A complete and accurate genome sequence provides a fundamental tool for functional genomics and DNA-informed breeding. Here, we assemble a high-quality genome (contig N50 of 6.99 Mb) of the apple anther-derived homozygous line HFTH1, including 22 telomere sequences, using a combination of PacBio single-molecule real-time (SMRT) sequencing, chromosome conformation capture (Hi-C) sequencing, and optical mapping. In comparison to the Golden Delicious reference genome, we identify 18,047 deletions, 12,101 insertions and 14 large inversions. We reveal that these extensive genomic variations are largely attributable to activity of transposable elements. Interestingly, we find that a long terminal repeat (LTR) retrotransposon insertion upstream of MdMYB1 , a core transcriptional activator of anthocyanin biosynthesis, is associated with red-skinned phenotype. This finding provides insights into the molecular mechanisms underlying red fruit coloration, and highlights the utility of this high-quality genome assembly in deciphering agriculturally important trait in apple.
In order to perform their normal physiological functions, it is important that cells maintain the intracellular pH within the physiological range. Intracellular enzyme activity, cytoskeleton component integration, and cellular growth and differentiation rates are all closely associated with the intracellular pH. It has been demonstrated that in nervous system diseases, such as ischemic stroke, traumatic brain injury, epilepsy, Parkinson's disease, and Alzheimer's disease (AD), the common characteristics are decreased pH or acidosis at both tissular and cellular levels. Particularly, some AD-associated enzymes will have altered activities under acidic conditions. We inferred that aging or ischemia may cause intracellular acidification. This acidification not only induces apoptosis but also substantially alters enzyme activities and promotes the development of AD or vascular dementia. The hypothesis of an intracellular pH role in sporadic AD or vascular dementia will be discussed in this paper. If confirmed, this hypothesis may lead to the formulation of new pathogenesis and new therapeutic approaches to AD or vascular dementia.
ABSTRACT.Purpose: To evaluate the biomechanical properties of the cornea using Corneal Visualization Scheimpflug Technology (CorVis ST, Oculus) in eyes with primary open-angle glaucoma (POAG) and normal control eyes. Methods: A comparative cross-sectional study that included 42 patients with POAG and 60 normal control subjects matched for intraocular pressure (IOP) and central corneal thickness (CCT). IOP was measured with a Goldmann applanation tonometer (GAT). Corneal tomography and biomechanical parameters were measured with Pentacam (Oculus) and CorVis ST, respectively. Corneal biomechanical properties were compared between groups, and the associations between corneal biomechanical parameters and ocular characteristics were evaluated. Receiver operating characteristic (ROC) curves were used to establish a cut-off value for the biomechanical parameters. Results: The following parameters of the CorVis ST showed a significant difference between eyes with POAG and normal eyes: first applanation velocity (V in ), second applanation time (A-time 2 ), peak distance (PD) and deformation amplitude (DA). In the univariate analysis, DA was negatively correlated with IOP in both groups. For all biomechanical parameters, the areas under the ROC curve were <0.80 and thus did not reach a good level of predictive accuracy for detecting POAG. Conclusion: CorVis ST offers an alternative method for measuring corneal biomechanical properties. Eyes with POAG exhibit a faster V in , longer A-time 2 , lower DA and longer PD than do IOP-and CCT-matched normal control eyes. The biomechanical parameters of the CorVis ST cannot readily be used for diagnosis of POAG in the individual patient.
PurposeTo investigate whether differences exist in lens position and other lens parameters among major ethnic groups with cataractous eyes, which may help explain racial differences in angle closure risk.MethodsThis retrospective, cross-sectional study included 807 adult patients who had cataract surgery between years 2014 and 2016 at the University of California, San Francisco (UCSF). Adult patients of white, Asian, Hispanic and African-American ethnicity were included. Lens position (LP), defined as anterior chamber depth (ACD) + 1/2 lens thickness (LT), was assessed using measurements from optical biometry. Other assessed biometric parameters included axial length (AL), relative lens position (RLP) (defined as LP/AL), and anterior chamber depth (ACD).ResultsA total of 807 patients and 1361 eyes were included in this study from a database of patients having cataract surgery. Mean age was 69.2 years (age range from 18 to 101 years old), and 60.3% of patients were women. The mean LP measurements were 5.54±0.32 mm for white, 5.38±0.32 mm for Asian, 5.32±0.30 mm for Hispanic, and 5.40±0.28 mm for African-American participants. After adjusting for age, sex, and AL, significant differences were found when comparing LP in paired comparisons among White cohort with Asians (P<0.001), Hispanics (P<0.001) and African-Americans (P = 0.003). Additionally, when comparing RLP, similar significant results were found when comparing Whites with Asians (P<0.001), Hispanics (P<0.001) and African-Americans (P = 0.002). Lastly, pair-wise comparison of LT between ethnic groups showed significant differences while comparing Asians with Whites (P = 0.001) and Asians with African-Americans (P<0.001).ConclusionThe results of this study suggest that the LP of Hispanic, Asian, and African-American patients are significantly smaller than that of White patients, and among all ethnic groups, Hispanics and after Asians have the smallest LP (P<0.001) and RLP (P<0.001). These findings may have implications for the relative risk of angle closure and the potential IOP response after cataract surgery among different ethnic groups.
BackgroundTo report our experience in planning and delivering total marrow irradiation (TMI) and total marrow and lymphatic irradiation (TMLI) in patients with hematologic malignancies.MethodsTwenty-seven patients undergoing bone marrow transplantation were treated with TMI/TMLI using Helical Tomotherapy (HT). All skeletal bones exclusion of the mandible comprised the treatment target volume and, for TMLI, lymph node chains, liver, spleen and/or brain were also included according to the clinical indication. Planned dose of 8Gy in 2 fractions was delivered over 1 day for TMI while 10Gy in 2 fractions BID was used for TMLI. Organs at risk (OAR) contoured included the brain, brainstem, lens, eyes, optic nerves, parotids, oral cavity, lungs, heart, liver, kidneys, stomach, small bowel, bladder and rectum. In particular, a simple method to avoid hot or cold doses in the overlapping region was implemented and the plan sum was adopted to evaluate dose inhomogeneity. Furthermore, setup errors from 54 treatments were summarized to gauge the effectiveness of immobilization.ResultsDuring the TMI/TMLI treatment, no acute adverse effects occurred during the radiation treatment. Two patients suffered nausea or vomiting right after radiation course. For the 9 patients treated with TMI, the median dose reduction of major organs varied 30–65% of the prescribed dose, substantially lower than the traditional total body irradiation (TBI). Meanwhile, average biological equivalent doses to OARs with 8Gy/2F TMI approach were not different from the conventional 12Gy/6F TMI approach. In the dose junction region, the 93% of PTV was covered by the prescribed dose without obvious hotspots. For the 27 patients, the overall setup corrections were lower than 3 mm except those in the SI direction for abdomen-pelvis region, demonstrating excellent immobilization.ConclusionThe present study confirmed the technical feasibility of HT-based TMI/TMLI delivering 8-10Gy in 2 fractions over 1 day. For patients undergoing hematopoietic cell transplantation the proposed 8Gy/2F TMI (or 10Gy/2F TMLI) strategy may be a novel approach to improve delivery efficiency, increase effective radiation dose to target while maintaining low risk of severe organ toxicities.
Allele-specific expression (ASE) can lead to phenotypic diversity and evolution. However, the mechanisms regulating ASE are not well understood, particularly in woody perennial plants. In this study, we investigated ASE genes in the apple cultivar 'Royal Gala' (RG). A high quality chromosome-level genome was assembled using a homozygous tetra-haploid RG plant, derived from anther cultures. Using RNA-sequencing (RNA-seq) data from RG flower and fruit tissues, we identified 2091 ASE genes. Compared with the haploid genome of 'Golden Delicious' (GD), a parent of RG, we distinguished the genomic sequences between the two alleles of 817 ASE genes, and further identified allele-specific presence of a transposable element (TE) in the upstream region of 354 ASE genes. These included MYB110a that encodes a transcription factor regulating anthocyanin biosynthesis. Interestingly, another ASE gene, MYB10 also showed an allele-specific TE insertion and was identified using genome data of other apple cultivars. The presence of the TE insertion in both MYB genes was positively associated with ASE and anthocyanin accumulation in apple petals through analysis of 231 apple accessions, and thus underpins apple flower colour evolution. Our study demonstrated the importance of TEs in regulating ASE on a genome-wide scale and presents a novel method for rapid identification of ASE genes and their regulatory elements in plants.
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