scholarly journals A comprehensive portrait of cilia and ciliopathies from a CRISPR-based screen for Hedgehog signaling

2017 ◽  
Author(s):  
David K. Breslow ◽  
Sascha Hoogendoorn ◽  
Adam R. Kopp ◽  
David W. Morgens ◽  
Brandon K. Vu ◽  
...  
Keyword(s):  
Hedgehog Signaling ◽  
Heart Defects ◽  
Functional Genomic ◽  
False Negatives ◽  
Systematic Analysis ◽  
Ciliary Function ◽  
Genome Wide ◽  
Ciliary Signaling ◽  
Selection Of

AbstractThe primary cilium organizes Hedgehog signaling, shapes embryonic development and is the unifying cause of the ciliopathies. We conducted a functional genomic screen for Hedgehog signaling by engineering antibiotic-based selection of Hedgehog-responsive cells and applying genome-wide CRISPR-mediated gene disruption. The screen robustly identifies factors required for ciliary signaling with few false positives or false negatives. Characterization of hit genes uncovers novel components of several ciliary structures including a protein complex containing ε- and δ- tubulin that is required for centriole maintenance. The screen also provides an unbiased tool for classifying ciliopathies and reveals that many forms of congenital heart defects are ciliopathies. Collectively, this screen enables a systematic analysis of ciliary function and of ciliopathies and also defines a versatile platform for dissecting signaling pathways through CRISPR-based screening.

scholarly journals Genome-Wide Identification and Characterization of SODs in Zhikong Scallop Reveals Gene Expansion and Regulation Divergence after Toxic Dinoflagellate Exposure

Marine Drugs ◽  
2019 ◽  
Vol 17 (12) ◽  
pp. 700 ◽  
Author(s):  
Shanshan Lian ◽  
Liang Zhao ◽  
Xiaogang Xun ◽  
Jiarun Lou ◽  
Moli Li ◽  
...  
Keyword(s):  
Alexandrium Minutum ◽  
Zhikong Scallop ◽  
Systematic Analysis ◽  
Toxic Algae ◽  
Gene Expansion ◽  
Paralytic Shellfish Toxins ◽  
Genome Wide ◽  
Paralytic Shellfish ◽  
Identification And Characterization

As filter-feeding animals mainly ingesting microalgae, bivalves could accumulate paralytic shellfish toxins (PSTs) produced by harmful algae through diet. To protect themselves from the toxic effects of PSTs, especially the concomitant oxidative damage, the production of superoxide dismutase (SOD), which is the only eukaryotic metalloenzyme capable of detoxifying superoxide, may assist with toxin tolerance in bivalves. To better understand this process, in the present study, we performed the first systematic analysis of SOD genes in bivalve Chlamys farreri, an important aquaculture species in China. A total of six Cu/Zn-SODs (SOD1-6) and two Mn-SODs (SOD7, SOD8) were identified in C. farreri, with gene expansion being revealed in Cu/Zn-SODs. In scallops exposed to two different PSTs-producing dinoflagellates, Alexandrium minutum and A. catenella, expression regulation of SOD genes was analyzed in the top ranked toxin-rich organs, the hepatopancreas and the kidney. In hepatopancreas, which mainly accumulates the incoming PSTs, all of the six Cu/Zn-SODs showed significant alterations after A. minutum exposure, with SOD1, 2, 3, 5, and 6 being up-regulated, and SOD4 being down-regulated, while no significant change was detected in Mn-SODs. After A. catenella exposure, up-regulation was observed in SOD2, 4, 6, and 8, and SOD7 was down-regulated. In the kidney, where PSTs transformation occurs, SOD4, 5, 6, and 8 were up-regulated, and SOD7 was down-regulated in response to A. minutum feeding. After A. catenella exposure, all the Cu/Zn-SODs except SOD1 were up-regulated, and SOD7 was down-regulated in kidney. Overall, in scallops after ingesting different toxic algae, SOD up-regulation mainly occurred in the expanded Cu/Zn-SOD group, and SOD6 was the only member being up-regulated in both toxic organs, which also showed the highest fold change among all the SODs, implying the importance of SOD6 in protecting scallops from the stress of PSTs. Our results suggest the diverse function of scallop SODs in response to the PST-producing algae challenge, and the expansion of Cu/Zn-SODs might be implicated in the adaptive evolution of scallops or bivalves with respect to antioxidant defense against the ingested toxic algae.

scholarly journals Hedgehog signaling controls segmentation dynamics and diversity via msx1 in a spider embryo

2020 ◽  
Vol 6 (37) ◽  
pp. eaba7261
Author(s):  
Yasuko Akiyama-Oda ◽  
Hiroki Oda
Keyword(s):  
Hedgehog Signaling ◽  
The Body ◽  
Body Region ◽  
Altered States ◽  
Genome Wide ◽  
Body Patterning ◽  
Genome Wide Data ◽  
Hh Signaling ◽  
Anterior Posterior

Hedgehog (Hh) signaling plays fundamental roles in animal body patterning. Understanding its mechanistic complexity requires simple tractable systems that can be used for these studies. In the early spider embryo, Hh signaling mediates the formation of overall anterior-posterior polarity, yet it remains unclear what mechanisms link the initial Hh signaling activity with body axis segmentation, in which distinct periodic stripe-forming dynamics occur depending on the body region. We performed genome-wide searches for genes that transcriptionally respond to altered states of Hh signaling. Characterization of genes negatively regulated by Hh signaling suggested that msx1, encoding a conserved transcription factor, functions as a key segmentation gene. Knockdown of msx1 prevented all dynamic processes causing spatial repetition of stripes, including temporally repetitive oscillations and bi-splitting, and temporally nonrepetitive tri-splitting. Thus, Hh signaling controls segmentation dynamics and diversity via msx1. These genome-wide data from an invertebrate illuminate novel mechanistic features of Hh-based patterning.

scholarly journals Genome-Wide Characterization of Arabian Peninsula Populations: Shedding Light on the History of a Fundamental Bridge between Continents

2019 ◽  
Vol 36 (3) ◽  
pp. 575-586 ◽  
Author(s):  
Veronica Fernandes ◽  
Nicolas Brucato ◽  
Joana C Ferreira ◽  
Nicole Pedro ◽  
Bruno Cavadas ◽  
...  
Keyword(s):  
South Asian ◽  
Arabian Peninsula ◽  
The West ◽  
Eye Color ◽  
Genome Wide ◽  
History Of ◽  
African Admixture ◽  
Sub Saharan ◽  
Selection Of

Abstract The Arabian Peninsula (AP) was an important crossroad between Africa, Asia, and Europe, being the cradle of the structure defining these main human population groups, and a continuing path for their admixture. The screening of 741,000 variants in 420 Arabians and 80 Iranians allowed us to quantify the dominant sub-Saharan African admixture in the west of the peninsula, whereas South Asian and Levantine/European influence was stronger in the east, leading to a rift between western and eastern sides of the Peninsula. Dating of the admixture events indicated that Indian Ocean slave trade and Islamization periods were important moments in the genetic makeup of the region. The western–eastern axis was also observable in terms of positive selection of diversity conferring lactose tolerance, with the West AP developing local adaptation and the East AP acquiring the derived allele selected in European populations and existing in South Asia. African selected malaria resistance through the DARC gene was enriched in all Arabian genomes, especially in the western part. Clear European influences associated with skin and eye color were equally frequent across the Peninsula.

scholarly journals Genome-Wide Characterization and Expression Analysis Provide Basis to the Biological Function of Cotton FBA Genes

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhong-Qing Li ◽  
Yao Zhang ◽  
He Li ◽  
Ting-Ting Su ◽  
Cheng-Gong Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Function Analysis ◽  
Pcr Analysis ◽  
Functional Domain ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Identification And Characterization

Fructose-1,6-biphosphate aldolase (FBA) is a multifunctional enzyme in plants, which participates in the process of Calvin-Benson cycle, glycolysis and gluconeogenesis. Despite the importance of FBA genes in regulating plant growth, development and abiotic stress responses, little is known about their roles in cotton. In the present study, we performed a genome-wide identification and characterization of FBAs in Gossypium hirsutum. Totally seventeen GhFBA genes were identified. According to the analysis of functional domain, phylogenetic relationship, and gene structure, GhFBA genes were classified into two subgroups. Furthermore, nine GhFBAs were predicted to be in chloroplast and eight were located in cytoplasm. Moreover, the promoter prediction showed a variety of abiotic stresses and phytohormone related cis-acting elements exist in the 2k up-stream region of GhFBA. And the evolutionary characteristics of cotton FBA genes were clearly presented by synteny analysis. Moreover, the results of transcriptome and qRT-PCR analysis showed that the expression of GhFBAs were related to the tissue distribution, and further analysis suggested that GhFBAs could respond to various abiotic stress and phytohormonal treatments. Overall, our systematic analysis of GhFBA genes would not only provide a basis for the understanding of the evolution of GhFBAs, but also found a foundation for the further function analysis of GhFBAs to improve cotton yield and environmental adaptability.

Applications of Transmission Electron Microscopy in the Characterization of Metal Machinability

1968 ◽  
Vol 26 ◽  
pp. 442-443 ◽  
Author(s):  
L.E. Murr ◽  
A.B. Draper
Keyword(s):  
Electron Microscopy ◽  
State Physics ◽  
Test Material ◽  
Milling Machine ◽  
Rotary Table ◽  
Solid State Physics ◽  
Materials Properties ◽  
Transmission Electron ◽  
Selection Of

The industrial characterization of the machinability of metals and alloys has always been a very arbitrarily defined property, subject to the selection of various reference or test materials; and the adoption of rather naive and misleading interpretations and standards. However, it seems reasonable to assume that with the present state of knowledge of materials properties, and the current theories of solid state physics, more basic guidelines for machinability characterization might be established on the basis of the residual machined microstructures. This approach was originally pursued by Draper; and our presentation here will simply reflect an exposition and extension of this research.The technique consists initially in the production of machined chips of a desired test material on a horizontal milling machine with the workpiece (specimen) mounted on a rotary table vice. A single cut of a specified depth is taken from the workpiece (0.25 in. wide) each at a new tool location.

Clinical and molecular cytogenetic characterization of two cases of inverted duplication deletion 8p

2020 ◽  
pp. 41-42
Author(s):  
Д.А. Юрченко ◽  
М.Е. Миньженкова ◽  
Е.Л. Дадали ◽  
Н.В. Шилова
Keyword(s):  
Mental Retardation ◽  
Congenital Heart ◽  
Heart Defects ◽  
Clinical Manifestations ◽  
Formation Mechanisms ◽  
Agenesis Of Corpus Callosum ◽  
Molecular Cytogenetic ◽  
Inverted Duplication ◽  
Cytogenetic Characterization

Синдром инвертированной дупликации короткого плеча хромосомы 8 со смежной терминальной делециенй (inv dup del(8p), ORPHA 96092) - редкая хромосомная аномалия (ХА) с частотой 1/10000-1/30000 живорожденных. В статье представлены клинические и молекулярно-цитогенетические характеристики двух неродственных пациентов с синдромом inv dup del(8p) и уточнены механизмы формирования хромосомного дисбаланса. Inverted duplication deletion 8p syndrome (inv dup del(8p), ORPHA 96092) is a rare chromosomal abnormality with a frequency of 1:10,000 - 30,000 newborns. Clinical manifestations of this syndrome include mental retardation, facial anomalies, hypoplasia/agenesis of corpus callosum, scoliosis and/or kyphosis, hypotonia, congenital heart defects. The article presents the clinical and molecular cytogenetic characteristics of two patients with inv dup del (8p) syndrome and clarifies the formation mechanisms.

Caracterização da Peneira Média em Clones de Coffea canephora

REVISTA FIMCA ◽  
2018 ◽  
Vol 5 (2) ◽  
pp. 28-31
Author(s):  
Darlan Darlan Sanches Barbosa Alves ◽  
Victor Mouzinho Spinelli ◽  
Marcos Santana Moraes ◽  
Carolina Augusto De Souza ◽  
Rodrigo da Silva Ribeiro ◽  
...  
Keyword(s):  
Genetic Improvement ◽  
Block Design ◽  
Coffea Canephora ◽  
Coffee Production ◽  
Randomized Block Design ◽  
Significant Difference ◽  
The Mean ◽  
Four Blocks ◽  
Selection Of

Introdução: O estado de Rondônia se destaca como tradicional produtor de café, sendo o segundo maior produtor brasileiro de C. canephora. No melhoramento genético de C. canephora, a seleção de plantas de elevada peneira média está associada à bebida de qualidade superior. Objetivos: O objetivo desse estudo foi avaliar a variabilidade genética de clones de C. canephora para o tamanho dos grãos, mensurado a partir da avaliação da peneira média (PM). Materiais e Métodos: Para isso, foi conduzido ao longo de dois anos agrícolas experimento no campo experimental da Embrapa no município de Ouro Preto do Oeste-RO, para a avaliação da peneira média de 130 genótipos (clones) com características das variedades botânicas Conilon, Robusta e híbridos intervarietais. O delineamento experimental utilizado foi de blocos ao acaso, com quatro repetições de quatro plantas por parcela. Resultados: Não houve resultados significativos para a interação clones X anos, indicando uma maior consistência no comportamento das plantas ao longo do tempo. Porém foram observadas diferenças significativas para o tamanho dos grãos entre os genótipos avaliados, possibilitando selecionar genótipos superiores. Conclusão: Os genótipos agruparam-se em cinco classes de acordo com o teste de média, subsidiando a caracterização de um gradiente de variabilidade da característica avaliada ABSTRACTIntroduction: Coffea canephora accounts for approximately 35% of the world's coffee production. The state of Rondônia stands out as a traditional coffee producer, being the second largest Brazilian producer of C. canephora. In the classical genetic improvement of C. anephora, the selection of plants of high average sieve is associated with a drink of superior quality. Objectives: The objective of this udy was to evaluate the genetic variability of Coffea canephora clones for the agronomic medium sieve (PM). Materials and Methods: The experiment was conducted in the experimental field of Embrapa, municipality of OuroPreto do Oeste-RO, located at coordinates 10º44'53 "S and 62º12'57". One hundred thirty genotypes (clones) of botanical characteristics Conilon, Robusta and intervarietal hybrids were evaluated in the agricultural years 2013-2014 and 2014-2015. The experimental design was a randomized block design with four blocks and four plants per plot, spacing 3.5 x 1.5 meters between plants. Results: Significant difference was found for the grain size. According to the F test, at 5% probability, the genotypes were grouped into five classes according to the mean test. Conclusion: The results obtained subsidized the characterization of a variability gradient of the evaluated trait.

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