Publications by authors named "Zhibin Zhang"

288 Publications

Broad-scale climate variation drives the dynamics of animal populations: a global multi-taxa analysis.

Biol Rev Camb Philos Soc 2022 Aug 9. Epub 2022 Aug 9.

State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.

Climate is a major extrinsic factor affecting the population dynamics of many organisms. The Broad-Scale Climate Hypothesis (BSCH) was proposed by Elton to explain the large-scale synchronous population cycles of animals, but the extent of support and whether it differs among taxa and geographical regions is unclear. We reviewed publications examining the relationship between the population dynamics of multiple taxa worldwide and the two most commonly used broad-scale climate indices, El Niño-Southern Oscillation (ENSO) and North Atlantic Oscillation (NAO). Our review and synthesis (based on 561 species from 221 papers) reveals that population changes of mammals, birds and insects are strongly affected by major oceanic shifts or irregular oceanic changes, particularly in ENSO- and NAO-influenced regions (Pacific and Atlantic, respectively), providing clear evidence supporting Elton's BSCH. Mammal and insect populations tended to increase during positive ENSO phases. Bird populations tended to increase in positive NAO phases. Some species showed dual associations with both positive and negative phases of the same climate index (ENSO or NAO). These findings indicate that some taxa or regions are more or less vulnerable to climate fluctuations and that some geographical areas show multiple weather effects related to ENSO or NAO phases. Beyond confirming that animal populations are influenced by broad-scale climate variation, we document extensive patterns of variation among taxa and observe that the direct biotic and abiotic mechanisms for these broad-scale climate factors affecting animal populations are very poorly understood. A practical implication of our research is that changes in ENSO or NAO can be used as early signals for pest management and wildlife conservation. We advocate integrative studies at both broad and local scales to unravel the omnipresent effects of climate on animal populations to help address the challenge of conserving biodiversity in this era of accelerated climate change.
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http://dx.doi.org/10.1111/brv.12888DOI Listing
August 2022

Author Correction: Streptococcal pyrogenic exotoxin B cleaves GSDMA and triggers pyroptosis.

Nature 2022 Jul 27. Epub 2022 Jul 27.

The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1038/s41586-022-05109-xDOI Listing
July 2022

Preparation of magnesium potassium phosphate cement using by-product MgO from Qarhan Salt Lake for low-carbon and sustainable cement production.

Environ Res 2022 Jul 19;214(Pt 2):113912. Epub 2022 Jul 19.

Department of Civil and Airport Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.

Herein, to reduce CO emissions and energy consumption and to promote the recycling of waste resources, two types of boron-containing MgO by-products, which were obtained by lithium extraction from Qarhan Salt Lake, China, were used as substitutes for dead-burned MgO to prepare magnesium phosphate potassium cement (MKPC) as a rapid repair material. First, the phase composition and particle-size distribution of the MgO by-product were investigated. The effects of different MgO sources, molar ratio of MgO to KHPO (M/P), and curing age on the setting time and mechanical properties of MKPC were then studied. Based on the results, the mix proportion of MKPC was optimized. Finally, X-ray diffractometry, scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), differential thermogravimetric (DTG) analysis, and mercury intrusion porosimetry were used to characterize the phase and microstructure evolution of MKPC prepared with different MgO contents. The results demonstrated that the by-product MgO prolonged the setting time of MKPC to more than 40 min. In addition, in the initial stage of hydration, the compressive strength of the MgO by-product was slightly lower than that of the dead-burned MgO; however, with increasing age, the mechanical properties of MKPC prepared by by-product MgO were excellent (up to 60 MPa). The phase and microstructure results revealed that the main hydration product of MKPC prepared using the three types of MgO was MgKPO·6HO. Combined with the physical and chemical properties of the raw materials, it was confirmed that the larger particle size and the coexisting impurities from the salt lake were the main reasons for the longer setting time of the MKPC prepared by the by-product MgO. We believe that this research will be of great significance for the preparation of low-carbon, low-cost, and high-performance MKPC materials.
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http://dx.doi.org/10.1016/j.envres.2022.113912DOI Listing
July 2022

Effects of homoeologous exchange on gene expression and alternative splicing in a newly formed allotetraploid wheat.

Plant J 2022 Jun 28. Epub 2022 Jun 28.

Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.

Homoeologous exchange (HE) is a major mechanism generating post-polyploidization genetic variation with important evolutionary consequences. However, the direct impacts of HE on gene expression and transcript diversity in allopolyploids without the intertwined evolutionary processes remain to be fully understood. Here, we analyzed high-throughput RNA-seq data of young leaves from plant groups of a synthetic allotetraploid wheat (AADD), which contained variable numbers of HEs. We aimed to investigate if and to which extent HE directly impacts gene expression and alternative splicing (AS). We found that HE impacts expression of genes located within HE regions primarily via a cis-acting dosage effect, which led to significant changes in the total expression level of homoeologous gene pairs, especially for homoeologs whose original expression was biased. In parallel, HE also influences expression of a large number of genes residing in non-HE regions by trans-regulation leading to convergent expression of homoeologs. Intriguingly, when taking the original relative homoeolog expression states into account, homoeolog pairs under trans-effect are more prone to manifesting a convergent response to the HEs whereas those under cis-regulation tended to show further exacerbated subgenome-biased expression. Moreover, HE-induced quantitative, largely individual-specific, changes of AS events were detected. Similar to homoeologous expression, homoeo-AS events under trans-effect were more responsive to HE. HE therefore exerts multifaceted immediate effects on gene expression and, to a less extent, on individualized transcript diversity in nascent allopolyploidy.
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http://dx.doi.org/10.1111/tpj.15886DOI Listing
June 2022

A Single-Cell Atlas of Tumor-Infiltrating Immune Cells in Pancreatic Ductal Adenocarcinoma.

Mol Cell Proteomics 2022 Jun 17;21(8):100258. Epub 2022 Jun 17.

School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China. Electronic address:

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies with limited treatment options. To guide the design of more effective immunotherapy strategies, mass cytometry was employed to characterize the cellular composition of the PDAC-infiltrating immune cells. The expression of 33 protein markers was examined at the single-cell level in more than two million immune cells from four types of clinical samples, including PDAC tumors, normal pancreatic tissues, chronic pancreatitis tissues, and peripheral blood. Based on the analyses, we identified 23 distinct T-cell phenotypes, with some cell clusters exhibiting aberrant frequencies in the tumors. Programmed cell death protein 1 (PD-1) was extensively expressed in CD4 and CD8 T cells and coexpressed with both stimulatory and inhibitory immune markers. In addition, we observed elevated levels of functional markers, such as CD137L and CD69, in PDAC-infiltrating immune cells. Moreover, the combination of PD-1 and CD8 was used to stratify PDAC tumors from The Cancer Genome Atlas database into three immune subtypes, with S1 (PD-1CD8) exhibiting the best prognosis. Further analysis suggested distinct molecular mechanisms for immune exclusion in different subtypes. Taken together, the single-cell protein expression data depicted a detailed cell atlas of the PDAC-infiltrating immune cells and revealed clinically relevant information regarding useful cell phenotypes and targets for immunotherapy development.
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http://dx.doi.org/10.1016/j.mcpro.2022.100258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9294203PMC
June 2022

Spatial and Temporal Transcriptomic Heredity and Asymmetry in an Artificially Constructed Allotetraploid Wheat (AADD).

Front Plant Sci 2022 16;13:887133. Epub 2022 May 16.

Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.

Polyploidy, or whole-genome duplication (WGD), often induces dramatic changes in gene expression due to "transcriptome shock. " However, questions remain about how allopolyploidy (the merging of multiple nuclear genomes in the same nucleus) affects gene expression within and across multiple tissues and developmental stages during the initial foundation of allopolyploid plants. Here, we systematically investigated the immediate effect of allopolyploidy on gene expression variation in an artificial allopolyploidy system consisting of a constructed allotetraploid wheat (AADD genome, accession AT2) and its diploid progenitors and . We performed comprehensive RNA sequencing of 81 samples from different genotypes, tissues, and developmental stages. First, we found that intrinsic interspecific differences between the diploid parents played a major role in establishing the expression architecture of the allopolyploid. Nonetheless, allopolyploidy also induced dramatic and asymmetric patterns of differential gene expression between the subgenomes, and genes from the D subgenome exhibited a more drastic response. Second, analysis of homoeolog expression bias (HEB) revealed that the D subgenome exhibited significant expression bias and that -generated HEB was attributed mainly to asymmetrical differential gene expression. Homoeolog-specific expression (HSE) analyses showed that the -only regulatory pattern was predominant in AT2, reflecting significant divergence between the parents. Co-expression network analysis revealed that homoeolog expression connectivity (HEC) was significantly correlated with sequence divergence in elements between subgenomes. Interestingly, allopolyploidy-induced reconstruction of network modules was also associated with different HSE patterns. Finally, a transcriptome atlas of spike development demonstrated that the phenotypic similarity of AT2 to may be attributed to the combination of relatively stable expression of A-subgenome genes and drastic downregulation of their D-subgenome homoeologs. These findings provide a broad, multidimensional characterization of allopolyploidy-induced transcriptomic responses and suggest that allopolyploidy can have immediate and complex regulatory effects on the expression of nuclear genes.
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http://dx.doi.org/10.3389/fpls.2022.887133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9150853PMC
May 2022

Revealing the real-time diversity and abundance of small mammals by using an Intelligent Animal Monitoring System (IAMS).

Integr Zool 2022 May 30. Epub 2022 May 30.

State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.

It is challenging to reveal the real-time spatio-temporal change of diversity and abundance of animals in natural systems by using traditional methods. The rapid advancement of new technologies such as the Internet of Things, artificial intelligence, and big-data processing, provide opportunities for developing novel technologies for monitoring biodiversity and population abundance of animals with high efficacy and accuracy. In this study, by using a recently developed Intelligent Animal Monitoring System, named "Vector Intelligent Monitoring System (VIMS)", we investigated the real-time diversity and abundance of small mammals in the Banruosi forest, Dujiangyan region, southwest China. To make a comparison of the VIMS with traditional methods, we also surveyed the diversity and abundance of small mammals using wired live traps. Compared to live traps, the VIMS has several advantages such as automatic data collection, intelligent identification of species, data visualization, whole-day and all-weather operation, little disturbance to animals, real-time monitoring, and is capable of revealing more small mammal species. However, the VIMS also has several disadvantages over live traps such as lower trapping efficiency and being more expensive than live traps. Our results suggest that the VIMS can be a complementary method to traditional ones in monitoring the real-time spatio-temporal change of diversity and abundance of small mammals (especially rare species). In addition, the VIMS is useful in monitoring other small animals like small carnivores, birds, amphibians, and reptiles.
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http://dx.doi.org/10.1111/1749-4877.12664DOI Listing
May 2022

Efficient capture of U(VI) by magnetic Zr(IV)-ethylenediamine tetramethylene phosphonic acid inorganic-organic hybrid.

Environ Sci Pollut Res Int 2022 May 10. Epub 2022 May 10.

State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, 330013, Jiangxi, China.

The separation of magnetic adsorbents from aqueous solutions is made simple by using an external magnetic field. Herein, magnetic Zr(IV)-ethylenediamine tetramethylene phosphonic acid (EDTMPA) hybrids (MZrOP-x-T, x, and T were the different quality of [email protected] and temperature in the synthesis process, respectively). A study was conducted on the uses of MZrOP-x-T in the capture of U(VI). The influences of pH, adsorption period, initial concentration, and temperature were all investigated. Furthermore, the desorption and reusability of the materials were explored. The optimal values of x and T were 0.2 g and 100 °C, respectively. At 298.15 K, the maximum adsorption capacity of MZrOP-0.2-100 was 330.30 mg·g. The current research demonstrates that MZrOP-0.2-100 is a potentially effective material in removing U(VI) from radioactive solution.
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http://dx.doi.org/10.1007/s11356-022-20548-9DOI Listing
May 2022

Antioxidant defense system responses, lysosomal membrane stability and DNA damage in earthworms () exposed to perfluorooctanoic acid: an integrated biomarker approach to evaluating toxicity.

RSC Adv 2021 Aug 3;11(43):26481-26492. Epub 2021 Aug 3.

School of Municipal and Environmental Engineering, Shandong Jianzhu University No. 1000 Fengming Road Jinan 250101 P. R. China

Perfluorooctanoic acid (PFOA) is one of the most representative perfluoroalkyl substances and has garnered intense human and ecological health concerns due to its ubiquity in the environment, bio-accumulative nature and potential toxicological effects. In this study, an artificial soil containing PFOA was used to evaluate the biological toxicity of PFOA to earthworms . Six kinds of oxidative stress biomarkers, including superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione S-transferase (GST), reduced glutathione (GSH) and lipid peroxidation (LPO), as well as lysosomal membrane stability (LMS) and DNA damage in earthworms were detected after exposure to 0, 10, 20, 40, 80 and 120 mg kg PFOA in the soil for 3, 7, 14, 28, and 42 days. The results of multi-biomarker responses indicated that PFOA can induce various adverse effects on earthworms, including growth inhibition, oxidative stress and genotoxicity, resulting in lipid membrane peroxidation, decreased lysosomal membrane stability and DNA damage. LPO, LMS and DNA damage all presented dose- and time-dependent relationships. An integrated biomarker response (IBR) index was applied to summarize the multi-biomarker responses to star plots, and the IBR value was calculated as the area of the plots to indicate the integrated stress of PFOA on earthworms. The IBR index showed that the integrated stress induced by PFOA increased markedly throughout the exposure period, exhibiting a concentration-related and exposure time-related effect. The graphical changing trend of the IBR star plots, along with the multi-biomarker responses, suggested that the biomarkers of the antioxidant defense system in earthworms are sufficiently sensitive for short-term PFOA biomonitoring programs, while the bioindicators that indicate actual damage in organisms are more suitable to be employed in long-term monitoring programs for the risk assessment of PFOA. This is the first study evaluating the biological toxicity of PFOA by using an integrated biomarker approach. Our results showed that PFOA can potentially damage soil ecosystems, which provides valuable information for chemical risk assessment of PFOA in the soil environment and early warning bioindicators of soils contaminated by PFOA.
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http://dx.doi.org/10.1039/d1ra04097aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9037344PMC
August 2021

Silicon Thermo-Optic Switches with Graphene Heaters Operating at Mid-Infrared Waveband.

Nanomaterials (Basel) 2022 Mar 25;12(7). Epub 2022 Mar 25.

State Key Laboratory of Modern Optical Instrumentation, College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, China.

The mid-infrared (MIR, 2-20 μm) waveband is of great interest for integrated photonics in many applications such as on-chip spectroscopic chemical sensing, and optical communication. Thermo-optic switches are essential to large-scale integrated photonic circuits at MIR wavebands. However, current technologies require a thick cladding layer, high driving voltages or may introduce high losses in MIR wavelengths, limiting the performance. This paper has demonstrated thermo-optic (TO) switches operating at 2 μm by integrating graphene onto silicon-on-insulator (SOI) structures. The remarkable thermal and optical properties of graphene make it an excellent heater material platform. The lower loss of graphene at MIR wavelength can reduce the required cladding thickness for the thermo-optics phase shifter from micrometers to tens of nanometers, resulting in a lower driving voltage and power consumption. The modulation efficiency of the microring resonator (MRR) switch was 0.11 nm/mW. The power consumption for 8-dB extinction ratio was 5.18 mW (0.8 V modulation voltage), and the rise/fall time was 3.72/3.96 μs. Furthermore, we demonstrated a 2 × 2 Mach-Zehnder interferometer (MZI) TO switch with a high extinction ratio of more than 27 dB and a switching rise/fall time of 4.92/4.97 μs. A comprehensive analysis of the device performance affected by the device structure and the graphene Fermi level was also performed. The theoretical figure of merit (2.644 mWμs) of graphene heaters is three orders of magnitude higher than that of metal heaters. Such results indicate graphene is an exceptional nanomaterial for future MIR optical interconnects.
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http://dx.doi.org/10.3390/nano12071083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9000650PMC
March 2022

Effect of application mode (capping and amendment) on the control of cadmium release from sediment by apatite/calcite mixture and its phosphorus release risk.

Environ Sci Pollut Res Int 2022 Apr 8. Epub 2022 Apr 8.

Department of Civil Engineering, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China.

In this research, the influence of application mode (capping and amendment) on the control of cadmium (Cd) liberation from sediment by apatite/calcite mixture and its phosphorus release risk were investigated. The results showed that calcite addition had a limited effect on the speciation of Cd in sediment, but apatite addition had a significant impact on the fractionation of Cd in sediment. Apatite amendment could effectively immobilize the most readily mobilized Cd by transferring the acid-soluble fraction to the reducible and residual fractions. Apatite addition also could effectively reduce the concentration of toxicity characteristic leaching procedure (TCLP)-leachable Cd in sediment, and apatite had a much higher reduction efficiency of TCLP-leachable Cd than calcite. Apatite/calcite mixture capping could reduce the risk of Cd liberation from sediment into the overlying water, and the controlling efficiency of apatite/calcite mixture capping was higher than that of apatite/calcite mixture amendment. The effect of apatite/calcite mixture addition on the concentration of reactive soluble phosphorus (SRP) in the overlying water was limited. The introduction of calcite into the apatite capping layer could lower the risk of phosphorus release from apatite to the overlying water as compared to single apatite capping. However, the apatite/calcite mixture capping layer still had a relatively high risk of phosphorus liberation into the overlying water. Results of this work suggest that apatite/calcite mixture has a high potential to be used as a capping material to control Cd release from sediment from the perspective of controlling efficiency and application convenience.
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http://dx.doi.org/10.1007/s11356-022-20113-4DOI Listing
April 2022

Salinity Tolerance in a Synthetic Allotetraploid Wheat (SSAA) Is Similar to Its Higher Tolerant Parent (SS) and Linked to Flavonoids Metabolism.

Front Plant Sci 2022 17;13:835498. Epub 2022 Mar 17.

Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.

Allotetraploidization between A and S (closely related to B) genome species led to the speciation of allotetraploid wheat (genome BBAA). However, the immediate metabolic outcomes and adaptive changes caused by the allotetraploidization event are poorly understood. Here, we investigated how allotetraploidization affected salinity tolerance using a synthetic allotetraploid wheat line (genome SSAA, labeled as 4x), its (genome SS, labeled as SS) and (AA genome, labeled as AA) parents. We found that the degree of salinity tolerance of 4x was similar to its SS parent, and both were substantially more tolerant to salinity stress than AA. This suggests that the SS subgenome exerts a dominant effect for this trait in 4x. Compared with SS and 4x, the salinity-stressed AA plants did not accumulate a higher concentration of Na in leaves, but showed severe membrane peroxidation and accumulated a higher concentration of ROS (HO and O ) and a lesser concentration of flavonoids, indicating that ROS metabolism plays a key role in saline sensitivity. Exogenous flavonoid application to roots of AA plants significantly relieved salinity-caused injury. Our results suggest that the higher accumulation of flavonoids in SS may contribute to ROS scavenging and salinity tolerance, and these physiological properties were stably inherited by the nascent allotetraploid SSAA.
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http://dx.doi.org/10.3389/fpls.2022.835498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8968947PMC
March 2022

Host and geographic barriers shape the competition, coexistence, and extinction patterns of influenza A (H1N1) viruses.

Ecol Evol 2022 Mar 21;12(3):e8732. Epub 2022 Mar 21.

State Key Laboratory of Integrated Management on Pest Insects and Rodents in Agriculture Institute of Zoology Chinese Academy of Sciences Beijing China.

The influenza virus mutates and spreads rapidly, making it suitable for studying evolutionary and ecological processes. The ecological factors and processes by which different lineages of influenza compete or coexist within hosts through time and across geographical space are poorly known. We hypothesized that competition would be stronger for influenza viruses infecting the same host compared to different hosts (the Host Barrier Hypothesis), and for those with a higher cross-region transmission intensity (the Geographic Barrier Hypothesis). Using available sequences of the influenza A (H1N1) virus in GenBank, we identified six lineages, twelve clades, and several replacement events. We found that human-hosted lineages had a higher cross-region transmission intensity than swine-hosted lineages. Co-occurrence probabilities of lineages infecting the same host were lower than those infecting different hosts, and human-hosted lineages had lower co-occurrence probabilities and genetic diversity than swine-hosted lineages. These results show that H1N1 lineages infecting the same host or with high cross-region transmission rates experienced stronger competition and extinction pressures than those infecting different hosts or with low cross-region transmission. Our study highlights how host and geographic barriers shape the competition, extinction, and coexistence patterns of H1N1 lineages and clades.
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http://dx.doi.org/10.1002/ece3.8732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8938227PMC
March 2022

Polyketide Derivatives from the Endophytic Fungus sp. LF5 Isolated from and Their Acetylcholinesterase Inhibitory Activities.

J Fungi (Basel) 2022 Feb 26;8(3). Epub 2022 Feb 26.

Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China.

The secondary metabolites of sp. LF5, an endophytic fungus with acetylcholinesterase (AChE) inhibitory activity isolated from , were investigated. Their structures and absolute configurations were elucidated by means of extensive spectroscopic data, including one- and two-dimensional nuclear magnetic resonance (NMR), high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) analyses, and calculations of electronic circular dichroism (ECD). A chemical study on the solid-cultured fungus LF5 resulted in 11 polyketide derivatives, which included three previously undescribed derivatives: aspilactonol I (), 2-(1-hydroxyethyl)-6-methylisonicotinic acid (), and 6,8-dihydroxy-3-(1', 2'-dihydroxypropyl)-isocoumarin (), and two new natural-source-derived aspilactonols (G, H) (, ). Moreover, the absolute configuration of de--methyldiaporthin () was identified for the first time. Compounds and exhibited inhibitory activity against AChE with half maximal inhibitory concentration (IC) values of 6.26 and 21.18 µM, respectively. Aspilactonol I () is the first reported furanone AChE inhibitor (AChEI). The results indicated that is a good source of polyketide derivatives. This study identified intriguing lead compounds for further research and development of new AChEIs.
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http://dx.doi.org/10.3390/jof8030232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8955197PMC
February 2022

Comparative transcriptome analysis of melon (Cucumis melo L.) reveals candidate genes and pathways involved in powdery mildew resistance.

Sci Rep 2022 03 23;12(1):4936. Epub 2022 Mar 23.

Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, Xinjiang, People's Republic of China.

Powdery mildew is a major disease in melon, primarily caused by Podosphaera xanthii (Px). Some melon varieties were resistant to powdery mildew, while others were susceptible. However, the candidate genes associated with resistance and the mechanism of resistance/susceptibility to powdery mildew in melon remain unclear. In this study, disease-resistant melon cultivar TG-1 and disease-susceptible melon cultivar TG-5 were selected for comparative transcriptome analysis. The results suggested that the numbers of differentially expressed genes (DEGs) in TG-5 was always more than that in TG-1 at each of the four time points after Px infection, indicating that their responses to Px infection may be different and that the active response of TG-5 to Px infection may be earlier than that of TG-1. Transcription factors (TFs) analysis among the DEGs revealed that the bHLH, ERF, and MYB families in TG-1 may play a vital role in the interaction between melon and powdery mildew pathogens. GO enrichment analysis of these DEGs in TG-5 showed that the SBP, HSF, and ERF gene families may play important roles in the early stage of melon development after Px infection. Finally, we speculated on the regulatory pathways of melon powdery mildew and found PTI and ABA signaling genes may be associated with the response to Px infection in melon.
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http://dx.doi.org/10.1038/s41598-022-08763-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8943038PMC
March 2022

L-Arginine enhanced perylenequinone production in the endophytic fungus Shiraia sp. Slf14(w) via NO signaling pathway.

Appl Microbiol Biotechnol 2022 Apr 15;106(7):2619-2636. Epub 2022 Mar 15.

Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, 330022, China.

Perylenequinones (PQ) are natural polyketides used as anti-microbial, -cancers, and -viral photodynamic therapy agents. Herein, the effects of L-arginine (Arg) on PQ biosynthesis of Shiraia sp. Slf14(w) and the underlying molecular mechanism were investigated. The total content of PQ reached 817.64 ± 72.53 mg/L under optimal conditions of Arg addition, indicating a 30.52-fold improvement over controls. Comparative transcriptome analysis demonstrated that Arg supplement promoted PQ precursors biosynthesis of Slf14(w) by upregulating the expression of critical genes associated with the glycolysis pathway, and acetyl-CoA and malonyl-CoA synthesis. By downregulating the expression of genes related to the glyoxylate cycle pathway and succinate dehydrogenase, more acetyl-CoA flow into the formation of PQ. Arg supplement upregulated the putative biosynthetic gene clusters for PQ and activated the transporter proteins (MFS and ABC) for exudation of PQ. Further studies showed that Arg increased the gene transcription levels of nitric oxide synthase (NOS) and nitrate reductase (NR), and activated NOS and NR, thus promoting the formation of nitric oxide (NO). A supplement of NO donor sodium nitroprusside (SNP) also confirmed that NO triggered promoted biosynthesis and efflux of PQ. PQ production stimulated by Arg or/and SNP can be significantly inhibited upon the addition of NO scavenger carboxy-PTIO, NOS inhibitor N-nitro-L-arginine, or soluble guanylate cyclase inhibitor NS-2028. These results showed that Arg-derived NO, as a signaling molecule, is involved in the biosynthesis and regulation of PQ in Slf14(W) through the NO-cGMP-PKG signaling pathway. Our results provide a valuable strategy for large-scale PQ production and contribute to further understanding of NO signaling in the fungal metabolite biosynthesis. KEY POINTS: • PQ production of Shiraia sp. Slf14(w) was significantly improved by L-arginine addition. • Arginine-derived NO was firstly reported to be involved in the biosynthesis and regulation of PQ. • The NO-cGMP-PKG signaling pathway was proposed for the first time to participate in PQ biosynthesis.
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http://dx.doi.org/10.1007/s00253-022-11877-3DOI Listing
April 2022

A rodent herbivore reduces its predation risk through ecosystem engineering.

Curr Biol 2022 04 11;32(8):1869-1874.e4. Epub 2022 Mar 11.

State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

Predator-prey interactions are ubiquitous and powerful forces that structure ecological communities. Habitat complexity has been shown to be particularly important in regulating the strength of predator-prey interactions. While it is well established that changes in habitat structure can alter the efficacy of predatory and anti-predatory behaviors, little is known about the consequences of engineering activity by prey species who modify the external environment to reduce their own predation risk. Using field surveys and manipulative experiments, we evaluated how habitat modification by Brandt's voles (Lasiopodomys brandtii) influences predation risk from a principal avian predator (shrike; Lanius spp.) in a steppe grassland, located in Inner Mongolia, China. We found that voles actively modify habitat structure by cutting down a large, unpalatable bunchgrass species (Achnatherum splendens) in the presence of shrikes, a behavior that disappeared when these avian predators were excluded experimentally. The damage activities of these voless dramatically decreased the volume of unpalatable grasses, which in turn reduced visitations by shrikes and thus mortality rates. Our study shows that herbivorous prey that act as ecosystem engineers can directly reduce their own predation risk by modifying habitat structure. Given the ubiquity of predation risks faced by consumers, and the likely ability of many consumers to alter the habitat structure in which they live, the interplay between predation risk and ecosystem engineering may be an important but unappreciated mechanism at play in natural communities.
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http://dx.doi.org/10.1016/j.cub.2022.02.074DOI Listing
April 2022

Immobilization of lead, copper, cadmium, nickel, and zinc in sediment by red mud: adsorption characteristics, mechanism, and effect of dosage on immobilization efficiency.

Environ Sci Pollut Res Int 2022 Jul 7;29(34):51793-51814. Epub 2022 Mar 7.

College of Marine Ecology and Environment, Shanghai Ocean University, Hucheng Ring Road No. 999, Shanghai, 201306, People's Republic of China.

The objective of this work was to determine the effect of dosage on the immobilization of lead (Pb), copper (Cu), cadmium (Cd), nickel (Ni), and zinc (Zn) in sediment by red mud (RM). To achieve this aim, the adsorption characteristics and mechanism of Pb, Cu, Cd, Ni, and Zn from aqueous solution on RM were studied at first, and then the influence of the RM dosage on the fractionation and leaching potential of Pb, Cu, Cd, Ni, and Zn in sediment was investigated. The results showed that RM possessed high adsorption capacities for Pb(II), Cu(II), Cd(II), Ni(II), and Zn(II) in aqueous solution. The maximum monolayer Pb(II), Cu(II), Cd(II), Ni(II), and Zn(II) adsorption capacities for RM derived from the Langmuir isotherm model were found to be 296, 39.2, 70.2, 46.0, and 50.7 mg/g, respectively. The addition of RM into sediment could effectively reduce the toxicity characteristic leaching procedure (TCLP)-leachable concentrations of Pb, Cu, Cd, Ni, and Zn in the sediment. The added RM could effectively immobilize the mobile (exchangeable, reducible, and oxidizable fractions) Pb in sediment by the conversion of the exchangeable and reducible fractions into the residual fraction, and it could effectively immobilize the mobile Cu, Cd, Ni, and Zn in sediment by the conversion of the exchangeable fraction into the residual fraction. The quantities of mobile Pb, Cu, Cd, and Ni immobilized by RM had a good linear relationship with the added RM. The above results suggest that RM is a promising amendment for the immobilization of mobile Pb, Cu, Cd, Ni, and Zn in sediment, and the linear relationship between the RM dosage and the quantities of immobilized Pb, Cu, Cd, and Ni by RM can be employed to determine the RM dosage required for the immobilization of mobile Pb, Cu, Cd, and Ni in sediment.
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http://dx.doi.org/10.1007/s11356-022-19506-2DOI Listing
July 2022

Endophytic fungi from Dongxiang wild rice ( Griff) show diverse catalytic potential for converting glycyrrhizin.

3 Biotech 2022 Mar 26;12(3):79. Epub 2022 Feb 26.

Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022 China.

Endophytic fungi inhabiting niche environments are novel biocatalyst resources that need to be exploited urgently. In this study, 63 endophytic fungi isolated from Dongxiang wild rice ( Griff.) were tested to assess their potentials to transform glycyrrhizin (GL) into glycyrrhetinic acid monoglucuronide (GAMG) or glycyrrhetinic acid (GA), of which 12 strains were shown to have β-d-glucuronidase activity. Based on morphological characteristics and rDNA ITS sequence analysis, the strains S59, L138, L55 and R57 with high GL molar conversion rates (55%, 45%, 65% and 89%) were further identified as S59, L138, L55 and R57, respectively. These four strains with four different types of GL conversion processes were identified, i.e., (1) GL → GAMG in S59, (2) GL → GAMG and GA in L55, (3) GL → GA in L138, and (4) GL → GAMG → GA in R57, in which the bioconversion type (4) is reported for the first time. The study not only provided abundant and diverse β-d-glucuronidase resources that can be used for GL bioconversion, especially for GAMG biosynthesis from endophytic fungi, but also expanded our knowledge of potential roles of endophytes as new biocatalysts in biotransformation.
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http://dx.doi.org/10.1007/s13205-022-03138-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8882211PMC
March 2022

Evolutionary and ecological patterns of scatter- and larder-hoarding behaviours in rodents.

Ecol Lett 2022 May 1;25(5):1202-1214. Epub 2022 Mar 1.

State Key Laboratory of Grassland Agro-ecosystems, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.

Scatter- and larder hoarding are the primary strategies of food-hoarding animals and have important implications for plant-animal interactions and plant recruitment. However, their origins and influencing factors have not been fully investigated across a wide range of taxa. Our systematic literature search amassed data for 183 seed-hoarding rodent species worldwide and tested relationships of seed-hoarding behaviours with phylogenetic signal, functional traits and environmental factors. We found that the evolution of hoarding strategies was not random in phylogeny, and scatter hoarding originated independently multiple times from larder hoarding. Rodents with higher encephalisation quotient (relative brain size), omnivorous diet (related to dependence on seeds) and inhabiting lower latitudes were disproportionately likely to scatter hoard. Despite body mass's potential relationship with competition through food defence, it was associated with food-hoarding strategy only in a few families. Our results show the need to study the community and ecological context of food-hoarding behaviours.
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http://dx.doi.org/10.1111/ele.13992DOI Listing
May 2022

Factors influencing range contraction of a rodent herbivore in a steppe grassland over the past decades.

Ecol Evol 2022 Feb 14;12(2):e8546. Epub 2022 Feb 14.

State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China.

Climate warming and human disturbance are known to be key drivers in causing range contraction of many species, but quantitative assessment on their distinctive and interactive effects on local disappearance is still rare.In this study, we examined the association of climate warming and human disturbance stressors with local disappearance probability of Brandt's voles () in a steppe grassland in northern China.We used logistic generalized additive models to quantify the relationship between local disappearance probability of Brandt's voles and environmental variables. The year following the last observation year was used to estimate the disappearance threshold of Brandt's voles. We projected the distribution change of Brandt's voles under future climate warming scenarios.We found climate warming attributed to local disappearance and range contraction for southern populations of Brandt's voles from 1971 to 2020. Human stressors and high vegetation coverage increased the probability of local disappearance of voles in years of abundant precipitation. The southern boundary retreated northward at a speed of 99.0 km per decade with the temperature rise of 0.36°C. The disappearance threshold of maximum air temperature of Brandt's voles in the warmest month (27.50 ± 1.61°C) was similar to the lower critical temperature of its thermal neutral zone.Our study suggests that the rapid climate change over the past decades contributed to the range contraction of its southern boundary of this keystone species in the steppe grassland of China. It is necessary to take actions to preserve the isolated populations of Brandt's voles from the effects of accelerated climate change and human disturbance.
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http://dx.doi.org/10.1002/ece3.8546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8843818PMC
February 2022

Habitats Show More Impacts Than Host Species in Shaping Gut Microbiota of Sympatric Rodent Species in a Fragmented Forest.

Front Microbiol 2022 7;13:811990. Epub 2022 Feb 7.

State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.

Gut microbiota play a significant role for animals to adapt to the changing environment. Host species and habitats are key drivers in shaping the diversity and composition of the microbiota, but the determinants of composition of the sympatric host gut microbiome remain poorly understood within an ecosystem. In this study, we examined the effects of habitats of different succession stages and host species on the diversity and composition of fecal gut microbiota in four sympatric rodent species (, , , and ) in a subtropical forest. We found, as compared to the differences between species, habitat types showed a much larger effect on the gut microbiota of rodents. Alpha diversity of the microbial community of , , and was highest in farmland, followed by primary forest and shrubland, and lowest in secondary forest. Beta diversity of the three rodent species showed significant different among habitats. The alpha diversity of gut microbiota of was significantly higher than those of and , and its beta diversity showed significant difference from . Our results suggested that gut microbiota were important for animals in responding to diet changes in different habitats under human disturbances.
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http://dx.doi.org/10.3389/fmicb.2022.811990DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8859092PMC
February 2022

Successful treatment of tuberculosis verrucosa cutis with fester as primary manifestation with photodynamic therapy and anti-tubercular drugs.

Photodiagnosis Photodyn Ther 2022 Jun 19;38:102763. Epub 2022 Feb 19.

Department of Dermatology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China; Institute of Dermatology, Jiangxi Academy of Clinical Medical Sciences, Nanchang, Jiangxi, China. Electronic address:

Tuberculosis verrucosa cutis (TBVC) is a rare type of cutaneous tuberculosis, which often occurs in the body with good immunity to tuberculosis bacilli. It usually presents as a hyperkeratotic verrucous plaque with polygonal boarders but can mimic or evolved into other dermatosis such as verruca vulgaris, chromoblastomycosis, hyperkeratotic lupus vulgaris, hypertrophic lichen planus, or squamous cell carcinoma, leading to delayed diagnosis. Here, we reported that a 62-year-old patient diagnosed by TBVC with fester as primary manifestation. Photodynamic therapy combined with anti-tuberculosis drugs is an effective method to treat TBVC lesions with fester, and it may shorten the treatment cycle of anti-tuberculosis drugs.
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http://dx.doi.org/10.1016/j.pdpdt.2022.102763DOI Listing
June 2022

Isolation and acetylcholinesterase inhibitory activity of asterric acid derivatives produced by FL15, an endophytic fungus from .

3 Biotech 2022 Mar 5;12(3):60. Epub 2022 Feb 5.

Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022 Jiangxi People's Republic of China.

Alzheimer's disease (AD) is a neurodegenerative disease and the fourth leading cause of death after cardiovascular disease, tumors, and stroke. Acetylcholinesterase (AChE) inhibitors, which are based on cholinergic damage, remain the mainstream drugs to alleviate AD-related symptoms. This study aimed to explore novel AChE inhibitors produced by the endophytic fungus FL15 from . The fungus was identified as FL15 according to its morphological characteristics and ITS, 18S rDNA, and 28S rDNA sequence analysis. Subsequently, seven natural metabolites were isolated from strain FL15, and identified as asterric acid , methyl asterrate , ethyl asterrate , emodin , physcion , chrysophanol , and sulochrin . Compounds , which possess a diphenyl ether structure, exhibited highly selective and moderate AChE inhibitory activities with IC values of 66.7, 23.3, and 20.1 μM, respectively. The molecular docking analysis showed that compounds interacted with the active catalytic site and peripheral anionic site of AChE, and the esterification substitution groups at position 8 of asterric acid may contribute to its bioactivity. The asterric acid derivatives showed highly selective and moderate AChE inhibitory activities, probably via interaction with the peripheral anionic site and catalytic site of AChE. To the best of our knowledge, this study was the first report of the AChE inhibitory activity of asterric acid derivatives, which opens new perspectives for the design of more effective derivatives that could serve as a drug carrier for new chemotherapeutic agents to treat AD.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03125-2.
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http://dx.doi.org/10.1007/s13205-022-03125-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8817963PMC
March 2022

GRAND: An Integrated Genome, Transcriptome Resources, and Gene Network Database for .

Front Plant Sci 2022 21;13:773107. Epub 2022 Jan 21.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.

With the increasing amount of cotton omics data, breeding scientists are confronted with the question of how to use massive cotton data to mine effective breeding information. Here, we construct a Resource And Network Database (GRAND), which integrates 18 cotton genome sequences, genome annotations, two cotton genome variations information, and also four transcriptomes for species. GRAND allows to explore and mine this data with the help of a toolbox that comprises a flexible search system, BLAST and BLAT suite, orthologous gene ID, networks of co-expressed genes, primer design, Gbrowse and Jbrowse, and drawing instruments. GRAND provides important information regarding resources and hopefully can accelerate the progress of cultivating cotton varieties.
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http://dx.doi.org/10.3389/fpls.2022.773107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8814657PMC
January 2022

Streptococcal pyrogenic exotoxin B cleaves GSDMA and triggers pyroptosis.

Nature 2022 02 2;602(7897):496-502. Epub 2022 Feb 2.

The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.

Gasdermins, a family of five pore-forming proteins (GSDMA-GSDME) in humans expressed predominantly in the skin, mucosa and immune sentinel cells, are key executioners of inflammatory cell death (pyroptosis), which recruits immune cells to infection sites and promotes protective immunity. Pore formation is triggered by gasdermin cleavage. Although the proteases that activate GSDMB, C, D and E have been identified, how GSDMA-the dominant gasdermin in the skin-is activated, remains unknown. Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a major skin pathogen that causes substantial morbidity and mortality worldwide. Here we show that the GAS cysteine protease SpeB virulence factor triggers keratinocyte pyroptosis by cleaving GSDMA after Gln246, unleashing an active N-terminal fragment that triggers pyroptosis. Gsdma1 genetic deficiency blunts mouse immune responses to GAS, resulting in uncontrolled bacterial dissemination and death. GSDMA acts as both a sensor and substrate of GAS SpeB and as an effector to trigger pyroptosis, adding a simple one-molecule mechanism for host recognition and control of virulence of a dangerous microbial pathogen.
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http://dx.doi.org/10.1038/s41586-021-04384-4DOI Listing
February 2022

Streptococcal pyrogenic exotoxin B cleaves GSDMA and triggers pyroptosis.

Nature 2022 02 2;602(7897):496-502. Epub 2022 Feb 2.

The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.

Gasdermins, a family of five pore-forming proteins (GSDMA-GSDME) in humans expressed predominantly in the skin, mucosa and immune sentinel cells, are key executioners of inflammatory cell death (pyroptosis), which recruits immune cells to infection sites and promotes protective immunity. Pore formation is triggered by gasdermin cleavage. Although the proteases that activate GSDMB, C, D and E have been identified, how GSDMA-the dominant gasdermin in the skin-is activated, remains unknown. Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a major skin pathogen that causes substantial morbidity and mortality worldwide. Here we show that the GAS cysteine protease SpeB virulence factor triggers keratinocyte pyroptosis by cleaving GSDMA after Gln246, unleashing an active N-terminal fragment that triggers pyroptosis. Gsdma1 genetic deficiency blunts mouse immune responses to GAS, resulting in uncontrolled bacterial dissemination and death. GSDMA acts as both a sensor and substrate of GAS SpeB and as an effector to trigger pyroptosis, adding a simple one-molecule mechanism for host recognition and control of virulence of a dangerous microbial pathogen.
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http://dx.doi.org/10.1038/s41586-021-04384-4DOI Listing
February 2022

Rapid Spread of Severe Fever with Thrombocytopenia Syndrome Virus by Parthenogenetic Asian Longhorned Ticks.

Emerg Infect Dis 2022 02;28(2):363-372

Severe fever with thrombocytopenia syndrome virus (SFTSV) is spreading rapidly in Asia. This virus is transmitted by the Asian longhorned tick (Haemaphysalis longicornis), which has parthenogenetically and sexually reproducing populations. Parthenogenetic populations were found in ≥15 provinces in China and strongly correlated with the distribution of severe fever with thrombocytopenia syndrome cases. However, distribution of these cases was poorly correlated with the distribution of populations of bisexual ticks. Phylogeographic analysis suggested that the parthenogenetic population spread much faster than bisexual population because colonization is independent of sexual reproduction. A higher proportion of parthenogenetic ticks was collected from migratory birds captured at an SFTSV-endemic area, implicating the contribution to the long-range movement of these ticks in China. The SFTSV susceptibility of parthenogenetic females was similar to that of bisexual females under laboratory conditions. These results suggest that parthenogenetic Asian longhorned ticks, probably transported by migratory birds, play a major role in the rapid spread of SFTSV.
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http://dx.doi.org/10.3201/eid2802.211532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8798674PMC
February 2022

The Lysosomal Rag-Ragulator Complex Licenses RIPK1 and Caspase-8-mediated Pyroptosis by .

Science 2021 06;372(6549)

The Joint Center for Infection and Immunity between Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center (Guangzhou, 510623, China) and Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.

Host cells initiate cell death programs to limit pathogen infection. Inhibition of transforming growth factor-β-activated kinase 1 (TAK1) by pathogenic in macrophages triggers receptor-interacting serine/threonine-protein kinase 1 (RIPK1)-dependent caspase-8 cleavage of gasdermin D (GSDMD) and inflammatory cell death (pyroptosis). A genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screen to uncover mediators of caspase-8-dependent pyroptosis identified an unexpected role of the lysosomal FLCN-FNIP2-Rag-Ragulator supercomplex, which regulates metabolic signalling and the mechanistic target of rapamycin complex 1 (mTORC1). In response to infection, FADD, RIPK1 and caspase-8 were recruited to Rag-Ragulator, causing RIPK1 phosphorylation and caspase-8 activation. Pyroptosis activation depended on Rag GTPase activity and lysosomal tethering of Rag-Ragulator, but not mTORC1. Thus, the lysosomal metabolic regulator Rag-Ragulator instructs the inflammatory response to .
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http://dx.doi.org/10.1126/science.abg0269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8769499PMC
June 2021

Genome sequence and transcriptome of Sorbus pohuashanensis provide insights into population evolution and leaf sunburn response.

J Genet Genomics 2022 Jun 5;49(6):547-558. Epub 2022 Jan 5.

Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China. Electronic address:

Sorbus pohuashanensis (Hance) Hedl. is a potential horticulture and medicinal plant, but its genomic and genetic backgrounds remain unknown. Here, we sequence and assemble the S. pohuashanensis reference genome using PacBio long reads. Based on the new reference genome, we resequence a core collection of 22 Sorbus spp. samples, which are divided into 2 groups (G1 and G2) based on phylogenetic and PCA analyses. These phylogenetic clusters are highly consistent with their classification based on leaf shape. Natural hybridization between the G1 and G2 groups is evidenced by a sample (R21) with a highly heterozygous genotype. Nucleotide diversity (π) analysis shows that G1 has a higher diversity than G2 and that G2 originated from G1. During the evolution process, the gene families involved in photosynthesis pathways expanded and the gene families involved in energy consumption contracted. RNA-seq data suggests that flavonoid biosynthesis and heat-shock protein (HSP)-heat-shock factor (HSF) pathways play important roles in protection against sunburn. This study provides new insights into the evolution of Sorbus spp. genomes. In addition, the genomic resources, and the identified genetic variations, especially those related to stress resistance, will help future efforts to produce and breed Sorbus spp.
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http://dx.doi.org/10.1016/j.jgg.2021.12.009DOI Listing
June 2022
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