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1.
Cell ; 2024 Aug 31.
Article in English | MEDLINE | ID: mdl-39326418

ABSTRACT

Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.

2.
Cell ; 185(23): 4298-4316.e21, 2022 11 10.
Article in English | MEDLINE | ID: mdl-36323317

ABSTRACT

After ingestion of toxin-contaminated food, the brain initiates a series of defensive responses (e.g., nausea, retching, and vomiting). How the brain detects ingested toxin and coordinates diverse defensive responses remains poorly understood. Here, we developed a mouse-based paradigm to study defensive responses induced by bacterial toxins. Using this paradigm, we identified a set of molecularly defined gut-to-brain and brain circuits that jointly mediate toxin-induced defensive responses. The gut-to-brain circuit consists of a subset of Htr3a+ vagal sensory neurons that transmit toxin-related signals from intestinal enterochromaffin cells to Tac1+ neurons in the dorsal vagal complex (DVC). Tac1+ DVC neurons drive retching-like behavior and conditioned flavor avoidance via divergent projections to the rostral ventral respiratory group and lateral parabrachial nucleus, respectively. Manipulating these circuits also interferes with defensive responses induced by the chemotherapeutic drug doxorubicin. These results suggest that food poisoning and chemotherapy recruit similar circuit modules to initiate defensive responses.


Subject(s)
Brain-Gut Axis , Parabrachial Nucleus , Vagus Nerve , Animals , Mice , Neurons/physiology , Neurons, Afferent/physiology , Vagus Nerve/physiology
3.
Cell ; 184(12): 3256-3266.e13, 2021 06 10.
Article in English | MEDLINE | ID: mdl-34048699

ABSTRACT

Northern East Asia was inhabited by modern humans as early as 40 thousand years ago (ka), as demonstrated by the Tianyuan individual. Using genome-wide data obtained from 25 individuals dated to 33.6-3.4 ka from the Amur region, we show that Tianyuan-related ancestry was widespread in northern East Asia before the Last Glacial Maximum (LGM). At the close of the LGM stadial, the earliest northern East Asian appeared in the Amur region, and this population is basal to ancient northern East Asians. Human populations in the Amur region have maintained genetic continuity from 14 ka, and these early inhabitants represent the closest East Asian source known for Ancient Paleo-Siberians. We also observed that EDAR V370A was likely to have been elevated to high frequency after the LGM, suggesting the possible timing for its selection. This study provides a deep look into the population dynamics of northern East Asia.


Subject(s)
Population Dynamics , DNA, Ancient/analysis , Asia, Eastern , Female , Genetic Variation , Genetics, Population , Genome, Human , Geography , Humans , Ice Cover , Likelihood Functions , Male , Models, Genetic , Phylogeny , Principal Component Analysis , Time Factors
4.
Cell ; 184(14): 3829-3841.e21, 2021 07 08.
Article in English | MEDLINE | ID: mdl-34171307

ABSTRACT

Past human genetic diversity and migration between southern China and Southeast Asia have not been well characterized, in part due to poor preservation of ancient DNA in hot and humid regions. We sequenced 31 ancient genomes from southern China (Guangxi and Fujian), including two ∼12,000- to 10,000-year-old individuals representing the oldest humans sequenced from southern China. We discovered a deeply diverged East Asian ancestry in the Guangxi region that persisted until at least 6,000 years ago. We found that ∼9,000- to 6,000-year-old Guangxi populations were a mixture of local ancestry, southern ancestry previously sampled in Fujian, and deep Asian ancestry related to Southeast Asian Hòabìnhian hunter-gatherers, showing broad admixture in the region predating the appearance of farming. Historical Guangxi populations dating to ∼1,500 to 500 years ago are closely related to Tai-Kadai and Hmong-Mien speakers. Our results show heavy interactions among three distinct ancestries at the crossroads of East and Southeast Asia.


Subject(s)
Genetics, Population , Asia, Southeastern , Asia, Eastern , Geography , Humans
5.
Nature ; 610(7931): 402-408, 2022 10.
Article in English | MEDLINE | ID: mdl-36131020

ABSTRACT

Chitin, the most abundant aminopolysaccharide in nature, is an extracellular polymer consisting of N-acetylglucosamine (GlcNAc) units1. The key reactions of chitin biosynthesis are catalysed by chitin synthase2-4, a membrane-integrated glycosyltransferase that transfers GlcNAc from UDP-GlcNAc to a growing chitin chain. However, the precise mechanism of this process has yet to be elucidated. Here we report five cryo-electron microscopy structures of a chitin synthase from the devastating soybean root rot pathogenic oomycete Phytophthora sojae (PsChs1). They represent the apo, GlcNAc-bound, nascent chitin oligomer-bound, UDP-bound (post-synthesis) and chitin synthase inhibitor nikkomycin Z-bound states of the enzyme, providing detailed views into the multiple steps of chitin biosynthesis and its competitive inhibition. The structures reveal the chitin synthesis reaction chamber that has the substrate-binding site, the catalytic centre and the entrance to the polymer-translocating channel that allows the product polymer to be discharged. This arrangement reflects consecutive key events in chitin biosynthesis from UDP-GlcNAc binding and polymer elongation to the release of the product. We identified a swinging loop within the chitin-translocating channel, which acts as a 'gate lock' that prevents the substrate from leaving while directing the product polymer into the translocating channel for discharge to the extracellular side of the cell membrane. This work reveals the directional multistep mechanism of chitin biosynthesis and provides a structural basis for inhibition of chitin synthesis.


Subject(s)
Chitin , Cryoelectron Microscopy , Acetylglucosamine/metabolism , Aminoglycosides/pharmacology , Binding Sites , Cell Membrane/metabolism , Chitin/biosynthesis , Chitin/chemistry , Chitin/metabolism , Chitin/ultrastructure , Chitin Synthase/metabolism , Phytophthora/enzymology , Uridine Diphosphate/metabolism , Uridine Diphosphate N-Acetylglucosamine/metabolism
6.
Nature ; 599(7884): 256-261, 2021 11.
Article in English | MEDLINE | ID: mdl-34707286

ABSTRACT

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious1. Here we present genomic data from 5 individuals dating to around 3000-2800 BC from the Dzungarian Basin and 13 individuals dating to around 2100-1700 BC from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early-Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo1,2 or to have originated among the Bactria-Margiana Archaeological Complex3 or Inner Asian Mountain Corridor cultures4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.


Subject(s)
Archaeology , Genome, Human/genetics , Genomics , Human Migration/history , Mummies/history , Phylogeny , Agriculture/history , Animals , Cattle , China , Cultural Characteristics , Dental Calculus/chemistry , Desert Climate , Diet/history , Europe , Female , Goats , Grassland , History, Ancient , Humans , Male , Milk Proteins/analysis , Phylogeography , Principal Component Analysis , Proteome/analysis , Proteomics , Sheep , Whole Genome Sequencing
7.
Cell ; 145(2): 300-11, 2011 Apr 15.
Article in English | MEDLINE | ID: mdl-21496647

ABSTRACT

Synaptotagmins Syt1, Syt2, Syt7, and Syt9 act as Ca(2+)-sensors for synaptic and neuroendocrine exocytosis, but the function of other synaptotagmins remains unknown. Here, we show that olfactory bulb neurons secrete IGF-1 by an activity-dependent pathway of exocytosis, and that Syt10 functions as the Ca(2+)-sensor that triggers IGF-1 exocytosis in these neurons. Deletion of Syt10 impaired activity-dependent IGF-1 secretion in olfactory bulb neurons, resulting in smaller neurons and an overall decrease in synapse numbers. Exogenous IGF-1 completely reversed the Syt10 knockout phenotype. Syt10 colocalized with IGF-1 in somatodendritic vesicles of olfactory bulb neurons, and Ca(2+)-binding to Syt10 caused these vesicles to undergo exocytosis, thereby secreting IGF-1. Thus, Syt10 controls a previously unrecognized pathway of Ca(2+)-dependent exocytosis that is spatially and temporally distinct from Ca(2+)-dependent synaptic vesicle exocytosis controlled by Syt1. Our findings thereby reveal that two different synaptotagmins can regulate functionally distinct Ca(2+)-dependent membrane fusion reactions in the same neuron.


Subject(s)
Exocytosis , Insulin-Like Growth Factor I/metabolism , Olfactory Bulb/metabolism , Synaptotagmins/metabolism , Animals , Cells, Cultured , In Vitro Techniques , Mice , Mice, Knockout , Neurons/metabolism , Olfactory Bulb/cytology
8.
PLoS Genet ; 19(9): e1010911, 2023 09.
Article in English | MEDLINE | ID: mdl-37708138

ABSTRACT

Understanding the mechanism of detoxification initiation in arthropods after pesticide exposure is crucial. Although the identity of transcription factors that induce and regulate the expression of detoxification genes in response to pesticides is beginning to emerge, whether transcription factors directly interact with xenobiotics is unclear. The findings of this study revealed that a nuclear hormone receptor, Tetranychus cinnabarinus hormone receptor (HR) TcHR96h, regulates the overexpression of the detoxification gene TcGSTm02, which is involved in cyflumetofen resistance. The nuclear translocation of TcHR96h increased after cyflumetofen exposure, suggesting direct binding with cyflumetofen. The direct binding of TcHR96h and cyflumetofen was supported by several independent proteomic assays that quantify interactions with small molecules. Together, this study proposes a model for the initiation of xenobiotic detoxification in a polyphagous agricultural pest. These insights not only provide a better understanding of the mechanisms of xenobiotic detoxification and metabolism in arthropods, but also are crucial in understanding adaptation in polyphagous herbivores.


Subject(s)
Arthropods , Tetranychidae , Animals , Proteomics , Xenobiotics , Receptors, Cytoplasmic and Nuclear/genetics , Transcription Factors , Tetranychidae/genetics
9.
J Biol Chem ; 300(5): 107294, 2024 May.
Article in English | MEDLINE | ID: mdl-38636665

ABSTRACT

Exenatide, a promising cardioprotective agent, protects against cardiac structural remodeling and diastolic dysfunction. Combined blockade of sodium and potassium channels is valuable for managing atrial fibrillation (AF). Here, we explored whether exenatide displayed anti-AF effects by inhibiting human Kv1.5 and Nav1.5 channels. We used the whole-cell patch-clamp technique to investigate the effects of exenatide on hKv1.5 and hNav1.5 channels expressed in human embryonic kidney 293 cells and studied the effects of exenatide on action potential (AP) and other cardiac ionic currents in rat atrial myocytes. Additionally, an electrical mapping system was used to explore the effects of exenatide on electrical properties and AF activity in isolated rat hearts. Finally, a rat AF model, established using acetylcholine and calcium chloride, was employed to evaluate the anti-AF potential of exenatide in rats. Exenatide reversibly suppressed IKv1.5 with IC50 of 3.08 µM, preferentially blocked the hKv1.5 channel in its closed state, and positively shifted the voltage-dependent activation curve. Exenatide also reversibly inhibited INav1.5 with IC50 of 3.30 µM, negatively shifted the voltage-dependent inactivation curve, and slowed its recovery from inactivation with significant use-dependency at 5 and 10 Hz. Furthermore, exenatide prolonged AP duration and suppressed the sustained K+ current (Iss) and transient outward K+ current (Ito), but without inhibition of L-type Ca2+ current (ICa,L) in rat atrial myocytes. Exenatide prevented AF incidence and duration in rat hearts and rats. These findings demonstrate that exenatide inhibits IKv1.5 and INav1.5in vitro and reduces AF susceptibility in isolated rat hearts and rats.


Subject(s)
Action Potentials , Atrial Fibrillation , Exenatide , Kv1.5 Potassium Channel , Myocytes, Cardiac , NAV1.5 Voltage-Gated Sodium Channel , Voltage-Gated Sodium Channel Blockers , Animals , Humans , Male , Rats , Action Potentials/drug effects , Atrial Fibrillation/drug therapy , Atrial Fibrillation/metabolism , Exenatide/pharmacology , Exenatide/therapeutic use , HEK293 Cells , Kv1.5 Potassium Channel/antagonists & inhibitors , Myocytes, Cardiac/drug effects , Myocytes, Cardiac/metabolism , NAV1.5 Voltage-Gated Sodium Channel/metabolism , NAV1.5 Voltage-Gated Sodium Channel/genetics , Rats, Sprague-Dawley , Voltage-Gated Sodium Channel Blockers/pharmacology , Voltage-Gated Sodium Channel Blockers/therapeutic use
10.
Plant J ; 119(1): 617-631, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38647454

ABSTRACT

Uncovering the function of phytopathogen effectors is crucial for understanding mechanisms of pathogen pathogenicity and for improving our ability to protect plants from diseases. An increasing number of effectors have been predicted in various plant pathogens. Functional characterization of these effectors has become a major focus in the study of plant-pathogen interactions. In this study, we designed a novel screening system that combines the TMV (tobacco mosaic virus)-GFP vector and Agrobacterium-mediated transient expression in the model plant Nicotiana benthamiana. This system enables the rapid identification of effectors that interfere with plant immunity. The biological function of these effectors can be easily evaluated by observing the GFP fluorescence signal using a UV lamp within just a few days. To evaluate the TMV-GFP system, we initially tested it with well-described virulence and avirulence type III effectors from the bacterial pathogen Ralstonia solanacearum. After proving the accuracy and efficiency of the TMV-GFP system, we successfully screened a novel virulence effector, RipS1, using this approach. Furthermore, using the TMV-GFP system, we reproduced consistent results with previously known cytoplasmic effectors from a diverse array of pathogens. Additionally, we demonstrated the effectiveness of the TMV-GFP system in identifying apoplastic effectors. The easy operation, time-saving nature, broad effectiveness, and low technical requirements of the TMV-GFP system make it a promising approach for high-throughput screening of effectors with immune interference activity from various pathogens.


Subject(s)
Genetic Vectors , Green Fluorescent Proteins , High-Throughput Screening Assays , Nicotiana , Plant Diseases , Ralstonia solanacearum , Tobacco Mosaic Virus , Tobacco Mosaic Virus/physiology , Tobacco Mosaic Virus/genetics , Tobacco Mosaic Virus/pathogenicity , Nicotiana/microbiology , Nicotiana/genetics , Nicotiana/virology , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Ralstonia solanacearum/pathogenicity , Ralstonia solanacearum/genetics , Ralstonia solanacearum/physiology , High-Throughput Screening Assays/methods , Plant Diseases/microbiology , Genetic Vectors/genetics , Virulence , Agrobacterium/genetics , Plant Immunity/genetics , Host-Pathogen Interactions/genetics
11.
Mol Biol Evol ; 41(7)2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38842255

ABSTRACT

The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3'UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds.


Subject(s)
Animal Fur , Selection, Genetic , Animals , Dogs/genetics , Polymorphism, Single Nucleotide , Breeding , Sweden , Genetic Variation , MicroRNAs/genetics
12.
Mol Biol Evol ; 41(4)2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38507661

ABSTRACT

Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.


Subject(s)
Genome, Mitochondrial , Animals , Dogs , Animals, Domestic/genetics , Asia, Eastern , DNA, Mitochondrial/genetics , Genetic Variation , Haplotypes , Mammals/genetics , Phylogeny
13.
Plant Physiol ; 2024 Sep 26.
Article in English | MEDLINE | ID: mdl-39325738

ABSTRACT

Ralstonia solanacearum causes lethal bacterial wilt diseases in numerous crops, resulting in considerable yield losses. Harnessing genetic resistance is desirable for safeguarding plants against phytopathogens. However, genetic resources resistant to bacterial wilt are limited in crops. RipE1, a conserved type Ⅲ effector with cysteine protease activity, is recognized in Nicotiana benthamiana and Arabidopsis (Arabidopsis thaliana). Here, using a virus-induced gene silencing approach, we identified the gene encoding N. benthamiana homologue of Ptr1 (NbPtr1a), a coiled-coil nucleotide-binding leucine-rich repeat receptor (NLR) recognizing RipE1. Silencing or editing NbPtr1a completely abolished RipE1-induced cell death, indicating recognition of RipE1 by NbPtr1a. Genetic complementation confirmed this recognition, which is conserved across multiple solanaceous plants. Expression of RipE1 in planta or within pathogenic bacteria promoted pathogen colonization of Nbptr1a mutant plants, demonstrating its virulence function independent of NLR recognition. Silencing NbRIN4 enhanced RipE1-induced cell death, while expressing NbRIN4 inhibited it, suggesting that NbRIN4 is involved in recognition of NbPtr1a-RipE1. Furthermore, RipE1 associated with and cleaved NbRIN4, AtRIN4, and tomato (Solanum lycopersicum) SlRIN4 proteins through its cysteine protease activity. Silencing NbRIN4 in Nbptr1a mutants did not prevent RipE1 from promoting pathogen colonization, suggesting that NbRIN4 is not the primary target for RipE1-mediated virulence. Additionally, NbRIN4 suppressed self-association of the coiled-coil domain of NbPtr1a, which is critical for NbPtr1a-mediated cell death and resistance. Finally, we demonstrated that activation of NbPtr1a requires RipE1-mediated elimination of NbRIN4. Given the conserved nature of RipE1, Ptr1 holds great potential for protecting crops from diverse R. solanacearum strains and other distinct pathogens.

14.
Chem Rev ; 123(2): 701-735, 2023 Jan 25.
Article in English | MEDLINE | ID: mdl-36577085

ABSTRACT

Self-healing materials open new prospects for more sustainable technologies with improved material performance and devices' longevity. We present an overview of the recent developments in the field of intrinsically self-healing polymers, the broad class of materials based mostly on polymers with dynamic covalent and noncovalent bonds. We describe the current models of self-healing mechanisms and discuss several examples of systems with different types of dynamic bonds, from various hydrogen bonds to dynamic covalent bonds. The recent advances indicate that the most intriguing results are obtained on the systems that have combined different types of dynamic bonds. These materials demonstrate high toughness along with a relatively fast self-healing rate. There is a clear trade-off relationship between the rate of self-healing and mechanical modulus of the materials, and we propose design principles of polymers toward surpassing this trade-off. We also discuss various applications of intrinsically self-healing polymers in different technologies and summarize the current challenges in the field. This review intends to provide guidance for the design of intrinsic self-healing polymers with required properties.

15.
Biochem Biophys Res Commun ; 690: 149256, 2024 Jan 01.
Article in English | MEDLINE | ID: mdl-37992525

ABSTRACT

14-3-3 proteins play important roles in plant metabolism and stress response. Tomato 14-3-3 proteins, SlTFT4 and SlTFT7, serve as hubs of plant immunity and are targeted by some pathogen effectors. Ralstonia solanacearum with more than 70 type Ⅲ effectors (T3Es) is one of the most destructive plant pathogens. However, little is known on whether R. solanacearum T3Es target SlTFT4 and SlTFT7 and hence interfere with plant immunity. We first detected the associations of SlTFT4/SlTFT7 with R. solanacearum T3Es by luciferase complementation assay, and then confirmed the interactions by yeast two-hybrid approach. We demonstrated that 22 Ralstonia T3Es were associated with both SlTFT4 and SlTFT7, and five among them suppressed the hypersensitive response induced by MAPKKKα, a protein kinase which associated with SlTFT4/SlTFT7. We further demonstrated that suppression of MAPKKKα-induced HR and plant basal defense by the T3E RipAC depend on its association with 14-3-3 proteins. Our findings firstly demonstrate that R. solanacearum T3Es can manipulate plant immunity by targeting 14-3-3 proteins, SlTFT4 and SlTFT7, providing new insights into plant-R. solanacearum interactions.


Subject(s)
14-3-3 Proteins , Ralstonia solanacearum , 14-3-3 Proteins/metabolism , Bacterial Proteins/metabolism , Plant Immunity , Ralstonia solanacearum/physiology , Plant Diseases , Plant Proteins/metabolism
16.
Magn Reson Med ; 92(3): 945-955, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38440832

ABSTRACT

PURPOSE: We aimed to incorporate a deep learning prior with k-space data fidelity for accelerating hyperpolarized carbon-13 MRSI, demonstrated on synthetic cancer datasets. METHODS: A two-site exchange model, derived from the Bloch equation of MR signal evolution, was firstly used in simulating training and testing data, that is, synthetic phantom datasets. Five singular maps generated from each simulated dataset were used to train a deep learning prior, which was then employed with the fidelity term to reconstruct the undersampled MRI k-space data. The proposed method was assessed on synthetic human brain tumor images (N = 33), prostate cancer images (N = 72), and mouse tumor images (N = 58) for three undersampling factors and 2.5% additive Gaussian noise. Furthermore, varied levels of Gaussian noise with SDs of 2.5%, 5%, and 10% were added on synthetic prostate cancer data, and corresponding reconstruction results were evaluated. RESULTS: For quantitative evaluation, peak SNRs were approximately 32 dB, and the accuracy was generally improved for 5 to 8 dB compared with those from compressed sensing with L1-norm regularization or total variation regularization. Reasonable normalized RMS error were obtained. Our method also worked robustly against noise, even on a data with noise SD of 10%. CONCLUSION: The proposed singular value decomposition + iterative deep learning model could be considered as a general framework that extended the application of deep learning MRI reconstruction to metabolic imaging. The morphology of tumors and metabolic images could be measured robustly in six times acceleration using our method.


Subject(s)
Brain Neoplasms , Deep Learning , Image Processing, Computer-Assisted , Magnetic Resonance Imaging , Phantoms, Imaging , Prostatic Neoplasms , Humans , Male , Prostatic Neoplasms/diagnostic imaging , Magnetic Resonance Imaging/methods , Brain Neoplasms/diagnostic imaging , Image Processing, Computer-Assisted/methods , Mice , Animals , Signal-To-Noise Ratio , Algorithms , Brain/diagnostic imaging , Carbon Isotopes/chemistry
17.
Magn Reson Med ; 91(6): 2417-2430, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38291598

ABSTRACT

PURPOSE: Recent work has shown MRI is able to measure and quantify signals of phospholipid membrane-bound protons associated with myelin in the human brain. This work seeks to develop an improved technique for characterizing this brain ultrashort- T 2 ∗ $$ {\mathrm{T}}_2\ast $$ component in vivo accounting for T 1 $$ {\mathrm{T}}_1 $$ weighting. METHODS: Data from ultrashort echo time scans from 16 healthy volunteers with variable flip angles (VFA) were collected and fitted into an advanced regression model to quantify signal fraction, relaxation time, and frequency shift of the ultrashort- T 2 ∗ $$ {\mathrm{T}}_2\ast $$ component. RESULTS: The fitted components show intra-subject differences of different white matter structures and significantly elevated ultrashort- T 2 ∗ $$ {\mathrm{T}}_2\ast $$ signal fraction in the corticospinal tracts measured at 0.09 versus 0.06 in other white matter structures and significantly elevated ultrashort- T 2 ∗ $$ {\mathrm{T}}_2\ast $$ frequency shift in the body of the corpus callosum at - $$ - $$ 1.5 versus - $$ - $$ 2.0 ppm in other white matter structures. CONCLUSION: The significantly different measured components and measured T 1 $$ {\mathrm{T}}_1 $$ relaxation time of the ultrashort- T 2 ∗ $$ {\mathrm{T}}_2\ast $$ component suggest that this method is picking up novel signals from phospholipid membrane-bound protons.


Subject(s)
Brain , Protons , Humans , Healthy Volunteers , Phantoms, Imaging , Brain/diagnostic imaging , Magnetic Resonance Imaging/methods , Phospholipids
18.
J Med Virol ; 96(8): e29882, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39185672

ABSTRACT

Establishing reliable noninvasive tools to precisely diagnose clinically significant liver fibrosis (SF, ≥F2) remains an unmet need. We aimed to build a combined radiomics-clinic (CoRC) model for triaging SF and explore the additive value of the CoRC model to transient elastography-based liver stiffness measurement (FibroScan, TE-LSM). This retrospective study recruited 595 patients with biopsy-proven liver fibrosis at two centers between January 2015 and December 2021. At Center 1, the patients before December 2018 were randomly split into training (276) and internal test (118) sets, the remaining were time-independent as a temporal test set (96). Another data set (105) from Center 2 was collected for external testing. Radiomics scores were built with selected features from Deep learning-based (ResUNet) automated whole liver segmentations on MRI (T2FS and delayed enhanced-T1WI). The CoRC model incorporated radiomics scores and relevant clinical variables with logistic regression, comparing routine approaches. Diagnostic performance was evaluated by the area under the receiver operating characteristic curve (AUC). The additive value of the CoRC model to TE-LSM was investigated, considering necroinflammation. The CoRC model achieved AUCs of 0.79 (0.70, 0.86), 0.82 (0.73, 0.89), and 0.81 (0.72-0.91), outperformed FIB-4, APRI (all p < 0.05) in the internal, temporal, and external test sets and maintained the discriminatory power in G0-1 subgroups (AUCs range, 0.85-0.86; all p < 0.05). The AUCs of joint CoRC-LSM model were 0.86 (0.79-0.94), and 0.81 (0.72-0.90) in the internal and temporal sets (p = 0.01). The CoRC model was useful for triaging SF, and may add value to TE-LSM.


Subject(s)
Elasticity Imaging Techniques , Liver Cirrhosis , Liver , Magnetic Resonance Imaging , Humans , Liver Cirrhosis/diagnostic imaging , Liver Cirrhosis/diagnosis , Male , Female , Middle Aged , Retrospective Studies , Magnetic Resonance Imaging/methods , Adult , Elasticity Imaging Techniques/methods , Liver/pathology , Liver/diagnostic imaging , ROC Curve , Deep Learning , Aged , Triage/methods
19.
Cancer Cell Int ; 24(1): 200, 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38840243

ABSTRACT

Ferroptosis, an iron-dependent regulated cell death mechanism, holds significant promise as a therapeutic strategy in oncology. In the current study, we explored the regulatory effects of epigallocatechin gallate (EGCG), a prominent polyphenol in green tea, on ferroptosis and its potential therapeutic implications for non-small cell lung cancer (NSCLC). Treatment of NSCLC cell lines with varying concentrations of EGCG resulted in a notable suppression of cell proliferation, as evidenced by a reduction in Ki67 immunofluorescence staining. Western blot analyses demonstrated that EGCG treatment led to a decrease in the expression of glutathione peroxidase 4 (GPX4) and solute carrier family 7 member 11 (SLC7A11) while increasing the levels of acyl-CoA synthetase long-chain family member 4 (ACSL4). These molecular changes were accompanied by an increase in intracellular iron, malondialdehyde (MDA), and reactive oxygen species (ROS), alongside ultrastructural alterations characteristic of ferroptosis. Through small RNA sequencing and RT-qPCR, transfer RNA-derived small RNA 13502 (tsRNA-13502) was identified as a significant target of EGCG action, with its expression being upregulated in NSCLC tissues compared to adjacent non-tumorous tissues. EGCG was found to modulate the ferroptosis pathway by downregulating tsRNA-13502 and altering the expression of key ferroptosis regulators (GPX4/SLC7A11 and ACSL4), thereby promoting the accumulation of iron, MDA, and ROS, and ultimately inducing ferroptosis in NSCLC cells. This study elucidates EGCG's multifaceted mechanisms of action, underscoring the modulation of ferroptosis as a viable therapeutic approach for enhancing NSCLC treatment outcomes.

20.
Chemistry ; : e202401727, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38979891

ABSTRACT

The development of innovative synthetic strategies to create functional polycaprolactones is highly demanded for advanced material applications. In this contribution, we reported a facile synthetic strategy to prepare a class of CL-based monomers (R-TO) derived from epoxides. They readily polymerize via well-controlled ring-opening polymerization (ROP) to afford a series of polyesters P(R-TO) with high molecular weight (Mn up to 350 kDa). Sequential addition copolymerization of MTO and L-lactide (L-LA) allowed to access of a series of ABA triblock copolymers with composition-dependent mechanical properties. Notably, P(L-LA)100-b-P(MTO)500-b-P(L-LA)100 containing the amorphous P(MTO) segment as a soft midblock and crystalline P(L-LA) domain as hard end block behaved as an excellent thermoplastic elastomer (TPE) with high elongation at break (1438±204 %), tensile strength (23.5±1.7 MPa), and outstanding elastic recovery (>88 %).

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