Induction of galectin-1 expression by HTLV-I Tax and its impact on HTLV-I infectivity

© 2008 Gauthier et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon

タイヌビエのゲノムを高精度解読 --除草剤に抵抗性を持つ水田の雑草タイヌビエの高精度ゲノム解読に成功--. 京都大学プレスリリース. 2023-11-07.Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32, 337, and 30, 889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production

A multilocular thymic cyst associated with mediastinal seminoma: evidence for its medullary epithelial origin highlighted by POU2F3-positive thymic tuft cells and concomitant myoid cell proliferation

Multilocular thymic cyst (MTC) and germ cell tumors are common diseases that impact the mediastinum. Correctly diagnosing these diseases can be difficult because several other conditions can mimic them. We report a male patient with MTC associated with mediastinal seminoma. A needle biopsy of the mediastinal tumor revealed numerous epithelioid cell granulomas that mimicked sarcoidosis or mycobacterial infection. However, large atypical cells positive for Oct3/4 and KIT were noted between the granulomas; thus, we diagnosed the patient with mediastinal seminoma. The resected tumor, after chemotherapy, consisted of multiple cystic lesions, and a residual germ cell tumor was first considered. However, thymic medulla-specific elements, namely, POU2F3-positive thymic tuft cells and rhabdomyomatous myoid cells accompanying the epithelium, led to the correct diagnosis of MTC. Our case underscores the importance of recognizing the histological features associated with mediastinal seminoma and provides novel findings for MTC pathogenesis, namely, the presence of thymic tuft cells

Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder’

We have established a high-quality, chromosome-level genome assembly for the hexaploid common wheat cultivar ‘Fielder’, an American, soft, white, pastry-type wheat released in 1974 and known for its amenability to Agrobacterium tumefaciens-mediated transformation and genome editing. Accurate, long-read sequences were obtained using PacBio circular consensus sequencing with the HiFi approach. Sequence reads from 16 SMRT cells assembled using the hifiasm assembler produced assemblies with N50 greater than 20 Mb. We used the Omni-C chromosome conformation capture technique to order contigs into chromosome-level assemblies, resulting in 21 pseudomolecules with a cumulative size of 14.7 and 0.3 Gb of unanchored contigs. Mapping of published short reads from a transgenic wheat plant with an edited seed-dormancy gene, TaQsd1, identified four positions of transgene insertion into wheat chromosomes. Detection of guide RNA sequences in pseudomolecules provided candidates for off-target mutation induction. These results demonstrate the efficiency of chromosome-scale assembly using PacBio HiFi reads and their application in wheat genome-editing studies

Zinc transport via ZNT5-6 and ZNT7 is critical for cell surface glycosylphosphatidylinositol-anchored protein expression

Glycosylphosphatidylinositol (GPI)-anchored proteins play crucial roles in various enzyme activities, cell signaling and adhesion, and immune responses. While the molecular mechanism underlying GPI-anchored protein biosynthesis has been well studied, the role of zinc transport in this process has not yet been elucidated. Zn transporter (ZNT) proteins mobilize cytosolic zinc to the extracellular space and to intracellular compartments. Here, we report that the early secretory pathway ZNTs [ZNT5-ZNT6 heterodimers (ZNT5-6) and ZNT7-ZNT7 homodimers (ZNT7)], which supply zinc to the lumen of the early secretory pathway compartments are essential for GPI-anchored protein expression on the cell surface. We show, using overexpression and gene disruption/re-expression strategies in cultured human cells, that loss of ZNT5-6 and ZNT7 zinc transport functions results in significant reduction in GPI-anchored protein levels similar to that in mutant cells lacking phosphatidylinositol glycan anchor biosynthesis (PIG) genes. Furthermore, medaka fish with disrupted Znt5 and Znt7 genes show touch-insensitive phenotypes similar to zebrafish Pig mutants. These findings provide a previously unappreciated insight into the regulation of GPI-anchored protein expression and protein quality control in the early secretory pathway

Image Evaluation of Free-breathing Navigator Echo and Triggered Cardiac-gated Delayed Myocardial Enhancement Magnetic Resonance Imaging in Sedated Infants

We validated a navigator-echo-triggered sequence that drives magnetization before cardiac-gated inversion recovery T1 turbo field echo acquisition, in the sedated free-breathing pediatric population. Cardiac magnetic resonance imaging was performed on sedated infants with single ventricle. We calculated the signal-to-noise ratios and contrast-to-noise ratios of 2 groups of images obtained using respiratory triggering with and without navigator echo. All images were then visually assessed by 2 observers. The signal-to-noise ratio and the contrast-to-noise ratio were significantly higher with than without navigator echo (p<0.01; p<0.05). The visual assessment scores were also consistently better with than without navigator echo (p<0.01). Free-breathing navigator echo was found to have the advantage of decreasing the motion artifact caused by respiration. Cardiacgated inversion recovery T1 turbo field echo sequence for free-breathing navigator-echo-triggered respiration allows for the acquisition, in sedated infants, of diagnostic images whose quality exceeds that of the non-navigator-echo-triggered alternative

Evaluation of Kidney Histological Images Using Unsupervised Deep Learning

[Introduction] Evaluating histopathology via machine learning has gained research and clinical interest, and the performance of supervised learning tasks has been described in various areas of medicine. Unsupervised learning of histological images has the advantage of reproducibility for labeling; however, the relationship between unsupervised evaluation and clinical information remains unclear in nephrology. [Methods] We propose an unsupervised approach combining convolutional neural networks (CNNs) and a visualization algorithm to cluster the histological images and calculate the score for patients. We applied the approach to the entire images or patched images of the glomerulus of kidney biopsy samples stained with hematoxylin and eosin obtained from 68 patients with immunoglobulin A nephropathy. We assessed the relationship between the obtained scores and clinical variables of urinary occult blood, urinary protein, serum creatinine (SCr), systolic blood pressure, and age. [Results] The glomeruli of the patients were classified into 12 distinct classes and 10 patches. The output of the fine-tuned CNN, which we defined as the histological scores, had significant relationships with assessed clinical variables. In addition, the clustering and visualization results suggested that the defined clusters captured important findings when evaluating renal histopathology. For the score of the patch-based cluster containing crescentic glomeruli, SCr (coefficient = 0.09, P = 0.019) had a significant relationship. [Conclusion] The proposed approach could successfully extract features that were related to the clinical variables from the kidney biopsy images along with the visualization for interpretability. The approach could aid in the quantified evaluation of renal histopathology

SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population

Average linkage disequilibrium coefficient (r2) values plotted against intermarker distance for all autosomal chromosomes. (PDF 407 kb