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Article ; Online: Primary cilia in skeletal development and disease.

Quadri, Neha / Upadhyai, Priyanka

2023 Volume 431, Issue 1, Page(s) 113751

Abstract: Primary cilia are non-motile, microtubule-based sensory organelle present in most vertebrate cells with a fundamental role in the modulation of organismal development, morphogenesis, and repair. Here we focus on the role of primary cilia in embryonic and ...

Abstract	Primary cilia are non-motile, microtubule-based sensory organelle present in most vertebrate cells with a fundamental role in the modulation of organismal development, morphogenesis, and repair. Here we focus on the role of primary cilia in embryonic and postnatal skeletal development. We examine evidence supporting its involvement in physiochemical and developmental signaling that regulates proliferation, patterning, differentiation and homeostasis of osteoblasts, chondrocytes, and their progenitor cells in the skeleton. We discuss how signaling effectors in mechanotransduction and bone development, such as Hedgehog, Wnt, Fibroblast growth factor and second messenger pathways operate at least in part at the primary cilium. The relevance of primary cilia in bone formation and maintenance is underscored by a growing list of rare genetic skeletal ciliopathies. We collate these findings and summarize the current understanding of molecular factors and mechanisms governing primary ciliogenesis and ciliary function in skeletal development and disease.
MeSH term(s)	Cilia ; Humans ; Animals ; Bone and Bones/cytology ; Bone and Bones/pathology ; Skeleton/growth & development ; Organogenesis ; Osteogenesis ; Signal Transduction ; Mechanotransduction, Cellular
Language	English
Publishing date	2023-08-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1493-x
ISSN	1090-2422 ; 0014-4827
ISSN (online)	1090-2422
ISSN	0014-4827
DOI	10.1016/j.yexcr.2023.113751
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Article ; Online: Early insights into the role of Exoc6B associated with spondyloepimetaphyseal dysplasia with joint laxity type 3 in primary ciliogenesis and chondrogenic differentiation in vitro.

Guleria, Vishal Singh / Quadri, Neha / Prasad, Keshava / Das, Ranajit / Upadhyai, Priyanka

Molecular biology reports

2024 Volume 51, Issue 1, Page(s) 274

Abstract: Background: Spondyloepimetaphyseal dysplasia with joint laxity type 3 (SEMDJL3) is a rare skeletal dysplasia associated with EXOC6B, a component of the exocyst complex, involved in vesicle tethering and exocytosis at the plasma membrane. So far, EXOC6B ... ...

Abstract	Background: Spondyloepimetaphyseal dysplasia with joint laxity type 3 (SEMDJL3) is a rare skeletal dysplasia associated with EXOC6B, a component of the exocyst complex, involved in vesicle tethering and exocytosis at the plasma membrane. So far, EXOC6B and the pathomechanisms underlying SEMDJL3 remain obscure. Methods and results: Exoc6b was detected largely at the perinuclear regions and the primary cilia base in ATDC5 prechondrocytes. Its shRNA lentiviral knockdown impeded primary ciliogenesis. In Exoc6b silenced prechondrocytes, Hedgehog signaling was attenuated, including when stimulated with Smoothened agonist. Exoc6b knockdown deregulated the mRNA and protein levels of Col2a1, a marker of chondrocyte proliferation at 7- and 14-days following differentiation. It led to the upregulation of Ihh another marker of proliferative chondrocytes. The levels of Col10a1, a marker of chondrocyte hypertrophy was enhanced at 14 days of differentiation. Congruently, Axin2, a canonical Wnt pathway modulator that inhibits chondrocyte hypertrophy was repressed. The expression of Mmp13 and Adamts4 that are terminal chondrocyte hypertrophy markers involved in extracellular matrix (ECM) remodelling were downregulated at 7 and 14 days of chondrogenesis. Bglap that encodes for the most abundant non-collagenous bone matrix constituent and promotes ECM calcification was suppressed at 14 days of chondrocyte differentiation. ECM mineralization was assessed by Alizarin Red staining. Gene expression and ciliogenesis were investigated by reverse transcription quantitative real-time PCR, immunoblotting, and immunocytochemistry. Conclusions: These findings provide initial insights into the potential role of Exoc6b in primary ciliogenesis and chondrogenic differentiation, contributing towards a preliminary understanding of the molecular pathomechanisms underlying SEMDJL3.
MeSH term(s)	Cell Differentiation/genetics ; Cells, Cultured ; Chondrogenesis/genetics ; Hedgehog Proteins/genetics ; Hedgehog Proteins/metabolism ; Hypertrophy ; Joint Instability ; Osteochondrodysplasias ; Wnt Signaling Pathway
Chemical Substances	Hedgehog Proteins
Language	English
Publishing date	2024-02-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-023-09114-9
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Article: Genomic and Ancestral Variation Underlies the Severity of COVID-19 Clinical Manifestation in Individuals of European Descent.

Upadhyai, Priyanka / Suresh, Gokul / Parit, Rahul / Das, Ranajit

Life (Basel, Switzerland)

2021 Volume 11, Issue 9

Abstract: The coronavirus disease (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by a wide spectrum of clinical phenotypes ranging from asymptomatic to symptomatic with mild or moderate presentation and ...

Abstract	The coronavirus disease (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by a wide spectrum of clinical phenotypes ranging from asymptomatic to symptomatic with mild or moderate presentation and severe disease. COVID-19 susceptibility, severity and recovery have demonstrated high variability worldwide. Variances in the host genetic architecture may underlie the inter-individual and population-scale differences in COVID-19 presentation. We performed a genome-wide association analysis employing the genotyping data from AncestryDNA for COVID-19 patients of European descent and used asymptomatic subjects as the control group. We identified 621 genetic variants that were significantly distinct between asymptomatic and acutely symptomatic COVID-19 patients (multiple-testing corrected
Language	English
Publishing date	2021-09-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life11090921
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Article ; Online: Investigating the West Eurasian ancestry of Pakistani Hazaras.

Das, Ranajit / Upadhyai, Priyanka

Journal of genetics

2019 Volume 98, Issue 2

Abstract: The Hazaras are a distinct ethnic group from central Afghanistan and northwestern Pakistan of Mongoloid descent. Here, we sought to dissect the genetic admixture history of the Pakistani Hazaras and investigated their likely affiliation to ancient and ... ...

Abstract	The Hazaras are a distinct ethnic group from central Afghanistan and northwestern Pakistan of Mongoloid descent. Here, we sought to dissect the genetic admixture history of the Pakistani Hazaras and investigated their likely affiliation to ancient and extant West Eurasian populations. Our results indicated that the likely proportion of West Eurasian ancestry was low in the Hazaras and could be attributed putatively to a combination of Steppe populations from Early/Middle Bronze Age or Middle/Late Bronze Age and the Neolithic Iranians. Our results expand upon the current understanding and provide an improved resolution into the population history of the Pakistani Hazaras.
MeSH term(s)	Cluster Analysis ; Ethnic Groups/genetics ; Genetic Variation ; Genetics, Population ; Genome, Human ; Genomics/methods ; Humans ; Models, Genetic ; Pakistan
Language	English
Publishing date	2019-06-10
Publishing country	India
Document type	Journal Article
ZDB-ID	3039-9
ISSN	0973-7731 ; 0958-8361 ; 0022-1333
ISSN (online)	0973-7731
ISSN	0958-8361 ; 0022-1333
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Article ; Online: Application of the geographic population structure (GPS) algorithm for biogeographical analyses of wild and captive gorillas.

Das, Ranajit / Upadhyai, Priyanka

BMC bioinformatics

2019 Volume 20, Issue Suppl 1, Page(s) 35

Abstract: Background: The utilization of high resolution genome data has important implications for the phylogeographical evaluation of non-human species. Biogeographical analyses can yield detailed understanding of their population biology and facilitate the geo- ...

Abstract	Background: The utilization of high resolution genome data has important implications for the phylogeographical evaluation of non-human species. Biogeographical analyses can yield detailed understanding of their population biology and facilitate the geo-localization of individuals to promote their efficacious management, particularly when bred in captivity. The Geographic Population Structure (GPS) algorithm is an admixture based tool for inference of biogeographical affinities and has been employed for the geo-localization of various human populations worldwide. Here, we applied the GPS tool for biogeographical analyses and localization of the ancestral origins of wild and captive gorilla genomes, of unknown geographic source, available in the Great Ape Genome Project (GAGP), employing Gorillas with known ancestral origin as the reference data. Results: Our findings suggest that GPS was successful in recapitulating the population history and estimating the geographic origins of all gorilla genomes queried and localized the wild gorillas with unknown geographical origin < 150 km of National Parks/Wildlife Reserves within the political boundaries of countries, considered as prominent modern-day abode for gorillas in the wild. Further, the GPS localization of most captive-born gorillas was congruent with their previously presumed ancestral homes. Conclusions: Currently there is limited knowledge of the ancestral origins of most North American captive gorillas, and our study highlights the usefulness of GPS for inferring ancestry of captive gorillas. Determination of the native geographical source of captive gorillas can provide valuable information to guide breeding programs and ensure their appropriate management at the population level. Finally, our findings shine light on the broader applicability of GPS for protecting the genetic integrity of other endangered non-human species, where controlled breeding is a vital component of their conservation.
MeSH term(s)	Algorithms ; Animals ; Cluster Analysis ; Gene Pool ; Genetics, Population ; Genome ; Gorilla gorilla/classification ; Gorilla gorilla/genetics ; Phylogeography ; Population Dynamics ; Principal Component Analysis
Language	English
Publishing date	2019-02-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-018-2568-5
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Article ; Online: Correction to: Application of geographic population structure (GPS) algorithm for biogeographical analyses of populations with complex ancestries: a case study of South Asians from 1000 genomes project.

Das, Ranajit / Upadhyai, Priyanka

BMC genetics

2018 Volume 19, Issue 1, Page(s) 96

Abstract: Following publication of the original article [1], the authors flagged that acknowledgment of their equal contribution is omitted in the article [1]. ...

Abstract	Following publication of the original article [1], the authors flagged that acknowledgment of their equal contribution is omitted in the article [1].
Language	English
Publishing date	2018-10-25
Publishing country	England
Document type	Journal Article ; Published Erratum
ISSN	1471-2156
ISSN (online)	1471-2156
DOI	10.1186/s12863-018-0683-y
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Article ; Online: An Ancestry Informative Marker Set Which Recapitulates the Known Fine Structure of Populations in South Asia.

Das, Ranajit / Upadhyai, Priyanka

Genome biology and evolution

2018 Volume 10, Issue 9, Page(s) 2408–2416

Abstract: The inference of genomic ancestry using ancestry informative markers (AIMs) can be useful for a range of studies in evolutionary genetics, biomedical research, and forensic analyses. However, the determination of AIMs for highly admixed populations with ... ...

Abstract	The inference of genomic ancestry using ancestry informative markers (AIMs) can be useful for a range of studies in evolutionary genetics, biomedical research, and forensic analyses. However, the determination of AIMs for highly admixed populations with complex ancestries has remained a formidable challenge. Given the immense genetic heterogeneity and unique population structure of the Indian subcontinent, here we sought to derive AIMs that would yield a cohesive and faithful understanding of South Asian genetic origins. To discern the most optimal strategy for extracting AIMs for South Asians we compared three commonly used AIMs-determining methods namely, Infocalc, FST, and Smart Principal Component Analysis with ADMIXTURE, using previously published whole genome data from the Indian subcontinent. Our findings suggest that the Infocalc approach is likely most suitable for delineation of South Asian AIMs. In particular, Infocalc-2,000 (N = 2,000) appeared as the most informative South Asian AIMs panel that recapitulated the finer structure within South Asian genomes with high degree of sensitivity and precision, whereas a negative control with an equivalent number of randomly selected markers when used to interrogate the South Asian populations, failed to do so. We discuss the utility of all approaches under evaluation for AIMs derivation and interpreting South Asian genomic ancestries. Notably, this is the first report of an AIMs panel for South Asian ancestry inference. Overall these findings may aid in developing cost-effective resources for large-scale demographic analyses and foster expansion of our knowledge of human origins and disease, in the South Asian context.
MeSH term(s)	Asia ; Asian People/genetics ; Gene Frequency ; Genetics, Population ; Genome, Human ; Genotype ; Humans ; Polymorphism, Single Nucleotide ; Principal Component Analysis
Language	English
Publishing date	2018-09-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evy182
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Article ; Online: Genomic and Ancestral Variation Underlies the Severity of COVID-19 Clinical Manifestation in Individuals of European Descent

Priyanka Upadhyai / Gokul Suresh / Rahul Parit / Ranajit Das

Life, Vol 11, Iss 921, p

2021 Volume 921

Abstract	The coronavirus disease (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by a wide spectrum of clinical phenotypes ranging from asymptomatic to symptomatic with mild or moderate presentation and severe disease. COVID-19 susceptibility, severity and recovery have demonstrated high variability worldwide. Variances in the host genetic architecture may underlie the inter-individual and population-scale differences in COVID-19 presentation. We performed a genome-wide association analysis employing the genotyping data from AncestryDNA for COVID-19 patients of European descent and used asymptomatic subjects as the control group. We identified 621 genetic variants that were significantly distinct between asymptomatic and acutely symptomatic COVID-19 patients (multiple-testing corrected p -value < 0.001). These variants were found to be associated with pathways governing host immunity, such as interferon, interleukin and cytokine signalling, and known COVID-19 comorbidities, such as obesity and cholesterol metabolism. Further, our ancestry analysis revealed that the asymptomatic COVID-19 patients possess discernibly higher proportions of the Ancestral North Eurasian (ANE) and Eastern Hunter-Gatherer (EHG) ancestry, which was introduced to Europe through Bell Beaker culture (Yamnaya related) and lower fractions of Western Hunter-Gatherer (WHG) ancestry, while severely symptomatic patients have higher fractions of WHG and lower ANE/EHG ancestral components, thereby delineating the likely ancestral differences between the two groups.
Keywords	ancestral genetic variation in COVID-19 patients ; genome-wide association study for COVID-19 patients ; asymptomatic COVID-19 patients as control ; ANE and WHG ancestries in COVID-19 ; multiple regression with ancestral fractions ; Science ; Q
Subject code	610
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article: Characterization of primary cilia features reveal cell-type specific variability in in vitro models of osteogenic and chondrogenic differentiation.

Upadhyai, Priyanka / Guleria, Vishal Singh / Udupa, Prajna

PeerJ

2020 Volume 8, Page(s) e9799

Abstract: Primary cilia are non-motile sensory antennae present on most vertebrate cell surfaces. They serve to transduce and integrate diverse external stimuli into functional cellular responses vital for development, differentiation and homeostasis. Ciliary ... ...

Abstract	Primary cilia are non-motile sensory antennae present on most vertebrate cell surfaces. They serve to transduce and integrate diverse external stimuli into functional cellular responses vital for development, differentiation and homeostasis. Ciliary characteristics, such as length, structure and frequency are often tailored to distinct differentiated cell states. Primary cilia are present on a variety of skeletal cell-types and facilitate the assimilation of sensory cues to direct skeletal development and repair. However, there is limited knowledge of ciliary variation in response to the activation of distinct differentiation cascades in different skeletal cell-types. C3H10T1/2, MC3T3-E1 and ATDC5 cells are mesenchymal stem cells, preosteoblast and prechondrocyte cell-lines, respectively. They are commonly employed in numerous in vitro studies, investigating the molecular mechanisms underlying osteoblast and chondrocyte differentiation, skeletal disease and repair. Here we sought to evaluate the primary cilia length and frequencies during osteogenic differentiation in C3H10T1/2 and MC3T3-E1 and chondrogenic differentiation in ATDC5 cells, over a period of 21 days. Our data inform on the presence of stable cilia to orchestrate signaling and dynamic alterations in their features during extended periods of differentiation. Taken together with existing literature these findings reflect the occurrence of not only lineage but cell-type specific variation in ciliary attributes during differentiation. These results extend our current knowledge, shining light on the variabilities in primary cilia features correlated with distinct differentiated cell phenotypes. It may have broader implications in studies using these cell-lines to explore cilia dependent cellular processes and treatment modalities for skeletal disorders centered on cilia modulation.
Language	English
Publishing date	2020-08-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.9799
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Article ; Online: Application of the geographic population structure (GPS) algorithm for biogeographical analyses of wild and captive gorillas

Ranajit Das / Priyanka Upadhyai

BMC Bioinformatics, Vol 20, Iss S1, Pp 17-

2019 Volume 26

Abstract: Abstract Background The utilization of high resolution genome data has important implications for the phylogeographical evaluation of non-human species. Biogeographical analyses can yield detailed understanding of their population biology and facilitate ... ...

Abstract	Abstract Background The utilization of high resolution genome data has important implications for the phylogeographical evaluation of non-human species. Biogeographical analyses can yield detailed understanding of their population biology and facilitate the geo-localization of individuals to promote their efficacious management, particularly when bred in captivity. The Geographic Population Structure (GPS) algorithm is an admixture based tool for inference of biogeographical affinities and has been employed for the geo-localization of various human populations worldwide. Here, we applied the GPS tool for biogeographical analyses and localization of the ancestral origins of wild and captive gorilla genomes, of unknown geographic source, available in the Great Ape Genome Project (GAGP), employing Gorillas with known ancestral origin as the reference data. Results Our findings suggest that GPS was successful in recapitulating the population history and estimating the geographic origins of all gorilla genomes queried and localized the wild gorillas with unknown geographical origin < 150 km of National Parks/Wildlife Reserves within the political boundaries of countries, considered as prominent modern-day abode for gorillas in the wild. Further, the GPS localization of most captive-born gorillas was congruent with their previously presumed ancestral homes. Conclusions Currently there is limited knowledge of the ancestral origins of most North American captive gorillas, and our study highlights the usefulness of GPS for inferring ancestry of captive gorillas. Determination of the native geographical source of captive gorillas can provide valuable information to guide breeding programs and ensure their appropriate management at the population level. Finally, our findings shine light on the broader applicability of GPS for protecting the genetic integrity of other endangered non-human species, where controlled breeding is a vital component of their conservation.
Keywords	Biogeography ; Admixture ; Geo-localization of non-human species ; Gorilla ancestry ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	333
Language	English
Publishing date	2019-02-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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