Distance measurements via the morphogen gradient of Bicoid in Drosophila embryos

<p>Abstract</p> <p>Background</p> <p>Patterning along the anterior-posterior (A-P) axis in <it>Drosophila </it>embryos is instructed by the morphogen gradient of Bicoid (Bcd). Despite extensive studies of this morphogen, how embryo geometry may affect gradient formation and target responses has not been investigated experimentally.</p> <p>Results</p> <p>In this report, we systematically compare the Bcd gradient profiles and its target expression patterns on the dorsal and ventral sides of the embryo. Our results support a hypothesis that proper distance measurement and the encoded positional information of the Bcd gradient are along the perimeter of the embryo. Our results also reveal that the dorsal and ventral sides of the embryo have a fundamentally similar relationship between Bcd and its target Hunchback (Hb), suggesting that Hb expression properties on the two sides of the embryo can be directly traced to Bcd gradient properties. Our 3-D simulation studies show that a curvature difference between the two sides of an embryo is sufficient to generate Bcd gradient properties that are consistent with experimental observations.</p> <p>Conclusions</p> <p>The findings described in this report provide a first quantitative, experimental evaluation of embryo geometry on Bcd gradient formation and target responses. They demonstrate that the physical features of an embryo, such as its shape, are integral to how pattern is formed.</p

SAR2EO: A High-resolution Image Translation Framework with Denoising Enhancement

Synthetic Aperture Radar (SAR) to electro-optical (EO) image translation is a fundamental task in remote sensing that can enrich the dataset by fusing information from different sources. Recently, many methods have been proposed to tackle this task, but they are still difficult to complete the conversion from low-resolution images to high-resolution images. Thus, we propose a framework, SAR2EO, aiming at addressing this challenge. Firstly, to generate high-quality EO images, we adopt the coarse-to-fine generator, multi-scale discriminators, and improved adversarial loss in the pix2pixHD model to increase the synthesis quality. Secondly, we introduce a denoising module to remove the noise in SAR images, which helps to suppress the noise while preserving the structural information of the images. To validate the effectiveness of the proposed framework, we conduct experiments on the dataset of the Multi-modal Aerial View Imagery Challenge (MAVIC), which consists of large-scale SAR and EO image pairs. The experimental results demonstrate the superiority of our proposed framework, and we win the first place in the MAVIC held in CVPR PBVS 2023

Relationship between Non-Pathogenic Bacteria from Eggs of Healthy Laying Ducks and Flora Structure in the Genital Tract and Cecum

Objective: The aim was to investigate whether a bacterial flora exists in the eggs of healthy laying ducks (Ma breed), and if yes, whether the bacterial flora could be associated with those in the genital tract and cecum. Methods: Healthy laying ducks were dissected to collect genital tract and cecum tissues, as well as soft- and hard-shelled duck eggs, and cultivable bacteria were counted by plate count method, and the diversity and correlation of uncultured bacterial flora were analyzed by MiSeq high-throughput sequencing. Results: The decreasing order of the total bacterial counts in the samples was cecum > genital tract > hard-shelled egg > soft-shelled egg. The bacterial gene sequences belonged to 56 phyla and 1 319 genera. The abundance and species evenness of bacteria in the cecum and genital tract were higher. The dominant genera included Bacteroides, Megamonas and Campylobacter. Species abundance and dominant concentration were higher in soft- and hard-shell eggs. Pseudomonas and Acinetobacter accounted for 19.01% and 10.01% of the total abundance, respectively. Gene function prediction showed that all samples had high abundance of metabolic and glycolytic functions. The gram-positive and anaerobic phenotypes in the cecum and genital tract were abundant. The pathogenicity and oxidative stress of bacteria in soft and hard shell eggs were significant. The dominant bacterial genera in the four samples were overlapped, and the overlap rates of egg content with the cecum and genital tract were 13.96% and 24.35%, respectively. In addition, the phylogenetic tree analysis showed that the genera in all samples were closely related to each other and shared homology with the significantly contributing genus Bacteroides in the cecum. Conclusion: Duck eggs are not formed in a sterile environment, the bacteria residing in the cecum and reproductive tract of healthy laying ducks can infect different egg structures during its formation and become a part of the internal flora in duck eggs. These results can provide a reference for further research on the characteristics and control of non-pathogenic bacteria in egg contents

Development of iFOX-hunting as a functional genomic tool and demonstration of its use to identify early senescence-related genes in the polyploid \u3ci\u3eBrassica napus\u3c/i\u3e

Functional genomic studies of many polyploid crops, including rapeseed (Brassica napus), are constrained by limited tool sets. Here we report development of a gain-of-function platform, termed ‘iFOX (inducible Full-length cDNA OvereXpressor gene)-Hunting’, for inducible expression of B. napus seed cDNAs in Arabidopsis. A Gateway-compatible plant gene expression vector containing a methoxyfenozide-inducible constitutive promoter for transgene expression was developed. This vector was used for cloning of random cDNAs from developing B. napus seeds and subsequent Agrobacterium-mediated transformation of Arabidopsis. The inducible promoter of this vector enabled identification of genes upon induction that are otherwise lethal when constitutively overexpressed and to control developmental timing of transgene expression. Evaluation of a subset of the resulting ~6000 Arabidopsis transformants revealed a high percentage of lines with full-length B. napus transgene insertions. Upon induction, numerous iFOX lines with visible phenotypes were identified, including one that displayed early leaf senescence. Phenotypic analysis of this line (rsl-1327) after methoxyfenozide induction indicated high degree of leaf chlorosis. The integrated B. napus cDNA was identified as a homolog of an Arabidopsis acyl-CoA binding protein (ACBP) gene designated BnACBP1-like. The early senescence phenotype conferred by BnACBP1-like was confirmed by constitutive expression of this gene in Arabidopsis and B. napus. Use of the inducible promoter in the iFOX line coupled with RNA-Seq analyses allowed mechanistic clues and a working model for the phenotype associated with BnACBP1-like expression. Our results demonstrate the utility of iFOX-Hunting as a tool for gene discovery and functional characterization of Brassica napus genome

Loss of ARHGEF6 Causes Hair Cell Stereocilia Deficits and Hearing Loss in Mice

ARHGEF6 belongs to the family of guanine nucleotide exchange factors (GEFs) for Rho GTPases, and it specifically activates Rho GTPases CDC42 and RAC1. Arhgef6 is the X-linked intellectual disability gene also known as XLID46, and clinical features of patients carrying Arhgef6 mutations include intellectual disability and, in some cases, sensorineural hearing loss. Rho GTPases act as molecular switches in many cellular processes. Their activities are regulated by binding or hydrolysis of GTP, which is facilitated by GEFs and GTPase-activating proteins, respectively. RAC1 and CDC42 have been shown to play important roles in hair cell (HC) stereocilia development. However, the role of ARHGEF6 in inner ear development and hearing function has not yet been investigated. Here, we found that ARHGEF6 is expressed in mouse cochlear HCs, including the HC stereocilia. We established Arhgef6 knockdown mice using the clustered regularly interspaced short palindromic repeat-associated Cas9 nuclease (CRISPR-Cas9) genome editing technique. We showed that ARHGEF6 was indispensable for the maintenance of outer hair cell (OHC) stereocilia, and loss of ARHGEF6 in mice caused HC stereocilia deficits that eventually led to progressive HC loss and hearing loss. However, the loss of ARHGEF6 did not affect the synapse density and did not affect the mechanoelectrical transduction currents in OHCs at postnatal day 3. At the molecular level, the levels of active CDC42 and RAC1 were dramatically decreased in the Arhgef6 knockdown mice, suggesting that ARHGEF6 regulates stereocilia maintenance through RAC1/CDC42

Tip60 Suppresses Cholangiocarcinoma Proliferation and Metastasis via PI3k-AKT

Background/Aims: Aberrant expression of Tip60 is associated with progression in many cancers. However, the role of Tip60 in cancer progression remains contradictory. The aim of this study was to investigate the clinical significance, biological functions and underlying mechanisms of Tip60 deregulation in cholangiocarcinoma (CCA) for the first time. Methods: Quantitative real-time PCR (QRT-PCR), western blotting and immunohistochemistry staining (IHC) were carried out to measure Tip60 expression in CCA tissues and cell lines. Kaplan–Meier analysis and the log-rank test were used for survival analysis. In vitro, cell proliferation was evaluated by flow cytometry and CCK-8, colony formation, and EDU assays. Migration/ invasion was evaluated by trans-well assays. Phosphokinase array was used to confirm the dominant signal regulated by Tip60. Tumor growth and metastasis were demonstrated in vivo using a mouse model. Results: Tip60 was notably downregulated in CCA tissues, which was associated with greater tumor size, venous invasion, and TNM stage. Down-regulation of Tip60 was associated with tumor progression and poorer survival in CCA patients. In vitro and in vivo studies demonstrated that Tip60 suppressed growth and metastasis throughout the progression of CCA. We further identified the PI3K/AKT pathway as a dominant signal of Tip60 and suggested that Tip60 regulated CCA cell proliferation and metastasis via PT3K-AKT pathway. Pearson analysis revealed that PTEN was positively correlated with the Tip60 level in CCA tissues. Conclusion: Tip60, as a tumor suppressor in CCA via the PI3K/AKT pathway, might be a promising therapeutic target or prognostic marker for CCA

Extraction Optimization of Water-Extracted Mycelial Polysaccharide from Endophytic Fungus Fusarium oxysporum Dzf17 by Response Surface Methodology

Water-extracted mycelial polysaccharide (WPS) from the endophytic fungus Fusarium oxysporum Dzf17 isolated from Dioscorea zingiberensis was found to be an efficient elicitor to enhance diosgenin accumulation in D. zingigerensis cultures, and also demonstrated antioxidant activity. In this study, response surface methodology (RSM) was employed to optimize the extraction process of WPS from F. oxysporum Dzf17 using Box-Behnken design (BBD). The ranges of the factors investigated were 1–3 h for extraction time (X1), 80–100 °C for extraction temperature (X2), and 20–40 (v/w) for ratio of water volume (mL) to raw material weight (g) (X3). The experimental data obtained were fitted to a second-order polynomial equation using multiple regression analysis. Statistical analysis showed that the polynomial regression model was in good agreement with the experimental results with the determination coefficient (R2) of 0.9978. By solving the regression equation and analyzing the response surface contour plots, the extraction parameters were optimized as 1.7 h for extraction time, 95 °C for extraction temperature, 39 (v/w) for ratio of water volume (mL) to raw material weight (g), and with 2 extractions. The maximum value (10.862%) of WPS yield was obtained when the WPS extraction process was conducted under the optimal conditions