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Article ; Online: Tracking footprints of artificial and natural selection signatures in breeding and non-breeding cats

Xuying Zhang / Kokila Jamwal / Ottmar Distl

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 20

Abstract: Abstract Stray non-breeding cats (stray) represent the largest heterogeneous cat population subject to natural selection, while populations of the Siamese (SIAM) and Oriental Shorthair (OSH) breeds developed through intensive artificial selection for ... ...

Abstract	Abstract Stray non-breeding cats (stray) represent the largest heterogeneous cat population subject to natural selection, while populations of the Siamese (SIAM) and Oriental Shorthair (OSH) breeds developed through intensive artificial selection for aesthetic traits. Runs of homozygosity (ROH) and demographic measures are useful tools to discover chromosomal regions of recent selection and to characterize genetic diversity in domestic cat populations. To achieve this, we genotyped 150 stray and 26 household non-breeding cats (household) on the Illumina feline 63 K SNP BeadChip and compared them to SIAM and OSH. The 50% decay value of squared correlation coefficients (r 2 ) in stray (0.23), household (0.25), OSH (0.24) and SIAM (0.25) corresponded to a mean marker distance of 1.12 Kb, 4.55 Kb, 62.50 Kb and 175.07 Kb, respectively. The effective population size (N e ) decreased in the current generation to 55 in stray, 11 in household, 9 in OSH and 7 in SIAM. In the recent generation, the increase in inbreeding per generation (ΔF) reached its maximum values of 0.0090, 0.0443, 0.0561 and 0.0710 in stray, household, OSH and SIAM, respectively. The genomic inbreeding coefficient (F ROH ) based on ROH was calculated for three length categories. The F ROH was between 0.014 (F ROH60 ) and 0.020 (F ROH5 ) for stray, between 0.018 (F ROH60 ) and 0.024 (F ROH5 ) for household, between 0.048 (F ROH60 ) and 0.069 (F ROH5 ) for OSH and between 0.053 (F ROH60 ) and 0.073 (F ROH5 ) for SIAM. We identified nine unique selective regions for stray through genome-wide analyses for regions with reduced heterozygosity based on F ST statistics. Genes in these regions have previously been associated with reproduction (BUB1B), motor/neurological behavior (GPHN, GABRB3), cold-induced thermogenesis (DIO2, TSHR), immune system development (TSHR), viral carcinogenesis (GTF2A1), host immune response against bacteria, viruses, chemoattractant and cancer cells (PLCB2, BAHD1, TIGAR), and lifespan and aging (BUB1B, FGF23). In addition, we ...
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis

Sergei Yu. Zaitsev / Nadezhda V. Bogolyubova / Xuying Zhang / Bertram Brenig

PeerJ, Vol 8, p e

a review

2020 Volume 8997

Abstract: The animal’s blood is the most complicated and important biological liquid for veterinary medicine. In addition to standard methods that are always in use, recent technologies such as dynamic tensiometry (DT) of blood serum and PCR analysis of particular ...

Abstract	The animal’s blood is the most complicated and important biological liquid for veterinary medicine. In addition to standard methods that are always in use, recent technologies such as dynamic tensiometry (DT) of blood serum and PCR analysis of particular markers are in progress. The standard and modern biochemical tests are commonly used for general screening and, finally, complete diagnosis of animal health. Interpretation of major biochemical parameters is similar across animal species, but there are a few peculiarities in each case, especially well-known for cattle. The following directions are discussed here: hematological indicators; “total protein” and its fractions; some enzymes; major low-molecular metabolites (glucose, lipids, bilirubin, etc.); cations and anions. As example, the numerous correlations between DT data and biochemical parameters of cattle serum have been obtained and discussed. Changes in the cell-free nucleic acids (cfDNA) circulating in the blood have been studied and analyzed in a variety of conditions; for example, pregnancy, infectious and chronic diseases, and cancer. CfDNA can easily be detected using standard molecular biological techniques like DNA amplification and next-generation sequencing. The application of digital PCR even allows exact quantification of copy number variations which are for example important in prenatal diagnosis of chromosomal aberrations.
Keywords	Blood ; Biochemical parameters ; Circulating nucleic acids ; Tensiometry ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	630
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Detection and classification of neurons and glial cells in the MADM mouse brain using RetinaNet.

Yuheng Cai / Xuying Zhang / Shahar Z Kovalsky / H Troy Ghashghaei / Alon Greenbaum

PLoS ONE, Vol 16, Iss 9, p e

2021 Volume 0257426

Abstract: The ability to automatically detect and classify populations of cells in tissue sections is paramount in a wide variety of applications ranging from developmental biology to pathology. Although deep learning algorithms are widely applied to microscopy ... ...

Abstract	The ability to automatically detect and classify populations of cells in tissue sections is paramount in a wide variety of applications ranging from developmental biology to pathology. Although deep learning algorithms are widely applied to microscopy data, they typically focus on segmentation which requires extensive training and labor-intensive annotation. Here, we utilized object detection networks (neural networks) to detect and classify targets in complex microscopy images, while simplifying data annotation. To this end, we used a RetinaNet model to classify genetically labeled neurons and glia in the brains of Mosaic Analysis with Double Markers (MADM) mice. Our initial RetinaNet-based model achieved an average precision of 0.90 across six classes of cells differentiated by MADM reporter expression and their phenotype (neuron or glia). However, we found that a single RetinaNet model often failed when encountering dense and saturated glial clusters, which show high variability in their shape and fluorophore densities compared to neurons. To overcome this, we introduced a second RetinaNet model dedicated to the detection of glia clusters. Merging the predictions of the two computational models significantly improved the automated cell counting of glial clusters. The proposed cell detection workflow will be instrumental in quantitative analysis of the spatial organization of cellular populations, which is applicable not only to preparations in neuroscience studies, but also to any tissue preparation containing labeled populations of cells.
Keywords	Medicine ; R ; Science ; Q
Subject code	006 ; 612
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Bulk and mosaic deletions of Egfr reveal regionally defined gliogenesis in the developing mouse forebrain

Xuying Zhang / Guanxi Xiao / Caroline Johnson / Yuheng Cai / Zachary K. Horowitz / Christine Mennicke / Robert Coffey / Mansoor Haider / David Threadgill / Rebecca Eliscu / Michael C. Oldham / Alon Greenbaum / H. Troy Ghashghaei

iScience, Vol 26, Iss 3, Pp 106242- (2023)

2023

Abstract: Summary: The epidermal growth factor receptor (EGFR) plays a role in cell proliferation and differentiation during healthy development and tumor growth; however, its requirement for brain development remains unclear. Here we used a conditional mouse ... ...

Abstract	Summary: The epidermal growth factor receptor (EGFR) plays a role in cell proliferation and differentiation during healthy development and tumor growth; however, its requirement for brain development remains unclear. Here we used a conditional mouse allele for Egfr to examine its contributions to perinatal forebrain development at the tissue level. Subtractive bulk ventral and dorsal forebrain deletions of Egfr uncovered significant and permanent decreases in oligodendrogenesis and myelination in the cortex and corpus callosum. Additionally, an increase in astrogenesis or reactive astrocytes in effected regions was evident in response to cortical scarring. Sparse deletion using mosaic analysis with double markers (MADM) surprisingly revealed a regional requirement for EGFR in rostrodorsal, but not ventrocaudal glial lineages including both astrocytes and oligodendrocytes. The EGFR-independent ventral glial progenitors may compensate for the missing EGFR-dependent dorsal glia in the bulk Egfr-deleted forebrain, potentially exposing a regenerative population of gliogenic progenitors in the mouse forebrain.
Keywords	Neuroscience ; Developmental neuroscience ; Omics ; Transcriptomics ; Science ; Q
Subject code	616
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Osteogenesis imperfecta in a male holstein calf associated with a possible oligogenic origin

Xuying Zhang / Marc Hirschfeld / Julia Beck / Alexandra Kupke / Kernt Köhler / Ekkehard Schütz / Bertram Brenig

Veterinary Quarterly, Vol 40, Iss 1, Pp 58-

2020 Volume 67

Abstract: Background Neuromusculoskeletal anomalies generally in combination with severe clinical symptoms, comprise a heterogeneous group of fairly common and mostly fatal disorders in man and animals. Osteogenesis imperfecta (OI), also known as brittle bone ... ...

Abstract	Background Neuromusculoskeletal anomalies generally in combination with severe clinical symptoms, comprise a heterogeneous group of fairly common and mostly fatal disorders in man and animals. Osteogenesis imperfecta (OI), also known as brittle bone disease, causes bone fragility and deformity. Prominent extra-skeletal accessory manifestations of OI comprise blue/gray sclerae, hearing impairment, lung abnormalities and hypercalciuria. Cases of OI in cattle have been reported. However, no causative mutations have been identified in cattle so far. Aim To report a possible oligogenic origin identified in a calf from clinically healthy parents suffering from OI. Materials and Methods A neonatal embryo transfer male Holstein calf developing multiple fractures with bone tissue showing marked osteopenia was used for whole genome re-sequencing as well as its parents. In addition, 2,612 randomly chosen healthy Holstein cattle were genotyped as well as controls. Results Sixteen candidate genes with potential protein-altering variants were selected revealing non-synonymous variants only within IFITM5 and CRTAP genes. However, in-depth gene analysis did not result in the identification of a single causative mutation in the OI calf. Conclusion The analysis of the OI case revealed a possible oligogenic origin of the disease attributable to additive effects of three candidate genes, i.e., ABCA13, QRFPR, and IFTIM5. Clinical relevance Most OI cases in humans and domestic animals reported so far are caused by distinct dominant or recessive monogenic mutations, therefore a potential oligogenic additive genetic effect is a novel finding. Furthermore, the case presented here demonstrates that cross-species genetic analyses might not always be straightforward.
Keywords	bovine ; cattle ; cow ; osteodysplasia ; osteodystrophy ; osteogenesis imperfecta ; brittle bone disease ; congenital bone disorder ; embryo transfer ; malformation ; Veterinary medicine ; SF600-1100
Subject code	616
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Taylor & Francis Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage

Xuying Zhang / Christine V. Mennicke / Guanxi Xiao / Robert Beattie / Mansoor Haider / Simon Hippenmeyer / H. Troy Ghashghaei

Cells, Vol 9, Iss 2662, p

2020 Volume 2662

Abstract: Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double ... ...

Abstract	Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis.
Keywords	cerebral cortex ; clonal analysis ; neurogenesis ; gliogenesis ; Egfr ; astrocyte ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Foxj1 expressing ependymal cells do not contribute new cells to sites of injury or stroke in the mouse forebrain

Nagendran Muthusamy / Andrew Brumm / Xuying Zhang / S. Thomas Carmichael / H. Troy Ghashghaei

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 9

Abstract: Abstract The stem cell source of neural and glial progenitors in the periventricular regions of the adult forebrain has remained uncertain and controversial. Using a cell specific genetic approach we rule out Foxj1+ ependymal cells as stem cells ... ...

Abstract	Abstract The stem cell source of neural and glial progenitors in the periventricular regions of the adult forebrain has remained uncertain and controversial. Using a cell specific genetic approach we rule out Foxj1+ ependymal cells as stem cells participating in neurogenesis and gliogenesis in response to acute injury or stroke in the mouse forebrain. Non stem- and progenitor-like responses of Foxj1+ ependymal cells to injury and stroke remain to be defined and investigated.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Optogenetic Mapping of Cerebellar Inhibitory Circuitry Reveals Spatially Biased Coordination of Interneurons via Electrical Synapses

Jinsook Kim / Soojung Lee / Sachiko Tsuda / Xuying Zhang / Brent Asrican / Bernd Gloss / Guoping Feng / George J. Augustine

Cell Reports, Vol 7, Iss 5, Pp 1601-

2014 Volume 1613

Abstract: We used high-speed optogenetic mapping technology to examine the spatial organization of local inhibitory circuits formed by cerebellar interneurons. Transgenic mice expressing channelrhodopsin-2 exclusively in molecular layer interneurons allowed us to ... ...

Abstract	We used high-speed optogenetic mapping technology to examine the spatial organization of local inhibitory circuits formed by cerebellar interneurons. Transgenic mice expressing channelrhodopsin-2 exclusively in molecular layer interneurons allowed us to focally photostimulate these neurons, while measuring resulting responses in postsynaptic Purkinje cells. This approach revealed that interneurons converge upon Purkinje cells over a broad area and that at least seven interneurons form functional synapses with a single Purkinje cell. The number of converging interneurons was reduced by treatment with gap junction blockers, revealing that electrical synapses between interneurons contribute substantially to the spatial convergence. Remarkably, gap junction blockers affected convergence in sagittal slices, but not in coronal slices, indicating a sagittal bias in electrical coupling between interneurons. We conclude that electrical synapse networks spatially coordinate interneurons in the cerebellum and may also serve this function in other brain regions.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2014-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Transcription factor C/EBPβ and 17β-estradiol promote transcription of the porcine p53 gene

Tao, Hu / Fenge Li / Huayu Wu / Jiahao Yang / Jiawei Zhou / Lei Wang / Lihua Zhu / Lun Hua / Shuqi Mei / Xianwen Peng / Xuying Zhang

international journal of biochemistry & cell biology. 2014 Feb., v. 47

2014

Abstract: The tumor protein 53 (p53) gene played a crucial role in maternal reproduction except its classic roles in maintaining genomic stability and preventing tumorigenesis. However, little is known concerning the regulatory elements which control the ... ...

Abstract	The tumor protein 53 (p53) gene played a crucial role in maternal reproduction except its classic roles in maintaining genomic stability and preventing tumorigenesis. However, little is known concerning the regulatory elements which control the expression of p53 gene. In this study, we predicted two binding sites (−490/−477 and −405/−392) of transcription factor CCAAT/enhancer binding protein beta (C/EBPβ) within the core promoter (−985/−273) determined by promoter deletion analysis, and discovered that the second site (−405/−392) was important for p53 promoter activity by site-directed mutagenesis. Then the binding of C/EBPβ to the p53 promoter was identified by electrophoretic mobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP). Moreover, evidence from C/EBPβ overexpression and RNAi studies showed C/EBPβ regulated p53 promoter activity and endogenous p53 expression. Meanwhile, we observed p53 mRNA at the peak in 10−6mol/L 17β-estradiol treated cells for 24h via enhancing its core promoter activity. Taken together, our study indicates that C/EBPβ and 17β-estradiol are the essential regulatory factors for p53 transcription.
Keywords	binding proteins ; binding sites ; carcinogenesis ; chromatin ; estradiol ; gel electrophoresis ; genes ; genomics ; messenger RNA ; precipitin tests ; regulatory sequences ; reproduction ; RNA interference ; site-directed mutagenesis ; swine ; transcription factors
Language	English
Dates of publication	2014-02
Size	p. 76-82.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1228429-4
ISSN	1878-5875 ; 1357-2725
ISSN (online)	1878-5875
ISSN	1357-2725
DOI	10.1016/j.biocel.2013.12.002
Database	NAL-Catalogue (AGRICOLA)

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