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Abstract Human ABC transporters ABCD1–3 are all localized on the peroxisomal membrane and participate in the β-oxidation of fatty acyl-CoAs, but they differ from each other in substrate specificity. The transport of branched-chain fatty acids from cytosol to peroxisome is specifically driven by ABCD3, dysfunction of which causes severe liver diseases such as hepatosplenomegaly. Here we report two cryogenic electron microscopy (cryo-EM) structures of ABCD3 bound to phytanoyl-CoA and ATP at resolutions of 2.9 Å and 3.2 Å, respectively. A pair of phytanoyl-CoA molecules were observed in ABCD3, each binding to one transmembrane domain (TMD), which is distinct from our previously reported structure of ABCD1, where each fatty acyl-CoA molecule strongly crosslinks two TMDs. Upon ATP binding, ABCD3 exhibits a conformation that is open towards the peroxisomal matrix, leaving two extra densities corresponding to two CoA molecules deeply embedded in the translocation cavity. Structural analysis combined with substrate-stimulated ATPase activity assays indicated that the present structures might represent two states of ABCD3 in the transport cycle. These findings advance our understanding of fatty acid oxidation and the molecular pathology of related diseases.

Ischemia-reperfusion (I/R) injury is an inevitable pathological process in many clinical practices, such as transplantation, myocardial infarction, cerebral infarction and current treatments for I/R injury are limited. Ferroptosis is an essential pathogenic mechanism for triggering I/R injury, characterized by excess reactive oxygen species (ROS) accompanied by lipid peroxidation and increased intracellular iron concentration consistent with the mechanical manifestations of I/R. Resveratrol (RES) is a polyphenolic compound found in red wine that acts as an iron chelator, lipophilic antioxidant, and lipid peroxidation inhibitor. It helps to inhibit I/R damage by reversing ferroptosis-induced cell death, providing insights into developing therapeutic strategies for this devastating disease. In this review, we used the keywords “ferroptosis”, “resveratrol”, and “ischemia-reperfusion” in conjunction with each other, collected 1039 papers from the last decade, 114 relevant papers were screened to review the research progress on the mitigating of I/R injury through ferroptosis in Res and its future perspectives.

Prestack amplitude versus offset (AVO) inversion is an essential tool to estimate elastic properties. Approximations of P-wave reflection coefficients based on the Zoeppritz equation are limited by the assumption of weak contrast and are inaccurate for far offset, and the existing nonlinear inversion method, like ant colony optimization (ACO), cannot converge to the global optimal solution within a limited time. Consequently, we propose a nonlinear AVO inversion method based on the exact Zoeppritz equation using hybrid quantum ant colony optimization (HQACO). The Zoeppritz equation is a forward modeling approach with high accuracy at far offset and is valid at the strong-contrast interface. HQACO, as a global optimization algorithm, not only has the potential of ACO to search global solutions but also exploits the power of quantum computing to speed up optimization procedures. The self-adaptive rotating strategy is proposed to improve the flexibility and efficiency of the conventional quantum rotating gate largely. Moreover, the quantum gate is introduced to enhance the global search ability. Numerical results show that the average evaluation number required for the global solution decreases largely and the solution converges to the global optimal solution closely using the proposed method. Synthetic applications verify that HQACO shows the most reliable exploring competence to find the global solution. The new inversion method is not only suitable for the strong-contrast interface with noise but also shows promising accuracy using the wide offset range.

Over the past 30 years, the survival rate for osteosarcoma (OS) has remained stagnant, indicating persistent challenges in diagnosis and treatment. Photodynamic therapy (PDT) has emerged as a novel and promising treatment modality for OS. Despite apoptosis being the primary mechanism attributed to PDT, it fails to overcome issues such as low efficacy and resistance. Ferroptosis, a Fe2+-dependent cell death process, has the potential to enhance PDT's efficacy by increasing reactive oxygen species (ROS) through the Fenton reaction. In this study, we investigated the anti-tumor mechanism of PDT and introduced an innovative therapeutic strategy that synergistically induces apoptosis and ferroptosis. Furthermore, we have identified HERC1 as a pivotal protein involved in the ubiquitination and degradation of NCOA4, while also uncovering a potential regulatory factor involving NRF2. Ultimately, by targeting the HERC1-NCOA4 axis during PDT, we successfully achieved full activation of ferroptosis, which significantly enhanced the anti-tumor efficacy of PDT. In conclusion, these findings provide new theoretical evidence for further characterizing mechanism of PDT and offer new molecular targets for the treatment of OS.

Abstract The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Following our recent report on the capsid structure of A-1(L), here we present the high-resolution cryo-EM structure of its intact tail machine including the neck, tail and attached fibers. Besides the dodecameric portal, the neck contains a canonical hexamer connected to a unique pentadecamer that anchors five extended bead-chain-like neck fibers. The 1045-Å-long contractile tail is composed of a helical bundle of tape measure proteins surrounded by a layer of tube proteins and a layer of sheath proteins, ended with a five-component baseplate. The six long and six short tail fibers are folded back pairwise, each with one end anchoring to the baseplate and the distal end pointing to the capsid. Structural analysis combined with biochemical assays further enable us to identify the dual hydrolytic activities of the baseplate hub, in addition to two host receptor binding domains in the tail fibers. Moreover, the structure of the intact A-1(L) also helps us to reannotate its genome. These findings will facilitate the application of A-1(L) as a chassis cyanophage in synthetic biology.

ABSTRACT The cyanosiphophage Mic1 specifically infects the bloom-forming Microcystis aeruginosa FACHB 1339 from Lake Chaohu, China. Previous genomic analysis showed that its 92,627 bp double-stranded DNA genome consists of 98 putative open reading frames, 63% of which are of unknown function. Here, we investigated the transcriptome dynamics of Mic1 and its host using RNA sequencing. In the early, middle, and late phases of the 10 h lytic cycle, the Mic1 genes are sequentially expressed and could be further temporally grouped into two distinct clusters in each phase. Notably, six early genes, including gp49 that encodes a TnpB-like transposase, immediately reach the highest transcriptional level in half an hour, representing a pioneer cluster that rapidly regulates and redirects host metabolism toward the phage. An in-depth analysis of the host transcriptomic profile in response to Mic1 infection revealed significant upregulation of a polyketide synthase pathway and a type III-B CRISPR system, accompanied by moderate downregulation of the photosynthesis and key metabolism pathways. The constant increase of phage transcripts and relatively low replacement rate over the host transcripts indicated that Mic1 utilizes a unique strategy to gradually take over a small portion of host metabolism pathways after infection. In addition, genomic analysis of a less-infective Mic1 and a Mic1-resistant host strain further confirmed their dynamic interplay and coevolution via the frequent horizontal gene transfer. These findings provide insights into the mutual benefit and symbiosis of the highly polymorphic cyanobacteria M. aeruginosa and cyanophages.IMPORTANCEThe highly polymorphic Microcystis aeruginosa is one of the predominant bloom-forming cyanobacteria in eutrophic freshwater bodies and is infected by diverse and abundant cyanophages. The presence of a large number of defense systems in M. aeruginosa genome suggests a dynamic interplay and coevolution with the cyanophages. In this study, we investigated the temporal gene expression pattern of Mic1 after infection and the corresponding transcriptional responses of its host. Moreover, the identification of a less-infective Mic1 and a Mic1-resistant host strain provided the evolved genes in the phage-host coevolution during the multiple-generation cultivation in the laboratory. Our findings enrich the knowledge on the interplay and coevolution of M. aeruginosa and its cyanophages and lay the foundation for the future application of cyanophage as a potential eco-friendly and bio-safe agent in controlling the succession of harmful cyanobacterial blooms.

Abstract Bilirubin is mainly generated from the breakdown of heme when red blood cells reach the end of their lifespan. Accumulation of bilirubin in human body usually leads to various disorders, including jaundice and liver disease. Bilirubin is conjugated in hepatocytes and excreted to bile duct via the ATP-binding cassette transporter ABCC2, dysfunction of which would lead to Dubin-Johnson syndrome. Here we determine the structures of ABCC2 in the apo, substrate-bound and ATP/ADP-bound forms using the cryo-electron microscopy, exhibiting a full transporter with a regulatory (R) domain inserted between the two half modules. Combined with substrate-stimulated ATPase and transport activity assays, structural analysis enables us to figure out transport cycle of ABCC2 with the R domain adopting various conformations. At the rest state, the R domain binding to the translocation cavity functions as an affinity filter that allows the substrates of high affinity to be transported in priority. Upon substrate binding, the R domain is expelled from the cavity and docks to the lateral of transmembrane domain following ATP hydrolysis. Our findings provide structural insights into a transport mechanism of ABC transporters finely tuned by the R domain.

Transportation is a major sector of anthropogenic emissions in urban areas and deteriorates air quality. The surface and vertical observational data were combined with the model results to reveal its impact on the horizontal and vertical variations of pollutants during the COVID-19 lockdown period. The evident reductions in ambient PM2.5 (∼30%) and NO2 (∼50%) concentrations but a ∼25% increase in O3 concentration were observed at the transportation sites. On the vertical scale, a uniform decrease of ∼28% in PM2.5 concentrations was observed within 600 m. However, the vertical profiles of NO2 and O3 exhibited increasing vertical variation rates with concentrations varying significantly within 400 m. Meanwhile, Ox shared a similar pattern of vertical profile with O3, with a uniform increase (∼5%) within 600 m in the urban area. The WRF-CMAQ model reproduced the variations, and revealed that the reduction of transportation emissions was the key factor contributing to the increase of urban O3 and Ox due to the weakened NO titration effect. The simulated vertical profile of NO2 was featured by a decreasing curve, while that of O3 exhibited the opposite trend. We find that the transportation emissions impact vertical concentrations of NO2 and O3 within at most 400 m. The process analysis revealed that the vertical transport and horizontal transport from bay areas contributed to O3 in the urban area, while chemical processes mainly consumed it. The reduction in transportation emissions weakened the consumption and resulted in O3 accumulation during rush hours and at night. The variation of planetary boundary layer height also favored the rise of urban O3 by promoting vertical transport at daytime and trapping it at night. The reduction in NOx emissions from the transportation enhanced O3 pollution, suggesting that collaborative reductions in VOCs from multiple sectors should be conducted. This study also indicated that regional collaborations in emission reductions were necessary for comprehensive air pollution prevention.

Background: The extracellular matrix (ECM) modeling induced by the metalloproteinases is a vital characteristic for tumor progression. Previous studies mainly focus on the functions of two subgroups of metalloproteinases: matrix metalloproteinases (MMPs) and a disintegrin and metalloproteases (ADAMs) in tumors. The roles of another important group: the ADAMs with thrombospondin motifs (ADAMTS) remain unclear. This study aimed to perform a pan-cancer analysis of procollagen N-propeptidase subgroup of ADAMTS (PNPSA). Methods: We systematically analyzed expression landscape, genomic variations, prognostic value, and cell expression clusters of PNPSA in pan-cancer based on the multiple integrated open databases. Besides, we also analyzed the impacts of expressions and genomic variations of PNPSA members on tumor immune microenvironment (TIME) and immune-related molecules in pan-cancer based on the immune-related open databases. The Gene Set Variation Analysis (GSVA) was performed to evaluate the associations of the whole PNPSA with prognosis, tumor indicators, TIME, and drug sensitivities. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed to reveal related signaling pathways. Finally, immunohistochemical staining was used to validate the differential analysis results. Results: We found a dual prognostic role of PNPSA members in pan-cancer and they were significantly correlated with TIME and immune-related molecules. Interestingly, the copy number variations (CNVs) of all PNPSA members were revealed to be negatively correlated with NK cell infiltration in most cancers. Single-cell sequencing analysis reveals expressions of PNPSA gene family members on some specific tumor and immune cells in addition to the fibroblasts. The GSVA score was found to have some predictive value for survival status in Brain Lower Grade Glioma (LGG), Mesothelioma (MESO), and Uveal Melanoma (UVM) and to be significantly correlated with tumorigenesis-related pathways such as PI3K-Akt, AGE-RAGE, etc. The GSVA score also shows some predictive value for chemotherapy and immunotherapy efficacy in some tumors. Conclusions: PNPSA was correlated with tumor development and might be potential tumor biomarker and therapeutic target.

Abstract Background Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date. Results Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0 kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the α-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and α-proteobacteria. Conclusion In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.

The authors identify nanobodies from immunized alpaca with broadly neutralizing activity against SARS-CoV-1, SARS-CoV-2 variants, and major sarbecoviruses. One representative nanobody binds to a highly conserved epitope on RBD and protects K18-hACE2 mice from Omicron and Delta infection.

Abstract RuBisCO is the most abundant enzyme in nature, catalyzing the fixation of CO2 in photosynthesis. Its common form consists of eight RbcL and eight RbcS subunits, the assembly of which requires a series of chaperones that include RbcX and RuBisCO accumulation factor 1 (Raf1). To understand how these RuBisCO-specific chaperones function during cyanobacterial RbcL8RbcS8 (L8S8) holoenzyme formation, we solved a 3.3-Å cryo-electron microscopy structure of a 32-subunit RbcL8Raf18RbcX16 (L8F8X16) assembly intermediate from Anabaena sp. PCC 7120. Comparison to the previously resolved L8F8 and L8X16 structures together with biochemical assays revealed that the L8F8X16 complex forms a rather dynamic structural intermediate, favoring RbcS displacement of Raf1 and RbcX. In vitro assays further demonstrated that both Raf1 and RbcX function to regulate RuBisCO condensate formation by restricting CcmM35 binding to the stably assembled L8S8 holoenzymes. Combined with previous findings, we propose a model on how Raf1 and RbcX work in concert to facilitate, and regulate, cyanobacterial RuBisCO assembly as well as disassembly of RuBisCO condensates.

The ternary chalcogenide AgBiS2 has attracted widespread attention in the field of photovoltaic and photoelectric devices due to its excellent properties. In this study, AgBiS2 powders with an average diameter of 200 nm were prepared via a simple and convenient reflux method from silver acetate, bismuth nitrate pentahydrate, and n-dodecyl mercaptan. The adjustment of the ratios of Ag:Bi:S raw materials and of the reaction temperatures were carried out to investigate the significance of the synthesis conditions toward the composition of the as-synthesized AgBiS2. The results of XRD indicated that the powders synthesized at a ratio of 1.05:1:2.1 and a synthesis temperature of 225 °C have the lowest bismuth content and the highest purity. The synthesized AgBiS2 crystallizes in a rock salt type structure with the cubic Fm3¯m space group. Scanning and transmission electron microscopy, thermogravimetric analysis, ultraviolet–visible–near-infrared spectra, and photocatalytic degradation performance were employed to characterize the as-synthesized samples. The results demonstrated that AgBiS2 powders display thermal stability; strong absorption in the ultraviolet, visible, and partial infrared regions; and an optical bandgap of 0.98 eV. The obtained AgBiS2 powders also have a good degradation effect on the methylene blue solution with a degradation efficiency of 58.61% and a rate constant of 0.0034 min−1, indicating that it is an efficient strategy for sewage degradation to reduce water pollution.

Abstract Background As important producers using photosynthesis on Earth, cyanobacteria contribute to the oxygenation of atmosphere and the primary production of biosphere. However, due to the eutrophication of urban waterbodies and global warming, uncontrollable growth of cyanobacteria usually leads to the seasonal outbreak of cyanobacterial blooms. Cyanophages, a group of viruses that specifically infect and lyse cyanobacteria, are considered as potential environment-friendly agents to control the harmful blooms. Compared to the marine counterparts, only a few freshwater cyanophages have been isolated and genome sequenced to date, largely limiting their characterizations and applications. Results Here, we isolated five freshwater cyanophages varying in tail morphology, termed Pam1~Pam5, all of which infect the cyanobacterium Pseudanabaena mucicola Chao 1806 that was isolated from the bloom-suffering Lake Chaohu in Anhui, China. The whole-genome sequencing showed that cyanophages Pam1~Pam5 all contain a dsDNA genome, varying in size from 36 to 142 Kb. Phylogenetic analyses suggested that Pam1~Pam5 possess different DNA packaging mechanisms and are evolutionarily distinct from each other. Notably, Pam1 and Pam5 have lysogeny-associated gene clusters, whereas Pam2 possesses 9 punctuated DNA segments identical to the CRISPR spacers in the host genome. Metagenomic data-based calculation of the relative abundance of Pam1~Pam5 at the Nanfei estuary towards the Lake Chaohu revealed that the short-tailed Pam1 and Pam5 account for the majority of the five cyanophages. Moreover, comparative analyses of the reference genomes of Pam1~Pam5 and previously reported cyanophages enabled us to identify three circular and seven linear contigs of virtual freshwater cyanophages from the metagenomic data of the Lake Chaohu. Conclusions We propose a high-throughput strategy to systematically identify cyanophages based on the currently available metagenomic data and the very limited reference genomes of experimentally isolated cyanophages. This strategy could be applied to mine the complete or partial genomes of unculturable bacteriophages and viruses. Transformation of the synthesized whole genomes of these virtual phages/viruses to proper hosts will enable the rescue of bona fide viral particles and eventually enrich the library of microorganisms that exist on Earth. Video abstract

Human ABC transporter ABCD1 transports very long-chain fatty acids from cytosol to peroxisome for βoxidation, dysfunction of which causes the X-ALD. Here, the authors report three structures of ABCD1: the ligand-free, C22:0-CoA- and ATP-bound forms.

Abstract Background Acute hemorrhagic conjunctivitis (AHC) is classified as a class C notifiable infectious disease in China and poses a great threat to public health. This study aimed to investigate the epidemiological trends and hotspots of AHC in mainland China. Sociodemographic factors that could contribute to early warning of AHC were further explored. Methods Yearly and monthly incidences of acute hemorrhagic conjunctivitis by date and region from 2004 to 2018 were extracted from the Data Center of China Public Health Science. Joinpoint regression and spatial autocorrelation analysis were performed to explore the epidemiological trends and hotspots of AHC. A generalized linear model was then applied to explore the relationship between sociodemographic factors and AHC incidence. Results The average annual AHC incidence was 3.58/100,000 in mainland China. The first-level spatial and temporal aggregation areas were distributed in Guangxi, Hainan, Guangdong, Guizhou, Hunan, Jiangxi, Fujian, Chongqing, Hubei, Anhui, and Zhejiang, with gathering times from 2010/1/1 to 2010/12/31 (RR = 20.13, LLR = 474,522.89, P

Video summarization aims to automatically generate a diverse and concise summary which is useful in large-scale video processing. Most of the methods tend to adopt self-attention mechanism across video frames, which fails to model the diversity of video frames. To alleviate this problem, we revisit the pairwise similarity measurement in self-attention mechanism and find that the existing inner-product affinity leads to discriminative features rather than diversified features. In light of this phenomenon, we propose global diverse attention which uses the squared Euclidean distance instead to compute the affinities. Moreover, we model the local contextual information by novel local contextual attention to remove the redundancy in the video. By combining these two attention mechanisms, a video SUMmarization model with Diversified Contextual Attention scheme is developed, namely SUM-DCA. Extensive experiments are conducted on benchmark data sets to verify the effectiveness and the superiority of SUM-DCA in terms of F-score and rank-based evaluation without any bells and whistles.

Background: Promoting cholesterol reverse transport (RCT) has been proven to be a promising hyperlipidemia therapy since it is more effective for the treatment of atherosclerosis (AS) caused by hyperlipidemia. Liver X receptor (LXR) agonists can accelerate RCT, but most of them trigger undesirable liver steatosis due to the activation of liver LXRα.Aim: We aim to figure out whether isochlorogenic acid C (ICAC) facilitates RCT without causing hepatic steatosis.Methods:In vitro study, we established foam macrophages and macrophages with loaded NBD-cholesterol models to investigate the competence of RCT promoting ICAC. RT-qPCR and Western blot were used to verify ICAC’s regulation of RCT and NF-κB inflammatory pathways. In this in vivo study, male 6-week-old C57BL/6 mice were fed a high-fat diet (HFD) to investigate ICAC’s anti-hyperlipidemic effect and its functions in regulating RCT. The anti-hyperlipidemic effect of ICAC was evaluated by blood and liver lipid levels, liver hematoxylin, oil red o staining, and liver coefficient. Finally, mRNA levels of genes involved in RCT and inflammation pathways in the liver and intestine were detected by RT-qPCR.Results: ICAC prevented macrophages from foaming by up-regulating the LXRα mediated RCT pathway and down-regulating expression of the cholesterol absorption genes LDLR and CD36, as well as suppressing iNOS, COX2, and IL-1β inflammatory factors. In HFD-fed mice, ICAC significantly lowered the lipid level both in the serum and the liver. Mechanistic studies showed that ICAC strengthened the RCT pathway in the liver and intestine but didn’t affect liver LXRα. Furthermore, ICAC impeded both adipogenesis and the inflammatory response in the liver.Conclusion: ICAC accelerated RCT without affecting liver LXRα, thus resulting in a lipid-lowering effect without increasing liver adipogenesis. Our results indicated that ICAC could be a new RCT promoter for hyperlipidemia treatment without causing liver steatosis.

Compared to the widely used compound semiconductor photoelectric sensors, all-silicon photoelectric sensors have the advantage of easy mass production because they are compatible with the complementary metal-oxide-semiconductor (CMOS) fabrication technique. In this paper, we propose an all-silicon photoelectric biosensor with a simple process and that is integrated, miniature, and with low loss. This biosensor is based on monolithic integration technology, and its light source is a PN junction cascaded polysilicon nanostructure. The detection device utilizes a simple refractive index sensing method. According to our simulation, when the refractive index of the detected material is more than 1.52, evanescent wave intensity decreases with the growth of the refractive index. Thus, refractive index sensing can be achieved. Moreover, it was also shown that, compared to a slab waveguide, the embedded waveguide designed in this paper has a lower loss. With these features, our all-silicon photoelectric biosensor (ASPB) demonstrates its potential in the application of handheld biosensors.

ObjectiveAccording to a recent study, serum total bile acids (TBA) may preserve lumbar bone mineral density (BMD) in Cushing syndrome patients, and BMD is directly linked to bone health. We were interested in examining the association between TBA and in Chinese adults aged 20–59 years.MethodsWe retrospectively analyzed the physical examination results of 2,490 general healthy subjects in Hainan West Central Hospital. Femoral neck BMD and TBA were measured, and the relationship between TBA and femoral neck BMD was evaluated by curve fitting, a generalized additive model, and multiple linear regression analysis.ResultsThe fitted smooth curve and generalized additive model showed a nonlinear relationship between TBA and femoral neck BMD, and a positive correlation between TBA and femoral neck BMD was found after we made adjustments for the potential confounders.ConclusionTBA is positively associated with femoral neck BMD in Chinese adults aged 20–59 years.

Background: Home quarantine as a non-pharmaceutical measure is a key strategy for preventing the spread of hand, foot, and mouth disease (HFMD) and herpangina (HA). However, the status of home quarantine remains unclear. This study aimed to provide a theoretical basis for the prevention and control of the HFMD and HA by investigating the situation and determining the factors influencing home quarantine in children with HFMD or HA. Methods: The convenience sampling method was used in this cross-sectional study involving parents whose children suffered from HFMD or HA in 2019. An online questionnaire tool was used to collect demographic information, socioeconomic status, clinical factors, sources of advice, and details of home quarantine. Logistic regression analysis was used to explore the factors influencing of home quarantine. Results: A total of 3145 parents answered the electronic questionnaire; among them, 317 had children diagnosed with HFMD or HA in 2019. After quality control, 298 questionnaires were included in the analysis. The whole compliance rate of home quarantine for HFMD and HA was 59.1%. Results of multivariate logistic regression analysis indicated that having grandparents as the primary caregiver (OR = 2.53, 95% CI: 1.20–5.43) was a risk factor of home-quarantine noncompliance, whereas doctor's notification (OR = 0.35, 95% CI: 0.18–0.67) and advice from parents of other infected children (OR = 0.53, 95% CI: 0.31–0.91) can increase the compliance with home quarantine. Conclusions: Home-quarantine measures for HFMD and HA were not well implemented. The caregivers, doctor's notification, and advice from parents of other infected children were associated with home-quarantine compliance. Corresponding measures should be taken to regulate home quarantine.

Abstract Background Bacterial gas vesicles, composed of two major gas vesicle proteins and filled with gas, are a unique class of intracellular bubble-like nanostructures. They provide buoyancy for cells, and thus play an essential role in the growth and survival of aquatic and soil microbes. Moreover, the gas vesicle could be applied to multimodal and noninvasive biological imaging as a potential nanoscale contrast agent. To date, cylinder-shaped gas vesicles have been found in several strains of cyanobacteria. However, whether the functional gas vesicles could be produced in the model filamentous cyanobacteria Anabaena sp. PCC 7120 remains controversial. Results In this study, we found that an intact gvp gene cluster indeed exists in the model filamentous cyanobacteria Anabaena sp. PCC 7120. Real-time PCR assays showed that the gvpA gene is constitutively transcribed in vivo, and its expression level is upregulated at low light intensity and/or high growth temperature. Functional expression of this intact gvp gene cluster enables the recombinant Escherichia coli to gain the capability of floatation in the liquid medium, thanks to the assembly of irregular gas vesicles. Furthermore, crystal structure of GvpF in combination with enzymatic activity assays of GvpN suggested that these two auxiliary proteins of gas vesicle are structurally and enzymatically conserved, respectively. Conclusions Our findings show that the laboratory strain of model filamentous cyanobacteria Anabaena sp. PCC 7120 possesses an intact but partially degenerated gas vesicle gene cluster, indicating that the natural isolate might be able to produce gas vesicles under some given environmental stimuli for better floatation.

Summary: The reverse cholesterol transport pathway is responsible for the maintenance of human cholesterol homeostasis, an imbalance of which usually leads to atherosclerosis. As a key component of this pathway, the ATP-binding cassette transporter ABCG1 forwards cellular cholesterol to the extracellular acceptor nascent high-density lipoprotein (HDL). Here, we report a 3.26-Å cryo-electron microscopy structure of cholesterol-bound ABCG1 in an inward-facing conformation, which represents a turnover condition upon ATP binding. Structural analyses combined with functional assays reveals that a cluster of conserved hydrophobic residues, in addition to two sphingomyelins, constitute a well-defined cholesterol-binding cavity. The exit of this cavity is closed by three pairs of conserved Phe residues, which constitute a hydrophobic path for the release of cholesterol in an acceptor concentration-dependent manner. Overall, we propose an ABCG1-driven cholesterol transport cycle initiated by sphingomyelin-assisted cholesterol recruitment and accomplished by the release of cholesterol to HDL.

The Candidate Phyla Radiation (CPR), as a newly discovered and difficult-to-culture bacterium, accounts for the majority of the bacterial domain, which may be related to various oral diseases, including dental caries. Restricted by laboratory culture conditions, there is limited knowledge about oral CPR. Advances in metagenomics provide a new way to study CPR through molecular biology. Here, we used metagenomic assembly and binning to reconstruct more and higher quality metagenome-assembled genomes (MAGs) of CPR from oral dental plaque. These MAGs represent novel CPR species, which differed from all known CPR organisms. Relative abundance of different CPR MAGs in the caries and caries-free group was estimated by mapping metagenomic reads to newly constructed MAGs. The relative abundance of two CPR MAGs was significantly increased in the caries group, indicating that there might be a relationship with caries activity. The detection of a large number of unclassified CPR MAGs in the dataset implies that the phylogenetic diversity of CPR is enormous. The results provide a reference value for exploring the ecological distribution and function of uncultured or difficult-to-culture microorganisms.

Background: More than 150 types of brain tumors have been documented. Accurate diagnosis is important for making appropriate therapeutic decisions in treating the diseases. The goal of this study is to develop a DNA methylation profile-based classifier to accurately identify various kinds of brain tumors.Methods: Thirteen datasets of DNA methylation profiles were downloaded from the Gene Expression Omnibus (GEO) database, of which GSE90496 and GSE109379 were used as the training set and the validation set, respectively, and the remaining 11 sets were used as the independent test set. The random forest algorithm was used to select the CpG sites based on the importance of the features and a multilayer perceptron (MLP) model was trained to classify the samples. Deconvolution with the debCAM package was used to explore the cellular composition difference among tumors.Results: From training datasets with 2,801 samples, 396,568 CpG sites were retained after preprocessing, of which 767 were selected as the modeling features. A three-layer MLP model was developed, which consists of 1,320 nodes in the hidden layer, to predict the histological types of brain tumors. The prediction accuracy is 99.2, 87.0, and 96.58%, respectively, on the training, validation and test sets. The results of deconvolution analysis showed that the cell proportions of different tumor subtypes were different, and it is approximately enough to distinguish different tumor entities.Conclusion: We developed a classifier that is robust for the classification of central nervous system tumors, and tried to analyze the reasons for the classification performance.

At the first step of phage infection, the receptor-binding proteins (RBPs) such as tail fibers are responsible for recognizing specific host surface receptors. The proper folding and assembly of tail fibers usually requires a chaperone encoded by the phage genome. Despite extensive studies on phage structures, the molecular mechanism of phage tail fiber assembly remains largely unknown. Here, using a minimal myocyanophage, termed Pam3, isolated from Lake Chaohu, we demonstrate that the chaperone gp25 forms a stable complex with the tail fiber gp24 at a stoichiometry of 3:3. The 3.1-Å cryo-electron microscopy structure of this complex revealed an elongated structure with the gp25 trimer embracing the distal moieties of gp24 trimer at the center. Each gp24 subunit consists of three domains: the N-terminal α-helical domain required for docking to the baseplate, the tumor necrosis factor (TNF)-like and glycine-rich domains responsible for recognizing the host receptor. Each gp25 subunit consists of two domains: a non-conserved N-terminal β-sandwich domain that binds to the TNF-like and glycine-rich domains of the fiber, and a C-terminal α-helical domain that mediates trimerization/assembly of the fiber. Structural analysis enabled us to propose the assembly mechanism of phage tail fibers, in which the chaperone first protects the intertwined and repetitive distal moiety of each fiber subunit, further ensures the proper folding of these highly plastic structural elements, and eventually enables the formation of the trimeric fiber. These findings provide the structural basis for the design and engineering of phage fibers for biotechnological applications.

Summary: How cells adapt to oncogenic transformation-associated cellular stress and become fully transformed is still unknown. Here we identified a novel GGCT-regulated glutathione (GSH)-reactive oxygen species (ROS) metabolic pathway in oncogenic stress alleviation. We identified GGCT as a target of oncogenic Ras and that it is required for oncogenic Ras-induced primary mouse cell proliferation and transformation and in vivo lung cancer formation in the LSL-Kras G12D mouse model. However, GGCT deficiency is compatible with normal mouse development, suggesting that GGCT can be a cancer-specific therapeutic target. Genetically amplified GGCT locus further supports the oncogenic driving function of GGCT. In summary, our study not only identifies an oncogenic function of GGCT but also identifies a novel regulator of GSH metabolism, with implications for further understanding of oncogenic stress and cancer treatment. : Biological Sciences; Cell Biology; Cancer Subject Areas: Biological Sciences, Cell Biology, Cancer

ABSTRACT The wall teichoic acid (WTA) is a major cell wall component of Gram-positive bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), a common cause of fatal clinical infections in humans. Thus, the indispensable ABC transporter TarGH, which flips WTA from cytoplasm to extracellular space, becomes a promising target of anti-MRSA drugs. Here, we report the 3.9-Å cryo-electron microscopy (cryo-EM) structure of a 50% sequence-identical homolog of TarGH from Alicyclobacillus herbarius at an ATP-free and inward-facing conformation. Structural analysis combined with activity assays enables us to clearly decode the binding site and inhibitory mechanism of the anti-MRSA inhibitor Targocil, which targets TarGH. Moreover, we propose a “crankshaft conrod” mechanism utilized by TarGH, which can be applied to similar ABC transporters that translocate a rather big substrate through relatively subtle conformational changes. These findings provide a structural basis for the rational design and optimization of antibiotics against MRSA. IMPORTANCE The wall teichoic acid (WTA) is a major component of cell wall and a pathogenic factor in methicillin-resistant Staphylococcus aureus (MRSA). The ABC transporter TarGH is indispensable for flipping WTA precursor from cytoplasm to the extracellular space, thus making it a promising drug target for anti-MRSA agents. The 3.9-Å cryo-EM structure of a TarGH homolog helps us to decode the binding site and inhibitory mechanism of a recently reported inhibitor, Targocil, and provides a structural platform for rational design and optimization of potential antibiotics. Moreover, we propose a “crankshaft conrod” mechanism to explain how a big substrate is translocated through subtle conformational changes of type II exporters. These findings advance our understanding of anti-MRSA drug design and ABC transporters.

Lake Chaohu, one of the five largest freshwater lakes in China, has been suffering from severe cyanobacterial blooms in the summer for many years. Cyanophages, the viruses that specifically infect cyanobacteria, play a key role in modulating cyanobacterial population, and thus regulate the emergence and decline of cyanobacterial blooms. Here we report a long-tailed cyanophage isolated from Lake Chaohu, termed Mic1, which specifically infects the cyanobacterium Microcystis aeruginosa. Mic1 has an icosahedral head of 88 nm in diameter and a long flexible tail of 400 nm. It possesses a circular genome of 92,627 bp, which contains 98 putative open reading frames. Genome sequence analysis enabled us to define a novel terminase large subunit that consists of two types of intein, indicating that the genome packaging of Mic1 is under fine control via posttranslational maturation of the terminase. Moreover, phylogenetic analysis suggested Mic1 and mitochondria share a common evolutionary origin of DNA polymerase γ gene. All together, these findings provided a start-point for investigating the co-evolution of cyanophages and its cyanobacterial hosts.

Infectious disease: A leap forward for disease models Rabbits offer a powerful complement to rodents as a model for studying human immunology, disease pathology, and responses to infectious disease. A review from Pedro Esteves at the University of Porto, Portugal, Rose Mage of the National Institute of Allergy and Infectious Disease, Bethesda, USA and colleagues highlights some of the areas of research where rabbits offer an edge over rats and mice. Rabbits have a particularly sophisticated adaptive immune system, which could provide useful insights into human biology and produce valuable research and clinical reagents. They are also excellent models for studying - infectious diseases such as syphilis and tuberculosis, which produce pathology that closely resembles that of human patients. Rabbit-specific infections such as myxomatosis are giving researchers insights into how pathogens and hosts can shape each other’s evolution.

Bacterial ATP-binding cassette (ABC)-type efflux pumps are involved in the resistance of antibiotics and antimicrobial peptides. Here authors report the crystal structures and ATPase activity of the MacAB-like efflux pump from Streptococcus pneumonia and describe a putative substrate transport mechanism.

Fiber gas sensing techniques have been applied for a wide range of industrial applications. In this paper, the basic fiber gas sensing principles and the development of different fibers have been introduced. In various specialty fibers, hollow-core photonic crystal fibers (HC-PCFs) can overcome the fundamental limits of solid fibers and have attracted intense interest recently. Here, we focus on the review of HC-PCF gas sensing, including the light-guiding mechanisms of HC-PCFs, various sensing configurations, microfabrication approaches, and recent research advances including the mid-infrared gas sensors via hollow core anti-resonant fibers. This review gives a detailed and deep understanding of HC-PCF gas sensors and will promote more practical applications of HC-PCFs in the near future.

Peptidoglycan recognition proteins (PGRPs), which have been identified in most animals, are pattern recognition molecules that involve antimicrobial defense. Resulting from extraordinary expansion of innate immune genes, the amphioxus encodes many PGRPs of diverse functions. For instance, three isoforms of PGRP encoded by Branchiostoma belcheri tsingtauense, termed BbtPGRP1~3, are fused with a chitin binding domain (CBD) at the N-terminus. Here we report the 2.7 Å crystal structure of BbtPGRP3, revealing an overall structure of an N-terminal hevein-like CBD followed by a catalytic PGRP domain. Activity assays combined with site-directed mutagenesis indicated that the individual PGRP domain exhibits amidase activity towards both DAP-type and Lys-type peptidoglycans (PGNs), the former of which is favored. The N-terminal CBD not only has the chitin-binding activity, but also enables BbtPGRP3 to gain a five-fold increase of amidase activity towards the Lys-type PGNs, leading to a significantly broadened substrate spectrum. Together, we propose that modular evolution via domain shuffling combined with gene horizontal transfer makes BbtPGRP1~3 novel PGRPs of augmented catalytic activity and broad recognition spectrum.

LicA plays a key role in the cell-wall phosphorylcholine biosynthesis of Streptococcus pneumonia. Here we determined the crystal structures of apo-form LicA at 1.94 Å and two complex forms LicA-choline and LicA-AMP-MES, at 2.01 and 1.45 Å resolution, respectively. The overall structure adopts a canonical protein kinase-like fold, with the active site located in the crevice of the N- and C-terminal domains. The three structures present distinct poses of the active site, which undergoes an open-closed-open conformational change upon substrate binding and product release. The structure analyses combined with mutageneses and enzymatic assays enabled us to figure out the key residues for the choline kinase activity of LicA. In addition, structural comparison revealed the loop between helices α7 and α8 might modulate the substrate specificity and catalytic activity. These findings shed light on the structure and mechanism of the prokaryotic choline kinase LicA, and might direct the rational design of novel anti-pneumococcal drugs.

Staphylococcus aureus, a Gram-positive bacterium causes a number of devastating human diseases, such as infective endocarditis, osteomyelitis, septic arthritis and sepsis. S. aureus SraP, a surface-exposed serine-rich repeat glycoprotein (SRRP), is required for the pathogenesis of human infective endocarditis via its ligand-binding region (BR) adhering to human platelets. It remains unclear how SraP interacts with human host. Here we report the 2.05 Å crystal structure of the BR of SraP, revealing an extended rod-like architecture of four discrete modules. The N-terminal legume lectin-like module specifically binds to N-acetylneuraminic acid. The second module adopts a β-grasp fold similar to Ig-binding proteins, whereas the last two tandem repetitive modules resemble eukaryotic cadherins but differ in calcium coordination pattern. Under the conditions tested, small-angle X-ray scattering and molecular dynamic simulation indicated that the three C-terminal modules function as a relatively rigid stem to extend the N-terminal lectin module outwards. Structure-guided mutagenesis analyses, in addition to a recently identified trisaccharide ligand of SraP, enabled us to elucidate that SraP binding to sialylated receptors promotes S. aureus adhesion to and invasion into host epithelial cells. Our findings have thus provided novel structural and functional insights into the SraP-mediated host-pathogen interaction of S. aureus.

The open reading frame SCO4226 of Streptomyces coelicolor A3(2) encodes an 82-residue hypothetical protein. Biochemical assays revealed that each SCO4226 dimer binds four nickel ions. To decipher the molecular function, we solved the crystal structures of SCO4226 in both apo- and nickel-bound (Ni-SCO4226) forms at 1.30 and 2.04 Å resolution, respectively. Each subunit of SCO4226 dimer adopts a canonical ferredoxin-like fold with five β-strands flanked by two α-helices. In the structure of Ni-SCO4226, four nickel ions are coordinated at the surface of the dimer. Further biochemical assays suggested that the binding of Ni2+ triggers the self-aggregation of SCO4226 in vitro. In addition, RT-qPCR assays demonstrated that the expression of SCO4226 gene in S. coelicolor is specifically up-regulated by the addition of Ni2+, but not other divalent ions such as Cu2+, Mn2+ or Co2+. All these results suggested that SCO4226 acts as a nickel binding protein, probably required for nickel sequestration and/or detoxification.

Peroxiredoxins (Prxs) are thiol-specific antioxidant proteins that exhibit peroxidase and peroxynitrite reductase activities involved in the reduction of reactive oxygen species. The peroxiredoxin Prx4 from the large yellow croaker Pseudosciaena crocea is a typical 2-Cys Prx with an N-terminal signal peptide. We solved the crystal structure of Prx4 at 1.90 Å and revealed an N-terminal antiparallel β-sheet that contributes to the dimer interface. Deletion of this β-sheet decreased the in vitro peroxidase activity to about 50% of the wild-type. In vivo assays further demonstrated that removal of this β-sheet led to some impairment in the ability of Prx4 to negatively regulate nuclear factor-κB (NF-κB) activity and to perform its role in anti-bacterial immunity. These results provide new insights into the structure and function relationship of a peroxiredoxin from bony fish.

Iron scarcity is one of the nutrition limitations that the Gram-positive infectious pathogens Streptococcus pneumoniae encounter in the human host. To guarantee sufficient iron supply, the ATP binding cassette (ABC) transporter Pia is employed to uptake iron chelated by hydroxamate siderophore, via the membrane-anchored substrate-binding protein PiaA. The high affinity towards ferrichrome enables PiaA to capture iron at a very low concentration in the host. We presented here the crystal structures of PiaA in both apo and ferrichrome-complexed forms at 2.7 and 2.1 Å resolution, respectively. Similar to other class III substrate binding proteins, PiaA is composed of an N-terminal and a C-terminal domain bridged by an α-helix. At the inter-domain cleft, a molecule of ferrichrome is stabilized by a number of highly conserved residues. Upon ferrichrome binding, two highly flexible segments at the entrance of the cleft undergo significant conformational changes, indicating their contribution to the binding and/or release of ferrichrome. Superposition to the structure of Escherichia coli ABC transporter BtuF enabled us to define two conserved residues: Glu119 and Glu262, which were proposed to form salt bridges with two arginines of the permease subunits. Further structure-based sequence alignment revealed that the ferrichrome binding pattern is highly conserved in a series of PiaA homologs encoded by both Gram-positive and negative bacteria, which were predicted to be sensitive to albomycin, a sideromycin antibiotic derived from ferrichrome.