Development of an interpretable machine learning model for Ki-67 prediction in breast cancer using intratumoral and peritumoral ultrasound radiomics features.

Background: Traditional immunohistochemistry assessment of Ki-67 in breast cancer (BC) via core needle biopsy is invasive, inaccurate, and nonrepeatable. While machine learning (ML) provides a promising alternative, its effectiveness depends on extensive data. Although the current mainstream MRI-centered radiomics offers sufficient data, its unsuitability for repeated examinations, along with limited accessibility and an intratumoral focus, constrain the application of predictive models in evaluating Ki-67 levels. Objective: This study aims to explore ultrasound (US) image-based radiomics, incorporating both intra- and peritumoral features, to develop an interpretable ML model for predicting Ki-67 expression in BC patients. Methods: A retrospective analysis was conducted on 263 BC patients, divided into training and external validation cohorts. From intratumoral and peritumoral regions of interest (ROIs) in US images, 849 distinctive radiomics features per ROI were derived. These features underwent systematic selection to analyze Ki-67 expression relationships. Four ML models-logistic regression, random forests, support vector machine (SVM), and extreme gradient boosting-were formulated and internally validated to identify the optimal predictive model. External validation was executed to ascertain the robustness of the optimal model, followed by employing Shapley Additive Explanations (SHAP) to reveal the significant features of the model. Results: Among 231 selected BC patients, 67.5% exhibited high Ki-67 expression, with consistency observed across both training and validation cohorts as well as other clinical characteristics. Of the 1698 radiomics features identified, 15 were significantly correlated with Ki-67 expression. The SVM model, utilizing combined ROI, demonstrated the highest accuracy [area under the receiver operating characteristic curve (AUROC): 0.88], making it the most suitable for predicting Ki-67 expression. External validation sustained an AUROC of 0.82, affirming the model's robustness above a 40% threshold. SHAP analysis identified five influential features from intra- and peritumoral ROIs, offering insight into individual prediction. Conclusion: This study emphasized the potential of SVM model using radiomics features from both intra- and peritumoral US images, for predicting elevated Ki-67 levels in BC patients. The model exhibited strong performance in validations, indicating its promise as a noninvasive tool to enable personalized decision-making in BC care.

Genome-Wide Detection of SPX Family and Profiling of CoSPX-MFS3 in Regulating Low-Phosphate Stress in Tea-Oil Camellia.

Camellia oleifera a member of the family Theaceae, is a phosphorus (P) tolerator native to southern China. The SPX gene family critically regulates plant growth and development and maintains phosphate (Pi) homeostasis. However, the involvement of SPX genes in Pi signaling in Tea-Oil Camellia remains unknown. In this work, 20 SPX genes were identified and categorized into four subgroups. Conserved domains, motifs, gene structure, chromosomal location and gene duplication events were also investigated in the SPX gene family. Defense and stress responsiveness cis-elements were identified in the SPX gene promoters, which participated in low-Pi stress responses. Based on transcriptome data and qRT-PCR results, nine CoSPX genes had similar expression patterns and eight genes (except CoPHO1H3) were up-regulated at 30 days after exposure to low-Pi stress. CoSPX-MFS3 was selected as a key candidate gene by WGCNA analysis. CoSPX-MFS3 was a tonoplast protein. Overexpression of CoSPX-MFS3 in Arabidopsis promoted the accumulation of total P content and decreased the anthocyanin content. Overexpression of CoSPX-MFS3 could enhance low-Pi tolerance by increased biomass and organic acid contents in transgenic Arabidopsis lines. Furthermore, the expression patterns of seven phosphate starvation genes were higher in transgenic Arabidopsis than those in the wild type. These results highlight novel physiological roles of the SPX family genes in C. oleifera under low-Pi stress, and lays the foundation for a deeper knowledge of the response mechanism of C. oleifera to low-Pi stress.

Cloning, subcellular localization and expression of phosphate transporter gene HvPT6 of hulless barley.

Deficiency of phosphate (Pi) is one of the main growth-limiting factors for crops. Generally, phosphate transporters play a key role in the uptake of P in the crops. However, current knowledge regarding the molecular mechanism underlying Pi transport is still limited. In this study, a phosphate transporter (PT) gene, designated HvPT6, was isolated from a cDNA library constructed from hulless barley "Kunlun 14." The promoter of HvPT6 showed a large number of elements related to plant hormones. The expression pattern also indicated that HvPT6 was highly induced by low phosphorus, drought, abscisic acid, methyl jasmonate and gibberellin. Phylogenetic tree analysis revealed that HvPT6 belongs to the same subfamily of the major facilitator superfamily as OsPT6 from Oryza sativa. Subcellular localization of HvPT6:GFP using transient expression of Agrobacterium tumefaciens showed the green fluorescent protein signal in the membrane and nucleus of the Nicotiana benthamiana leaves. Overexpressing HvPT6 led to a longer and higher lateral root length and dry matter yield in the transgenic Arabidopsis lines under low Pi conditions, indicating that HvPT6 improves plant tolerance under Pi-deficient conditions. This study will lay a molecular basis for phosphate absorption mechanism in barley and breeding barley with high-efficient phosphate uptake.

Transcriptome Analysis of Resistant and Susceptible Pecan (Carya illinoinensis) Reveals the Mechanism of Resistance to Black Spot Disease (Colletotrichum fioriniae).

Pecan, Carya illinoinensis (Wangenh.) K. Koch, is an important dried fruit and woody oil tree species grown worldwide. With continuous expansion of pecan cultivation, the frequency and scope of diseases, especially black spot disease, are increasing, damaging trees and reducing yields. In this study, the key factors in resistance to black spot disease (Colletotrichum fioriniae) were investigated between the high-resistance pecan variety "Kanza" and the low-resistance variety "Mahan". Leaf anatomy and antioxidase activities confirmed much stronger resistance to black spot disease in "Kanza" than in "Mahan". Transcriptome analysis indicated that the increased expression of genes associated with defense response, oxidation-reduction, and catalytic activity was involved in disease resistance. A connection network identified a highly expressed hub gene CiFSD2 (CIL1242S0042), which might participate in redox reactions to affect disease resistance. Overexpression of CiFSD2 in tobacco inhibited enlargement of necrotic spots and increased disease resistance. Overall, the expression of differentially expressed genes differed in pecan varieties with different levels of resistance to C. fioriniae infection. In addition, the hub genes associated with black spot resistance were identified and the functions clarified. The in-depth understanding of resistance to black spot disease provides new insights for early screening of resistant varieties and molecular-assisted breeding in pecan.

Safety and efficacy of short-term dual antiplatelet therapy combined with intensive rosuvastatin in acute ischemic stroke

Abstract Objective: To investigate the safety and efficacy of short-term (7-day) Dual Antiplatelet Therapy (DAPT) with intensive rosuvastatin in Acute Ischemic Stroke (AIS). Methods: In this study, patients with AIS in the emergency department of the hospital from October 2016 to December 2019 were registered and divided into the control group (Single Antiplatelet Therapy [SAPT] + rosuvastatin) and the study group (7-day DAPT + intensive rosuvastatin) according to the therapy regimens. The generalized linear model was used to compare the National Institute of Health Stroke Scale (NIHSS) scores between the two groups during the 21-day treatment. A Cox regression model was used to compare recurrent ischemic stroke, bleeding events, Statin-Induced Liver Injury (SILI), and Statin-Associated Myopathy (SAM) between the two groups during the 90-day follow-up. Results: Comparison of NIHSS scores after 21-day treatment: NIHSS scores in the study group decreased significantly, 0.273-times as much as that in the control group (Odds Ratio [OR] 0.273; 95% Confidence Interval [95% CI] 0.208-0.359; p < 0.001). Comparison of recurrent ischemic stroke during the 90-day follow-up: The therapy of the study group reduced the risk of recurrent stroke by 65% (7.76% vs. 22.82%, Hazard Ratio [HR] 0.350; 95% CI 0.167-0.730; p = 0.005). Comparison of bleeding events: There was no statistical difference between the two groups (7.79% vs. 6.71%, HR = 1.076; 95% CI 0.424-2.732; p = 0.878). No cases of SILI and SAM were found. Conclusions: Short-term DAPT with intensive rosuvastatin effectively relieved the clinical symptoms and significantly reduced the recurrent stroke for patients with mild-to-moderate AIS within 90 days, without increasing bleeding events, SILI and SAM.

Overexpression of dihydroflavonol 4-reductase (CoDFR) boosts flavonoid production involved in the anthracnose resistance.

The outbreak of anthracnose caused by Colletotrichum spp. represents a devastating epidemic that severely affects oil tea (Camellia oleifera) production in China. However, the unknown resistance mechanism to anthracnose in C. oleifera has impeded the progress of breeding disease-resistant varieties. In this study, we investigated the physiological responses of resistant and susceptible lines during C. gloeosporioides infection. Our results showed that the accumulation of malondialdehyde (MDA), catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) in both disease-resistant and susceptible lines increased by C. gloeosporioides infection. Also, disease-resistant lines exhibited lower MDA, but higher POD, SOD, and CAT activities compared to susceptible lines. The accumulation of flavonoids in both resistant and susceptible C. oleifera leaves increased following C. gloeosporioides infection, and the increase was greater in resistant lines. Further, we identified and functionally characterized the dihydroflavonol 4-reductase (CoDFR) from the resistant C. oleifera line. We showed that the full-length coding sequence (CDS) of CoDFR is 1044 bp encoding 347 amino acids. The overexpression of CoDFR in tobacco altered the expression of flavonoid biosynthetic genes, resulting in an increased flavonoid content in leaves. CoDFR transgenic tobacco plants exhibited increased anthracnose resistance. Furthermore, the transgenic plants had higher salicylic acid content. These findings offer potential insights into the pivotal role of CoDFR involved in flavonoid-mediated defense mechanisms during anthracnose invasion in resistant C. oleifera.

Comparative Genomic Analysis Uncovers the Chloroplast Genome Variation and Phylogenetic Relationships of Camellia Species.

Camellia is the largest genus in the family Theaceae. Due to phenotypic diversity, frequent hybridization, and polyploidization, an understanding of the phylogenetic relationships between Camellia species remains challenging. Comparative chloroplast (cp) genomics provides an informative resource for phylogenetic analyses of Camellia. In this study, 12 chloroplast genome sequences from nine Camellia species were determined using Illumina sequencing technology via de novo assembly. The cp genome sizes ranged from 156,545 to 157,021 bp and were organized into quadripartite regions with the typical angiosperm cp genomes. Each genome harbored 87 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes in the same order and orientation. Differences in long and short sequence repeats, SNPs, and InDels were detected across the 12 cp genomes. Combining with the complete cp sequences of seven other species in the genus Camellia, a total of nine intergenic sequence divergent hotspots and 14 protein-coding genes with high sequence polymorphism were identified. These hotspots, especially the InDel (~400 bp) located in atpH-atpI region, had sufficient potential to be used as barcode markers for further phylogenetic analysis and species identification. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These cp genomes could facilitate the development of new molecular markers, accurate species identification, and investigations of the phylogenomic relationships of the genus Camellia.

Effects of Quinoa Flour on Wheat Dough Quality, Baking Quality, and in vitro Starch Digestibility of the Crispy Biscuits.

Quinoa is a pseudo-cereal which has excellent nutritional and functional properties due to its high content of nutrients, such as polyphenols and flavonoids, and therefore quinoa serves as an excellent supplement to make healthy and functional foods. The present study was aimed to evaluate the quality characteristics of wheat doughs and crispy biscuits supplemented with different amount of quinoa flour. The results showed that when more wheat flour was substituted by quinoa flour, proportion of unextractable polymeric protein to the total polymeric protein (UPP%) of the reconstituted doughs decreased and the gluten network structure was destroyed at a certain substitution level. The content of B-type starch and the gelatinization temperature of the reconstituted flours increased. The storage modulus, loss modulus, development time, and stability time of the dough increased as well. Moreover, hardness and toughness of the formulated crispy biscuits significantly decreased. Analyses suggested that starch digestibility was reduced and resistant starch content increased significantly. Taken together, quinoa flour improved dough rheological properties, enhanced the textural properties, and increased resistant starch content in crispy biscuits, thus adding to high nutritional value.

Effect of Highland Barley on Rheological Properties, Textural Properties and Starch Digestibility of Chinese Steamed Bread.

Highland barley has a different composition and structure to other crops. It has higher contents of total polyphenol (TPC), total flavonoid (TFC) and ß-glucan, which can be supplemented to improve the nutrition of wheat-flour-based food. In this study, the flours of three different grain-colored highland barley varieties Beiqing 6 (BQ), Dulihuang (DLH), and Heilaoya (HLY), were added to Jimai60 (JM, a wheat variety with medium gluten) wheat flour at different substitution levels to investigate their effects on the unextractable polymeric protein (UPP) content, micro-structure, rheological properties and mixing properties of dough, and the color, texture, flavor, and in vitro digestion of Chinese steam bread (CSB). The results showed that the moderate substitution of highland barley (20%) increased the UPP%, optimized the micro-structure of gluten, and improved its rheological properties by increasing dough viscoelasticity. The CSBs made from the composite flours exhibited a similar specific volume, cohesiveness, springiness and resilience to wheat CSB, while the firmness of composite CSBs (particularly JM-HLY-20) was delayed during storage. Importantly, the addition of highland barley increased the contents of TPC, TFC and ß-glucan, but decreased the in vitro starch digestibility of CSBs. A sensory evaluation showed that JM-HLY CSB was the most preferable. Taken together, highland barley can be used as a fine supplement to food products, with health-promoting properties.

Impacts of Continuous Cropping on Fungal Communities in the Rhizosphere Soil of Tibetan Barley.

Microbial community structures and keystone species play critical roles in soil ecological processes; however, their responses to the continuous cropping of plants are virtually unknown. Here, we investigated the community dynamics and keystone species of fungal communities in the rhizosphere soils of continuously cropped Tibetan barley (a principal cereal cultivated on the Qinghai-Tibetan Plateau). We found that the Chao1 and Phylogenetic Diversity (PD) indices decreased with increased cropping years. The relative abundance of the genera Cystofilobasidium, Mucor, and Ustilago increased with the extension of continuous cropping years, whereas Fusarium showed the opposite pattern. Furthermore, long-term monocropped Tibetan barley simplified the complexity of the co-occurrence networks. Keystone operational taxonomic units (OTUs) changed with continuous cropping, and most of the keystone OTUs belonged to the phylum Ascomycota, suggesting their important roles in rhizosphere soil. Overall, this study revealed that the continuous cropping of Tibetan barley impacted both on the richness, phylogenetic diversity, and co-occurrence network of fungal community in the rhizosphere. These findings enhance our understanding of how rhizosphere fungal communities respond to monocropped Tibetan barley.

The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication.

BACKGROUND: As a perennial crop, oil-Camellia possesses a long domestication history and produces high-quality seed oil that is beneficial to human health. Camellia oleifera Abel. is a sister species to the tea plant, which is extensively cultivated for edible oil production. However, the molecular mechanism of the domestication of oil-Camellia is still limited due to the lack of sufficient genomic information. RESULTS: To elucidate the genetic and genomic basis of evolution and domestication, here we report a chromosome-scale reference genome of wild oil-Camellia (2.95 Gb), together with transcriptome sequencing data of 221 cultivars. The oil-Camellia genome, assembled by an integrative approach of multiple sequencing technologies, consists of a large proportion of repetitive elements (76.1%) and high heterozygosity (2.52%). We construct a genetic map of high-density corrected markers by sequencing the controlled-pollination hybrids. Genome-wide association studies reveal a subset of artificially selected genes that are involved in the oil biosynthesis and phytohormone pathways. Particularly, we identify the elite alleles of genes encoding sugar-dependent triacylglycerol lipase 1, ß-ketoacyl-acyl carrier protein synthase III, and stearoyl-acyl carrier protein desaturases; these alleles play important roles in enhancing the yield and quality of seed oil during oil-Camellia domestication. CONCLUSIONS: We generate a chromosome-scale reference genome for oil-Camellia plants and demonstrate that the artificial selection of elite alleles of genes involved in oil biosynthesis contributes to oil-Camellia domestication.

Effect of Hulless Barley Flours on Dough Rheological Properties, Baking Quality, and Starch Digestibility of Wheat Bread.

Hulless barley (Hordeum vulgare L.), also known as highland barley, contains nutritional compounds, such as ß-glucan and polyphenol, which can be added to wheat flour to improve the dough nutritional quality. In this study, different formulated dough samples were obtained by individually adding four hulless barley flours into flour of a wheat variety (Jimai 44, designated as JM) which has very strong gluten. The effects of hulless barley supplementation on gluten structure, dough rheological properties, bread-making properties, and starch digestibility were assessed. The results showed that compared with JM dough, substitution of hulless barley flour to wheat flour at levels ranging from 10 to 40% negatively affected gluten micro-structure and dough mixing behavior, because the cross-links of gluten network were partially broken and the dough development time and stability time were shortened. For the hulless barley-supplemented bread, specific volume was significantly (P < 0.05) increased while springiness was not greatly changed. Furthermore, the hydrolysed starch rate in hulless barley-supplemented bread was decreased, compared with that in JM bread. Importantly, the contents of ß-glucan, polyphenols and flavonoids in hulless barley-supplemented bread were 132.61-160.87%, 5.71-48.57%, and 25-293.75% higher than those in JM bread, respectively. Taken together, the hulless barley-supplemented bread has been fortified with enhanced nutritional components, more desirable bread-making quality, and improved starch hydrolytic properties, which shows a great potential to use hulless barley as a health supplement.

Synthesis and characterization of tannic acid pillared bentonite composite for the efficient adsorption of aflatoxins.

Tannic acid (TA) is a hydrolysable polyphenol with established antioxidant and antibacterial activity along with its tendency to bind both organic and inorganic ions/molecules. In the present study, the sequestration performance of TA pillared bentonite for various aflatoxins (AFs) including AFB1, AFB2, AFG1 and AFG2 from aqueous solutions and simulated poultry gastrointestinal model solution was studied via adsorption. The adsorbents were characterized by scanning electron microscopy (SEM), energy dispersive X-ray (EDX) analysis, Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), N2 adsorption-desorption study and X-ray photoelectron spectroscopy (XPS). The reaction conditions including pH, agitation time, initial toxin concentration and temperature were systematically optimized. The Langmuir adsorption capacity of the adsorbent reached to 86, 71, 74 and 149 mg/g for AFB1, AFB2, AFG1 and AFG2 respectively. Adsorption kinetics and thermodynamic studies showed rapid AFs uptake and the exothermicity of the adsorption reaction respectively. Simultaneous removal of AFs by BTA3 revealed their independent and uninterrupted adsorption and the adsorption mechanism of AFs over BTA3 was elaborated with the help of XPS results. The outstanding AFs sequestering capability of BTA3 in aqueous solution and simulated poultry gastrointestinal model can be envisioned of great promise for the remediation of AFs and other hazardous pollutants from food and poultry industrial products.

Effects of Harvest Time on the Yield, Quality and Active Substance of Torreya grandis Nut and Its Oil.

Torreya grandis is an important economic tree species in China. It provides nutritional value and is important to the health care industry. There are ongoing issues with product quality which are primarily related to improper management and early harvest. This study was carried out during the fruit ripening processes to evaluate the influence of harvesting date on T. grandis quality, and to determine the optimal harvest period. The effects of harvest time on the variation of quality and nutritional parameters of T. grandis nuts and its oil were evaluated, and the optimal harvest period was determined. The results showed that harvest timing had a strong effect on both oil yield and quality. Prolonged ripening could induce higher levels of kernel rate, fruit inclusions, oil and nutritional quality. When the sample harvested in the mid-September, the kernel rate and oil content were increased by 1.88±0.31% and 6.65±0.47%, respectively, compared to samples harvested in the beginning of late-August. Similarly, the mid-September harvest resulted in total unsaturated fatty acids content of the oil being increased by 5.3±0.34%, the FFA and peroxide value being decreased by 40.7±0.15% and 76±0.08%, respectively, and total tocopherols and free amino acids were increased 7.5±0.24% and 47.3±0.15%, respectively, compared to the samples harvested on Aug. 25. The results indicated that the optimal harvest time of T. grandis fruits was mid-September as it was beneficial for improving the quality of T. grandis nut and its oil. It was suggested that T. grandis fruit should be harvested later.

Value of Ultrasound Combined with Immunohistochemistry Evaluation of Central Lymph Node Metastasis for the Prognosis of Papillary Thyroid Carcinoma.

BACKGROUND: Papillary thyroid carcinoma (PTC) is often accompanied by cervical lymph node metastasis (LNM). The accuracy of the preoperative ultrasound diagnosis of central LNM (CLNM) is limited. LNM is a high-risk factor for local recurrence and may affect the prognosis. Factors not directly related to tumor proliferation are used for risk assessment in the tumor-node-metastasis (TNM) staging system for thyroid cancer. The present study aimed to investigate the value of ultrasound and immunohistochemistry in predicting the presence of CLNM and the prognosis of PTC. PATIENTS AND METHODS: The ultrasound and immunohistochemistry features of 303 patients with first-ever PTC and who underwent surgery between 01/2014 to 12/2016 were analyzed, as well as the prognosis of the patients. Univariable and multivariable analyses were carried out to determine the risk factors of CLNM and recurrence. RESULTS: Among 303 patients, 125 (41.3%) were pathologically confirmed with CLNM. Multivariable analysis showed that multifocality, taller-than-wide shape, grade III-IV blood flow, capsular invasion, Ki-67 >10%, p53 ≥5%, T2 or T3 stages were independent risk factors for CLNM. The median follow-up was 56 months. Cox regression analysis showed that age ≥55 years, maximum tumor diameter >20 mm, multifocality, capsular invasion, Ki-67 5-10%, Ki-67 >10%, p53 ≥5%, T3 stage and N1a stage were independent risk factors for PTC recurrence. The Kaplan-Meier showed that recurrence-free survival (RFS) was different according to age (P=0.017), tumor size multifocality, capsular invasion, Ki-67, p53, T stage and N stage (all P<0.001). CONCLUSION: For PTC with rich blood flow, taller-than-wide shape, multifocality, capsular invasion, p53 ≥5%, Ki-67 >10%, T2 or T3 stages prophylactic CLNM dissection might be indicated. Age≥55 years, maximum tumor diameter >20 mm, multifocality, capsular invasion, high Ki-67, p53 ≥5%, T3 and N1a stages affected the clinical outcome.

A polyphasic study of Aspergillus section Flavi isolated from corn in Guangxi, China- a hot spot of aflatoxin contamination.

Aspergillus section Flavi is widely known as a potential threat to contaminate agricultural products and food commodities. In this study, a polyphasic approach consisting of micro- and macro-morphological, chemical and molecular features, was applied to survey the Aspergillus section Flavi population in corn collected from Guangxi, China. Based on multigene phylogenies as well as morphological observations, Aspergillus flavus (192/195), A. arachidicola (1/195), A. pseudonomius (1/195) and A. novoparasiticus (1/195) were found to be the predominant section Flavi population. Among them, 31 representative isolates were selected for mycotoxin determination. The results showed that Aspergillus flavus chemotype I was most common, chemotype IV was also detected with low incidence and low CPA amounts, while chemotypes II and III were absent. Other tested species including A. arachidicola, A. pseudonomius, and A. novoparasiticus produced all types of aflatoxins, but none of them produced CPA. The polyphasic approach applied in this study permitted reliable understanding of the prevailing Aspergillus section Flavi population and their mycotoxin profiles. Knowledge of the prevailing section Flavi population will aid in developing a sustainable strategy to mitigate the effects of aflatoxin contamination. This study suggests that CPA contamination of food should be considered while conducting mycotoxigenic surveys of food commodities, and the same should be considered while planning a bio-control strategy to control aflatoxin contamination.

Association Genetics Identifies Single Nucleotide Polymorphisms Related to Kernel Oil Content and Quality in Camellia oleifera.

Camellia oleifera, as an important nonwood tree species for seed oil in China, has received enormous attention owing to its high unsaturated fatty acid contents benefited to human health. It is necessary to examine allelic diversity of key genes that are associated with oil production in C. oleifera cultivars with a large variation of fatty acid compositions. In this study, we performed the association analysis between four key genes (two CoSAD and two Cofad2) coding fatty acid desaturases and traits including oil content and fatty acid composition. We identified two single nucleotide insertion-deletion (InDel) and 362 single-nucleotide polymorphisms (SNPs) within the four candidate genes by sequencing an association population (216 accessions). Single-marker (or haplotype) and traits association tests were conducted by linkage disequilibrium (LD) approaches to detect significant marker-trait associations. Validation population (279 hybrid individuals from six full-sibs families) studies were performed to validate the function of allelic variations significantly associated. In all, 90 single marker-trait and one haplotype-trait associations were significant in association population, and these loci explained 1.87-17.93% proportion of the corresponding phenotypic variance. Further, six SNP marker-trait associations ( Q < 0.10) from Cofad2-A, CoSAD1, and CoSAD2 were successfully validated in the validation population. The SNP markers identified in this study can potentially be applied for future marker-assisted selection to improve oil content and quality in C. oleifera.

Correlations of PCNA expression with thyroid cancer ultrasound and histopathologic features.

OBJECTIVE: To investigate the correlations of proliferating cell nuclear antigen (PCNA) gene expression with thyroid cancer (TC) ultrasound (US) features, histopathology and clinical stage. METHODS: A total of 66 TC patients admitted and treated in the Department of Oncology of our hospital from April 2014 to April 2018 were enrolled randomly. The conventional US imaging data of the patients were collected. Paired carcinoma and para-carcinoma tissues were obtained after operation to detect the expression of PCNA protein by immunohistochemistry (IHC). The correlations of PCNA expression with the patients' US manifestations and clinical stages were analyzed. RESULTS: The positive rate of PCNA was 72.73% (48/66) in TC tissues and 13.64% (9/66) in paired para-carcinoma tissues, displaying a statistically significant difference between the two groups (P<0.05). The PCNA and US features suggested that there was no significant difference in tumor boundary between the PCNA positive group and PCNA negative group (P>0.05). However, significant differences in tumor diameter, echo, calcification and blood flow were found between the two groups (P<0.05). The pathologic data of preoperative US diagnosis and PCNA expression in postoperative TC specimens were analyzed, and the results indicated that PCNA expression was prominently associated with T stage and N stage in US diagnosis (P<0.05). The total correct rate of US in assessing the T stage was 75.8% (50/66), and the over-staging rate and under-staging rate in evaluating the T stage were 13.6% (9/66) and 10.6% (7/66), respectively. CONCLUSION: The expression of PCNA protein in TC tissues is significantly correlated with the diameter, echo, calcification and blood flow of US features as well as clinical stage detected by US. PCNA level and US examination can provide certain clinical values for TC treatment.

Seed Transcriptomics Analysis in Camellia oleifera Uncovers Genes Associated with Oil Content and Fatty Acid Composition.

Camellia oleifera is a major tree species for producing edible oil. Its seed oil is well known for the high level of oleic acids; however, little is known regarding the molecular mechanism of lipid biosynthesis in C. oleifera. Here, we measured the oil contents and fatty acid (FA) compositions at four developmental stages and investigated the global gene expression profiles through transcriptomics sequencing. We identified differentially-expressed genes (DEGs) among the developmental stages and found that the distribution of numbers of DEGs was associated with the accumulation pattern of seed oil. Gene Ontology (GO) enrichment analysis revealed some critical biological processes related to oil accumulation, including lipid metabolism and phosphatidylcholine metabolism. Furthermore, we investigated the expression patterns of lipid biosynthesis genes. We showed that most of the genes were identified with single or multiple copies, and some had correlated profiles along oil accumulation. We proposed that the higher levels of stearoyl-ACP desaturases (SADs) coupled with lower activities of fatty acid desaturase 2 (FAD2) might be responsive to the boost of oleic acid at the late stage of C. oleifera seeds' development. This work presents a comprehensive transcriptomics study of C. oleifera seeds and uncovers valuable DEGs that are associated with the seed oil accumulation.

CbRCI35, a Cold Responsive Peroxidase from Capsella bursa-pastoris Regulates Reactive Oxygen Species Homeostasis and Enhances Cold Tolerance in Tobacco.

Low temperature affects gene regulatory networks and alters cellular metabolism to inhibit plant growth. Peroxidases are widely distributed in plants and play a large role in adjusting and controlling reactive oxygen species (ROS) homeostasis in response to abiotic stresses such as low temperature. The Rare Cold-Inducible 35 gene from Capsella bursa-pastoris (CbRCI35) belongs to the type III peroxidase family and has been reported to be a cold responsive gene in plants. Here we performed an expressional characterization of CbRCI35 under cold and ionic liquid treatments. The promoter of CbRCI35 was also cloned and its activity was examined using the GUS reporter system. CbRCI35 protein was localized in the cytoplasm according to sequence prediction and GFP fusion assay. Heterologous expression tests revealed that CbRCI35 conferred enhanced resistance to low temperature and activated endogenous cold responsive signaling in tobacco. Furthermore, in the normal condition the ROS accumulation was moderately enhanced while after chilling exposure superoxide dismutase activity was increased in CbRCI53 transgenic plants. The ROS metabolism related genes expression was altered accordingly. We conclude that CbRCI35 modulates ROS homeostasis and contributes to cold tolerance in plants.