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https://www.readbyqxmd.com/read/28207000/spatial-transcriptomic-analysis-of-cryosectioned-tissue-samples-with-geo-seq
#1
Jun Chen, Shengbao Suo, Patrick Pl Tam, Jing-Dong J Han, Guangdun Peng, Naihe Jing
Conventional gene expression studies analyze multiple cells simultaneously or single cells, for which the exact in vivo or in situ position is unknown. Although cellular heterogeneity can be discerned when analyzing single cells, any spatially defined attributes that underpin the heterogeneous nature of the cells cannot be identified. Here, we describe how to use Geo-seq, a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology. The combination of these two methods enables the elucidation of cellular heterogeneity and spatial variance simultaneously...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28196891/insights-into-immune-system-development-and-function-from-mouse-t-cell-repertoires
#2
Zachary Sethna, Yuval Elhanati, Chrissy S Dudgeon, Curtis G Callan, Arnold J Levine, Thierry Mora, Aleksandra M Walczak
The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors. This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts on the surface receptor gene each time a new immune cell is created from a stem cell. By analyzing T-cell receptor (TCR) sequence repertoires taken from the blood and thymus of mice of different ages, we quantify the changes in the VDJ recombination process that occur from embryo to young adult...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28192080/evo-engineering-and-the-cellular-and-molecular-origins-of-the-vertebrate-spinal-cord
#3
REVIEW
Ben Steventon, Alfonso Martinez Arias
The formation of the spinal cord during early embryonic development in vertebrate embryos is a continuous process that begins at gastrulation and continues through to the completion of somitogenesis. Despite the conserved usage of patterning mechanisms and gene regulatory networks that act to generate specific spinal cord progenitors, there now exists two seemingly disparate models to account for their action. In the first, a posteriorly localized signalling source transforms previously anterior-specified neural plate into the spinal cord...
February 9, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28190810/visualization-of-the-spatial-arrangement-of-nuclear-organization-using-three-dimensional-fluorescence-in-situ-hybridization-in-early-mouse-embryos-a-new-easi-fish-chamber-glass-for-mammalian-embryos
#4
Masataka Nakaya, Hideyuki Tanabe, Shingo Takamatsu, Misaki Hosokawa, Tasuku Mitani
The fertilized oocyte begins cleavage, leading to zygotic gene activation (ZGA), which re-activates the resting genome to acquire totipotency. In this process, genomic function is regulated by the dynamic structural conversion in the nucleus. Indeed, a considerable number of genes that are essential for embryonic development are located near the pericentromeric regions, wherein the heterochromatin is formed. These genes are repressed transcriptionally in somatic cells. Three-dimensional fluorescence in situ hybridization (3D-FISH) enables the visualization of the intranuclear spatial arrangement, such as gene loci, chromosomal domains, and chromosome territories (CTs)...
February 11, 2017: Journal of Reproduction and Development
https://www.readbyqxmd.com/read/28177917/cytoskeleton-associated-protein-5-and-clathrin-heavy-chain-binding-regulates-spindle-assembly-in-mouse-oocytes
#5
Angeleem Lu, Cheng-Jie Zhou, Dong-Hui Wang, Zhe Han, Xiang-Wei Kong, Yu-Zhen Ma, Zhi-Zhong Yun, Cheng-Guang Liang
Mammalian oocyte meiotic maturation is the precondition of early embryo development. Lots of microtubules (MT)-associated proteins participate in oocyte maturation process. Cytoskeleton-associated protein 5 (CKAP5) is a member of the XMAP215 family that regulates microtubule dynamics during mitosis. However, its role in meiosis has not been fully studied. Here, we investigated the function of CKAP5 in mouse oocyte meiotic maturation and early embryo development. Western blot showed that CKAP5 expression increased from GVBD, maintaining at high level at metaphase, and decreased after late 1-cell stage...
February 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28174238/functional-characterisation-of-cis-regulatory-elements-governing-dynamic-eomes-expression-in-the-early-mouse-embryo
#6
Claire S Simon, Damien J Downes, Matthew E Gosden, Jelena Telenius, Douglas R Higgs, Jim R Hughes, Ita Costello, Elizabeth K Bikoff, Elizabeth J Robertson
The T-box transcription factor (TF) Eomes is a key regulator of cell fate decisions during early mouse development. The cis-acting regulatory elements that direct expression in the anterior visceral endoderm (AVE), primitive streak (PS) and definitive endoderm (DE) have yet to be defined. Here, we identified three gene-proximal enhancer-like sequences (PSE_a, PSE_b and VPE) that faithfully activate tissue specific expression in transgenic embryos. However, targeted deletion experiments demonstrate that PSE_a and PSE_b are dispensable and only the VPE is required for optimal Eomes expression in vivo Embryos lacking this enhancer display variably penetrant defects in anterior-posterior axis orientation and DE formation...
February 7, 2017: Development
https://www.readbyqxmd.com/read/28167653/orai1-activates-proliferation-of-lymphatic-endothelial-cells-in-response-to-laminar-flow-through-kr%C3%A3-ppel-like-factors-2-and-4
#7
Dongwon Choi, Eunkyung Park, Eunson Jung, Young Jin Seong, Mingu Hong, Sunju Lee, James Burford, Georgina Gyarmati, Janos Peti-Peterdi, Sonal Srikanth, Yousang Gwack, Chester J Koh, Evgenii Boriushkin, Anne Hamik, Alex K Wong, Young-Kwon Hong
RATIONALE: Lymphatic vessels function to drain interstitial fluid from a variety of tissues. Although shear stress generated by fluid flow is known to trigger lymphatic expansion and remodeling, the molecular basis underlying flow-induced lymphatic growth is unknown. OBJECTIVE: We aimed to gain a better understanding of the mechanism by which laminar shear stress activates lymphatic proliferation. METHODS AND RESULTS: Primary endothelial cells from dermal blood and lymphatic vessels (BECs and LECs) were exposed to low-rate steady laminar flow...
February 6, 2017: Circulation Research
https://www.readbyqxmd.com/read/28165496/small-rna-directed-epigenetic-programming-of-embryonic-stem-cell-cardiac-differentiation
#8
Hossein Ghanbarian, Nicole Wagner, Jean-François Michiels, François Cuzin, Kay-Dietrich Wagner, Minoo Rassoulzadegan
Microinjection of small noncoding RNAs in one-cell embryos was reported in several instances to result in transcriptional activation of target genes. To determine the molecular mechanisms involved and to explore whether such epigenetic regulations could play a role in early development, we used a cell culture system as close as possible to the embryonic state. We report efficient cardiac differentiation of embryonic stem (ES) cells induced by small non-coding RNAs with sequences of Cdk9, a key player in cardiomyocyte differentiation...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28152580/quantifying-three-dimensional-morphology-and-rna-from-individual-embryos
#9
Rebecca M Green, Courtney L Leach, Natasha Hoehn, Ralph S Marcucio, Benedikt Hallgrímsson
Quantitative analysis of morphogenesis aids our understanding of developmental processes by providing a method to link changes in shape with cellular and molecular processes. Over the last decade many methods have been developed for 3D imaging of embryos using microCT scanning to quantify the shape of embryos during development. These methods generally involve a powerful, cross-linking fixative such as paraformaldehyde to limit shrinkage during the CT scan. However, the extended time frames that these embryos are incubated in such fixatives prevent use of the tissues for molecular analysis after microCT scanning...
February 2, 2017: Developmental Dynamics: An Official Publication of the American Association of Anatomists
https://www.readbyqxmd.com/read/28152074/multiple-ubxn-family-members-inhibit-retrovirus-and-lentivirus-production-and-canonical-nf%C3%AE%C2%BA%C3%AE-signaling-by-stabilizing-i%C3%AE%C2%BAb%C3%AE
#10
Yani Hu, Kaitlin O'Boyle, Jim Auer, Sagar Raju, Fuping You, Penghua Wang, Erol Fikrig, Richard E Sutton
UBXN proteins likely participate in the global regulation of protein turnover, and we have shown that UBXN1 interferes with RIG-I-like receptor (RLR) signaling by interacting with MAVS and impeding its downstream effector functions. Here we demonstrate that over-expression of multiple UBXN family members decreased lentivirus and retrovirus production by several orders-of-magnitude in single cycle assays, at the level of long terminal repeat-driven transcription, and three family members, UBXN1, N9, and N11 blocked the canonical NFκB pathway by binding to Cullin1 (Cul1), inhibiting IκBα degradation...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28134930/xist-dependent-imprinted-x-inactivation-and-the-early-developmental-consequences-of-its-failure
#11
Maud Borensztein, Laurène Syx, Katia Ancelin, Patricia Diabangouaya, Christel Picard, Tao Liu, Jun-Bin Liang, Ivaylo Vassilev, Rafael Galupa, Nicolas Servant, Emmanuel Barillot, Azim Surani, Chong-Jian Chen, Edith Heard
The long noncoding RNA Xist is expressed from only the paternal X chromosome in mouse preimplantation female embryos and mediates transcriptional silencing of that chromosome. In females, absence of Xist leads to postimplantation lethality. Here, through single-cell RNA sequencing of early preimplantation mouse embryos, we found that the initiation of imprinted X-chromosome inactivation absolutely requires Xist. Lack of paternal Xist leads to genome-wide transcriptional misregulation in the early blastocyst and to failure to activate the extraembryonic pathway that is essential for postimplantation development...
January 30, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28127704/effect-of-potential-role-of-p53-on-embryo-development-arrest-induced-by-h2o2-in-mouse
#12
De-Bao Hu, Zhong-Shu Li, Ihsan Ali, Li-Jie Xu, Nan-Zhu Fang
During mammalian embryo development in vitro, mechanism of embryonic development arrest caused by oxidative stress has not been clear so far. The tumor suppressor protein p53 controls cell cycle and programmed cell death by regulating relevant signal pathway. Recent researches revealed that the concentration and distribution of p53 are closely related with reactive oxygen species (ROS). The main objective of this experiment was to explore the role of p53 on embryonic development arrest caused by oxidative stress...
January 27, 2017: In Vitro Cellular & Developmental Biology. Animal
https://www.readbyqxmd.com/read/28123425/ankfy1-is-dispensable-for-neural-stem-precursor-cell-development
#13
Chao Weng, Man Ding, Lian-Sheng Chang, Ming-Xin Ren, Hong-Feng Zhang, Zu-Neng Lu, Hui Fu
There are few studies on the membrane protein Ankfy1. We have found Ankfy1 is specifically expressed in neural stem/precursor cells during early development in mice (murine). To further explore Ankfy1 function in neural development, we developed a gene knockout mouse with a mixed Balb/C and C57/BL6 genetic background. Using immunofluorescence and in situ hybridization, neural defects were absent in mixed genetic Ankfy1 null mice during development and in adults up to 2 months old. However, Ankfy1 gene knockout mice with a pure genetic background were found to be lethal in the C57/BL6 inbred mice embryos, even after seven generations of backcrossing...
November 2016: Neural Regeneration Research
https://www.readbyqxmd.com/read/28120088/one-pot-aqueous-synthesization-of-near-infrared-quantum-dots-for-bioimaging-and-photodynamic-therapy-of-gliomas
#14
Ming-Xing Liu, Jun Zhong, Ning-Ning Dou, Massimiliano Visocchi, Guo Gao
BACKGROUND: As the early detection and total destruction of gliomas are essential for longer survival, we attempted to synthesize a quantum dot (QD) that is capable of recognizing glioma cells for imaging and photodynamic therapy. METHODS: Using a one-pot aqueous approach, near infrared-emitting CdTe was produced. After detection of its physicochemical characteriistics, it was conjugated with RGD. The emission images were observed with confocal microscopy. To test its toxicity, CdTe-RGD at various concentrations was separately added to a human glioma cell line (U251) and a mouse embryo fibroblast cell line (3T3) (control) for incubation in dark conditions...
2017: Acta Neurochirurgica. Supplement
https://www.readbyqxmd.com/read/28114387/gene-expression-noise-enhances-robust-organization-of-the-early-mammalian-blastocyst
#15
William R Holmes, Nabora Soledad Reyes de Mochel, Qixuan Wang, Huijing Du, Tao Peng, Michael Chiang, Olivier Cinquin, Ken Cho, Qing Nie
A critical event in mammalian embryo development is construction of an inner cell mass surrounded by a trophoectoderm (a shell of cells that later form extraembryonic structures). We utilize multi-scale, stochastic modeling to investigate the design principles responsible for robust establishment of these structures. This investigation makes three predictions, each supported by our quantitative imaging. First, stochasticity in the expression of critical genes promotes cell plasticity and has a critical role in accurately organizing the developing mouse blastocyst...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28103468/poly-a-binding-proteins-are-required-for-translational-regulation-in-vertebrate-oocytes-and-early-embryos
#16
Saffet Ozturk, Fatma Uysal
Poly(A)-binding proteins (PABPs) function in the timely regulation of gene expression during oocyte maturation, fertilisation and early embryo development in vertebrates. To this end, PABPs bind to poly(A) tails or specific sequences of maternally stored mRNAs to protect them from degradation and to promote their translational activities. To date, two structurally different PABP groups have been identified: (1) cytoplasmic PABPs, including poly(A)-binding protein, cytoplasmic 1 (PABPC1), embryonic poly(A)-binding protein (EPAB), induced PABP and poly(A)-binding protein, cytoplasmic 3; and (2) nuclear PABPs, namely embryonic poly(A)-binding protein 2 and nuclear poly(A)-binding protein 1...
January 20, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28101448/acetylsalicylic-acid-interferes-with-embryonic-kidney-growth-and-development-by-a-prostaglandin-independent-mechanism
#17
Simon J M Welham, Alexander J Sparrow, David S Gardner, Matthew J Elmes
AIM: To evaluate the effects of the non-selective, non-steroidal anti-inflammatory drug (NSAID) acetylsalicylic acid (ASA), on ex vivo embryonic kidney growth and development. METHODS: Pairs of fetal mouse kidneys at embryonic day 12.5 were cultured ex vivo in increasing concentrations of ASA (0.04-0.4 mg/mL) for up to 7 d. One organ from each pair was grown in control media and was used as the internal control for the experimental contralateral organ. In some experiments, organs were treated with ASA for 48 h and then transferred either to control media alone or control media containing 10 μmol/L prostaglandin E2 (PGE2) for a further 5 d...
January 6, 2017: World Journal of Nephrology
https://www.readbyqxmd.com/read/28087626/snail2-and-zeb2-repress-p-cadherin-to-define-embryonic-territories-in-the-chick-embryo
#18
Hervé Acloque, Oscar H Ocaña, Diana Abad, Claudio D Stern, M Angela Nieto
Snail and Zeb transcription factors induce epithelial to mesenchymal transition (EMT) in embryonic and adult tissues by direct repression of E-Cadherin transcription. The repression of E-Cadherin transcription by the EMT inducers Snail1 and Zeb2 plays a fundamental role in defining embryonic territories in the mouse, as E-Cadherin needs to be downregulated in the primitive streak and in the epiblast concomitant with the formation of mesendodermal precursors and the neural plate, respectively. Here we show that in the chick embryo, E-Cadherin is weakly expressed in the epiblast at pre-primitive streak stages where it is substituted by P-Cadherin We also show that Snail2 and Zeb2 repress P-Cadherin transcription in the primitive streak and the neural plate, respectively...
January 13, 2017: Development
https://www.readbyqxmd.com/read/28073917/the-e3-ubiquitin-ligase-rnf114-and-tab1-degradation-are-required-for-maternal-to-zygotic-transition
#19
Ye Yang, Cheng Zhou, Ying Wang, Weixiao Liu, Chao Liu, Liying Wang, Yujiao Liu, Yongliang Shang, Mingrui Li, Shuai Zhou, Yuanting Wang, Wentao Zeng, Jianli Zhou, Ran Huo, Wei Li
The functional role of the ubiquitin-proteasome pathway during maternal-to-zygotic transition (MZT) remains to be elucidated. Here we show that the E3 ubiquitin ligase, Rnf114, is highly expressed in mouse oocytes and that knockdown of Rnf114 inhibits development beyond the two-cell stage. To study the underlying mechanism, we identify its candidate substrates using a 9,000-protein microarray and validate them using an in vitro ubiquitination system. We show that five substrates could be degraded by RNF114-mediated ubiquitination, including TAB1...
February 2017: EMBO Reports
https://www.readbyqxmd.com/read/28069738/fbxl5-inactivation-in-mouse-brain-induces-aberrant-proliferation-of-neural-stem-progenitor-cells
#20
Takayoshi Yamauchi, Masaaki Nishiyama, Toshiro Moroishi, Atsuki Kawamura, Keiichi I Nakayama
FBXL5 is the substrate recognition subunit of an SCF-type ubiquitin ligase that serves as a master regulator of iron metabolism in mammalian cells. We previously showed that mice with systemic deficiency of FBXL5 fail to sense intracellular iron levels and die in utero at embryonic day (E) 8.5 as a result of iron overload and subsequent oxidative stress. This early embryonic mortality has thus impeded study of the role of FBXL5 in brain development. We have now generated mice lacking FBXL5 specifically in Nestin-expressing neural stem-progenitor cells (NSPCs) in the brain...
January 9, 2017: Molecular and Cellular Biology
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