Respiration; Complex I; Mitochondria; Embryogenesis; Arabidopsis; Angiosperms.
Online: 10 January 2022 (12:46:06 CET)
Mitochondria play key roles in cellular energy metabolism in eukaryotes. Mitochondria of most organisms contain their own genome and specific transcription and translation machineries. The expression of angiosperm mtDNA involves extensive RNA-processing steps, such as RNA trimming, editing, and the splicing of numerous group II-type introns. Pentatricopeptide repeat (PPR) proteins are key players of plant organelle gene expression and RNA metabolism. In the present analysis, we reveal the function of the MITOCHONDRIAL SPLICING FACTOR 2 gene (MISF2, AT3G22670) and show that it encodes a mitochondria-localized PPR protein that is crucial for early embryo-development in Arabidopsis. Molecular characterization of embryo-rescued misf2 plantlets indicates that the splicing of nad2 intron 1 and thus respiratory complex I biogenesis are strongly compromised. Moreover, the molecular function seems conserved between MISF2 protein in Arabidopsis and its orthologous gene (EMP10) in maize, suggesting that the ancestor of MISF2/EMP10 was recruited to function in nad2 processing before the monocot-dicot divergence, ~200 million years ago. These data provide new insights into the function of nuclear-encoded factors in mitochondrial gene expression and respiratory chain biogenesis during plant embryo development.
REVIEW | doi:10.20944/preprints201912.0211.v1
Subject: Life Sciences, Biochemistry Keywords: retinoic acid; retinol; retinaldehyde; short-chain dehydrogenase; vitamin a; retinol dehydrogenase; retinaldehyde reductase; embryogenesis
Online: 16 December 2019 (07:18:46 CET)
The concentration of all-trans-retinoic acid, the bioactive derivative of vitamin A, is critically important for the optimal performance of numerous physiological processes. Either too little or too much of retinoic acid in developing or adult tissues is equally harmful. All-trans-retinoic acid is produced by the irreversible oxidation of all-trans-retinaldehyde. Thus, the concentration of retinaldehyde as the immediate precursor of retinoic acid has to be tightly controlled. However, the enzymes that produce all-trans-retinaldehyde for retinoic acid biosynthesis and the mechanisms responsible for the control of retinaldehyde levels have not yet been fully defined. The goal of this review is to summarize the current state of knowledge regarding the identities of physiologically relevant retinol dehydrogenases, their enzymatic properties and tissue distribution, and to discuss potential mechanisms for the regulation of the flux from retinol to retinaldehyde.
REVIEW | doi:10.20944/preprints202109.0507.v1
Subject: Biology, Plant Sciences Keywords: epigenetics; plant development; microsporogenesis; megasporogenesis; male and female gametophytes; embryogenesis; endospermogenesis; sexual and asexual reproduction
Online: 30 September 2021 (09:16:17 CEST)
Plants are exposed to highly fluctuating effects of light, temperature, weather conditions and many other environmental factors throughout their life. As sessile or-ganisms, unlike animals, they are unable to escape, hide or even change their position. Therefore, the growth and development of plants is largely determined by interaction with the external environment, the success of this interaction depends on the ability of the phenotype plasticity, which is largely determined by epigenetic regulation. In addi-tion to how environmental factors can change the patterns of genes expression, epige-netic regulation determines how genetic expression changes during the differentiation of one cell type into another, and how patterns of gene expression are passed from one cell to its descendants. Thus, one genome can generate many 'epigenomes'. Epigenetic modifications acquire special significance during the formation of gametes and plant reproduction, when epigenetic marks are eliminated during meiosis and early embry-ogenesis and later reappear. However, during asexual plant reproduction, when meio-sis is absent or suspended, epigenetic modifications that have arisen in the parental sporophyte can be transmitted to the next clonal generation practically unchanged. In plants that reproduce sexually and asexually, epigenetic variability has different adap-tive significance. In asexuals, epigenetic regulation is of particular importance for im-parting plasticity to the phenotype, when the genotype remains unchanged for many generations of individuals. Of particular interest is the question of the possibility of transferring acquired epigenetic memory to future generations and its potential role for natural selection and evolution. All these issues will be discussed to some extent in this review. In the last two decades, a lot of data on the epigenetic regulation of plants has appeared, as well as works summarizing the accumulated knowledge (Verhoeven and Preite 2013; Pikaard and Scheid 2014; Gehring 2019; Ono and Kinoshita 2021), nevertheless, many questions remain unclear, and a number of results are contradic-tory. New in this area data is constantly emerging. We tried to take into account and discuss the main findings and conclusions in this field.
REVIEW | doi:10.20944/preprints202208.0203.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: neural induction; embryogenesis; tumorigenesis; conjoined twin; Spemann organizer; node; neural default model; neural stemness; tumorigenicity; pluripotency; epithelial-mesenchymal transition; tumor microenvironment
Online: 10 August 2022 (12:10:36 CEST)
Some concepts/hypotheses have been proposed to explain the general rules behind the complexity of tumorigenesis. Characterization of the property of cancer cells and neural stem cells indicates that neural stemness underlies tumorigenicity and pluripotency, leading to the proposal that tumorigenesis represents a process of progressive loss of original cell identity and gain of neural stemness. This reminds of a most fundamental process required for the development of the nervous system and body axis during embryogenesis, i.e., embryonic neural induction. The principle of neural induction is that, in response to extracellular signals that are secreted by the Spemann-Mangold organizer in amphibians or the node in mammals and inhibit epidermal fate in ectoderm, the ectodermal cells assume the neural default fate and turn into neuroectodermal cells. These cells further differentiate into the nervous system and also some non-neural cells via interaction with adjacent tissues. Failure in neural induction leads to failure of embryogenesis, and ectopic neural induction due to ectopic organizer or node activity or activation of embryonic neural genes causes a formation of secondary body axis or conjoined twins. A similar principle underlies tumorigenesis. Increasing evidence has demonstrated that the core property of cancer cells is neural stemness. Therefore, cancer cells are cells with the loss of original cell identity and gain of neural stemness, and consequently tumorigenicity and pluripotency, due to various intra-/extracellular insults in postnatal animals. Unlike that pluripotent cells (embryonic pluripotent cells, neural stem cells and cancer cells) can differentiate and integrate into embryonic development, cancer cells are capable of self-renewal and differentiation, but cannot integrate into normal tissues in a 2 postnatal animal, ultimately leading to tumor formation. Neural induction and the unique property of neural stemness provide an inclusive explanation for embryogenesis, conjoined twin formation and tumorigenesis. Based on these findings, I discuss about some confusion in cancer research, e.g., epithelial-mesenchymal transition, and propose to distinguish the causality and associations, and the causal and supporting factors involved in tumorigenesis, and suggest revisiting the focus of cancer research. Integration of evidence from developmental and cancer biology indicates that neural stemness determines tumorigenicity and pluripotency, and neural induction drives embryogenesis in gastrulating embryos but a similar process drives tumorigenesis in a postnatal animal.