HERV1-env Induces Unfolded Protein Response Activation in Autoimmune Liver Disease: A Potential Mechanism for Regulatory T Cell Dysfunction.

Regulatory T cells (Tregs) are not terminally differentiated but can acquire effector properties. Here we report an increased expression of human endogenous retrovirus 1 (HERV1-env) proteins in Tregs of patients with de novo autoimmune hepatitis and autoimmune hepatitis, which induces endoplasmic reticulum (ER) stress. HERV1-env-triggered ER stress activates all three branches (IRE1, ATF6, and PERK) of the unfolded protein response (UPR). Our coimmunoprecipitation studies show an interaction between HERV1-env proteins and the ATF6 branch of the UPR. The activated form of ATF6α activates the expression of RORC and STAT3 by binding to promoter sequences and induces IL-17A production. Silencing of HERV1-env results in recovery of Treg suppressive function. These findings identify ER stress and UPR activation as key factors driving Treg plasticity (species: human).

Cotton peroxisome-localized lysophospholipase counteracts the toxic effects of Verticillium dahliae NLP1 and confers wilt resistance.

Plasma membrane represents a critical battleground between plants and attacking microbes. Necrosis-and-ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs), cytolytic toxins produced by some bacterial, fungal and oomycete species, are able to target on lipid membranes by binding eudicot plant-specific sphingolipids (glycosylinositol phosphorylceramide) and form transient small pores, causing membrane leakage and subsequent cell death. NLP-producing phytopathogens are a big threat to agriculture worldwide. However, whether there are R proteins/enzymes that counteract the toxicity of NLPs in plants remains largely unknown. Here we show that cotton produces a peroxisome-localized enzyme lysophospholipase, GhLPL2. Upon Verticillium dahliae attack, GhLPL2 accumulates on the membrane and binds to V. dahliae secreted NLP, VdNLP1, to block its contribution to virulence. A higher level of lysophospholipase in cells is required to neutralize VdNLP1 toxicity and induce immunity-related genes expression, meanwhile maintaining normal growth of cotton plants, revealing the role of GhLPL2 protein in balancing resistance to V. dahliae and growth. Intriguingly, GhLPL2 silencing cotton plants also display high resistance to V. dahliae, but show severe dwarfing phenotype and developmental defects, suggesting GhLPL2 is an essential gene in cotton. GhLPL2 silencing results in lysophosphatidylinositol over-accumulation and decreased glycometabolism, leading to a lack of carbon sources required for plants and pathogens to survive. Furthermore, lysophospholipases from several other crops also interact with VdNLP1, implying that blocking NLP virulence by lysophospholipase may be a common strategy in plants. Our work demonstrates that overexpressing lysophospholipase encoding genes have great potential for breeding crops with high resistance against NLP-producing microbial pathogens.

Dual Hole Transport Layers Heterojunction and Band Alignment Engineered Mo:BiVO4 Photoanodes for Efficient Water Splitting.

BiVO4-based photoanode is one of the most promising photoanodes for photoelectrocatalytic water splitting. However, the serious problem of interface charge recombination limits its further development. Here, a Mo:BiVO4/NiOx/CPF-TCzB/NiCoBi photoanode is constructed with double hole transport layer and an energy level gradient to achieve an effective photo-generated holes extraction and accumulation at the surface electrocatalyst. The conjugated polycarbazole framework CPF-TCzB is used as hole transport layer to eliminate the charge recombination center between Mo:BiVO4 and NiCoBi electrocatalyst and realize the extraction and storage of photo-generated hole; NiOx nanoparticles are further inserted between Mo:BiVO4 and CPF-TCzB to form a gradient energy level, eliminating the energy level barrier and optimizing band alignment. As a result, Mo:BiVO4/NiOx/CPF-TCzB/NiCoBi achieves a much higher photocurrent densities of 3.14 mA cm-2 than that of Mo:BiVO4 (0.42 mA cm-2) at 0.6 V versus RHE. This work provides an specific way to adjust the band structure of BiVO4-based photoanodes and realize efficient hole extraction and storage for PEC water splitting.

Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes.

There are currently limited Food and Drug Administration (FDA)-approved drugs and vaccines for the treatment or prevention of Coronavirus Disease 2019 (COVID-19). Enhanced understanding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and pathogenesis is critical for the development of therapeutics. To provide insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface (ALI) cultures over a time course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target at the onset of infection, which we confirmed by electron and immunofluorescence microscopy. Over the course of infection, the cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III interferons (IFNs) and interleukin (IL)-6 but not IL-1. This results in expression of interferon-stimulated genes (ISGs) in both infected and bystander cells. This provides a detailed characterization of genes, cell types, and cell state changes associated with SARS-CoV-2 infection in the human airway.

First-principle calculations study of the ORR/OER electrocatalytic activity of ruthenium polyphthalocyanine axially modified with aliphatic thiol groups.

In this study, the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) catalytic activity of ruthenium polyphthalocyanine axially modified with different aliphatic thiol groups, RuPPc-SR (SR = -SCH3, -SC2H5, -SC3H7, -SC4H9, -SC5H11, and -SC6H13), in an acidic medium were simulated using DFT. All -SR groups can effectively enhance the ORR and OER catalytic activities of RuPPc. The ORR and OER overpotentials of RuPPc-SC4H9 are 0.237 V and 0.436 V, respectively, which are far lower than those of RuPPc (0.960 V and 0.903 V). For RuPPc-SC4H9, the four C and S atoms of the -SC4H9 chain and Ru atom are coplanar, and thus, conjugate effects and inductive effects exist between the -SC4H9 chain and Ru atom. This makes the Ru atom exhibit the least positive Bader charge and smallest spin density, and the anti-bonding orbitals of dxz, dyz, and dz2 of the Ru atom shift below the Fermi level (Ef). This makes the adsorption strength of RuPPc-SC4H9 toward ORR and OER intermediates the weakest, which accelerates the reaction process, thus resulting in better ORR and OER catalytic activity. Therefore, the introduction of the aliphatic thiol groups might effectively improve the OER/ORR catalytic activity of RuPPc.

Promoting Plasmonic Hot Hole Extraction and Photothermal Effect for the Oxygen Evolution Reactions.

Boosting oxygen evolution reaction by local surface plasmon resonance (LSPR) provides breakthrough opportunities for the promotion of solar energy conversion; the potential of LSPR, however, has rarely been tapped and investigated. Here, we report the precise regulation of commercial Au nanoparticles plasmonic nanomaterial and OER electrocatalysts, viz., the NiCoOx electrocatalytic layer with hole transport ability and photothermal effect is prepared on the surface of Au nanoparticles by photoelectrodeposition. The NiCoOx layer not only increases the transmission distance of holes generated by plasmonic Au nanoparticles, but also reduce the agglomeration of plasmonic Au nanoparticles during long-time OER reaction, which greatly improves the OER catalytic ability. The current density of NiCoOx /Au anode achieves 16.58 mA cm-2 at 2.0 V versus RHE, which is about 6.5 times of pristine NiCoOx anode (2.56 mA cm-2 ) and 47 times of pristine Au anode (0.35 mA cm-2 ). More importantly, with the LSPR and photothermal effect of plasmonic Au nanoparticles, the NiCoOx /Au anode provides additional current density of 7.01 mA cm-2 after illumination, and maintains no attenuation for more than 2000 s. Benefiting from the solution of agglomeration problem of plasmonic Au nanoparticles in the long-time OER process and the effective utilization of generated holes of plasmonic Au nanoparticles, this design can provide guidance for the application of plasmonic materials in the field of electrocatalysis.

A theoretical study on the ORR electrocatalytic activity of axial ligand modified cobalt polyphthalocyanine.

In this work, the catalytic activity in the oxygen reduction reaction (ORR) of cobalt polyphthalocyanine whose central Co atom is coordinated at the axial position by ligands (L = -F, -OH, -OCH3, -N3, -Cl, -Br, -I, -SCN, and -CN) (CoPPc-L) was investigated using theoretical calculations in alkaline medium. Among all CoPPc-L, CoPPc-N3 exhibited the lowest ORR overpotential of 0.23 V vs. a standard hydrogen electrode, which is significantly lower than those of CoPPc (0.48 V) and Pt(111) (0.43 V). There is a good linear relationship between ΔG*OOH and the electronegativity of ligating atoms in axial ligands of CoPPc-L. The greater the electronegativity, the stronger the adsorption of the catalyst to the intermediate. Additionally, the adsorption strength of CoPPc to the intermediate is modified by the axial ligands, which adjust the distribution of anti-bonding electronic states of dz2, dxz, and dyz orbitals near the Fermi level, Ef. A larger Mayer bond order of the Co-L bond resulted in a smaller bond order of the Co-O bond. CoPPc-N3 exhibited a moderate Co-O bond order of 0.737, corresponding to moderate adsorption energy to the OOH intermediate. This study demonstrates that the interaction strength between CoPPc and ORR intermediates can be adjusted by selecting appropriate axial ligands, which can modulate the ORR catalytic activity.

Theoretical Study on ORR/OER Bifunctional Catalytic Activity of Axial Functionalized Iron Polyphthalocyanine.

Designing efficient ORR/OER bifunctional electrocatalysts is very significant for reducing energy consumption and environmental protection. Hence, we studied the ORR/OER bifunctional catalytic activity of iron polyphthalocyanine (FePPc) coordinated by a series of axial ligands which has different electronegative coordination atom (FePPc-L) (L = -CN, -SH, -SCH3, -SC2H5, -I, -Br, -NH2, -Cl, -OCH3, -OH, and -F) in alkaline medium by DFT calculations. Among all FePPc-L, FePPc-CN, FePPc-SH, FePPc-SCH3, and FePPc-SC2H5 exhibit excellent ORR/OER bifunctional catalytic activities. Their ORR/OER overpotential is 0.256 V/0.234 V, 0.278 V/0.256 V, 0.280 V/0.329 V, and 0.290 V/0.316 V, respectively, which are much lower than that of the FePPc (0.483 V/0.834 V). The analysis of the electronic structure of the above catalysts shows that the electronegativity of the coordination atoms in the axial ligand is small, resulting in less distribution of dz2, dyz, and dxz orbitals near Ef, weak orbital polarization, small charge and magnetic moment of the central Fe atom, and weak adsorption strength for *OH. All these prove that the introduction of axial ligands with appropriate electronegativity coordinating atoms can adjust the adsorption of catalyst to intermediates and modify the ORR/OER bifunctional catalytic activities. This is an effective strategy for designing efficient ORR/OER bifunctional electrocatalysts.

Dual-tracer PET/CT-targeted, mpMRI-targeted, systematic biopsy, and combined biopsy for the diagnosis of prostate cancer: a pilot study.

PURPOSE: Growing evidence proved the efficacy of multi-parametric MRI (mpMRI) and prostate-specific membrane antigen (PSMA) positron emission tomography/computed tomography (PET/CT)-guided targeted biopsy (TB) in prostate cancer (PCa) diagnosis, but there is no direct comparison between mpMRI-TB and PSMA PET/CT-TB. Gastrin-releasing peptide receptor (GRPR) is highly expressed in PCa, which can compensate for the unstable expression of PSMA in PCa. Therefore, we designed a study to compare the efficiency of mpMRI-TB, dual-tracer (GRPR and PSMA) PET/CT-TB, systematic biopsy, and combined biopsy for the diagnosis of prostate cancer. METHODS: One hundred twelve suspicious PCa patients were enrolled from September 2020 to June 2021. Patients with anyone of positive dual-tracer PET/CT or mpMRI underwent TB, and all enrolled patients underwent systematic biopsy (SB) after TB. The primary outcome was the detection rates of PCa in different biopsy strategies. Secondary outcomes were the performance of three imaging methods, omission diagnostic rates, and upgrading and downgrading of biopsy samples relative to those of prostatectomy specimens in different biopsy strategies. McNemar's tests and Bonferroni correction in multiple comparisons were used to compare the primary and secondary outcomes. RESULTS: In 112 men, clinically significant PCa (grade group[GG] ≥ 2) accounted for 34.82% (39/112), and nonclinically significant PCa (GG = 1) accounted for 4.46% (5/112). 68 Ga-PSMA PET/CT-TB achieved higher PCa detection rate (69.77%) and positive ratio of biopsy cores (0.44) compared with SB (39.29% and 0.12) and mpMRI-TB (36.14% and 0.23), respectively (P < 0.005). Dual-tracer PET/CT screen out patients for avoiding 52.67% (59/112) unnecessary biopsy, whereas dual-tracer PET/CT-TB plus SB achieved high detection rate (77.36%) without misdiagnosis of csPCa. CONCLUSION: Dual-tracer PET/CT might screen patients for avoiding unnecessary biopsy. Dual-tracer PET/CT-TB plus SB might be a more effective and promising strategy for the definite diagnosis of clinically significant PCa than mpMRI-TB.

An anti-scratch flexible SERS substrate for pesticide residue detection on the surface of fruits and vegetables.

We propose an anti-scratch flexible surface-enhanced Raman scattering substrate with arrayed nanocavity microstructures fabricated by colloidal lithography. The nanocavity microstructure of the substrate can well protect the inner gold nanoparticles during wipe sampling. The prepared flexible substrate was able to detect 4-aminothiophenol (4-ATP) with a concentration down to 1 fM. Furthermore, the substrate was used to detect 6-BA residues on the surface of apples and bean sprouts through wipe sampling, which shows great potential in the field of rapid on-site detection, especially in the detection of pesticide residues on the surface of fruits and vegetables.

DNA methylation on N(6)-adenine in mammalian embryonic stem cells.

It has been widely accepted that 5-methylcytosine is the only form of DNA methylation in mammalian genomes. Here we identify N(6)-methyladenine as another form of DNA modification in mouse embryonic stem cells. Alkbh1 encodes a demethylase for N(6)-methyladenine. An increase of N(6)-methyladenine levels in Alkbh1-deficient cells leads to transcriptional silencing. N(6)-methyladenine deposition is inversely correlated with the evolutionary age of LINE-1 transposons; its deposition is strongly enriched at young (<1.5 million years old) but not old (>6 million years old) L1 elements. The deposition of N(6)-methyladenine correlates with epigenetic silencing of such LINE-1 transposons, together with their neighbouring enhancers and genes, thereby resisting the gene activation signals during embryonic stem cell differentiation. As young full-length LINE-1 transposons are strongly enriched on the X chromosome, genes located on the X chromosome are also silenced. Thus, N(6)-methyladenine developed a new role in epigenetic silencing in mammalian evolution distinct from its role in gene activation in other organisms. Our results demonstrate that N(6)-methyladenine constitutes a crucial component of the epigenetic regulation repertoire in mammalian genomes.

lnc-Rps4l-encoded peptide RPS4XL regulates RPS6 phosphorylation and inhibits the proliferation of PASMCs caused by hypoxia.

Pulmonary artery smooth muscle cells (PASMCs) proliferation caused by hypoxia is an important pathological process of pulmonary hypertension (PH). Prevention of PASMCs proliferation can effectively reduce PH mortality. Long non-coding RNAs (lncRNAs) are involved in the proliferation process. Recent evidence has demonstrated that functional peptides encoded by lncRNAs play important roles in cell pathophysiological process. Our previous study has demonstrated that lnc-Rps4l with high coding ability mediates the PASMCs proliferation under hypoxic conditions. We hypothesize in this study that a lnc-Rps4l-encoded peptide is involved in hypoxic-induced PASMCs proliferation. The presence of peptide 40S ribosomal protein S4 X isoform-like (RPS4XL) encoded by lnc-Rps4l in PASMCs under hypoxic conditions was confirmed by bioinformatics, immunofluorescence, and immunohistochemistry. Inhibition of proliferation by the peptide RPS4XL was demonstrated in hypoxic PASMCs by MTT, bromodeoxyuridine (BrdU) incorporation, and immunofluorescence assays. By using the bioinformatics, coimmunoprecipitation (coIP), and mass spectrometry, RPS6 was identified to interact with RPS4XL. Furthermore, lnc-Rps4l-encoded peptide RPS4XL inhibited the RPS6 process via binding to RPS6 and inhibiting RPS6 phosphorylation at p-RPS6 (Ser240+Ser244) phosphorylation site. These results systematically elucidate the role and regulatory network of Rps4l-encoded peptide RPS4XL in PASMCs proliferation. These discoveries provide potential targets for early diagnosis and a leading compound for treatment of hypoxic PH.

Prevalence of phase variable epigenetic invertons among host-associated bacteria.

Type I restriction-modification (R-M) systems consist of a DNA endonuclease (HsdR, HsdM and HsdS subunits) and methyltransferase (HsdM and HsdS subunits). The hsdS sequences flanked by inverted repeats (referred to as epigenetic invertons) in certain Type I R-M systems undergo invertase-catalyzed inversions. Previous studies in Streptococcus pneumoniae have shown that hsdS inversions within clonal populations produce subpopulations with profound differences in the methylome, cellular physiology and virulence. In this study, we bioinformatically identified six major clades of the tyrosine and serine family invertases homologs from 16 bacterial phyla, which potentially catalyze hsdS inversions in the epigenetic invertons. In particular, the epigenetic invertons are highly enriched in host-associated bacteria. We further verified hsdS inversions in the Type I R-M systems of four representative host-associated bacteria and found that each of the resultant hsdS allelic variants specifies methylation of a unique DNA sequence. In addition, transcriptome analysis revealed that hsdS allelic variations in Enterococcus faecalis exert significant impact on gene expression. These findings indicate that epigenetic switches driven by invertases in the epigenetic invertons broadly operate in the host-associated bacteria, which may broadly contribute to bacterial host adaptation and virulence beyond the role of the Type I R-M systems against phage infection.

Modulating the plasmon-mediated silver oxidation using thiophenol molecules as monitored by in situ SERS spectroscopy.

Effective charge separation is essential in plasmon-mediated photochemistry and is usually achieved by constructing plasmon-semiconductor interfaces, which is usually challenging. In this work, by monitoring the plasmon-mediated silver oxidation with in situ Raman spectroscopy, we demonstrate that the adsorbed thiophenol molecules could modulate the rate of photochemical reactions by tuning the charge separation at the plasmon-molecule interfaces. It is found that the thiophenol molecules with strong electron-withdrawing or donating functional groups could accelerate or decelerate the rate of plasmon-mediated silver oxidation, respectively. Owing to the easy tuning of the electronic structures of organic molecules via substitution, our method provides a versatile and convenient approach for the fine modulation of plasmon-mediated photochemical reactions.

GbCYP86A1-1 from Gossypium barbadense positively regulates defence against Verticillium dahliae by cell wall modification and activation of immune pathways.

Suberin acts as stress-induced antipathogen barrier in the root cell wall. CYP86A1 encodes cytochrome P450 fatty acid ω-hydroxylase, which has been reported to be a key enzyme for suberin biosynthesis; however, its role in resistance to fungi and the mechanisms related to immune responses remain unknown. Here, we identified a disease resistance-related gene, GbCYP86A1-1, from Gossypium barbadense cv. Hai7124. There were three homologs of GbCYP86A1 in cotton, which are specifically expressed in roots and induced by Verticillium dahliae. Among them, GbCYP86A1-1 contributed the most significantly to resistance. Silencing of GbCYP86A1-1 in Hai7124 resulted in severely compromised resistance to V. dahliae, while heterologous overexpression of GbCYP86A1-1 in Arabidopsis improved tolerance. Tissue sections showed that the roots of GbCYP86A1-1 transgenic Arabidopsis had more suberin accumulation and significantly higher C16-C18 fatty acid content than control. Transcriptome analysis revealed that overexpression of GbCYP86A1-1 not only affected lipid biosynthesis in roots, but also activated the disease-resistant immune pathway; genes encoding the receptor-like kinases (RLKs), receptor-like proteins (RLPs), hormone-related transcription factors, and pathogenesis-related protein genes (PRs) were more highly expressed in the GbCYP86A1-1 transgenic line than control. Furthermore, we found that when comparing V. dahliae -inoculated and noninoculated plants, few differential genes related to disease immunity were detected in the GbCYP86A1-1 transgenic line; however, a large number of resistance genes were activated in the control. This study highlights the role of GbCYP86A1-1 in the defence against fungi and its underlying molecular immune mechanisms in this process.

The structure and chemical bonding in inverse sandwich B6Ca2 and B8Ca2 clusters: conflicting aromaticity vs. double aromaticity.

The typical electron-deficiency of the boron element renders fascinating architectures and chemical bonding to boron-based nanoclusters. We theoretically predict two di-Ca-doped boron clusters, B6Ca2 (D2h, 1Ag) and B8Ca2 (D8h, 1A1g), and both adopt interesting inverse sandwich geometries, showing an elongated D2h B6 or perfectly planar D8h B8 ring being sandwiched by two Ca atoms only, respectively. Natural atomic charge analyses indicate that the Ca atoms donate nearly all the 4s electrons to the B6 (or B8) ring, forming [Ca]2+[B6]4-[Ca]2+ and [Ca]2+[B8]4-[Ca]2+ charge transfer complexes. The interaction between the two Ca atoms and the boron rings is governed by robust electrostatics albeit by weaker B-Ca covalent interaction. Chemical bonding analyses show that B6Ca2 has 4σ and 6π delocalized electrons on the elongated B6 ring, leading to a conflicting aromatic system. B8Ca2, possessing 6σ and 6π delocalized electrons on the B8 ring, is doubly aromatic. Additionally, the B6Ca2 and B8Ca2 clusters show noticeable structural and electronic transmutation relative to their equivalent electronic B6Be2 and B8Mg2 clusters, respectively. The intrinsic reasons behind the transmutations are elucidated via in-depth bonding analyses.

The time-resolved transcriptome of C. elegans.

We generated detailed RNA-seq data for the nematode Caenorhabditis elegans with high temporal resolution in the embryo as well as representative samples from post-embryonic stages across the life cycle. The data reveal that early and late embryogenesis is accompanied by large numbers of genes changing expression, whereas fewer genes are changing in mid-embryogenesis. This lull in genes changing expression correlates with a period during which histone mRNAs produce almost 40% of the RNA-seq reads. We find evidence for many more splice junctions than are annotated in WormBase, with many of these suggesting alternative splice forms, often with differential usage over the life cycle. We annotated internal promoter usage in operons using SL1 and SL2 data. We also uncovered correlated transcriptional programs that span >80 kb. These data provide detailed annotation of the C. elegans transcriptome.

Silver Nanowire-Templated Molecular Nanopatterning and Nanoparticle Assembly for Surface-Enhanced Raman Scattering.

Developing simple and cost-efficient methods for fabricating molecular patterns is of great importance in the field of nanoscience and nanotechnology. Here, a simple and convenient method was developed for fabricating nanopatterns composed of positively charged silane molecules by using silver nanowires as templates. The as-obtained silane pattern copies the shape of the silver nanowires and is only 0.7 nm thick, which can later be used for templated assembly of small molecules and nanoparticles of opposite charges. As a proof of concept, the resultant assembly could be further used for surface-enhanced Raman scattering.