Search Results (7)

One out of every hundred live births present with congenital heart abnormalities caused by the aberrant development of the embryonic cardiovascular system. The conserved zinc finger transcription factor proteins, which include GATA binding protein 5 (GATA5) and GATA binding protein (GATA6) play important roles in embryonic development and their inactivation may result in congenital heart defects (CHDs). In this study, we performed genotypic–phenotypic analyses in two families affected by right-sided CHD diagnosed by echocardiography imaging. Proband A presented with pulmonary valve stenosis, and proband B presented with complex CHD involving the right heart structures. For variant detection, we employed whole-genome single-nucleotide polymorphism (SNP) microarray and family-based whole-exome sequencing (WES) studies. Proband A is a full-term infant who was admitted to the neonatal intensive care unit (NICU) at five days of life for pulmonary valve stenosis (PVS). Genomic studies revealed a normal SNP microarray; however, quad WES analysis identified a novel heterozygous [Chr20:g.61041597C>G (p.Arg237Pro)] variant in the GATA5 gene. Further analysis confirmed that the novel variant was inherited from the mother but was absent in the father and the maternal uncle with a history of heart murmur. Proband B was born prematurely at 35 weeks gestation with a prenatally diagnosed complex CHD. A postnatal evaluation revealed right-sided heart defects including pulmonary atresia with intact ventricular septum (PA/IVS), right ventricular hypoplasia, tricuspid valve hypoplasia, hypoplastic main and bilateral branch pulmonary arteries, and possible coronary sinusoids. Cardiac catheterization yielded anatomy and hemodynamics unfavorable to repair. Hence, heart transplantation was indicated. Upon genomic testing, a normal SNP microarray was observed, while trio WES analysis identified a novel heterozygous [Chr18:c.1757C>T (p.Pro586Leu)] variant in the GATA6 gene. This variant was inherited from the father, who carries a clinical diagnosis of tetralogy of Fallot. These findings provide new insights into novel GATA5/6 variants, elaborate on the genotypic and phenotypic association, and highlight the critical role of GATA5 and GATA6 transcription factors in a wide spectrum of right-sided CHDs. Full article

A recombinant Ross River virus (RRV) that contains the fluorescent protein mCherry fused to the non-structural protein 3 (nsP3) was constructed, which allowed real-time imaging of viral replication. RRV-mCherry contained either the natural opal stop codon after the nsP3 gene or was constructed without a stop codon. The mCherry fusion protein did not interfere with the viral life cycle and deletion of the stop codon did not change the replication capacity of RRV-mCherry. Comparison of RRV-mCherry and chikungunya virus-mCherry infections, however, showed a cell type-dependent delay in RRV-mCherry replication in HEK 293T cells. This delay was not caused by differences in cell entry, but rather by an impeded nsP expression caused by the RRV inhibitor ZAP (zinc finger CCCH-Type, antiviral 1). The data indicate that viral replication of alphaviruses is cell-type dependent, and might be unique for each alphavirus. Full article

Over the years, our vision of the genome has changed from a linear molecule to that of a complex 3D structure that follows specific patterns and possesses a hierarchical organization. Currently, genomics is becoming “four-dimensional”: our attention is increasingly focused on the study of chromatin dynamics over time, in the fourth dimension. Recent methods for visualizing the movements of chromatin loci in living cells by targeting fluorescent proteins can be divided into two groups. The first group requires the insertion of a special sequence into the locus of interest, to which proteins that recognize the sequence are recruited (e.g., FROS and ParB-INT methods). In the methods of the second approach, “programmed” proteins are targeted to the locus of interest (i.e., systems based on CRISPR/Cas, TALE, and zinc finger proteins). In the present review, we discuss these approaches, examine their strengths and weaknesses, and identify the key scientific problems that can be studied using these methods. Full article

VIVIPAROUS1/ABSCISIC ACID INSENSITIVE3-LIKE1 (VAL1) encodes a DNA-binding B3 domain protein and plays essential roles in seed maturation and flowering transition by repressing genes through epigenetic silencing in Arabidopsis. SWI-INDEPENDENT3 (SIN3)-LIKEs (SNLs), which encode scaffold proteins for the assembly of histone deacetylase complexes and have six SIN3 homologues (SNL1–SNL6) in Arabidopsis thaliana, directly repress gene expression to regulate seed maturation and flowering transition. However, it remains unclear whether VAL1 and SNLs work together in repressing the expression of related genes. In this study, yeast two-hybrid and firefly luciferase complementation imaging assays revealed that VAL1 interacts with SNLs, which can be attributed to its own zinc-finger CW (conserved Cys (C) and Trp (W) residues) domain and the PAH (Paired Amphipathic Helices) domains of SNLs. Furthermore, pull-down experiments confirmed that the CW domain of VAL1 interacts with both intact protein and the PAH domains of SNLs proteins, and the co-immunoprecipitation assays also confirmed the interaction between VAL1 and SNLs. In addition, quantitative real-time PCR (qRT-PCR) analysis showed that VAL1 and SNLs were expressed in seedlings, and transient expression assays showed that VAL1 and SNLs were localized in the nucleus. Considered together, these results reveal that VAL1 physically interacts with SNLs both in vitro and in vivo, and suggest that VAL1 and SNLs may work together to repress the expression of genes related to seed maturation and flowering transition in Arabidopsis. Full article

High-throughput phenotypic identification is a prerequisite for large-scale identification and gene mining of important traits. However, existing work has rarely leveraged high-throughput phenotypic identification into quantitative trait locus (QTL) acquisition in wheat crops. Clarifying the feasibility and effectiveness of high-throughput phenotypic data obtained from UAV multispectral images in gene mining of important traits is an urgent problem to be solved in wheat. In this paper, 309 lines of the spring wheat Worrakatta × Berkut recombinant inbred line (RIL) were taken as materials. First, we obtained the leaf area index (LAI) including flowering, filling, and mature stages, as well as the flag leaf chlorophyll content (CC) including heading, flowering, and filling stages, from multispectral images under normal irrigation and drought stress, respectively. Then, on the basis of the normalized difference vegetation index (NDVI) and green normalized difference vegetation index (GNDVI), which were determined by multispectral imagery, the LAI and CC were comprehensively estimated through the classification and regression tree (CART) and cross-validation algorithms. Finally, we identified the QTLs by analyzing the predicted and measured values. The results show that the predicted values of determination coefficient (R²) ranged from 0.79 to 0.93, the root-mean-square error (RMSE) ranged from 0.30 to 1.05, and the relative error (RE) ranged from 0.01 to 0.18. Furthermore, the correlation coefficients of predicted and measured values ranged from 0.93 to 0.94 for CC and from 0.80 to 0.92 for LAI at different wheat growth stages under normal irrigation and drought stress. Additionally, a linkage map of this RIL population was constructed by 11,375 SNPs; eight QTLs were detected for LAI on wheat chromosomes 1BL, 2BL (four QTLs), 3BL, 5BS, and 5DL, and three QTLs were detected for CC on chromosomes 1DS (two QTLs) and 3AL. The closely linked QTLs formed two regions on chromosome 2BL (from 54 to 56 cM and from 96 to 101 cM, respectively) and one region on 1DS (from 26 to 27 cM). Each QTL explained phenotypic variation for LAI from 2.5% to 13.8% and for CC from 2.5% to 5.8%. For LAI, two QTLs were identified at the flowering stage, two QTLs were identified at the filling stage, and three QTLs were identified at the maturity stage, among which QLAI.xjau-5DL-pre was detected at both filling and maturity stages. For CC, two QTLs were detected at the heading stage and one QTL was identified at the flowering stage, among which QCC.xjau-1DS was detected at both stages. Three QTLs (QLAI.xjau-2BL-pre.2, QLAI.xjau-2BL.2, and QLAI.xjau-3BL-pre) for LAI were identified under drought stress conditions. Five QTLs for LAI and two QTLs for CC were detected by imagery-predicted values, while four QTLs for LAI and two QTLs for CC were identified by manual measurement values. Lastly, investigations of these QTLs on the wheat reference genome identified 10 candidate genes associated with LAI and three genes associated with CC, belonging to F-box family proteins, peroxidase, GATA transcription factor, C₂H₂ zinc finger structural protein, etc., which are involved in the regulation of crop growth and development, signal transduction, and response to drought stress. These findings reveal that UAV sensing technology has relatively high reliability for phenotyping wheat LAI and CC, which can play an important role in crop genetic improvement. Full article

Speckle-type POZ (pox virus and zinc finger protein) protein (SPOP) is the most commonly mutated gene in prostate cancer (PCa). Recent evidence reports a role of SPOP in DNA damage response (DDR), indicating a possible impact of SPOP deregulation on PCa radiosensitivity. This study aimed to define the role of SPOP deregulation (by gene mutation or knockdown) as a radiosensitizing factor in PCa preclinical models. To express WT or mutant (Y87N, K129E and F133V) SPOP, DU145 and PC-3 cells were transfected with pMCV6 vectors. Sensitivity profiles were assessed using clonogenic assay and immunofluorescent staining of γH2AX and RAD51 foci. SCID xenografts were treated with 5 Gy single dose irradiation using an image-guided small animal irradiator. siRNA and miRNA mimics were used to silence SPOP or express the SPOP negative regulator miR-145, respectively. SPOP deregulation, by either gene mutation or knockdown, consistently enhanced the radiation response of PCa models by impairing DDR, as indicated by transcriptome analysis and functionally confirmed by decreased RAD51 foci. SPOP silencing also resulted in a significant downregulation of RAD51 and CHK1 expression, consistent with the impairment of homologous recombination. Our results indicate that SPOP deregulation plays a radiosensitizing role in PCa by impairing DDR via downregulation of RAD51 and CHK1. Full article

In this paper, we introduce a transparent fingerprint sensing system using a thin film transistor (TFT) sensor panel, based on a self-capacitive sensing scheme. An armorphousindium gallium zinc oxide (a-IGZO) TFT sensor array and associated custom Read-Out IC (ROIC) are implemented for the system. The sensor panel has a 200 × 200 pixel array and each pixel size is as small as 50 μm × 50 μm. The ROIC uses only eight analog front-end (AFE) amplifier stages along with a successive approximation analog-to-digital converter (SAR ADC). To get the fingerprint image data from the sensor array, the ROIC senses a capacitance, which is formed by a cover glass material between a human finger and an electrode of each pixel of the sensor array. Three methods are reviewed for estimating the self-capacitance. The measurement result demonstrates that the transparent fingerprint sensor system has an ability to differentiate a human finger’s ridges and valleys through the fingerprint sensor array. Full article