107 research outputs found
An improved fruit transcriptome and the identification of the candidate genes involved in fruit abscission induced by carbohydrate stress in litchi
Developing a Semantic-Driven Hybrid Segmentation Method for Point Clouds of 3D Shapes
With the rapid development of point cloud processing technologies and the availability of a wide range of 3D capturing devices, a geometric object from the real world can be directly represented digitally as a dense and fine point cloud. Decomposing a 3D shape represented in point cloud into meaningful parts has very important practical implications in the fields of computer graphics, virtual reality and mixed reality. In this paper, a semantic-driven automated hybrid segmentation method is proposed for 3D point cloud shapes. Our method consists of three stages: semantic clustering, variational merging, and region remerging. In the first stage, a new feature of point cloud, called Local Concave-Convex Histogram, is introduced to first extract saddle regions complying with the semantic boundary feature. All other types of regions are then aggregated according to this extracted feature. This stage often leads to multiple over-segmentation convex regions, which are then remerged by a variational method established based on the narrow-band theory. Finally, in order to recombine the regions with the approximate shapes, order relation is introduced to improve the weighting forms in calculating the conventional Shape Diameter Function. We have conducted extensive experiments with the Princeton Dataset. The results show that the proposed algorithm outperforms the state-of-the-art algorithms in this area. We have also applied the proposed algorithm to process the point cloud data acquired directly from the real 3D objects. It achieves excellent results too. These results demonstrate that the method proposed in this paper is effective and universal
A fast responsive chromogenic and near-infrared fluorescence lighting-up probe for visual detection of toxic thiophenol in environmental water and living cells
Thiophenols as high toxic environmental pollutants are poisonous for animals and aquatic organisms. Therefore,
it is indispensable to monitor thiophenols in the environment. Herein, a novel near-infrared fluorescent probe
was developed for the detection of thiophenols, which was easily prepared by one-step coupling of 2,4-dini trobenzenesulfonyl chloride with Nile blue. The probe showed a significant near infrared (∼675 nm) fluores cence “turn-on” response to thiophenols with some good features including chromogenic reaction, high sensi tivity and selectivity, fast response, near-infrared emission along with low detection limit (1.8 nM). The probe
was employed to rapidly and visually determine thiophenols in several industrial wastewaters with good re coveries (90–110%). Moreover, this probe has been demonstrated good capability for imaging thiophenol in
HeLa cellsinfo:eu-repo/semantics/publishedVersio
Rapid short-pulse sequences enhance the spatiotemporal uniformity of acoustically driven microbubble activity during flow conditions
Despite the promise of microbubble-mediated focused ultrasound therapies, in vivo findings have revealed over-treated and under-treated regions distributed throughout the focal volume. This poor distribution cannot be improved by conventional pulse shapes and sequences, due to their limited ability to control acoustic cavitation dynamics within the ultrasonic focus. This paper describes the design of a rapid short-pulse (RaSP) sequence which is comprised of short pulses separated by μs off-time intervals. Improved acoustic cavitation distribution was based on the hypothesis that microbubbles can freely move during the pulse off-times. Flowing SonoVue® microbubbles (flow velocity: 10 mm/s) were sonicated with a 0.5 MHz focused ultrasound transducer using RaSP sequences (peak-rarefactional pressures: 146–900 kPa, pulse repetition frequency: 1.25 kHz, and pulse lengths: 5–50 cycles). The distribution of cavitation activity was evaluated using passive acoustic mapping. RaSP sequences generated uniform distributions within the focus in contrast to long pulses (50 000 cycles) that produced non-uniform distributions. Fast microbubble destruction occurred for long pulses, whereas microbubble activity was sustained for longer durations for shorter pulses. High-speed microscopy revealed increased mobility in the direction of flow during RaSP sonication. In conclusion, RaSP sequences produced spatiotemporally uniform cavitation distributions and could result in efficient therapies by spreading cavitation throughout the treatment area
Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission
Auxin response factors (ARFs) play fundamental roles in modulating various biological processes including fruit development and abscission via regulating the expression of auxin response genes. Currently, little is known about roles of ARFs in litchi (Litchi chinensis Sonn.), an economically important subtropical fruit tree whose production is suffering from fruit abscission. In this study, a genome-wide analysis of ARFs was conducted for litchi, 39 ARF genes (LcARFs) were identified. Conserved domain analysis showed that all the LcARFs identified have the signature B3 DNA-binding (B3) and ARF (Aux_rep) domains, with only 23 members having the dimerization domain (Aux_IAA). The number of exons in LcARF genes ranges from 2 to 16, suggesting a large variation for the gene structure of LcARFs. Phylogenetic analysis showed that the 39 LcARFs could be divided into three main groups: class I, II, and III. In total, 23 LcARFs were found to be potential targets of small RNAs, with three conserved and one novel miRNA-ARF (miRN43-ARF9) regulatory pathways discovered in litchi. Expression patterns were used to evaluate candidate LcARFs involved in various developmental processes, especially in flower formation and organ abscission. The results revealed that most ARF genes likely acted as repressors in litchi fruit abscission, that is, ARF2D/2E, 7A/7B, 9A/9B, 16A/16B, while a few LcARFs, such as LcARF5A/B, might be positively involved in this process. These findings provide useful information and resources for further studies on the roles of ARF genes in litchi growth and development, especially in the process of fruit abscission
Research on concentration and distribution of cadmium in crabs sold in Wenzhou
Objective To investigate the contamination and distribution of cadmium (Cd) in crabs sold in Wenzhou, and instruct consumers to eat healthily. Methods Three crab species were collected from 51 markets in 6 counties and districts of Wenzhou. The content of Cd was determined by inductively coupled plasma mass spectrometry based on GB 5009.268-2016. Results The detection rate of Cd was 100% in 235 samples. The Cd pollution in Portunus crab increase during 2013, 2015 to 2017. The Cd content of muscle and hepatopancreas in Portunus crab and Scylla serrata was higher than that in Eriocheir sinensis Milne-Edwards (P0.05). The distribution of Cd in Portunus crab was hepatopancreas and gonad> pectoral muscle > leg muscle, there was no significant difference of cadmium content in different parts between female and male crabs (P>0.05). Conclusion Cd was mainly concentrated in hepatopancreas, which was irrelevant to crab species, sex and individual difference. Cd content of Portunus crab and Scylla serrata exceeded the standard seriously, especially in hepatopancreas. People should pay more attention to the Cd pollution of crabs, and reduce the intake of hepatopancreas if necessary
Comprehensive characterization of ERV-K (HML-8) in the chimpanzee genome revealed less genomic activity than humans
Endogenous retroviruses (ERVs) originate from ancestral germline infections caused by exogenous retroviruses. Throughout evolution, they have become fixed within the genome of the animals into which they were integrated. As ERV elements coevolve with the host, they are normally epigenetically silenced and can become upregulated in a series of physiological and pathological processes. Generally, a detailed ERV profile in the host genome is critical for understanding the evolutionary history and functional performance of the host genome. We previously characterized and cataloged all the ERV-K subtype HML-8 loci in the human genome; however, this has not been done for the chimpanzee, the nearest living relative of humans. In this study, we aimed to catalog and characterize the integration of HML-8 in the chimpanzee genome and compare it with the integration of HML-8 in the human genome. We analyzed the integration of HML-8 and found that HML-8 pervasively invaded the chimpanzee genome. A total of 76 proviral elements were characterized on 23/24 chromosomes, including detailed elements distribution, structure, phylogeny, integration time, and their potential to regulate adjacent genes. The incomplete structure of HML-8 proviral LTRs will undoubtedly affect their activity. Moreover, the results indicated that HML-8 integration occurred before the divergence between humans and chimpanzees. Furthermore, chimpanzees include more HML-8 proviral elements (76 vs. 40) and fewer solo long terminal repeats (LTR) (0 vs. 5) than humans. These results suggested that chimpanzee genome activity is less than the human genome and that humans may have a better ability to shape and screen integrated proviral elements. Our work is informative in both an evolutionary and a functional context for ERVs
Identification of differentially expressed HERV-K(HML-2) loci in colorectal cancer
Colorectal cancer is one of the malignant tumors with the highest mortality rate in the world. Survival rates vary significantly among patients at various stages of the disease. A biomarker capable of early diagnosis is required to facilitate the early detection and treatment of colorectal cancer. Human endogenous retroviruses (HERVs) are abnormally expressed in various diseases, including cancer, and have been involved in cancer development. Real-time quantitative PCR was used to detect the transcript levels of HERV-K(HML-2) gag, pol, and env in colorectal cancer to systematically investigate the connection between HERV-K(HML-2) and colorectal cancer. The results showed that HERV-K(HML-2) transcript expression was significantly higher than healthy controls and was consistent at the population and cell levels. We also used next-generation sequencing to identify and characterize HERV-K(HML-2) loci that were differentially expressed between colorectal cancer patients and healthy individuals. The analysis revealed that these loci were concentrated in immune response signaling pathways, implying that HERV-K impacts the tumor-associated immune response. Our results indicated that HERV-K might serve as a screening tumor marker and a target for tumor immunotherapy in colorectal cancer
Sensitizing Leukemia Stem Cells to NF-κB Inhibitor Treatment in Vivo by Inactivation of Both TNF and IL-1 Signaling
We previously reported that autocrine TNF-α (TNF) is responsible for JNK pathway activation in a subset of acute myeloid leukemia (AML) patient samples, providing a survival/proliferation signaling parallel to NF-κB in AML stem cells (LSCs). In this study, we report that most TNF-expressing AML cells (LCs) also express another pro-inflammatory cytokine, IL1β, which acts in a parallel manner. TNF was produced primarily by LSCs and leukemic progenitors (LPs), whereas IL1β was mainly produced by partially differentiated leukemic blasts (LBs). IL1β also stimulates an NF-κB-independent pro-survival and proliferation signal through activation of the JNK pathway. We determined that co-inhibition of signaling stimulated by both TNF and IL1β synergizes with NF-κB inhibition in eliminating LSCs both ex vivo and in vivo. Our studies show that such treatments are most effective in M4/5 subtypes of AML
Screening of an individualized treatment strategy for an advanced gallbladder cancer using patient-derived tumor xenograft and organoid models
Gallbladder cancer is a highly aggressive malignancy with poor sensitivity to postoperative radiotherapy or chemotherapy; therefore, the development of individualized treatment strategies is paramount to improve patient outcomes. Both patient-derived tumor xenograft (PDX) and patient-derived tumor organoid (PDO) models derived from surgical specimens can better preserve the biological characteristics and heterogeneity of individual original tumors, display a unique advantage for individualized therapy and predicting clinical outcomes. In this study, PDX and PDO models of advanced gallbladder cancer were established, and the consistency of biological characteristics between them and primary patient samples was confirmed using pathological analysis and RNA-sequencing. Additionally, we tested the efficacy of chemotherapeutic drugs, targeted drugs, and immune checkpoint inhibitors using these two models. The results demonstrated that gemcitabine combined with cisplatin induced significant therapeutic effects. Furthermore, treatment with immune checkpoint inhibitors elicited promising responses in both the humanized mice and PDO immune models. Based on these results, gemcitabine combined with cisplatin was used for basic treatment, and immune checkpoint inhibitors were applied as a complementary intervention for gallbladder cancer. The patient responded well to treatment and exhibited a clearance of tumor foci. Our findings indicate that the combined use of PDO and PDX models can guide the clinical treatment course for gallbladder cancer patients to achieve individualized and effective treatment
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