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ALES: cell lineage analysis and mapping of developmental events

V. Braun, R. B. R. Azevedo, M. Gumbel, P.-M. Agapow, A. M. Leroi, H.-P. Meinzer
2003 Bioinformatics  
ALES introduces a series of algorithms that locate putative developmental events.  ...  Results: ALES (A Lineage Evaluation System) allows the display, evaluation and comparison of cell lineages with the aim of identifying molecular and cellular events underlying development.  ...  P-MA was supported by Natural Environment Research Council (UK) grant GR3/11526 and Biotechnology and Biological Sciences Research Council (UK) grant 45/G09600.  ... 
doi:10.1093/bioinformatics/btg087 pmid:12724295 fatcat:3hbus2dh4bf3xhpifyxgjl56b4

Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS

Raphaelle Luisier, Giulia E. Tyzack, Claire E. Hall, Jamie S. Mitchell, Helen Devine, Doaa M. Taha, Bilal Malik, Ione Meyer, Linda Greensmith, Jia Newcombe, Jernej Ule, Nicholas M. Luscombe (+1 others)
2018 Nature Communications  
Collectively, we demonstrate SFPQ IR and nuclear loss as molecular hallmarks of familial and sporadic ALS.  ...  To understand the molecular impact of ALS-causing mutations on neuronal development and disease, we analysed transcriptomes during in vitro differentiation of motor neurons (MNs) from human control and  ...  We thank Benjamin Clarke, Mhoriam Ahmed and members of the Schiavo and Greensmith Labs for valuable technical support. We thank Selina Wray for kindly providing access to the VCP mutant iPSC lines.  ... 
doi:10.1038/s41467-018-04373-8 pmid:29789581 pmcid:PMC5964114 fatcat:dersoymtcbgormy4vvdomv4cra

Post-transcriptional remodelling is temporally deregulated during motor neurogenesis in human ALS models [article]

Raphaelle Luisier, Giulia E. Tyzack, Claire E. Hall, Jernej Ule, Nicholas M. Luscombe, Rickie Patani
2017 bioRxiv   pre-print
To understand the molecular impact of ALS-causing mutations on early neuronal development and disease, we performed transcriptomic analysis of differentiated human control and VCP-mutant induced pluripotent  ...  Together with related effects on 3'UTR length variation, these findings implicate alternative RNA-processing in regulating distinct stages of lineage restriction from iPSCs to MNs, and reveal a temporal  ...  Doublets were excluded from analysis and 10,000 events were collected in the single cell gate per sample.  ... 
doi:10.1101/180372 fatcat:fk54gj3lvje2hg6prprdv3c2wi

A comprehensive evaluation of CRISPR lineage recorders using TraceQC [article]

Jingyuan Hu, Hyun-Hwan Jeong, Rami Al-Ouran, Igor Bado, Weijie Zhang, Xiang Zhang, Zhandong Liu
2021 bioRxiv   pre-print
The CRISPR-Cas9 genome editing-based lineage tracing system is emerging as a powerful tool to track cell lineages at unprecedented scale and resolution.  ...  Second, by using the TraceQC package, we performed a comprehensive analysis across multiple CRISPR lineage recorders to uncover the speed and distribution of CRISPR-induced mutations.  ...  Subsequently, several studies have integrated the CRISPR lineage recorder with single-cell RNA sequencing to provide a cell-level lineage mapping of zebrafish [9] [10] [11] and mouse 12, 13 .  ... 
doi:10.1101/2021.10.29.466515 fatcat:nx3gvbnmmfbpzbcl3mklzrhybi

Developmental Programming of Branching Morphogenesis in the Kidney

R. V. Sampogna, L. Schneider, Q. Al-Awqati
2015 Journal of the American Society of Nephrology  
Our map identifies and quantitates the contribution of four developmental mechanisms that guide organogenesis: growth, patterning, branching rate, and nephron induction.  ...  This morphogenetic map is expected to find widespread applications and help identify modifiable targets to prevent developmental programming of common diseases.  ...  to study other organs that develop via repetitive branching and make tractable rigorous analysis of morphologic events at any age.  ... 
doi:10.1681/asn.2014090886 pmid:25644110 pmcid:PMC4587701 fatcat:ox3ozn2t5rchfcctdkgoqovaci

An aberrant cytoplasmic intron retention programme is a blueprint for ALS-related RBP mislocalization [article]

Giulia E Tyzack, Jacob Neeves, Pierre Klein, Hamish Crerar, Oliver Ziff, Doaa M Taha, Raphaelle Luisier, Nicholas M Luscombe, Rickie Patani
2020 bioRxiv   pre-print
In summary we uncover a distinct class of cytoplasmic IRTs that serve as blueprints for established molecular hallmarks of ALS (nuclear-to-cytoplasmic mislocalisation of TDP-43, SFPQ and FUS) and therefore  ...  We recently described intron retention as the predominant splicing programme characterizing early stages of motor neurogenesis from human induced pluripotent stem cells (hiPSCs) and it's perturbation in  ...  Mapping and analysis of CLIP data To identify RBPs that bind to aberrantly retained introns, we examined iCLIP data for 21 RBPs (Attig et al. , 2018) , and eCLIP data from K562 and HepG2 cells for 112  ... 
doi:10.1101/2020.07.20.211557 fatcat:ffnryrj5vveutbp5fxvqcgxk4m

The Genome of the Mimosoid Legume Prosopis cineraria, a Desert Tree

Naganeeswaran Sudalaimuthuasari, Rashid Ali, Martin Kottackal, Mohammed Rafi, Mariam Al Al Nuaimi, Biduth Kundu, Raja Saeed Al-Maskari, Xuewen Wang, Ajay Kumar Mishra, Jithin Balan, Srinivasa R. Chaluvadi, Fatima Al Al Ansari (+4 others)
2022 International Journal of Molecular Sciences  
that approximately occurred at the same time of divergence of P. cineraria from a common lineage with P. alba~23 Mya.  ...  The mimosoid legumes are a clade of ~40 genera in the Caesalpinioideae subfamily of the Fabaceae that grow in tropical and subtropical regions.  ...  of Sweihan area (Figure 1A ; 24°17′18.3″ N 55°43′36.2″ E), Al Ain, Abu Dhabi Emirates, UAE.  ... 
doi:10.3390/ijms23158503 pmid:35955640 pmcid:PMC9369113 fatcat:g4phug3gfzerpdgoxi6b4sqke4

Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology

Jeanne M. Serb, Todd H. Oakley
2005 Bioessays  
Phylogenetics has inherent utility in evolutionary developmental biology (EDB) as it is an established methodology for estimating evolutionary relationships and for making comparisons between levels of  ...  We present examples at and between different hierarchical levels of organization to address questions central to EDB.  ...  Roe, members of the Oakley lab group, A. Wilkins and two reviewers for valuable comments that greatly improved this article.  ... 
doi:10.1002/bies.20291 pmid:16237676 fatcat:z2rybsytnfhtfafubgg3idglqi

Astrocytes in Pathogenesis of ALS Disease and Potential Translation into Clinic [chapter]

Izrael Michal, Slutsky Shalom Guy, Joseph Itskovitz-Eldor, Revel Michel
2018 Astrocyte - Physiology and Pathology  
Here, we will mainly focus on the role of astrocytes in ALS disease, the major cell sources for generation of human astrocytes, or astrocyte like cells and show how multiple preclinical studies demonstrate  ...  the efficacy of these cells in animal models.  ...  stem cells toward neural and glial lineage.  ... 
doi:10.5772/intechopen.72862 fatcat:yf3zmlqu4nchbmpgrberqjgdau

Profiling microRNA expression during multi-staged date palm ( Phoenix dactylifera L.) fruit development

Chengqi Xin, Wanfei Liu, Qiang Lin, Xiaowei Zhang, Peng Cui, Fusen Li, Guangyu Zhang, Linlin Pan, Ali Al-Amer, Hailiang Mei, Ibrahim S. Al-Mssallem, Songnian Hu (+2 others)
2015 Genomics  
MicroRNAs (miRNAs) play crucial roles in multiple stages of plant development and regulate gene expression at posttranscriptional and translational levels.  ...  Our data define a comprehensive set of conserved and novel FDA miRNAs along with their expression profiles, which provide a basis for further experimentation in assigning discrete functions of these miRNAs  ...  Acknowledgment We acknowledge my colleagues Saeed Mohammed Al-Qahtani, Majed Abdullah Majrashi, and Abdullah Ganim Al-Salem, who kindly assisted us to collect the samples, and Dr.  ... 
doi:10.1016/j.ygeno.2015.01.004 pmid:25638647 fatcat:oiqaxorobbajzhnyqwwd7wswpu

Stochasticity and stereotypy in the Ciona notochord

Maia Carlson, Wendy Reeves, Michael Veeman
2015 Developmental Biology  
The lineages giving rise to the 40 cells of the Ciona notochord are invariant, but the intercalation of those cells into a single-file column is not.  ...  Our results indicate that the interplay between stereotyped and stochastic cell behaviors in morphogenesis can only be assessed by fate mapping experiments that have both cellular resolution and large  ...  Acknowledgements We thank the KSU CVM Confocal Core for use of their excellent facility.  ... 
doi:10.1016/j.ydbio.2014.11.016 pmid:25459659 pmcid:PMC4378655 fatcat:uddf6qcusrgbxeaqrgh4tkmhqa

Single-cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS iPSC-derived motor neurons

Seema C. Namboori, Patricia Thomas, Ryan Ames, Sophie Hawkins, Lawrence O. Garrett, Craig R.G. Willis, Alessandro Rosa, Lawrence W. Stanton, Akshay Bhinge
2021 Stem Cell Reports  
Differential gene expression and network analysis identified activation of developmental pathways and core transcriptional factors driving the ALS motor neuron gene dysregulation.  ...  Our results demonstrate the utility of single-cell transcriptomics in mapping disease-relevant gene regulatory networks driving neurodegeneration in ALS motor neurons.  ...  ACKNOWLEDGMENTS We thank the sequencing center at the Genome Institute of Singapore for help with Illumina sequencing.  ... 
doi:10.1016/j.stemcr.2021.10.010 pmid:34767750 pmcid:PMC8693652 fatcat:7bbrc3z27fak7dymws2wjefiyy

Single-cell biology: resolving biological complexity, one cell at a time

Anna M. Ranzoni, Ana Cvejic
2018 Development  
A highly interdisciplinary meeting, the Single Cell Biology conference covered a variety of topics, ranging from cutting-edge technological innovation, developmental biology and stem cell research to evolution  ...  In March 2018, over 250 researchers came together at the Wellcome Genome Campus in Hinxton, Cambridge, UK, to present their latest research in the area of single-cell biology.  ...  Acknowledgements This conference is funded and organised by the Wellcome Genome Campus, Advanced Courses and Scientific Conferences programme.  ... 
doi:10.1242/dev.163972 pmid:29986899 fatcat:ruswmqz52jbqnce5uwrg5jzssy

Tracing Cells for Tracking Cell Lineage and Clonal Behavior

Margaret E. Buckingham, Sigolène M. Meilhac
2011 Developmental Cell  
With the approaches of prospective clonal analysis, fate maps can be drawn and partial lineages reconstructed.  ...  The rarity of the event makes clonal analysis possible (Bonnerot and Nicolas, 1993) .  ... 
doi:10.1016/j.devcel.2011.07.019 pmid:21920310 fatcat:lqm3dnkgwvafvhy6qny2gtxjwq

Page 929 of The Plant Journal Vol. 4, Issue 6 [page]

1993 The Plant Journal  
The uncertainties implicit in this map include: the biological meaning of the distance term and the timing and location of events determining cell fate.  ...  The analysis of these large sectors affecting the cotyledons and early leaves showed distinct developmental restrictions termed ‘compartments’.  ... 
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