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1.
Cell ; 182(1): 162-176.e13, 2020 07 09.
Article in English | MEDLINE | ID: mdl-32553274

ABSTRACT

Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.


Subject(s)
Genome, Plant , Glycine max/growth & development , Glycine max/genetics , Base Sequence , Chromosomes, Plant/genetics , Domestication , Ecotype , Gene Duplication , Gene Expression Regulation, Plant , Gene Fusion , Geography , Molecular Sequence Annotation , Phylogeny , Polymorphism, Single Nucleotide/genetics , Polyploidy
2.
Nature ; 630(8018): 847-852, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38839959

ABSTRACT

The recent discovery of superconductivity in La3Ni2O7-δ under high pressure with a transition temperature around 80 K (ref. 1) has sparked extensive experimental2-6 and theoretical efforts7-12. Several key questions regarding the pairing mechanism remain to be answered, such as the most relevant atomic orbitals and the role of atomic deficiencies. Here we develop a new, energy-filtered, multislice electron ptychography technique, assisted by electron energy-loss spectroscopy, to address these critical issues. Oxygen vacancies are directly visualized and are found to primarily occupy the inner apical sites, which have been proposed to be crucial to superconductivity13,14. We precisely determine the nanoscale stoichiometry and its correlation to the oxygen K-edge spectra, which reveals a significant inhomogeneity in the oxygen content and electronic structure within the sample. The spectroscopic results also reveal that stoichiometric La3Ni2O7 has strong charge-transfer characteristics, with holes that are self-doped from Ni sites into O sites. The ligand holes mainly reside on the inner apical O and the planar O, whereas the density on the outer apical O is negligible. As the concentration of O vacancies increases, ligand holes on both sites are simultaneously annihilated. These observations will assist in further development and understanding of superconducting nickelate materials. Our imaging technique for quantifying atomic deficiencies can also be widely applied in materials science and condensed-matter physics.

3.
Nucleic Acids Res ; 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38686791

ABSTRACT

In plant chloroplasts, certain ribosomal proteins (RPs) and ribosome biogenesis factors (RBFs) are present in nucleoids, implying an association between nucleoids and ribosome biogenesis. In Arabidopsis, the YqeH-type GTPase Brassinazole-Insensitive Pale Green2 (BPG2) is a chloroplast nucleoid-associated RBF. Here, we investigated the relationship between nucleoids and BPG2-involved ribosome biogenesis steps by exploring how BPG2 targets ribosomes. Our findings demonstrate that BPG2 interacts with an essential plastid RP, uS10c, in chloroplast nucleoids in a ribosomal RNA (rRNA)-independent manner. We also discovered that uS10c is a haploinsufficient gene, as the heterozygous deletion of this gene leads to variegated shoots and chlorophyll aggregation. uS10c is integrated into 30S ribosomal particles when rRNA is relatively exposed and also exists in polysome fractions. In contrast, BPG2 exclusively associates with 30S ribosomal particles. Notably, the interaction between BPG2 and 30S particles is influenced by the absence of uS10c, resulting in BPG2 diffusing in chloroplasts instead of targeting nucleoids. Further, our results reveal that the loss of BPG2 function and the heterozygous deletion of uS10c impair the processing of 16S and 23S-4.5S rRNAs, reduce plastid protein accumulation, and trigger the plastid signaling response. Together, these findings indicate that the uS10c-BPG2 module mediates ribosome biogenesis in chloroplast nucleoids.

4.
EMBO J ; 39(24): e105896, 2020 12 15.
Article in English | MEDLINE | ID: mdl-33140861

ABSTRACT

COVID-19 is characterized by dysregulated immune responses, metabolic dysfunction and adverse effects on the function of multiple organs. To understand host responses to COVID-19 pathophysiology, we combined transcriptomics, proteomics, and metabolomics to identify molecular markers in peripheral blood and plasma samples of 66 COVID-19-infected patients experiencing a range of disease severities and 17 healthy controls. A large number of expressed genes, proteins, metabolites, and extracellular RNAs (exRNAs) exhibit strong associations with various clinical parameters. Multiple sets of tissue-specific proteins and exRNAs varied significantly in both mild and severe patients suggesting a potential impact on tissue function. Chronic activation of neutrophils, IFN-I signaling, and a high level of inflammatory cytokines were observed in patients with severe disease progression. In contrast, COVID-19-infected patients experiencing milder disease symptoms showed robust T-cell responses. Finally, we identified genes, proteins, and exRNAs as potential biomarkers that might assist in predicting the prognosis of SARS-CoV-2 infection. These data refine our understanding of the pathophysiology and clinical progress of COVID-19.


Subject(s)
COVID-19/blood , COVID-19/pathology , Biomarkers/blood , COVID-19/immunology , COVID-19/virology , Female , Genomics/methods , Humans , Lipoproteins/metabolism , Male , Metabolomics/methods , SARS-CoV-2/physiology , Severity of Illness Index , Viral Load
5.
Small ; 20(12): e2306928, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37953415

ABSTRACT

The development of lithium-sulfur batteries is seriously hindered by the shuttle effect of lithium polysulfides (LiPSs) and the low electrical conductivity of sulfur. To solve these problems, efficient catalysts can be used to improve the conversion rate of LiPSs and the conductivity of sulfur cathode. Herein, annealed melamine foam supported MoSe2 (NCF@MoSe2) is used as interlayer and the MoSe2/MoP heterojunction obtained by phosphating MoSe2 is further used as the catalyst material for metal fusion with a sulfur element. The interlayer can not only improve the electrical conductivity and effectively adsorb and catalyze LiPSs, but more importantly, the MoSe2/MoP heterojunction can also effectively adsorb and catalyze LiPSs, so that the batteries have a dual inhibition shuttling effect strategy. Furthermore, the rapid anchor-diffusion transition of LiPSs, and the suppression of shuttling effects by catalyst materials are elucidated using theoretical calculations and in situ Raman spectroscopy. The two-step catalytic strategy exhibits a high reversibility of 983 mAh g-1 after 200 cycles at 0.5 C and a high-rate capacity of 889 mAh g-1 at 5 C. This work provides a feasible solution for the rational design of interlayer and heterojunction materials and is also conducive to the development of more advanced Li-S batteries.

6.
Opt Express ; 32(5): 6887-6902, 2024 Feb 26.
Article in English | MEDLINE | ID: mdl-38439384

ABSTRACT

Laser speckle contrast imaging (LSCI) has gained significant attention in the biomedical field for its ability to map the spatio-temporal dynamics of blood perfusion in vivo. However, LSCI faces difficulties in accurately resolving blood perfusion in microvessels. Although the transmissive detecting geometry can improve the spatial resolution of tissue imaging, ballistic photons directly transmitting forward through tissue without scattering will cause misestimating in the flow speed by LSCI because of the lack of a quantitative theoretical model of transmissvie LSCI. Here, we develop a model of temporal LSCI which accounts for the effect of nonscattered light on estimating decorrelation time. Based on this model, we further propose a dual-exposure temporal laser speckle imaging method (dEtLSCI) to correct the overestimation of background speed when performing traditional transmissive LSCI, and reconstruct microvascular angiography using the scattered component extracted from total transmitted light. Experimental results demonstrated that our new method opens an opportunity for LSCI to simultaneously resolve the blood vessels morphology and blood flow speed at microvascular level in various contexts, ranging from the drug-induced vascular response to angiogenesis and the blood perfusion monitoring during tumor growth.


Subject(s)
Angiography , Laser Speckle Contrast Imaging , Microvessels/diagnostic imaging , Perfusion , Lasers
7.
Opt Lett ; 49(13): 3600-3603, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38950219

ABSTRACT

Visualizing a 3D blood flow velocity field through noninvasive imaging is crucial for analyzing hemodynamic mechanisms in areas prone to disorders. However, traditional correlation-based optical coherence tomography (OCT) velocimetry techniques have a maximum measurable flow velocity depending on the A-line rate. We presented the ergodic speckle contrast OCT (ESCOCT) to break the bottleneck in measuring the rapid blood flow velocity. It achieved a measurement of blood flow velocity ranging from 9.5 to 280 mm/s using a 100 kHz swept-source (SS) OCT based on 100 A-repeats scanning mode. Addressing the non-ergodic problem of temporal OCT signals by integrating more consecutive A-scans, ESCOCT can enable the estimation for lower velocity flows by increasing A-repeats. ESCOCT provided a wide dynamic range with no upper limit on measuring blood flow velocity with an adequate signal-to-noise ratio and improved the sensitivity and accuracy of the hemodynamic assessment.


Subject(s)
Tomography, Optical Coherence , Tomography, Optical Coherence/methods , Blood Flow Velocity/physiology , Rheology/methods , Humans , Signal-To-Noise Ratio
8.
FASEB J ; 37(6): e22942, 2023 06.
Article in English | MEDLINE | ID: mdl-37178006

ABSTRACT

Extracellular vesicles (EVs) possess great potential in the modulation of cardiovascular diseases. Our current work intended to assay the clinical significance of endothelial cell (EC)-derived EVs in atherosclerosis (AS). Expression of HIF1A-AS2, miR-455-5p, and ESRRG in plasma from AS patients and mice and EVs from ox-LDL-treated ECs was measured. Interactions among HIF1A-AS2, miR-455-5p, ESRRG, and NLRP3 were analyzed. Next, EVs were co-cultured with ECs, and ectopic expression and depletion experimentations of HIF1A-AS2, miR-455-5p, ESRRG, and/or NLRP3 were carried out to assay their roles in pyroptosis and inflammation of ECs in AS. At last, the effects of HIF1A-AS2 shuttled by EC-derived EVs on EC pyroptosis and vascular inflammation in AS were verified in vivo. HIF1A-AS2 and ESRRG were highly expressed, while miR-455-5p was poorly expressed in AS. HIF1A-AS2 could sponge miR-455-5p to elevate the expression of ESRRG and NLRP3. Both in vitro and in vivo experiments revealed that ECs-derived EVs carrying HIF1A-AS2 induced the pyroptosis and vascular inflammation of ECs to promote the progression of AS by sponging miR-455-5p via ESRRG/NLRP3. HIF1A-AS2 shuttled by ECs-derived EVs can accelerate the progression of AS by downregulating miR-455-5p and upregulating ESRRG and NLRP3.


Subject(s)
Atherosclerosis , Extracellular Vesicles , MicroRNAs , Mice , Animals , MicroRNAs/metabolism , NLR Family, Pyrin Domain-Containing 3 Protein/genetics , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Pyroptosis , Endothelial Cells/metabolism , Inflammation/metabolism , Atherosclerosis/metabolism , Extracellular Vesicles/metabolism
9.
Theor Appl Genet ; 137(5): 102, 2024 Apr 12.
Article in English | MEDLINE | ID: mdl-38607439

ABSTRACT

KEY MESSAGE: A total of 389 and 344 QTLs were identified by GWAS and QTL mapping explaining accumulatively 32.2-65.0% and 23.7-63.4% of phenotypic variation for 14 shoot-borne root traits using more than 1300 individuals across multiple field trails. Efficient nutrient and water acquisition from soils depends on the root system architecture (RSA). However, the genetic determinants underlying RSA in maize remain largely unexplored. In this study, we conducted a comprehensive genetic analysis for 14 shoot-borne root traits using 513 inbred lines and 800 individuals from four recombinant inbred line (RIL) populations at the mature stage across multiple field trails. Our analysis revealed substantial phenotypic variation for these 14 root traits, with a total of 389 and 344 QTLs identified through genome-wide association analysis (GWAS) and linkage analysis, respectively. These QTLs collectively explained 32.2-65.0% and 23.7-63.4% of the trait variation within each population. Several a priori candidate genes involved in auxin and cytokinin signaling pathways, such as IAA26, ARF2, LBD37 and CKX3, were found to co-localize with these loci. In addition, a total of 69 transcription factors (TFs) from 27 TF families (MYB, NAC, bZIP, bHLH and WRKY) were found for shoot-borne root traits. A total of 19 genes including PIN3, LBD15, IAA32, IAA38 and ARR12 and 19 GWAS signals were overlapped with selective sweeps. Further, significant additive effects were found for root traits, and pyramiding the favorable alleles could enhance maize root development. These findings could contribute to understand the genetic basis of root development and evolution, and provided an important genetic resource for the genetic improvement of root traits in maize.


Subject(s)
Genome-Wide Association Study , Zea mays , Humans , Zea mays/genetics , Genomics , Chromosome Mapping , Alleles
10.
Org Biomol Chem ; 22(17): 3420-3424, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38619101

ABSTRACT

Thiols and thioesters play crucial roles in pharmaceuticals, biology, and material science as essential organosulfur compounds. Leveraging readily available and cost-effective inert alkanes through direct thioetherification holds promise for yielding high-value-added products. Herein, we present a photoinduced strategy for sulfur-containing modification of inert alkanes utilizing decatungstate as hydrogen atom transfer reagent, offering a straightforward and practical approach for synthesizing thioethers and thioesters.

11.
BMC Infect Dis ; 24(1): 501, 2024 May 17.
Article in English | MEDLINE | ID: mdl-38760687

ABSTRACT

BACKGROUND: The study aims were to evaluate the species distribution and antimicrobial resistance profile of Gram-negative pathogens isolated from specimens of intra-abdominal infections (IAI), urinary tract infections (UTI), respiratory tract infections (RTI), and blood stream infections (BSI) in emergency departments (EDs) in China. METHODS: From 2016 to 2019, 656 isolates were collected from 18 hospitals across China. Minimum inhibitory concentrations were determined by CLSI broth microdilution and interpreted according to CLSI M100 (2021) guidelines. In addition, organ-specific weighted incidence antibiograms (OSWIAs) were constructed. RESULTS: Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) were the most common pathogens isolated from BSI, IAI and UTI, accounting for 80% of the Gram-negative clinical isolates, while Pseudomonas aeruginosa (P. aeruginosa) was mainly isolated from RTI. E. coli showed < 10% resistance rates to amikacin, colistin, ertapenem, imipenem, meropenem and piperacillin/tazobactam. K. pneumoniae exhibited low resistance rates only to colistin (6.4%) and amikacin (17.5%) with resistance rates of 25-29% to carbapenems. P. aeruginosa exhibited low resistance rates only to amikacin (13.4%), colistin (11.6%), and tobramycin (10.8%) with over 30% resistance to all traditional antipseudomonal antimicrobials including ceftazidime, cefepime, carbapenems and levofloxacin. OSWIAs were different at different infection sites. Among them, the susceptibility of RTI to conventional antibiotics was lower than for IAI, UTI or BSI. CONCLUSIONS: Gram-negative bacteria collected from Chinese EDs exhibited high resistance to commonly used antibiotics. Susceptibilities were organ specific for different infection sites, knowledge which will be useful for guiding empirical therapies in the clinic.


Subject(s)
Anti-Bacterial Agents , Emergency Service, Hospital , Gram-Negative Bacteria , Gram-Negative Bacterial Infections , Microbial Sensitivity Tests , Humans , China/epidemiology , Anti-Bacterial Agents/pharmacology , Gram-Negative Bacteria/drug effects , Gram-Negative Bacteria/isolation & purification , Emergency Service, Hospital/statistics & numerical data , Gram-Negative Bacterial Infections/microbiology , Gram-Negative Bacterial Infections/epidemiology , Urinary Tract Infections/microbiology , Urinary Tract Infections/epidemiology , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/epidemiology , Intraabdominal Infections/microbiology , Intraabdominal Infections/epidemiology , Drug Resistance, Bacterial , Female , Male
12.
Bioorg Chem ; 144: 107117, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38266324

ABSTRACT

The scope of bioengineering is expanding from the design of single strain to the microbial communities, allowing for the division-of-labor in synthesizing the multi-protein systems. Predicting the composition of the final product during the biomanufacturing process, however, can be difficult. Consortia-based manufacturing has the potential to boost production efficiency, but this benefit primarily holds in the upstream. The current format of downstream process heavily relies on the centralized facility, and is not economical and flexible to address the demands in small-scale. Here, we present a concise and manageable platform to enable the multi-protein system assembly. We engineer a self-lysis microbial consortium, where each strain lyses autonomously at high densities and produces a single protein component. The product fraction can be precisely tuned by varying the inoculation ratio. Utilizing this platform, we assemble a classical 34-component PURE (protein synthesis using recombinant elements) system. We have further optimized the downstream process of the biomanufacturing by incorporating the porous structure of polymeric materials. The encapsulated autolysis consortium can produce and release the proteins while maintaining the cell factories enclosed in the materials by exporting the multi-protein system for collection. Our research provides a novel approach to the flexible and controllable production of multi-protein systems, opening up new possibilities for pathway assembly and portable biomanufacturing.


Subject(s)
Bioengineering , Microbial Consortia , Proteins/chemistry
13.
J Chem Phys ; 160(2)2024 Jan 14.
Article in English | MEDLINE | ID: mdl-38189619

ABSTRACT

We investigate the "roughness" of the energy landscape of a system that diffuses in a heterogeneous medium with a random position-dependent friction coefficient α(x). This random friction acting on the system stems from spatial inhomogeneity in the surrounding medium and is modeled using the generalized Caldira-Leggett model. For a weakly disordered medium exhibiting a Gaussian random diffusivity D(x) = kBT/α(x) characterized by its average value ⟨D(x)⟩ and a pair-correlation function ⟨D(x1)D(x2)⟩, we find that the renormalized intrinsic diffusion coefficient is lower than the average one due to the fluctuations in diffusivity. The induced weak internal friction leads to increased roughness in the energy landscape. When applying this idea to diffusive motion in liquid water, the dissociation energy for a hydrogen bond gradually approaches experimental findings as fluctuation parameters increase. Conversely, for a strongly disordered medium (i.e., ultrafast-folding proteins), the energy landscape ranges from a few to a few kcal/mol, depending on the strength of the disorder. By fitting protein folding dynamics to the escape process from a metastable potential, the decreased escape rate conceptualizes the role of strong internal friction. Studying the energy landscape in complex systems is helpful because it has implications for the dynamics of biological, soft, and active matter systems.

14.
Mar Drugs ; 22(5)2024 Apr 29.
Article in English | MEDLINE | ID: mdl-38786596

ABSTRACT

The escalation of jellyfish stings has drawn attention to severe skin reactions, underscoring the necessity for novel treatments. This investigation assesses the potential of hydroxybenzoic acid derivatives, specifically protocatechuic acid (PCA) and gentisic acid (DHB), for alleviating Nemopilema nomurai Nematocyst Venom (NnNV)-induced injuries. By employing an in vivo mouse model, the study delves into the therapeutic efficacy of these compounds. Through a combination of ELISA and Western blot analyses, histological examinations, and molecular assays, the study scrutinizes the inflammatory response, assesses skin damage and repair mechanisms, and investigates the compounds' ability to counteract venom effects. Our findings indicate that PCA and DHB significantly mitigate inflammation by modulating critical cytokines and pathways, altering collagen ratios through topical application, and enhancing VEGF and bFGF levels. Furthermore, both compounds demonstrate potential in neutralizing NnNV toxicity by inhibiting metalloproteinases and phospholipase-A2, showcasing the viability of small-molecule compounds in managing toxin-induced injuries.


Subject(s)
Cnidarian Venoms , Hydroxybenzoates , Skin , Animals , Hydroxybenzoates/pharmacology , Mice , Cnidarian Venoms/pharmacology , Skin/drug effects , Skin/pathology , Skin/metabolism , Gentisates/pharmacology , Nematocyst/drug effects , Disease Models, Animal , Cytokines/metabolism
15.
J Med Internet Res ; 26: e54107, 2024 Mar 08.
Article in English | MEDLINE | ID: mdl-38457223

ABSTRACT

BACKGROUND: Younger generations actively use social media to access health information. However, research shows that they also avoid obtaining health information online at times when confronted with uncertainty. OBJECTIVE: This study aims to examine the phenomenon of health information avoidance among Generation Z, a representative cohort of active web users in this era. METHODS: Drawing on the planned risk information avoidance model, we adopted a qualitative approach to explore the factors related to information avoidance within the context of health and risk communication. The researchers recruited 38 participants aged 16 to 25 years for the focus group discussion sessions. RESULTS: In this study, we sought to perform a deductive qualitative analysis of the focus group interview content with open, focused, and theoretical coding. Our findings support several key components of the planned risk information avoidance model while highlighting the underlying influence of cognition on emotions. Specifically, socioculturally, group identity and social norms among peers lead some to avoid health information. Cognitively, mixed levels of risk perception, conflicting values, information overload, and low credibility of information sources elicited their information avoidance behaviors. Affectively, negative emotions such as anxiety, frustration, and the desire to stay positive contributed to avoidance. CONCLUSIONS: This study has implications for understanding young users' information avoidance behaviors in both academia and practice.


Subject(s)
Health Behavior , Information Avoidance , Humans , Focus Groups , Communication
16.
Arthroscopy ; 40(2): 553-566, 2024 02.
Article in English | MEDLINE | ID: mdl-37315745

ABSTRACT

PURPOSE: To systematically review the current evidence to compare the differences in outcomes of the suture button (SB) versus hook plate (HP) fixations for treating acute acromioclavicular joint dislocation (ACD). METHODS: Two independent reviewers performed the literature search based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. A literature search of the Embase, PubMed, and Cochrane Library databases was performed and Level I-IV evidence studies comparing the SB and HP procedures for acute ACD were included. Studies that met the following exclusion criteria were excluded: (1) letters, comments, case reports, reviews, animal studies, cadaveric studies, biomechanical studies, and study protocols; (2) incomplete data; and (3) repeated studies and data. The Newcastle-Ottawa Scale was used to evaluate the quality of nonrandomized studies. Constant score, visual analog scale (VAS) score, operation time, coracoclavicular distance (CCD), and complications were recorded and the mean differences of VAS and Constant were compared with preset minimal clinically important difference. RESULTS: Fourteen studies with 363 patients treated with SB procedures and 432 patients with the HP procedure were included. In terms of patient-reported outcomes, 5 of the 13 included studies reported significantly greater Constant score in SB group and most (4/5) used arthroscopic SB technique. Statistically significant differences in favor of SB were found in 3 of the 7 included studies in terms of VAS score whereas none of them reached the minimal clinically important difference. In terms of recurrent instability, no statistically significant difference was noted. All studies showed that the SB technique resulted in lower estimated blood loss. No difference was detected in CCD and complications. CONCLUSIONS: Based on the current body of evidence, it is suggested that employment of the SB technique may confer advantageous outcomes when compared to the HP technique in acute ACD patients. These potential benefits may include higher Constant scores, lower pain levels, and no discernible increases in operation time, CCD, or complication rates. LEVEL OF EVIDENCE: Level IV, systematic review of Level II-IV studies.


Subject(s)
Acromioclavicular Joint , Joint Dislocations , Shoulder Dislocation , Humans , Joint Dislocations/surgery , Acromioclavicular Joint/surgery , Treatment Outcome , Shoulder Dislocation/surgery , Bone Plates , Sutures , Pain
17.
Genomics ; 115(6): 110709, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37739021

ABSTRACT

Recent studies on marine organisms have made use of third-generation sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). While these specialized bioinformatics tools have different algorithmic designs and performance capabilities, they offer scalability and can be applied to various datasets. We investigated the effectiveness of PacBio and ONT RNA sequencing methods in identifying the venom of the jellyfish species Nemopilema nomurai. We conducted a detailed analysis of the sequencing data from both methods, focusing on key characteristics such as CD, alternative splicing, long-chain noncoding RNA, simple sequence repeat, transcription factor, and functional transcript annotation. Our findings indicate that ONT generally produced higher raw data quality in the transcriptome analysis, while PacBio generated longer read lengths. PacBio was found to be superior in identifying CDs and long-chain noncoding RNA, whereas ONT was more cost-effective for predicting alternative splicing events, simple sequence repeats, and transcription factors. Based on these results, we conclude that PacBio is the most specific and sensitive method for identifying venom components, while ONT is the most cost-effective method for studying venogenesis, cnidocyst (venom gland) development, and transcription of virulence genes in jellyfish. Our study has implications for future sequencing technologies in marine jellyfish, and highlights the power of full-length transcriptome analysis in discovering potential therapeutic targets for jellyfish dermatitis.


Subject(s)
Cnidarian Venoms , Scyphozoa , Animals , RNA , Sequence Analysis, RNA , RNA, Untranslated , High-Throughput Nucleotide Sequencing/methods
18.
Pediatr Emerg Care ; 40(5): 390-394, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38459619

ABSTRACT

OBJECTIVES: Early wound management for pediatric patients with partial-thickness burns in the emergency department remains debatable. This study aims to evaluate the value of emergency conservative debridement under topical anesthesia in improving short-term prognosis of pediatric partial-thickness burns. METHODS: This retrospective cohort study enrolled children with partial-thickness thermal burns presenting to the emergency department within 6 hours postburn. All the enrolled patients were divided into 2 groups: the debridement group and the dressing group. The associations between emergency conservative debridement and time to reepithelialization was analyzed by using Kaplan-Meier curves with log rank test and multivariate Cox regression analysis. Moreover, the associations between emergency conservative debridement and in-hospital cost and length of stay were also evaluated. RESULTS: All baseline characteristics between groups were comparable (all P > 0.05). Emergency conservative debridement under topical anesthesia significantly decreased the median value of time to reepithelialization (13 vs 14 days, P = 0.02). Cox regression analysis showed that emergency conservative debridement significantly improved wound reepithelialization after adjusting for burn size (odds ratio, 4.07; 95% confidence interval, 1.64-10.11; P < 0.01). The mean length of stay of patients receiving conservative wound debridement was lower than that of patients in the wound dressing group (14.3 ± 7.3 vs 18.8 ± 10.4 days, P < 0.01), but not in terms of mean in-hospital cost per 1% total body surface area (2.8 ± 1.9 vs 3.0 ± 2.1 × 103 RMB per 1% total body surface area, P = 0.58). CONCLUSIONS: Emergency conservative debridement of pediatric partial-thickness burns under topical anesthesia significantly improves the wound healing outcomes without increasing health care burden.


Subject(s)
Anesthesia, Local , Burns , Debridement , Humans , Debridement/methods , Male , Retrospective Studies , Female , Burns/therapy , Child, Preschool , Prognosis , Infant , Child , Wound Healing , Length of Stay/statistics & numerical data , Bandages/economics , Emergency Service, Hospital , Conservative Treatment/methods , Treatment Outcome
19.
J Fish Biol ; 104(5): 1350-1365, 2024 May.
Article in English | MEDLINE | ID: mdl-38332499

ABSTRACT

Dam construction alters the hydrodynamic conditions, consequently impacting the swimming behavior of fish. To explore the effect of flow hydrodynamics on fish swimming behavior, five endemic fish species in the upper Yangtze River basin were selected. Through high-speed video visualization and computer analysis, these species' swimming patterns under different flow velocities (0.1-1.2 m/s) were investigated. The kinematic and morphological characteristics of the fish were presented. The principal component analysis was used to analyse the main factors influencing the swimming ability of fish and to determine the correlation coefficients among fish behavior indicators. Fish exhibited three different swimming patterns under different flow velocities. Low velocity (0.1-0.3 m/s) corresponds to free motion, middle velocity (0.4-0.7 m/s) corresponds to cruising motion, and high velocity corresponds to stress motion (0.8-1.2 m/s). The fish kinematic index curves were obtained, and four of five fish species showed two extreme points, which means the optimal and adverse swimming strategies can be determined. With the increase in flow velocity, the tail-beat frequency showed an increasing trend, whereas the tail-beat angle and amplitude showed a decreasing trend. Morphological and kinematic parameters were the two main indexes that affect the swimming ability of fish, which accounts for 41.9% and 26.9%, respectively.


Subject(s)
Hydrodynamics , Rivers , Swimming , Animals , China , Biomechanical Phenomena , Fishes/physiology , Fishes/anatomy & histology , Principal Component Analysis , Video Recording
20.
J Sci Food Agric ; 104(2): 993-1007, 2024 Jan 30.
Article in English | MEDLINE | ID: mdl-37715565

ABSTRACT

BACKGROUND: Type 2 diabetes mellitus (T2DM) is a prevalent metabolic disease that poses significant health risks due to its numerous complications. However, the effects of eumelanin on oxidative stress, hyperglycemia and depression in diabetic mice have not been extensively studied. RESULTS: Our study employed an enzymatic approach to extract eumelanin from squid ink and characterized it using spectroscopic techniques. Remarkably, eumelanin extracted with alkaline-neutral-flavor protease (ANF) displayed superior inhibitory activity against α-glucosidase and α-amylase, while enhancing glucose utilization and hepatic glycogen synthesis in human hepatocellular carcinoma cell line (HepG2) insulin resistance model. Further evaluation of ANF in a T2DM ICR mouse model demonstrated its significant potential in alleviating hyperglycemia, reducing glycosylated serum protein levels, improving glucose tolerance and modulating total cholesterol and low-density lipoprotein levels, as well as antioxidant indices at a dosage of 0.04 g kg-1 . Additionally, ANF exhibited positive effects on energy levels and reduced immobility time in antidepressant behavioral experiments. Moreover, ANF positively influenced the density and infiltration state of renal cells, while mitigating inflammatory enlargement and deformation of liver cells, without inducing any adverse effects in mice. CONCLUSION: Overall, these findings underscore the significant therapeutic potential of ANF in the treatment of T2DM and its associated complications. By augmenting lipid and glucose metabolism, mitigating oxidative stress and alleviating depression, ANF emerges as a promising candidate for multifaceted intervention. © 2023 Society of Chemical Industry.


Subject(s)
Diabetes Mellitus, Experimental , Diabetes Mellitus, Type 2 , Hyperglycemia , Humans , Mice , Animals , Diabetes Mellitus, Type 2/metabolism , Mice, Inbred ICR , Hypoglycemic Agents/metabolism , Insulin , Diabetes Mellitus, Experimental/metabolism , Depression , Ink , Blood Glucose/metabolism , Hyperglycemia/drug therapy , Hyperglycemia/metabolism , Oxidative Stress , Liver/metabolism
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