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1.
Biochem Biophys Res Commun ; 557: 8-13, 2021 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-33857842

RESUMO

Precise quantification of vascular developments in Zebrafish requires continuous in-vivo 3D imaging. Here we employed a bi-directional light-sheet illumination microscope to characterize the development process of Zebrafish's intersegmental vessels. A Virtual Reality-based method was used to measure the lengths of intersegmental vessels (ISVs). The quantified growth rates of typical ISVs can be plotted, and unusual growth of some specific vessels was also observed.

2.
Philos Trans R Soc Lond B Biol Sci ; 376(1825): 20200160, 2021 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-33813888

RESUMO

Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations. Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) has also brought about a large variety of assemblers. Although these have been extensively tested on model species such as Homo sapiens and Drosophila melanogaster, such benchmarking has not been done in Mollusca, which lacks widely adopted model species. Molluscan genomes are notoriously rich in repeats and are often highly heterozygous, making their assembly challenging. Here, we benchmarked 10 assemblers based on ONT raw reads from two published molluscan genomes of differing properties, the gastropod Chrysomallon squamiferum (356.6 Mb, 1.59% heterozygosity) and the bivalve Mytilus coruscus (1593 Mb, 1.94% heterozygosity). By optimizing the assembly pipeline, we greatly improved both genomes from previously published versions. Our results suggested that 40-50X of ONT reads are sufficient for high-quality genomes, with Flye being the recommended assembler for compact and less heterozygous genomes exemplified by C. squamiferum, while NextDenovo excelled for more repetitive and heterozygous molluscan genomes exemplified by M. coruscus. A phylogenomic analysis using the two updated genomes with 32 other published high-quality lophotrochozoan genomes resulted in maximum support across all nodes, and we show that improved genome quality also leads to more complete matrices for phylogenomic inferences. Our benchmarking will ensure efficiency in future assemblies for molluscs and perhaps also for other marine phyla with few genomes available. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

3.
Philos Trans R Soc Lond B Biol Sci ; 376(1825): 20200161, 2021 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-33813889

RESUMO

The extraordinary diversity in molluscan body plans, and the genomic mechanisms that enable it, remains one of the great questions of evolution. The eight distinct living taxonomic classes of molluscs are each unambiguously monophyletic; however, significant controversy remains about the phylogenetic relationships among those eight branches. Molluscs are the second-largest animal phylum, with over 100 000 living species with broad biological, economic and medical interest. To date, only around 53 genome assemblies have been accessioned to NCBI GenBank covering only four of the eight living molluscan classes. Furthermore, the molluscan taxa where partial or whole-genome assemblies are available are often aberrantly fast evolving or recently derived lineages. Characteristic adaptations provide interesting targets for whole-genome projects, in animals like the scaly-foot snail or octopus, but without basal-branching lineages for comparison, the context of recently derived features cannot be assessed. The currently available genomes also create a non-optimal set of taxa for resolving deeper phylogenetic branches: they are a small sample representing a large group, and those that are available come primarily from a rarefied pool. Thoughtful selection of taxa for future projects should focus on the blank areas of the molluscan tree, which are ripe with opportunities to delve into peculiarities of genome evolution, and reveal the biology and evolutionary history of molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

4.
Sci Rep ; 11(1): 8700, 2021 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-33888800

RESUMO

The neurobiological literature implicates chronic stress induced decision-making deficits as a major contributor to depression and anxiety. Given that females are twice as likely to suffer from these disorders, we hypothesized the existence of sex difference in the effects of chronic stress on decision-making. Here employing a decision-making paradigm that relies on reinforcement learning of probabilistic predictive relationships, we show female volunteers with a high level of perceived stress in the past month are more likely to make suboptimal choices than males. Computational characterizations of this sex difference suggest that while under high stress, females and males differ in their weighting but not learning of the expected uncertainty in the predictive relationships. These findings provide a mechanistic account of the sex difference in decision-making under chronic stress and may have important implications for the epidemiology of sex difference in depression and anxiety.

5.
Inorg Chem ; 2021 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-33890781

RESUMO

The two acentric aluminoborates (ABOs) [M(dap)3]2{Al[B5O7(OH)3][B5O8(OH)2][B6O9(OH)2]} (M and dap represent Co(1)/Ni(2) and 1,2-diaminopropane, respectively) templated by chiral metal complexes (CMCs) have been solvothermally synthesized. The isostructural 1 and 2 crystallize in the chiral space group P21. Both feature unprecedented 2D wavelike layers built by three kinds of oxoboron (B-O) clusters ([B5O7(OH)3]2-, [B5O8(OH)2]3-, and [B6O9(OH)2]2-) and AlO4 tetrahedra. In the frameworks of 1 and 2, AlO4 and [B6O9(OH)2]2- units are strictly alternating into 1D chains. Further, [B5O8(OH)2]3- clusters link adjacent chains to form 2D wavelike layers. In addition, the [B5O7(OH)3]2- units as the hanging clusters are supported on two sides of the wavelike layers through AlO4 groups, resulting in the first example of a wavelike layer ABO composed of three kinds of B-O clusters and four types of channels. 1 and 2 display second-harmonic generation (SHG) signals about ∼1.3 and ∼0.93 times that of KH2PO4 (KDP) and belong to the class of wide-band-gap semiconductors.

6.
Brief Bioinform ; 2021 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-33834194

RESUMO

Transcriptional regulation is associated with complicated mechanisms including multiple molecular interactions and collaborative drive. Long noncoding RNAs (lncRNAs) have highly structured characteristics and play vital roles in the regulation of transcription in organisms. However, the specific contributions of conformation feature and underlying molecular mechanisms are still unclear. In the present paper, a hypothesis regarding molecular structure effect is presented, which proposes that lncRNAs fold into a complex spatial architecture and act as a skeleton to recruit transcription factors (TF) targeted binding, and which is involved in cooperative regulation. A candidate set of TF-lncRNA coregulation was constructed, and it was found that structural accessibility affected molecular binding force. In addition, transcription factor binding site (TFBS) regions of myopia-related lncRNA transcripts were disturbed, and it was discovered that base mutations affected the occurrence of significant molecular allosteric changes in important elements and variable splicing regions, mediating the onset and development of myopia. The results originated from structureomics and interactionomics and created conditions for systematic research on the mechanisms of structure-mediated TF-lncRNA coregulation in transcriptional regulation. Finally, these findings will help further the understanding of key regulatory roles of molecular allostery in cell physiological and pathological processes.

7.
Curr Eye Res ; : 1-8, 2021 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-33870816

RESUMO

Purpose: To assess the anti-neovascularization effect of a novel peptide NT/K-CFY derived from the kringle domain of neurotrypsin.Materials and Methods: Cell migration, lumen formation and cell proliferation assays were performed to determine the anti-neovascularization effect of NT/K-CFY in primary human umbilical vein endothelial cells (HUVECs). Chick chorioallantoic membrane (CAM) and oxygen-induced retinopathy (OIR) models were established to assess the anti-angiogenic role of NT/K-CFY in vivo. The retinal expression of vascular endothelial growth factor (VEGF) and pigment epithelium-derived factor (PEDF) was examined by western blot and real-time PCR in OIR model.Results: The in vitro results showed that NT/K-CFY effectively and safely decreased VEGF-induced cell migration, cell proliferation and tube formation in HUVECs. In addition, NT/K-CFY showed certain efficacy in angiogenesis inhibition in chicken embryos and oxygen-treated mouse pups. Moreover, the CFY peptide also improved retinal blood perfusion and reversed the abnormal expression of VEGF and PEDF in OIR mouse model.Conclusion: NT/K-CFY peptide strongly inhibits neovascularization in vitro and vivo. This novel peptide may become a promising therapeutic agent for ocular angiogenesis-related diseases.

8.
Food Chem ; 354: 129534, 2021 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-33752116

RESUMO

The effect of using highly unsaturated 2-monoglycerides as oleogelators on the properties of soybean oil oleogels designed to eliminate saturated and trans fatty acids was investigated in this study. We adopted a novel two-step synthesis aiming to increase the yield of the 2-monoglycerides. The optimal synthesis conditions were a substrate weight ratio of 2:1 (w/w), 10% Lipozyme 435 (w/w total reactants), and 4 h of reaction time at room temperature. Under these conditions, the 2-monoglyceride yield (40.69%) increased by 10% compared to that of the conventional synthesis route. Additionally, soybean oil oleogels prepared using 10% 2-monoglycerides with or without rice bran wax were systematically characterized by polarized light microscopy, a texture analyzer, XRD spectroscopy, and rheometry. Comparative studies indicated that a combination of rice bran wax and 2-monoglycerides had synergistic effects on gel properties. A mixture of 4% rice bran wax and 6% 2-monoglycerides was found to provide better oleogels.

9.
Artigo em Inglês | MEDLINE | ID: mdl-33656621

RESUMO

PURPOSE: The sperm DNA fragmentation index (DFI) was quantitatively measured and its relationship with age, semen quality, and infertility conditions was investigated. METHODS: Semen routine test and sperm DFI were performed in 2760 infertile male and 2354 male whose spouse experienced at least one unexplained miscarriage to analyze the correlation between sperm DNA damage, semen routine parameters, and age. RESULTS: Sperm DFI was significantly lower from patients whose wife experienced unexplained miscarriage compared to infertility males (p = 0.000). An inverse correlation between sperm DFI and sperm progressive motility was observed (rs = - 0.465, p = 0.000) and sperm DFI was positively correlated with age (rs = 0.255, p = 0.000). However, the correlation between sperm DFI and sperm concentration, semen volume, total sperm count, and motile sperm count were not proved. CONCLUSIONS: Sperm DFI is an important indicator for evaluating the quality of semen. Sperm DNA integrity testing is preferentially recommended to those who have decreased sperm progressive motility, especially older men. An integrative analysis of sperm DFI, sperm progressive motility, age, and infertility conditions can provide a more comprehensive assessment of male fertility.

10.
Dysphagia ; 2021 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-33661332

RESUMO

Dysphagia is one of the most common complaints after anterior cervical spine surgery. The Bazaz scale, the Dysphagia Short Questionnaire (DSQ), and the Hospital for Special Surgery-Dysphagia and Dysphonia Inventory (HSS-DDI) were patient-reported outcome measures assessing the patients' perceptions of their swallowing functions after surgery. This prospective diagnostic test study aimed to compare these surveys' psychometric properties in the Chinese population. We evaluated 150 consecutive patients after anterior cervical spine surgery with the Bazaz scale, DSQ, HSS-DDI, and M.D. Anderson Dysphagia Inventory (MDADI). The reliability and validity of the Bazaz scale, DSQ, and HSS-DDI were compared. Receiver operating characteristic (ROC) curves of the DSQ, Bazaz scale, and HSS-DDI were constructed using the MDADI as a reference criterion. Their areas under the curve (AUCs) were further analyzed. In total, 132 participants completed all of the surveys. The results showed that all surveys were significantly correlated with each other. The HSS-DDI and HSS-Dysphagia subscale showed near-perfect reliability (Cronbach α = 0.969 and 0.957, respectively). ROC curves showed both HSS-DDI and HSS-Dysphagia subscale had greater accuracy (AUCs > 0.9) in detecting mild dysphagia and moderate/severe dysphagia. The HSS-Dysphagia subscale achieved higher accuracy in assessing the dysphagia symptoms after anterior cervical spine surgery. The Bazaz scale was considered less accurate than other scales. Our results provided guidance for selecting the appropriate measuring tool during clinical and research practices.

11.
BMC Surg ; 21(1): 106, 2021 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-33648467

RESUMO

BACKGROUND: Early onset scoliosis (EOS) may cause malnutrition in affected patients. Growing-rod treatment has been an effective protocol for treating EOS. The objective of this study is to demonstrate whether growing-rod treatment improves nutritional status of EOS patients. METHODS: Fifty-two EOS patients who had dual growing-rod surgery was enrolled. The minimum follow-up was 3-years. Their body weights were normalized based on the data of two National Population Census of China. Z-scores were used to indicate the standard deviation from the median body weight-for-age. RESULTS: The median follow-up time was 6 years. Preoperatively, the prevalence of malnutrition (Z < - 2) was 21.2%, and reduced to 9.6% at the end of the follow-up. Preoperatively, the average Z-score was - 0.94, and it increased to - 0.65 at the latest follow-up (p < 0.05). Patients with preoperative Z-score below - 1 had more significant increase of Z-scores (- 2.15 vs - 1.26, p < 0.001). A significant negative correlation between the change of Z-score and the preoperative Z-score (correlation coefficient - 0.65, p < 0.001). CONCLUSIONS: The growing rod surgery and lengthening procedures significantly improves the nutrition status of EOS patients. The body weight gains are more significant in patients with lower body weights.


Assuntos
Estado Nutricional , Escoliose , China , Seguimentos , Humanos , Escoliose/cirurgia , Resultado do Tratamento
12.
Genomics ; 2021 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-33711452

RESUMO

Ancestry informative markers have extensive uses and advantages in inferring ancestral origins and estimating ancestral genetic information components of admixed populations. With the characteristics of highly cultural exchange and the admixed genetic structure of the Kyrgyz group, it is essential to enrich the genetic data of the Kyrgyz group. In this study, we used a self-developed ancestry informative marker-deletion/insertion polymorphic (AIM-DIP) panel to explore ancestral components of the Chinese Kyrgyz group and population genetic relationships between the Kyrgyz group and reference populations. Results showed that all AIM-DIP loci were conformed to Hardy-Weinberg equilibrium. There were 36 AIM-DIP loci with a significant contribution to genetic information inference. Multiple statistical analyses revealed that the Chinese Kyrgyz group had a closer genetic relationship with the Chinese Uyghur group and the ancestral components of the Kyrgyz group, being mostly composed of genetic components of European and East Asian populations, which were more similar to the Chinese Uyghur group.

13.
Int J Legal Med ; 2021 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-33754178

RESUMO

Evaluating the short tandem repeat (STR) in the field is important for the timely identification of a suspect. Several lines showed that the RapidHIT® ID system is reliable for DNA genotyping with buccal swabs and naked DNA. However, the application of this approach with blood samples has been poorly investigated. Because blood samples are among the most common forensic samples in our laboratory, further studies should be conducted. Here, we assessed the analytical performance of 19 STR loci with a newly developed RapidINTEL (RI) Sample Cartridge Kit by using the blood samples with known genotypes. Several commonly used substrates were included in the sensitivity study, and FTA cards proved to be the most promising sample carrier for blood storage and later identification. There was superior sensitivity and specificity with a 100% concordance rate for 0.5 µL of blood or 7 ng of genomic DNA. The performance for blood samples was comparable with that for the standard protocol. High success rate (90.57%) and high-concordance (100%) genotyping were automatically achieved over a wide range of operating conditions except for TH01. No contamination was observed throughout the study. Hematin, indigo, and humic acid had limited influence on the instrument system, while urea and melanin dramatically affected the genotyping results. Generally, the newly developed RI sample cartridge provided an alternative method for the STR genotyping of single-source blood samples over a wide range of operating conditions.

14.
Oncol Rep ; 45(5)2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33760175

RESUMO

Hypoxia is a common phenomenon during tumorigenesis and tumour development. In recent years, studies have found that hypoxia­inducible factor (HIF)­2α, also referred to as endothelial PAS domain protein­1, plays an important role in tumours. HIF­2α is an important oncogene and a critical prognostic indicator in non­small cell lung cancer. However, no unified conclusion can be drawn concerning HIF­2α and small cell lung cancer, since few studies to date have focused on their association. An increasing number of studies have confirmed that HIF­2α is involved in tumorigenesis, cell proliferation, angiogenesis, metastasis, drug resistance and radiotherapy failure in lung cancer. Of note, HIF­2α plays a crucial role in lung cancer to maintain cancer cell stemness. Based on the importance of HIF­2α in lung cancer, HIF­2α­targeted therapy has been attracting increasing attention. Although this strategy currently appears to be promising in vitro, it has never been assessed as a therapy for lung cancer. The aim of the present review was to summarize the contribution of HIF­2α to various aspects of lung cancer, as well as its potential as targeted therapy.

15.
JACC Cardiovasc Interv ; 14(3): 247-257, 2021 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-33541535

RESUMO

OBJECTIVES: The aim of this study was to explore the difference in target vessel failure (TVF) 3 years after intravascular ultrasound (IVUS) guidance versus angiographic guidance among all comers undergoing second-generation drug-eluting stent (DES) implantation. BACKGROUND: The multicenter randomized ULTIMATE (Intravascular Ultrasound Guided Drug Eluting Stents Implantation in "All-Comers" Coronary Lesions) trial showed a lower incidence of 1-year TVF after IVUS-guided DES implantation among all comers compared with angiographic guidance. However, the 3-year clinical outcomes of the ULTIMATE trial remain unknown. METHODS: A total of 1,448 all comers undergoing DES implantation who were randomly assigned to either IVUS guidance or angiographic guidance in the ULTIMATE trial were followed for 3 years. The primary endpoint was the risk for TVF at 3 years. The safety endpoint was definite or probable stent thrombosis (ST). RESULTS: At 3 years, TVF occurred in 47 patients (6.6%) in the IVUS-guided group and in 76 patients (10.7%) in the angiography-guided group (p = 0.01), driven mainly by the decrease in clinically driven target vessel revascularization (4.5% vs. 6.9%; p = 0.05). The rate of definite or probable ST was 0.1% in the IVUS-guided group and 1.1% in the angiography-guided group (p = 0.02). Notably, the IVUS-defined optimal procedure was associated with a significant reduction in 3-year TVF relative to that with the suboptimal procedure. CONCLUSIONS: IVUS-guided DES implantation was associated with significantly lower rates of TVF and ST during 3-year follow-up among all comers, particularly those who underwent the IVUS-defined optimal procedure compared with those with angiographic guidance. (Intravascular Ultrasound Guided Drug Eluting Stents Implantation in "All-Comers" Coronary Lesions; NCT02215915).

16.
Poult Sci ; 100(2): 461-466, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33518097

RESUMO

Feed consumption represents a major cost in poultry production and improving feed efficiency is one of the important goals in breeding strategies. The present study aimed to analyze the relationship between feed efficiency and relevant traits and find the proper selection method for improving feed efficiency by using the Northeast Agricultural University High and Low Fat broiler lines that were divergently selected for abdominal fat content. A total of 899 birds were used to measure the feed intake (FI), abdominal fat weight (AFW), and body weight traits. The abdominal fat percentage (AFP), feed conversion ratio (FCR), and the residual feed intake (RFI) were calculated for each individual broiler. The differences in the AFW, AFP, and in traits relevant to feed efficiency, such as FCR and RFI, between the fat line and the lean line were analyzed, and the genetic parameters were estimated for AFW, AFP, and feed efficiency relevant traits. The results showed that AFW, AFP, body weight gain (BWG), FI, FCR, and RFI were significantly higher in the fat line compared with the lean line. The heritability of FI, BWG, FCR, RFI, AFW, and AFP were 0.45, 0.28, 0.36, 0.38, 0.33, and 0.30, respectively. Both FCR and RFI showed high positive genetic correlations with FI, AFW, and AFP and relatively low, negative genetic correlations with BWG. The RFI showed much higher positive genetic correlation with the abdominal fat traits than FCR. In addition, the FCR showed negative genetic correlation with body weight of 4 wk (BW4) and 7 wk (BW7), whereas RFI showed positive genetic correlation with BW4 and BW7. The results showed that both RFI and FCR could be used for improving feed efficiency. When selecting against RFI, the AFP could be significantly reduced, and by selecting against FCR, the body weight could be improved simultaneously.


Assuntos
Gordura Abdominal/crescimento & desenvolvimento , Galinhas/genética , Ingestão de Alimentos/fisiologia , Ganho de Peso , Ração Animal/análise , Animais , Peso Corporal , Galinhas/crescimento & desenvolvimento , Ingestão de Alimentos/genética , Fenótipo
17.
Biomed Pharmacother ; 137: 111308, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33556877

RESUMO

BACKGROUND AND OBJECTIVE: Doxorubicin (DOX) is an anthracycline antitumor antibiotic widely utilized in treating various tumors. Nevertheless, the toxicity of DOX toward normal cells limits its applicability, with nephrotoxicity considered a major dose-limiting adverse effect. Apigenin (APG), a flavonoid widely distributed in natural plants, has been reported to have antioxidant, anti-inflammatory, and mild tumor-suppressive properties. In this study, we investigated the role of APG in DOX-induced nephrotoxicity and chemotherapeutic efficacy. METHODS: Male BALB/c mice were administered DOX (11.5 mg/kg) via the tail vein to establish the DOX nephropathy model. After treatment with or without APG (125, 250, and 500 mg/kg) for two weeks, urine, serum, and tissue samples were collected to evaluate proteinuria, serum albumin, serum creatinine (Scr), blood urea nitrogen (BUN), superoxide dismutase (SOD) activity, malondialdehyde (MDA), glutathione (GSH), and pathological changes. Rat renal tubular epithelial cells (NRK52E), murine podocyte cells (MPC5), and murine breast cancer cells (4T1) were utilized to verify the effect of APG on DOX-induced cell injury. An MTT assay was employed to analyze cell viability. Apoptosis was evaluated using a colorimetric TUNEL staining and cleaved caspase-3 protein analysis by western blotting. A reactive oxygen species (ROS)/superoxide (O2-) fluorescence probe was employed to determine oxidative injury. Western blotting was used to analyze nephrin, α-smooth muscle actin (α-SMA), collagen I (Col1), fibronectin (FN), and SOD2 expression. The mRNA levels of tumor necrosis factor-α (TNF-α), interleukin-18 (IL-18), IL-6, NACHT, LRR, PYD domain-containing protein 3 (NLRP3), caspase-1, and IL-1ß were tested by reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: APG ameliorated DOX-elicited renal injuries in both the glomeruli and tubules. The DOX + APG groups had much lower tissue MDA, IL-6, TNF-α, NLRP3, caspase-1, and IL-1ß levels and generation of intracellular ROS, but significantly higher SOD activity and GSH levels compared to those of the DOX group. Additionally, APG attenuated DOX-induced morphological changes, loss of cellular viability, and apoptosis in NRK-52E and MPC-5 cells, but not in 4T1 cells. CONCLUSION: APG has a protective role against DOX-induced nephrotoxicity, without weakening DOX cytotoxicity in malignant tumors. Thus, APG may serve as a potential protective agent against renal injury and inflammatory diseases and may be a promising candidate to attenuate renal toxicity in cancer patients treated with DOX.

18.
Genes (Basel) ; 12(2)2021 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-33572856

RESUMO

A growing number of studies have shown immunotherapy to be a promising treatment strategy for several types of cancer. Short tandem repeats (STRs) have been proven to be alternative markers for the evaluation of hypermutability in gastrointestinal (GI) cancers. However, the status of STRs and microsatellite instability (MSI) in other tumors have not yet been investigated. To further compare STR and MSI alterations in different tumors, a total of 407 paired DNAs were analyzed from the following eight tumor types: breast cancer (BC), hepatocellular cancer (HCC), pancreatic cancer (PC), colorectal cancer (CRC), gastric cancer (GC), lung cancer (LC), esophageal cancer (EC), and renal cell cancer (RCC). The STR alteration frequencies varied in different tumors as expected. Interestingly, none of the patients possessed MSI-low (MSI-L) or MSI-high (MSI-H), except for the GI patients. The highest STR alteration was detected in EC (77.78%), followed by CRC (69.77%), HCC (63.33%), GC (54.55%), LC (48.00%), RCC (40.91%), BC (36.11%), and PC (25.71%). The potential cutoff for hypermutability was predicted using the published objective response rate (ORR), and the cutoff of LC and HCC was the same as that of GI cancers (26.32%). The cutoffs of 31.58% and 10.53% should be selected for BC and RCC, respectively. In summary, we compared MSI and STR status in eight tumor types, and predicted the potential threshold for hypermutability of BC, HCC, CRC, GC, LC, EC, and RCC.

19.
Genes (Basel) ; 12(2)2021 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-33572950

RESUMO

In recent years, trafficking and abuse of hallucinogenic mushrooms have become a serious social problem. It is therefore imperative to identify hallucinogenic mushrooms of the genus Psilocybe for national drug control legislation. An internal transcribed spacer (ITS) is a DNA barcoding tool utilized for species identification. Many methods have been used to discriminate the ITS region, but they are often limited by having a low resolution. In this study, we sought to analyze the ITS and its fragments, ITS1 and ITS2, by using high-resolution melting (HRM) analysis, which is a rapid and sensitive method for evaluating sequence variation within PCR amplicons. The ITS HRM assay was tested for specificity, reproducibility, sensitivity, and the capacity to analyze mixture samples. It was shown that the melting temperatures of the ITS, ITS1, and ITS2 of Psilocybe cubensis were 83.72 ± 0.01, 80.98 ± 0.06, and 83.46 ± 0.08 °C, and for other species, we also obtained species-specific results. Finally, we performed ITS sequencing to validate the presumptive taxonomic identity of our samples, and the sequencing output significantly supported our HRM data. Taken together, these results indicate that the HRM method can quickly distinguish the DNA barcoding of Psilocybe cubensis and other fungi, which can be utilized for drug trafficking cases and forensic science.

20.
Nat Commun ; 12(1): 1165, 2021 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-33608555

RESUMO

Animals endemic to deep-sea hydrothermal vents often form obligatory symbioses with bacteria, maintained by intricate host-symbiont interactions. Most genomic studies on holobionts have not investigated both sides to similar depths. Here, we report dual symbiosis in the peltospirid snail Gigantopelta aegis with two gammaproteobacterial endosymbionts: a sulfur oxidiser and a methane oxidiser. We assemble high-quality genomes for all three parties, including a chromosome-level host genome. Hologenomic analyses reveal mutualism with nutritional complementarity and metabolic co-dependency, highly versatile in transporting and using chemical energy. Gigantopelta aegis likely remodels its immune system to facilitate dual symbiosis. Comparisons with Chrysomallon squamiferum, a confamilial snail with a single sulfur-oxidising gammaproteobacterial endosymbiont, show that their sulfur-oxidising endosymbionts are phylogenetically distant. This is consistent with previous findings that they evolved endosymbiosis convergently. Notably, the two sulfur-oxidisers share the same capabilities in biosynthesising nutrients lacking in the host genomes, potentially a key criterion in symbiont selection.


Assuntos
Bactérias/genética , Fontes Hidrotermais/microbiologia , Caramujos/genética , Caramujos/microbiologia , Simbiose/genética , Animais , Bactérias/metabolismo , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Expressão Gênica , Genoma Bacteriano , Genômica , Filogenia , Caramujos/metabolismo , Enxofre/metabolismo , Simbiose/fisiologia , Transcriptoma
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