The impact of cross-kingdom molecular forensics on genetic privacy

stjosephs-hospital

Recent advances in metagenomic technology and computational prediction may inadvertently weaken an individual’s reasonable expectation of privacy. Through cross-kingdom genetic and metagenomic forensics, we can already predict at least a dozen human phenotypes with varying degrees of accuracy.

There is also growing potential to detect a “molecular echo” of an individual’s microbiome from cells deposited on public surfaces. At present, host genetic data from somatic or germ cells provide more reliable information than microbiome samples.

However, the emerging ability to infer personal details from different microscopic biological materials left behind on surfaces requires in-depth ethical and legal scrutiny. There is potential to identify and track individuals, along with new, surreptitious means of genetic discrimination.

This commentary underscores the need to update legal and policy frameworks for genetic privacy with additional considerations for the information that could be acquired from microbiome-derived data. The article also aims to stimulate ubiquitous discourse to ensure the protection of genetic rights and liberties in the post-genomic era. Video abstract.

MiR-340 promotes the proliferation of vascular smooth muscle cells by targeting von Hippel-Lindau tumor suppressor (VHL) gene

MiRNAs play key roles in the proliferation of vascular smooth muscle cells (VSMCs). However, the roles and underlying mechanism of miRNAs in VSMCs are not fully understood. The aim of this study was to evaluate the role of miR-340 in the proliferation of VSMCs.

The expression levels of miR-340 and von Hippel-Lindau tumor-suppressor (VHL) in VSMCs induced by platelet-derived growth factor (PDGF) -BB or fetal bovine serum (FBS) were measured by q-PCR. The effects of miR-340 and VHL on cell proliferation and invasion were evaluated by CCK-8 assay. Target gene prediction and screening as well as luciferase reporter assay were performed to verify the downstream target genes of miR-340. Western blotting was used to detect the protein expression levels of vascular endothelial growth factor (VEGF) and VHL.

Our results showed that the miR-340 was up-regulated in PDGF-BB_ENREF_1or FBS induced VSMCs. In addition, overexpression of miR-340 promoted VSMCs proliferation and invasion. Moreover, VHL was found to be a potential target for miR-340, and up-regulation of VHL inhibited VSMCs proliferation.

MiR-340 plays a critical role in VSMC proliferation and neointimal hyperplasia in rats carotid balloon injury model. Reduced expression levels of miR-340 promoted VHL-inhibited VSMCs proliferation. In conclusion, miR-340 may play a role in the regulation of proliferation of VSMCs by inhibition of VHL.

 

ECM2 and GLT8D2 in human pulmonary artery hypertension: fruits from weighted gene co-expression network analysis

Background: Pulmonary artery hypertension (PAH) is an incurable disease with a high mortality rate. Current medications ameliorate symptoms but cannot target adverse vascular remodeling. New therapeutic strategies for PAH need to be established.

 

Methods: Using the weighted gene coexpression network analysis (WGCNA) algorithm, we constructed a coexpression network of dataset GSE117261 from the Gene Expression Omnibus (GEO) database. Key modules were identified by the relationship between module eigengenes and clinical traits.

 

Hub genes were screened out based on gene significance (GS), module membership (MM), and mean pulmonary artery pressure (mPAP). External validations were conducted in GSE48149 and GSE113439. Functional enrichment and immune cell infiltration were analyzed using Metascape and CIBERSORTx.

Results: The WGCNA analysis revealed 13 coexpression modules. The pink module had the highest correlation with PAH in terms of module eigengene (r=0.79; P=2e-18) and module significance (MS =0.43).

 

Functional enrichment indicated genes in the pink module contributed to the immune system process and extracellular matrix (ECM). In the pink module, ECM2 (GS =0.65, MM =0.86, ρ=0.407, P=0.0019) and GLT8D2 (GS =0.63, MM =0.85, ρ=0.443, P=0.006) were identified as hub genes. For immune cells infiltration in PAH lung tissue, hub genes were positively correlated with M2 macrophages and resting mast cells, and were negatively correlated with monocytes, neutrophils, and CD4-naïve T cells.

 

Conclusions: Our research identified 2 hub genes ECM2 and GLT8D2 related to PAH. The functions of these hub genes were involved in the immune process and ECM, indicating that they might serve as candidate therapeutic targets for PAH.

stjosephs-hospital

stjosephs-hospital

Genomes of 12 fig wasps provide insights into the adaptation of pollinators to fig syconia

Figs and fig pollinators are one of the few classic textbook examples of obligate pollination mutualism. The specific dependence of fig pollinators on the relatively safe living environment with sufficient food sources in the enclosed fig syconia implies that they are vulnerable to habitat changes.

 

  • However, there is still no extensive genomic evidence to reveal the evolutionary footprint of this long-term mutually beneficial symbiosis in fig pollinators. In fig syconia, there are also non-pollinator species.
  • The non-pollinator species differ in their evolutionary and life histories from pollinators. We conducted comparative analyses on 11 newly sequenced fig wasp genomes and one previously published genome.
  • The pollinators colonized the figs approximately 66.9 million years ago, consistent with the origin of host figs. Compared with non-pollinators, many more genes in pollinators were subject to relaxed selection.
  • Seven genes were absent in pollinators in response to environmental stress and immune activation. Pollinators had more streamlined gene repertoires in the innate immune system, chemosensory toolbox, and detoxification system.
  • Our results provide genomic evidence for the differentiation between pollinators and nonpollinators. The data suggest that owing to the long-term adaptation to the fig, some genes related to functions no longer required are absent in pollinators.

Byrsonima Rich. is one of the largest genera of the Malpighiaceae family with 97 species occurrence in Brazil and multiple potentialities, including pharmaceutical and food industries. In this study, 17 microsatellite markers characterized in Byrsonima cydoniifolia were tested for seven related taxa, all species are native to Brazil and four are endemic. Genomic DNA was extracted from leaves tissues and 17 microsatellite markers were used to cross-amplification of microsatellite regions.

 

Polymorphism and genetic diversity were evaluated for B. intermedia, B. verbascifolia, B. laxiflora, B. subterranea, B. umbellata, B. linearifolia. from 16 individuals and for B. viminifolia from 14 individuals. Transferred microsatellite markers panels ranged from 11 (64.8%) in B. viminifolia to 6 (35.2%) in B. umbellata. The total number of alleles per locus ranged from 5 (B. linearifolia) to 8 (B. subterranea) alleles. B. umbellata showed lower values of observed and expected heterozygosity (HO = 0.312; HE = 0.436) and B. subterranea presented the highest values (HO = 0.687; HE = 0.778).

A greater number of microsatellite markers should be developed for B. umbellata. The microsatellite marker panels transferred to the species B. intermedia, B. verbascifolia, B. laxiflora, B. subterranea, B. viminifolia and B. linearifolia are very informative, with a high combined probability of exclusion of paternity (Q ≥ 0.976) and the low combined probability of identity (I ≤ 9.91 × 10-6), potentially suitable for future genetic-population studies, supporting strategies for maintaining the genetic diversity and for exploration of Byrsonima species as genetic resources.

 

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EpiQuik Total Histone H3 Acetylation Detection Fast Kit (Colorimetric)

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Rapid Animal Total RNA Extraction Kit

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Total Protein Extraction Kit: 50X PI

K3011010-2 260 ul
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AffiSelect Total Protein Extraction Solution

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Bacterial Total Protein Extraction Reagent

abx090632-50100assays 50-100 assays
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Plant Total Protein Extraction Reagent

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EpiQuik Methyl-Histone H3K4 ChIP Kit

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EpiQuik Histone H3 Citrullination ELISA Kit

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3-min Bacterial Total Protein Extraction Kit

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Human Total PSA (t-PSA) ELISA Kit

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EpiQuik Tri-Methyl-Histone H3K9 ChIP Kit

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EpiQuik Tissue Methyl-Histone H3K9 ChIP Kit

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EpiQuik Tissue Methyl-Histone H3K4 ChIP Kit

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EpiQuik Tissue Acetyl-Histone H3 ChIP Kit

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EpiQuik Global Histone H3K4 Methylation Assay Kit

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3-min Total Protein Extraction Kit (Animal cells)

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AnaPrep Total RNA Extraction Kit with DNase-Treatment

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EpiQuik Histone Methyltransferase Activity/Inhibition Assay Kit (H3K4)

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EpiQuik Histone Methyltransferase Activity/Inhibition Assay Kit (H3K27)

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EpiQuik In Situ Histone H3K4 Methylation Assay Kit

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EpiQuik Global Histone H3K27 Tri-Methylation Assay Kit

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EpiQuik Circulating Dimethyl Histone H3K4 ELISA Kit (Colorimetric)

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EpiQuik Circulating Trimethyl Histone H3K9 ELISA Kit (Colorimetric)

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EpiQuik Circulating Monomethyl Histone H3K27 ELISA Kit (Colorimetric)

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EpiQuik Circulating Trimethyl Histone H3K36 ELISA Kit (Colorimetric)

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EpiQuik Circulating Acetyl Histone H3K9 ELISA Kit (Colorimetric)

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EpiQuik Circulating Acetyl Histone H3K18 ELISA Kit (Colorimetric)

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EpiQuik Global Acetyl Histone H3K9 Quantification Kit (Colorimetric)

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EpiQuik Global Acetyl Histone H3K14 Quantification Kit (Colorimetric)

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EpiQuik Global Acetyl Histone H3K14 Quantification Kit (Fluorometric)

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EpiQuik Global Acetyl Histone H3K18 Quantification Kit (Fluorometric)

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EpiQuik Global Acetyl Histone H3K23 Quantification Kit (Colorimetric)

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