Pollutant removal in an experimental bioretention cell situated in a northern Chinese sponge city.

To assess the viability and effectiveness of bioretention cell in enhancing rainwater resource utilization within sponge cities, this study employs field monitoring, laboratory testing, and statistical analysis to evaluate the water purification capabilities of bioretention cell. Findings indicate a marked purification impact on surface runoff, with removal efficiencies of 59.81% for suspended solids (SS), 39.01% for chemical oxygen demand (COD), 37.53% for ammonia nitrogen (NH3-N), and 30.49% for total phosphorus (TP). The treated water largely complies with rainwater reuse guidelines and tertiary sewage discharge standards. Notably, while previous research in China has emphasized water volume control in sponge city infrastructures, less attention has been given to the qualitative aspects and field-based evaluations. This research not only fills that gap but also offers valuable insights and practical implications for bioretention cell integration into sponge city development. Moreover, the methodology and outcomes of this study serve as a benchmark for future sponge city project assessments, offering guidance to relevant authorities.

A novel bacterial sulfite dehydrogenase that requires three c-type cytochromes for electron transfer.

c-type Cytochromes (c-Cyts), primarily as electron carriers and oxidoreductases, play a key role in energy transduction processes in virtually all living organisms. Many bacteria, such as Shewanella oneidensis, are particularly rich in c-Cyts, supporting respiratory versatility not seen in eukaryotes. Unfortunately, a large number of c-Cyts are underexplored, and their biological functions remain unknown. In this study, we identify SorCABD of S. oneidensis as a novel sulfite dehydrogenase (SDH), which catalyzes the oxidation of sulfite to sulfate. In addition to catalytic subunit SorA, this enzymatic complex includes three c-Cyt subunits, which all together carry out electron transfer. The electrons extracted from sulfite oxidation are ultimately delivered to oxygen, leading to oxygen reduction, a process relying on terminal oxidase cyt cbb3. Genomic analysis suggests that the homologs of this SDH are present in a small number of bacterial genera, Shewanella and Vibrio in particular. Because these bacteria are generally capable of reducing sulfite under anaerobic conditions, the co-existence of a sulfite oxidation system implies that they may play especially important roles in the transformation of sulfur species in natural environments.Importancec-type Cytochromes (c-Cyts) endow bacteria with high flexibility in their oxidative/respiratory systems, allowing them to extracellularly transform diverse inorganic and organic compounds for survival and growth. However, a large portion of the bacterial c-Cyts remain functionally unknown. Here, we identify three c-Cyts that work together as essential electron transfer partners for the catalytic subunit of a novel SDH in sulfite oxidation in Shewanella oneidensis. This characteristic makes S. oneidensis the first organism known to be capable of oxidizing and reducing sulfite. The findings suggest that Shewanella, along with a small number of other aquatic bacteria, would serve as a particular driving force in the biogeochemical sulfur cycle in nature.

Discovery of a potent inhibitor targeting the cap-binding domain of the PB2 subunit of influenza RNA-dependent RNA polymerase.

Influenza pandemics have emerged as a significant global public health and security concern. PB2, a crucial subunit of the influenza RNA-dependent RNA polymerase (RdRP), has been identified as a promising target for influenza treatment. We herein report the discovery of a potent novel PB2 inhibitor, 7-51A, with a KD value of 1.64 nM as determined by ITC. The high activity of 7-51A was elucidated by the co-crystal structure of the PB2-7-51A complex, and comparative analysis revealed unique interactions that had never been observed before. The preliminary pharmacological evaluation indicated that 7-51A exhibited commendable cellular safety, hepatic microsomal metabolic safety and stability. Collectively, 7-51A was found to be an effective PB2 inhibitor and could be used as a lead compound for further studies.

Design, synthesis, and biological screening of a series of pyrazolo [1,5-a]quina-zoline derivatives as SIRT6 activators.

SIRT6 has emerged as a novel therapeutic target for a variety of diseases. In this study, a total of 102 pyrazolo [1,5-a]quinazoline derivatives were designed and synthesized. The result revealed that 2-methyl-N-(4-phenoxy-phenyl)pyrazolo [1,5-a]quinazoline-5-amine (21q) was the most active compound by structure-activity relationship study, which significantly enhanced SIRT6 defatty-acylation activity with an EC1.5 value of 1.85±0.41 µM and EC50 value of 11.15±0.33 µM. The biological activity of 21q was further verified by differential scanning fluorimetry assay (DSF) and surface plasmon resonance assay (SPR). Molecular docking showed that the pyrazolo [1,5-a]quinazoline of 21q formed a hydrogen bond with Val115 and four π- π interactions with Phe64, Phe82 and Phe86. 21q can significantly improve the thermal stability of SIRT6 protein and inhibit the PI3K/Akt signaling pathway in mouse embryonic fibroblasts (MEFs), thereby inhibiting the proliferation of MEFs. Collectively, we discovered a new potent SIRT6 activator, which can be taken as a lead compound for later studies.

Biotransformation of 2D Nanomaterials through Stimulated Bacterial Respiration-Produced Extracellular Reactive Oxygen Species: A Common but Overlooked Process.

The biotransformation of 2D nanomaterials is still poorly understood, although their environmental fates are becoming an increasing concern with their broad applications. Here, we found that Ti3C2Tx nanosheets, a typical 2D nanomaterial, could be oxidized by reactive oxygen species (ROS) produced by both Gram-negative (Escherichia coli and Shewanella oneidensis) and Gram-positive (Bacillus subtilis) bacteria, with the formation of titanium dioxide (TiO2) on the nanosheet surfaces and impairment of structural integrity. Specifically, Ti3C2Tx nanosheets stimulated bacterial respiration Complex I, leading to increased generation of extracellular O2•- and the formation of H2O2 and •OH via Fenton-like reactions, which intensified the oxidation of the nanosheets. Surface modifications with KOH and hydrazine (HMH), especially HMH, could limit bacterial oxidation of the nanosheets. These findings reveal a common but overlooked process in which oxygen-respiring bacteria are capable of oxidizing 2D nanosheets, providing new knowledge for environmental fate evaluation and future design of functional 2D nanomaterials.

NapB Restores cytochrome c biosynthesis in bacterial dsbD-deficient mutants.

Cytochromes c (cyts c), essential for respiration and photosynthesis in eukaryotes, confer bacteria respiratory versatility for survival and growth in natural environments. In bacteria having a cyt c maturation (CCM) system, DsbD is required to mediate electron transport from the cytoplasm to CcmG of the Ccm apparatus. Here with cyt c-rich Shewanella oneidensis as the research model, we identify NapB, a cyt c per se, that suppresses the CCM defect of a dsbD mutant during anaerobiosis, when NapB is produced at elevated levels, a result of activation by cAMP-Crp. Data are then presented to suggest that NapB reduces CcmG, leading to the suppression. We further show that NapB proteins capable of rescuing CCM in the dsbD mutant form a small distinct clade. The study sheds light on multifunctionality of cyts c, and more importantly, unravels a self-salvation strategy through which bacteria have evolved to better adjust to the natural world.

Functional Irreplaceability of Escherichia coli and Shewanella oneidensis OxyRs Is Critically Determined by Intrinsic Differences in Oligomerization.

LysR-type transcriptional regulators (LTTRs), which function in diverse biological processes in prokaryotes, are composed of a conserved structure with an N-terminal DNA-binding domain (DBD) and a C-terminal signal-sensing regulatory domain (RD). LTTRs that sense and respond to the same signal are often functionally exchangeable in bacterial species across wide phyla, but this phenomenon has not been demonstrated for the H2O2-sensing and -responding OxyRs. Here, we systematically examined the biochemical and structural determinants differentiating activator-only OxyRs from dual-activity ones by comparing OxyRs from two Gammaproteobacteria, Escherichia coli and Shewanella oneidensis. Our data show that EcOxyR could function as neither an activator nor a repressor in S. oneidensis. Using SoOxyR-based OxyR chimeras and mutants, we demonstrated that residues 283 to 289, which form the first half of the last C-terminal α-helix (α10), are critical for the proper function of SoOxyR and cannot be replaced with the EcOxyR counterpart. Crystal structural analysis reveals that α10 is important for the oligomerization of SoOxyR, which, unlike EcOxyR, forms several high-order oligomers upon DNA binding. As the mechanisms of OxyR oligomerization vary substantially among bacterial species, our findings underscore the importance of subtle structural features in determining regulatory activities of structurally similar proteins descending from a common ancestor. IMPORTANCE Evolution may drive homologous proteins to be functionally nonexchangeable in different organisms. However, much is unknown about the mechanisms underlying this phenomenon beyond amino acid substitutions. Here, we systematically examined the biochemical and structural determinants differentiating functionally nonexchangeable OxyRs, H2O2-responding transcriptional regulators from two Gammaproteobacteria, Escherichia coli and Shewanella oneidensis. Using SoOxyR-based OxyR chimeras and mutants, we demonstrated that residues 283 to 289, which form the first half of the last C-terminal α-helix (α10), are critical for the proper function of SoOxyR and cannot be replaced with the EcOxyR counterpart. Crystal structural analysis reveals that this last helix is critical for formation of high-order oligomers upon DNA binding, a phenomenon not observed with EcOxyR. Our findings provide a new dimension to differences in sequence and structural features among bacterial species in determining regulatory activities of homologous regulators.

Promoting Extracellular Electron Transfer of Shewanella oneidensis MR-1 by Optimizing the Periplasmic Cytochrome c Network.

The low efficiency of extracellular electron transfer (EET) is a major bottleneck for Shewanella oneidensis MR-1 acting as an electroactive biocatalyst in bioelectrochemical systems. Although it is well established that a periplasmic c-type cytochrome (c-Cyt) network plays a critical role in regulating EET efficiency, the understanding of the network in terms of structure and electron transfer activity is obscure and partial. In this work, we attempted to systematically investigate the impacts of the network components on EET in their absence and overproduction individually in microbial fuel cell (MFC). We found that overexpression of c-Cyt CctA leads to accelerated electron transfer between CymA and the Mtr system, which function as the primary quinol oxidase and the outer-membrane (OM) electron hub in EET. In contrast, NapB, FccA, and TsdB in excess severely impaired EET, reducing EET capacity in MFC by more than 50%. Based on the results from both strategies, a series of engineered strains lacking FccA, NapB, and TsdB in combination while overproducing CctA were tested for a maximally optimized c-Cyt network. A strain depleted of all NapB, FccA, and TsdB with CctA overproduction achieved the highest maximum power density in MFCs (436.5 mW/m2), ∼3.62-fold higher than that of wild type (WT). By revealing that optimization of periplasmic c-Cyt composition is a practical strategy for improving EET efficiency, our work underscores the importance in understanding physiological and electrochemical characteristics of c-Cyts involved in EET.

Thiosulfate oxidation in sulfur-reducing Shewanella oneidensis and its unexpected influences on the cytochrome c content.

Thiosulfate, an important form of sulfur compounds, can serve as both electron donor and acceptor in various microorganisms. In Shewanella oneidensis, a bacterium renowned for respiratory versatility, thiosulfate reduction has long been recognized but whether it can catalyse thiosulfate oxidation remains elusive. In this study, we discovered that S. oneidensis is capable of thiosulfate oxidation, a process specifically catalysed by two periplasmic cytochrome c (cyt c) proteins, TsdA and TsdB, which act as the catalytic subunit and the electron transfer subunit respectively. In the presence of oxygen, oxidation of thiosulfate has priority over reduction. Intriguingly, thiosulfate oxidation negatively regulates the cyt c content in S. oneidensis cells, largely by reducing intracellular levels of cAMP, which as the cofactor modulates activity of global regulator Crp required for transcription of many cyt c genes. This unexpected finding provides an additional dimension to interplays between the respiration regulator and the respiratory pathways in S. oneidensis. Moreover, the data presented here identified S. oneidensis as the first bacterium known to date owning both functional thiosulfate reductase and dehydrogenase, and importantly, genomics analyses suggested that the number of bacterial species possessing this feature is rather limited.

SARS-CoV-2 Mpro inhibitors with antiviral activity in a transgenic mouse model.

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continually poses serious threats to global public health. The main protease (Mpro) of SARS-CoV-2 plays a central role in viral replication. We designed and synthesized 32 new bicycloproline-containing Mpro inhibitors derived from either boceprevir or telaprevir, both of which are approved antivirals. All compounds inhibited SARS-CoV-2 Mpro activity in vitro, with 50% inhibitory concentration values ranging from 7.6 to 748.5 nM. The cocrystal structure of Mpro in complex with MI-23, one of the most potent compounds, revealed its interaction mode. Two compounds (MI-09 and MI-30) showed excellent antiviral activity in cell-based assays. In a transgenic mouse model of SARS-CoV-2 infection, oral or intraperitoneal treatment with MI-09 or MI-30 significantly reduced lung viral loads and lung lesions. Both also displayed good pharmacokinetic properties and safety in rats.

Discovery of Potent Small-Molecule SIRT6 Activators: Structure-Activity Relationship and Anti-Pancreatic Ductal Adenocarcinoma Activity.

SIRT6 activation is thought to be a promising target for the treatment of many diseases, particularly cancer. Herein, we report the discovery of a series of new small-molecule SIRT6 activators. Structure-activity relationship analyses led to the identification of the most potent compound, 2-(1-benzofuran-2-yl)-N-(diphenylmethyl) quinoline-4-carboxamide (12q), which showed an EC1.5 value of 0.58 ± 0.12 µM and an EC50 value of 5.35 ± 0.69 µM against SIRT6-dependent peptide deacetylation in FLUOR DE LYS assay. It exhibited weak or no activity against other HDAC family members as well as 415 kinases, indicating good selectivity for SIRT6. 12q significantly inhibited the proliferation and migration of pancreatic ductal adenocarcinoma (PDAC) cells in vitro. It also markedly suppressed the tumor growth in a PDAC tumor xenograft model. This compound showed attractive pharmacokinetic properties. Overall, 12q could be a good lead compound for the treatment of PDAC, and it is worthy of further study.

Association Between Vitamins and Amyotrophic Lateral Sclerosis: A Center-Based Survey in Mainland China.

To date, conflicting results about the role of vitamins in amyotrophic lateral sclerosis (ALS) have been reported along with a lack of systematic studies on all types of serum vitamins in patients with ALS. Moreover, extensive studies have been conducted on vitamins in other neurodegenerative diseases; however, whether serum vitamin alterations in ALS are similar to those in other neurodegenerative diseases remains unclear. Therefore, we performed a study involving a large Chinese cohort of patients with ALS to address this gap. In this study, 202 patients with ALS, 214 with a neurodegenerative disease that mimicked ALS (mimics), and 208 healthy controls were enrolled. Serum vitamins of all subjects were examined under fasting state in Clinical Laboratory. As a result, we found that higher vitamin A and E levels and lower vitamin B2, B9, and C levels were in patients with ALS compared to healthy controls, and that high vitamin A and E levels, and low vitamin B2, B9, and C levels were associated with an increased risk for ALS. In addition, serum vitamin C was lower in early-onset ALS patients compared to those in late-onset ALS patients; however, there was no significant correlation between serum vitamins and age at onset, sites at onset, disease duration, or disease severity of ALS. We also found that patients with ALS showed similar vitamin alterations to mimics, with the exception of vitamin E. In summary, our study adds information to the literature on the role of vitamins in ALS and provides support for clinical guidance regarding dietary changes and vitamin supplements in patients with ALS.

Discovery of 5-(4-methylpiperazin-1-yl)-2-nitroaniline derivatives as a new class of SIRT6 inhibitors.

SIRT6 is a deacetylase of histone H3 and inhibitors of SIRT6 have been thought as potential agents for treatment of diabetes. Herein we report the discovery of a series of new SIRT6 inhibitors containing the skeleton 1-phenylpiperazine. Among them, compound 5-(4-methylpiperazin-1-yl)-2-nitroaniline (6d) is the most potent one, which showed an IC50 value of 4.93 µM against SIRT6 in the Fluor de Lys (FDL) assay. It displayed KD values of 9.76 µM and 10 µM in surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) assays, respectively. In selectivity assay, 6d showed no activity against other members of the HDAC family (SIRT1-3 and HDAC1-11) at concentrations up to 200 µM. In a mouse model of type 2 diabetes, 6d could significantly increase the level of glucose transporter GLUT-1, thereby reducing blood glucose. Overall, this study provides a promising lead compound for subsequent drug discovery targeting SIRT6.

Mutation analysis of GLT8D1 and ARPP21 genes in amyotrophic lateral sclerosis patients from mainland China.

Variants in exon 4 of gene encoding GLT8D1 (glycosyltransferase 8 domain containing 1) gene have recently been suggested as a novel cause of amyotrophic lateral sclerosis (ALS). In addition, there is a synergism between GLT8D1 and ARPP21 (cAMP Regulated Phosphoprotein 21) variants for ALS. However, this observation has not been validated in other ALS cohorts. In this study, we analyzed the rare pathogenic variants in GLT8D1 and ARPP21 genes in a cohort of 512 ALS patients and 3210 healthy controls from mainland China. A total of 25 rare variants in ARPP21 were identified in the patients and controls, but we did not find rare variants in exon 4 of GLT8D1 in the patients. By using Fisher's exact test, we did not find significant association between ALS and GLT8D1 or ARPP21. Therefore, GLT8D1 and ARPP21 are not likely the causative genes for ALS in mainland China.

Clinical findings of autosomal-dominant striatal degeneration and PDE8B mutation screening in parkinsonism and related disorders.

BACKGROUND: Autosomal-dominant striatal degeneration (ADSD) is a rare neurodegenerative movement disorder caused by mutations in the Phosphodiesterase 8B (PDE8B) gene. OBJECTIVE: To summarize the clinical and imaging features of a Chinese ADSD family and determine whether mutations in PDE8B are associated with Parkinson's disease (PD) or Parkinsonism. METHODS: Clinical, imaging and genetic findings in a Chinese ADSD family are reported. Rare, potentially pathogenic variants in PDE8B were searched in whole-exome sequencing datasets from 1714 PD or parkinsonism patients and 1039 controls. RESULTS: An ADSD diagnosis was confirmed by a nonsense mutation in PDE8B (p.E102X) in a patient and a presymptomatic carrier. Clinically, the patient exhibited progressive parkinsonism without tremor and ataxia phenotype. Neuroimaging showed an inhomogeneous increased signal in the patient's striatum on T1-weighted images but a decreased signal in the presymptomatic carrier. Diffusion tensor imaging (DTI) showed a disturbance in the white matter fiber distribution, especially between the lentiform nucleus and caudate nucleus, which was more prominent in the patient than in the presymptomatic carrier. Within the 1714 patients, three PDE8B missense variants were identified that were unlikely to be the cause of the parkinsonism phenotype according to the functional prediction and mutation types reported in ADSD. CONCLUSIONS: For the first time, we described the typical ataxia phenotype in ADSD. A loss of white matter fiber integrity was shown on DTI scanning. No causative PDE8B mutation was discovered in our cohort of PD or Parkinsonism patients.

Distinct Roles of Shewanella oneidensis Thioredoxin in Regulation of Cellular Responses to Hydrogen and Organic Peroxides.

The thioredoxin (Trx) and glutaredoxin (Grx) antioxidant systems are deeply involved in bacterial response to oxidative stress, but to date, we know surprisingly little about the roles of these systems in response to reactive oxygen species (ROS) other than hydrogen peroxide (H2O2). In this study, we used Shewanella oneidensis, an environmental bacterium, as a research model to investigate the roles of Trx and Grx in oxidative stress response because it has functionally intertwined ROS responsive regulators OxyR and OhrR. We found that Trx1 is the major thiol/disulfide redox system and that in its absence a Grx system becomes essential under normal conditions. Although overshadowed by Trx1 in the wild type, Trx2 can fully replace Trx1 in physiology when overproduced. Trx1 is required for OxyR to function as a repressor but, more importantly, plays a critical role in the cellular response to organic peroxide (OP) by mediating the redox status of OhrR but not OP scavenger OhrA. While none of the trx and grx genes are OxyR dependent, trxA and trxC are affected by OhrR indirectly. Additional data suggest that depletion of glutathione is likely the cue to trigger induced expression of trxA and trxC These findings underscore the particular importance of Trx in the bacterial OP stress response.IMPORTANCE The Trx and Grx systems are deeply involved in bacterial responses to H2O2-induced oxidative stress. However, little is known about their roles in response to other ROS, such as organic peroxides (OPs). In this study, we used S. oneidensis as a research model to investigate the interplay between Trx/Grx and OxyR/OhrR. We show that Trxs mediate the redox status of transcriptional OP-responding regulator OhrR. Although none of the trx or grx genes are directly controlled by OxyR or OhrR, expression of trxA and trxC is induced by tert-butyl hydroperoxide (t-BHP). We further show that the trxA and trxC genes respond to effects of glutathione (GSH) depletion rather than oxidation. These findings underscore the particular importance of Trx in the bacterial OP stress response.

Oxidized OxyR Up-Regulates ahpCF Expression to Suppress Plating Defects of oxyR- and Catalase-Deficient Strains.

It is well established that in bacteria, such as Escherichia coli, OxyR is a transcriptional regulator that mediates the response to H2O2 by activating the OxyR regulon, which consists of many genes that play vital roles in oxidative stress resistance. In Shewanella, OxyR regulates, however, in both reduced and oxidized states, the production of H2O2 scavengers, including major catalase KatB and NADH peroxidase AhpCF. Here we showed that the oxyR mutant carried a plating defect manifested as division arresting, a phenotype that can be completely suppressed by an OxyR variant constitutively existing in oxidized form (OxyRL197P). This effect of OxyRL197P could not be solely attributed to the increment in KatB production, since the suppression was also observed in the absence of KatB. Although expression of peroxidase CcpA was greatly activated by OxyRL197P, the contribution of the protein in alleviating plating defect was negligible. We eventually identified AhpCF as the critical factor, when produced at substantially elevated levels by OxyRL197P, to protect the cell from H2O2 attack. Our data indicate that AhpCF is a particularly important peroxidase in oxidative stress resistance in Shewanella, not only playing a compensatory role for catalase, but also by itself providing sufficient protection from killing of H2O2 generated abiotically.

Discovery of human TyrRS inhibitors by structure-based virtual screening, structural optimization, and bioassays.

The human tyrosyl transfer-RNA (tRNA) synthetase (TyrRS), which is well known for its essential aminoacylation function in protein synthesis, has been shown to translocate to the nucleus and protect against DNA damage caused by external stimuli. Small molecules that can fit into the active site pocket of TyrRS are thought to affect the nuclear role. The exploitation of TyrRS inhibitors has attracted attention recently. In this investigation, we adopted a structure-based virtual screening strategy and subsequent structure-activity relationship analysis to discover new TyrRS inhibitors, and identified a potent compound 5,7-dihydroxy-6,8-bis((3-hydroxyphenyl)thio)-2-phenyl-4H-chromen-4-one (compound 11, K i = 8.8 µM). In intact HeLa cells, this compound showed a protective effect against DNA damage. Compound 11 is a good lead compound for the further development of drugs against disorders caused by DNA damage.

[Analysis of spinocerebellar ataxia type 31 related mutations among patients from mainland China].

OBJECTIVE: To determine the frequency of spinocerebellar ataxia type 31 (SCA31) related mutations among patients from mainland China. METHODS: For a cohort of molecularly unassigned patients comprised of 295 SCA patients (including 98 probands from families featuring autosomal dominant SCA and 197 sporadic cases) and 81 patients with hereditary spastic paraplegia (HSP) (including 23 probands from families with autosomal dominant HSP and 58 sporadic cases),TGGAA pentanucleotide expansion insertional mutation of the BEAN/TK2 gene was detected using repeat-primed PCR followed by capillary gel electrophoresis. RESULTS: No TGGAA pentanucleotide insertion expansion in BEAN/TK2 gene was identified in the above cohort. CONCLUSION: SCA31 is an extremely rare subtype of SCA and should not be included in routine genetic screening in mainland China.

Fe2O3/BiOI-Based Photoanode with n-p Heterogeneous Structure for Photoelectric Conversion.

We report a promising photoanode material of Fe2O3/BiOI for efficient photoelectric conversion in solar cells, which was fabricated with BiOI attached to a one-dimensional Fe2O3 nanorod array. The two semiconductors of p-type BiOI and n-type Fe2O3 formed a heterogeneous structure for efficient charge separation. The highest open circuit voltage and short circuit current of the solar cell can reach 0.41 V and 4.89 mA/cm2, respectively. This study opens an available field to develop low-cost and environmentally friendly photoelectric materials for solar cells.