Structural basis of BAM-mediated outer membrane ß-barrel protein assembly.

The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane ß-barrel proteins (OMPs) that are essential interchange portals of materials1-3. All known OMPs share the antiparallel ß-strand topology4, implicating a common evolutionary origin and conserved folding mechanism. Models have been proposed for bacterial ß-barrel assembly machinery (BAM) to initiate OMP folding5,6; however, mechanisms by which BAM proceeds to complete OMP assembly remain unclear. Here we report intermediate structures of BAM assembling an OMP substrate, EspP, demonstrating sequential conformational dynamics of BAM during the late stages of OMP assembly, which is further supported by molecular dynamics simulations. Mutagenic in vitro and in vivo assembly assays reveal functional residues of BamA and EspP for barrel hybridization, closure and release. Our work provides novel insights into the common mechanism of OMP assembly.

Distinct antiviral activities of IFNφ1 and IFNφ4 in zebrafish.

Interferons (IFNs) are a group of secreted cytokines that play a crucial role in antiviral immunity. Type I IFNs display functional disparities. In teleosts, type I IFNs are categorized into two subgroups containing one or two pairs of disulfide bonds. However, their functional differences have not been fully elucidated. In this study, we comparatively characterized the antiviral activities of zebrafish IFNφ1 and IFNφ4 belonging to the group I type I IFNs. It was found that ifnφ1 and ifnφ4 were differentially modulated during viral infection. Although both IFNφ1 and IFNφ4 activated JAK-STAT signaling pathway via CRFB1/CRFB5 receptor complex, IFNφ4 was less potent in inducing phosphorylation of STAT1a, STAT1b and STAT2 and the expression of antiviral genes than IFNφ1, thereby conferring weaker antiviral resistance of target cells. Taken together, our results provide insights into the functional divergence of type I IFNs in lower vertebrates.

Incongruent gray matter atrophy and functional connectivity of striatal subregions in behavioral variant frontotemporal dementia.

Previous studies on the striatum demonstrated that it is involved in the regulation of cognitive function and psychiatric symptoms in patients with behavioral variant frontotemporal dementia (bvFTD). Multiple lines of evidence have shown that striatal subregions have their own functions. However, the results of the existing studies on striatal subregions are inconsistent and unclear. In this study, we found that structural imaging analysis revealed that the bvFTD patients had smaller volumes of striatal subregions than the controls. We found that the degree of atrophy varied across the striatal subregions. Additionally, the right striatal subregions were significantly more atrophic than the left in bvFTD. Functional imaging analysis revealed that bvFTD patients exhibited different changed patterns of resting-state functional connectivity (RSFC) when striatal subregions were selected as regions of interest (ROI). The RSFC extending range on the right ROIs was more significant than on the left in the same subregion. Interestingly, the RSFC of the subregions extending to the insula were consistent. In addition, the left dorsolateral putamen may be involved in executive function regulation. This suggests that incongruence in striatal subregions may be critical to the bvFTD characteristics.

Leveraging Electron Push-Pull Effect for Catalytic Polymerization and Degradation of a Cyclobutane Monomer System.

Ring-opening polymerization (ROP) offers a striking solution to solve problems encountered in step-growth condensation polymerization, including precise control over molecular weight, molecular weight distribution, and topology. This has inspired our interest in ROP of cycloalkanes with an ultimate goal to rethink polyolefins, which clearly poses a number of challenges. Practicality of ROP of cycloalkanes is actually limited by their low polymerizability and elusive mechanisms which arise from significantly varied ring size and non-polar C-C bonds in monomers. In this work, by using Lewis acid/Brønsted base/C(sp3)-H initiator system previously developed in our laboratory, we focus on cyclobutanes and explore the positional and electronic effects of substituents on the ring, namely electron push-pull effect, in promoting controlled polymerization to afford densely functionalized poly(cyclobutanes), as well as catalytic degradation of obtained polymers for upcycling. More importantly, experiments and DFT calculations unveil considerable population of Lewis-acid-induced thermostabilized 1,4-zwitterions, which distinguish cyclobutanes from cyclopropanes and others. All these findings would shed light on catalytic synthesis and degradation of saturated all-carbon main-chain polymers, as well as small molecule transformations of cyclobutanes.

Effect of Chain Architecture on Self-Assembled Aggregates from Cyclic AB Diblock and Linear ABA Triblock Copolymers in Solution.

The self-assembly behaviors of two block copolymers with the same chain length but different chain architectures (cyclic AB, linear ABA) in B-selective solvents are investigated using Monte Carlo simulations. A morphological transition sequence, from spherical micelles to cylindrical micelles, to vesicles and then to multicompartment vesicles, is observed for both copolymer systems when the interaction between the solvophobic A-block and the solvent is increased. In particular, toroidal micelles could be formed in triblock systems due to the presence of the bridging chains at the parameter region between cylindrical micelles and vesicles whereas disklike micelles are formed in cyclic systems. The simulation results demonstrated that the architecture of block copolymers could be used to regulate the structural characteristics and thermal stability of these self-assembled aggregates.

A Ni(OH)2-modified Ti-doped α-Fe2O3 photoanode for improved photoelectrochemical oxidation of urea: the role of Ni(OH)2 as a cocatalyst.

For semiconductor-based PEC systems, loading an appropriate cocatalyst on a semiconductor (such as a solar-active material) can significantly improve the PEC activity due to the suppression of photogenerated charge recombination. But there is little direct information about the role of a cocatalyst in the spatial separation of photogenerated charge carriers. In our work, a combination of surface photovoltage spectroscopy (SPS), transient photovoltage (TPV) technique, photoelectrochemical impedance spectroscopy (PEIS) and transient photocurrent measurements was used to study the real role of Ni(OH)2 as a cocatalyst for the enhanced PEC performance of Ni(OH)2-modified Ti-doped α-Fe2O3. It was found that Ni(OH)2 as a hole storage layer enhances the separation of photogenerated charge carriers and increases the lifetime of holes, which contributed to the enhanced photocurrent. In addition, Ni(OH)2 is a good cocatalyst for urea oxidation which suppresses the over-potential, resulting in a negative shift of the onset potential.

Different topological organization of human brain functional networks with eyes open versus eyes closed.

Opening and closing the eyes are fundamental behaviors for directing attention to the external versus internal world. However, it remains unclear whether the states of eyes-open (EO) relative to eyes-closed (EC) are associated with different topological organizations of functional neural networks for exteroceptive and interoceptive processing (processing the external world and internal state, respectively). Here, we used resting-state functional magnetic resonance imaging and neural network analysis to investigate the topological properties of functional networks of the human brain when the eyes were open versus closed. The brain networks exhibited higher cliquishness and local efficiency, but lower global efficiency during the EO state compared to the EC state. These properties suggest an increase in specialized information processing along with a decrease in integrated information processing in EO (vs. EC). More importantly, the "exteroceptive" network, including the attentional system (e.g., superior parietal gyrus and inferior parietal lobule), ocular motor system (e.g., precentral gyrus and superior frontal gyrus), and arousal system (e.g., insula and thalamus), showed higher regional nodal properties (nodal degree, efficiency and betweenness centrality) in EO relative to EC. In contrast, the "interoceptive" network, composed of visual system (e.g., lingual gyrus, fusiform gyrus and cuneus), auditory system (e.g., Heschl's gyurs), somatosensory system (e.g., postcentral gyrus), and part of the default mode network (e.g., angular gyrus and anterior cingulate gyrus), showed significantly higher regional properties in EC vs. EO. In addition, the connections across sensory modalities were altered by volitional eye opening. The synchronicity between the visual system and the motor, somatosensory and auditory systems, characteristic of EC, was attenuated in EO. Further, the connections between the visual system and the attention, arousal and subcortical systems were increased in EO. These results may indicate that EO leads to a suppression of sensory modalities (other than visual) to allocate resources to exteroceptive processing. Our findings suggest that the topological organization of human brain networks dynamically switches corresponding to the information processing modes as we open or close our eyes.

Cortical thinning correlates with cognitive change in multiple sclerosis but not in neuromyelitis optica.

OBJECTIVES: To compare spatial patterns of cortical thickness alterations in neuromyelitis optica (NMO) and multiple sclerosis (MS); and to investigate the correlations between cortical thinning and clinical variables in NMO and MS. METHODS: We studied 23 patients with NMO, 27 patients with MS and 26 healthy controls (HCs). The global, brain region and vertex-based cortical thickness (CTh) were analysed and compared among the three groups. A general linear model was used to investigate the correlations between cortical thinning and clinical measures. RESULTS: A limited number of cortical regions in visual cortex were found to be significantly thinner in NMO patients than in HCs. The MS patients exhibited more widespread cortical thinning compared with HCs, and significantly greater cortical thinning in the insula and the parahippocampus compared with NMO. The extent of cortical thinning in several brain regions correlated with cognitive measures in MS, but not in NMO. CONCLUSIONS: Neocortical thinning in NMO mainly affects visual cortex, while MS patients show much more extensive cortical thinning. Cognitive changes are correlated with cortical atrophy in MS not in NMO. The substrates of cognitive changes in MS and NMO could therefore be different. KEY POINTS: MS patients show much more extensive cortical thinning than NMO. Cortical thinning of insula and parahippocampus particularly distinguishes MS from NMO. Cognitive changes are correlated with cortical atrophy in MS but not in NMO.

[In silico cloning and bioinformatics analysis of an AP2/EFR family gene from Arnebia euchroma].

A cDNA sequence of Arnebia euchroma AP2/ERF named AeAP2/ERF was cloned by in silico cloning in this study, using ACX71873 sequence from Lithospermum erythrorhizon as the probe sequence. Some characters of the AP2/ERF gene and encoded protein sequences were predicted and analyzed by the bioinformatics methods, including general physical and chemical properties, hydrophobieity, signal peptide, secondary structure, localization sites in cells. Results showed that the 876 bp long gene included a 1 077 bp ORF and encoding 205 amino acid. The AeAP2/ERF protein had no signal peptide, it was a hydrophilic proteins located in nucleus. The function of the AP2/ERF protein was mainly involved with metabolism controlling and signal transduction.

[Transcriptome-based bioinformatics analysis of Arnebia euchroma ERF transcription factor family].

Twenty-seven ERF transcription factor family genes were isolated from Arnebia euchroma, with an average size of 1,010 bp, each gene encoded a 212 amino acids on average. The gene structure and expression of physicochemical properties, subcellular localization, signal peptides, senior structural domains and conservative forecasting, and analysis of A. euchroma were studied comparing with ERF gene gi261363612 of Lithospermum erythrorhizon, and phylogenetic analysis of A. euchroma ERF family was carried out. The results showed the existence of three conserved domains in this family, the senior structure based on random coil and it clustered into CBF/DREB and ERF subfamilies.

[Overexpression and RNAi vectors built for key secondary metabolic pathway genes PAL, HMGR, PGT of Arnebia euchroma].

Arnebia euchroma is the main source for medicinal herb Zicao. and its most important component shikonin compounds have high medicinal and industrial value. This research is aimed to build overexpression vectors and RNAi vectors for key secondary metabolism genes of A. euchroma, and bulid platform for constructions of related transgenic lines using GATEWAY technology. To build genetic material based genetic research platform is to provide a great convenience for digging and functional verification of the genes on secondary metabolic pathway, and also to fill the gaps in transgenic research of A. euchroma. This study is also important for the cultivation of shikonin high-yielding strains of A. euchroma.

Directional Pumpless Transport of Biomolecules through Self-Propelled Nanodroplets on Patterned Heterostructures.

The surface patterning in natural systems has exhibited appreciable functional advantages for life activities, which serve as inspiration for the design of artificial counterparts to achieve functions such as directional liquid transport at the nanoscale. Here, we propose a patterned two-dimensional (2D) in-plane heterostructure with a triangle-shaped hexagonal boron nitride (hBN) track embedded in graphene nanosheets, which can achieve unidirectional and self-propelled transport of nanodroplets carrying various biomolecules such as DNA, RNA, and peptides. Our extensive MD simulations show that the wettability gradient on the patterned heterostructure can drive the motion of nanodroplet with an instantaneous acceleration, which also permits long-distance transport (>100 nm) at the microsecond time scale. The different behaviors of various types of biomolecules have been further studied systematically within the transporting nanodroplets. These findings suggest that these specially designed, patterned heterostructures have the potential for spontaneous, directional transport of important biomolecules, which might be useful in biosensing, drug delivery, and biomedical nanodevices.

Inhibition of DEF-p65 Interactions as a Potential Avenue to Suppress Tumor Growth in Pancreatic Cancer.

The limited success of current targeted therapies for pancreatic cancer underscores an urgent demand for novel treatment modalities. The challenge in mitigating this malignancy can be attributed to the digestive organ expansion factor (DEF), a pivotal yet underexplored factor in pancreatic tumorigenesis. The study uses a blend of in vitro and in vivo approaches, complemented by the theoretical analyses, to propose DEF as a promising anti-tumor target. Analysis of clinical samples reveals that high expression of DEF is correlated with diminished survival in pancreatic cancer patients. Crucially, the depletion of DEF significantly impedes tumor growth. The study further discovers that DEF binds to p65, shielding it from degradation mediated by the ubiquitin-proteasome pathway in cancer cells. Based on these findings and computational approaches, the study formulates a DEF-mimicking peptide, peptide-031, designed to disrupt the DEF-p65 interaction. The effectiveness of peptide-031 in inhibiting tumor proliferation has been demonstrated both in vitro and in vivo. This study unveils the oncogenic role of DEF while highlighting its prognostic value and therapeutic potential in pancreatic cancer. In addition, peptide-031 is a promising therapeutic agent with potent anti-tumor effects.

The Deinococcus protease PprI senses DNA damage by directly interacting with single-stranded DNA.

Bacteria have evolved various response systems to adapt to environmental stress. A protease-based derepression mechanism in response to DNA damage was characterized in Deinococcus, which is controlled by the specific cleavage of repressor DdrO by metallopeptidase PprI (also called IrrE). Despite the efforts to document the biochemical, physiological, and downstream regulation of PprI-DdrO, the upstream regulatory signal activating this system remains unclear. Here, we show that single-stranded DNA physically interacts with PprI protease, which enhances the PprI-DdrO interactions as well as the DdrO cleavage in a length-dependent manner both in vivo and in vitro. Structures of PprI, in its apo and complexed forms with single-stranded DNA, reveal two DNA-binding interfaces shaping the cleavage site. Moreover, we show that the dynamic monomer-dimer equilibrium of PprI is also important for its cleavage activity. Our data provide evidence that single-stranded DNA could serve as the signal for DNA damage sensing in the metalloprotease/repressor system in bacteria. These results also shed light on the survival and acquired drug resistance of certain bacteria under antimicrobial stress through a SOS-independent pathway.

Sequential transcriptomic alterations in the cerebral cortex of mice after cerebral venous sinus thrombosis.

To investigate the expression alterations of specific genes that occur after venous stroke, we identified differentially expressed genes (DEGs) between sham and damaged cortical tissues at 2 and 7 days after induction of cerebral venous sinus thrombosis (CVST) model. The profiles of DEGs were analyzed using GO, KEGG, GSEA, and PPI, and the crucial gene was further verified by western blot and immunofluorescence. We found 969 and 883 DEGs at 2 and 7 days after CVST, respectively. A marked increase in biological-process categories, such as immune system process and inflammatory response, and a decrease in neuropeptide signaling pathway were observed both at 2 and 7 days post-CVST. The KEGG pathway was enriched to varying degrees on complement and coagulation cascades, cytokine-cytokine receptor interaction, and multiple immune-inflammatory signaling pathways at 2 and 7 days post-CVST, separately. Furthermore, GSEA highlights the potential roles of the NOD-like receptor signaling pathway and cytokine-cytokine receptor interaction in CVST. Importantly, numerous genes related to KEGG pathways above featured prominently in the PPI network analysis, with IL1b being one of the most conspicuous. These time-dependent alterations in gene profiles and enrichment pathways reveal the unique pathophysiological characteristics of CVST and indicate novel therapeutic targets for venous stroke. SIGNIFICANCE: Cerebral venous sinus thrombosis (CVST) is an underrated and potentially fatal cause of stroke with a reported mortality of 5-10% worldwide. Currently, in addition to anticoagulant and thrombolytic therapy, effective treatments targeting the injured brain parenchyma after CVST remain limited. Besides, accurate diagnostic markers are still sorely lacking. In the present study, we will detect the transcriptomic alterations of the cerebral cortex of mice post-CVST by RNA-sequencing, screen differentially expressed genes and abnormal pathways through bioinformatics methods, analyze the correlation of these signals and CVST pathology, and finally validate the key molecules through western blot and immunofluorescence assays. Collectively, the study aimed to offer a reference for the discovery of specific genes/pathway alterations in the damaged cortical tissues of CVST mice and further reveal the underlying pathogenesis, thereby providing evidence for the diagnosis and treatment of CVST.

Metabolome and transcriptome integration reveals cerebral cortical metabolic profiles in rats with subarachnoid hemorrhage.

Subarachnoid hemorrhage (SAH) is a severe subtype of hemorrhagic stroke. The molecular mechanisms of its secondary brain damage remain obscure. To investigate the alterations in gene and metabolite levels following SAH, we construct the transcriptome and metabolome profiles of the rat cerebral cortex post-SAH using whole transcriptome sequencing and untargeted metabolomics assays. Transcriptomic analysis indicated that there were 982 differentially expressed genes (DEGs) and 540 differentially expressed metabolites (DEMs) between the sham group and SAH 1d, and 292 DEGs and 254 DEMs between SAH 1d and SAH 7d. Most notably, DEGs were predominantly involved in the activation of immune and inflammatory pathways, particularly the Complement and coagulation cascades, TNF signaling pathway, and NOD-like receptor signaling pathway. Metabolic analysis revealed that the metabolic pathways of Arginine and proline, Arachidonic acid, Folate biosynthesis, Pyrimidine, and Cysteine and methionine were remarkably affected after SAH. Metabolites of the above pathways are closely associated not only with immune inflammation but also with oxidative stress, endothelial cell damage, and blood-brain barrier disruption. This study provides new insights into the underlying pathologic mechanisms of secondary brain injury after SAH and further characterization of these aberrant signals could enable their application as potential therapeutic targets for SAH.

[Growth and accumulation of shikonin compounds of two kinds of cells in suspension culture of Arnebia euchroma].

Via studying the phenotype, growth curve and secondary metabolites of two kinds of suspension culture cell of Arnebia euchroma, the kinetics parameters of growth and accumulation of shikonin compounds in cell suspension culture of A. euchroma was obtained through simulating and modeling. This Study found that the red high-yielding one was a fine cell line for producing shikonin compounds, and the white low-yielding one may be a mutant. The first-order and second-order derivative of the fitting function were obtained by fitting the Logistic model of growth curve to get the growth rate and growth acceleration curve of the suspended cells. It is found that the best period to subculture was the 15th day cultured in fresh medium, and the best period of the induction process was the 13th-14th day. When compared the growth rate of the red line and the shikonin compounds accumulation curve, it is found that the rapid growth of the biomass of cells was not conducive to the synthesis and accumulation of shikonin compounds.

Predicted superconductivity in one-dimensional A3Hf2B3-type electrides.

Inorganic electrides are considered potential superconductors due to the unique properties of their anionic electrons. However, most electrides require external high-pressure conditions to exhibit considerable superconducting transition temperatures (Tc). Therefore, searching for superconducting electrides under low or moderate external pressures is of significant research interest and importance. In this work, a series of A3Hf2B3-type compounds (A = Mg, Ca, Sr, Ba; B = Si, Ge, Sn, Pb) were constructed and systematically studied based on density functional theory calculations. According to the analysis of the electronic structures and phonon dispersion spectrums, stable one-dimensional electrides Ca3Hf2Ge3, Ca3Hf2Sn3, and Sr3Hf2Pb3, were screened out. Interestingly, the superconductivity of these electrides were predicted from electron phonon coupling calculations. It is highlighted that Sr3Hf2Pb3 showed the highest Tc, reaching 4.02 K, while the Tc values of Ca3Hf2Ge3 and Ca3Hf2Sn3 were 1.16 K and 1.04 K, respectively. Moreover, the Tc value of Ca3Hf2Ge3 can be increased to 1.96 K under 20 GPa due to the effect of phonon softening. This work enriches the types of superconducting electrides and has important guiding significance for the research on constructing electrides and related superconducting materials.

Characteristics of Odor Identification and Hedonics and Their Association with Piriform Cortex-Based Resting-State Functional Connectivity in Amnestic Mild Cognitive Impairment.

BACKGROUND: Olfactory identification dysfunction (OID) might be an early sign of amnestic mild cognitive impairment (aMCI). However, odor hedonics, the ability to perceive odor pleasantness, is neglected. Also, the neural substrate of OID remains unclear. OBJECTIVE: To explore the characteristics of odor identification and hedonics in aMCI and examine the potential neural correlates of OID by analyzing olfactory functional connectivity (FC) patterns in MCI. METHODS: Forty-five controls and 83 aMCI patients were examined. The Chinese smell identification test was used to assess olfaction. Global cognition, memory, and social cognition were assessed. Resting-state functional networks associated with olfactory cortex seeds were compared between the cognitively normal (CN) and aMCI groups, as well as between aMCI subgroups by the degree of OID. RESULTS: Compared to controls, aMCI patients had a significant deficit in olfactory identification, mainly reflected in the identification of pleasant and neutral odors. aMCI patients also rated pleasant and neutral odors much lower than controls. A positive correlation between olfaction and social cognition was found in aMCI. The seed-based FC analysis found that aMCI patients had higher FC between the right orbitofrontal cortex and right frontal lobe/middle frontal gyrus than controls. Subgroup analysis showed that, compared to aMCI without OID, aMCI with severe OID had abnormal FC in the bilateral piriform region. CONCLUSION: Our results suggest that OID in aMCI primarily refers to the identification of pleasant and neutral odors. The FC alterations in bilateral orbitofrontal cortex and piriform cortices might contribute to the impairment in odor identification.

Co-pyrolysis of biomass and polyethylene: Insights into characteristics, kinetic and evolution paths of the reaction process.

Investigation on the distribution and mechanism of co-pyrolysis products is vital to the directional control and high-value utilization of agriculture solid wastes. Co-pyrolysis, devolatilization, kinetics characteristics, and evolution paths of corn stalk (CS) and low-density-polyethylene (LDPE) were investigated via thermogravimetric experiments. The co-pyrolysis behaviors could be separated into two stages: firstly, the degradation of CS (150- 400 °C); secondly, the degradation of CS (400- 550 °C). The devolatilization index (DI) increased with the addition of LDPE. Furthermore, a combination of devolatilization chemical analysis with product analysis to analyze the intrinsic mechanism during co-pyrolysis. The results indicated that the yield of alkanes and olefin in gas products increased with the addition of LDPE. Additionally, LDPE pyrolysis maybe abstract hydrogen from CS pyrolysis and evolved into hydrogen, methane, and ethylene. Further, the co-pyrolysis kinetic parameters were computed by using model-free isoconversion methods, which showed promotion of CS pyrolysis and the reduced activation energy. All the activation energy were declined, which indicated a "bidirectional positive effect" during co-pyrolysis. The mean activation energy of P-cellulose (P-CE), P-hemicellulose (P-HM), P-lignin (P-LG), and LDPE decreased by 23.49 %, 12.89 %, 15.36 %, and 27.82 %, respectively. This study further proves the hydrogen donor transfer pathway in the co-pyrolysis process of CS and LDPE, providing theoretical support for the resource utilization of agricultural solid waste.