An effective strategy for identifying autogenous regulation of transcription factors in filamentous fungi.

IMPORTANCE: Transcription factors (TFs) play a crucial role in deciphering biological information from the DNA of living organisms. Improper regulation of their functions can disrupt cellular physiology and lead to diseases in humans. As one of the key regulatory mechanisms, some TFs control their own expression levels through autogenous regulation. However, identifying autogenous regulation events of TFs has been a tedious task. In this study, we present a straightforward approach that provides a reliable means to identify TF autogenous regulation events. Our method provides a valuable means for understanding the function of this important class of proteins in cells.

Electroacupuncture-Modulated MiR-106b-5p Expression Enhances Autophagy by Targeting Beclin-1 to Promote Motor Function Recovery After Spinal Cord Injury in Rats.

OBJECTIVE: Electroacupuncture (EA) has a definite effect on the treatment of spinal cord injuries (SCIs), but its underlying molecular mechanism remains unclear. Meanwhile, MiR106b-5p is an autophagy- and apoptosis-related microribonucleic acid, but whether it regulates the progression of autophagy and apoptosis in SCIs is yet undetermined. As such, this study aimed to elucidate the involvement of miR-106b-5p in the EA treatment of an SCI. METHODS: The miR-106b-5p level was detected by quantitative real-time polymerase chain reaction. In vitro, SH-SY5Y cells were transfected with miR-106b-5p mimics or inhibitors to regulate the miR-106b-5p expression, while in vivo, SCI rats were treated with EA for 7 days at the bilateral Zusanli (ST36) and Jiaji (EX-B2) acupoints. The motor function was evaluated using the Basso-Beattie-Bresnahan (BBB) criteria. Further, autophagic vacuoles, pathological damage, and neuronal cell morphology were observed by transmission electron microscopy, as well as by hematoxylin and eosin and Nissl staining, respectively. RESULTS: The miR-106b-5p level, which can interact directly with Beclin-1 by influencing its expression, as well as the expressions of P62, Caspase-3, and Bax, was upregulated after an SCI, but it decreased after EA. Moreover, the ratio of LC3-II to LC3-I was upregulated after EA. EA can enhance autophagy, reduce neuronal apoptosis, and minimize motor dysfunction and histopathological deficits after an SCI. More importantly, however, all the above effects induced by EA can be reversed after an injection of miR-106-5p agomir to produce an overexpression of miR-106b-5p. CONCLUSION: EA treatment could downregulate miR-106b-5p to alleviate SCI-mediated injuries by promoting autophagy and inhibiting apoptosis.

Visible-light-driven photoreforming of poly(ethylene terephthalate) plastics via carbon nitride porous microtubes.

It is highly desirable but challenging to realize efficient photoreforming of plastic waste over metal-free semiconductors. Here, we synthesized metal-free carbon nitride porous microtube (CNxPM) photocatalysts by carrying out a pyrolysis of the supramolecular assembly formed by the self-assembly of L-arginine (L-Arg) and melamine, the modification of L-Arg rationally engineering the microstructure and electronic structure of the CNxPM system for efficient visible-light-driven photoreforming of poly(ethylene terephthalate) (PET) to hydrogen (H2) and high-value chemicals. In particular, the amount of formate converted from PET substrate under visible light was highest in metal-free semiconductors without any co-catalyst reported so far, presenting the first example of visible-light-driven photoreforming of PET over a completely metal-free single-component semiconductor without any co-catalyst.

Applying causal discovery to single-cell analyses using CausalCell.

Correlation between objects is prone to occur coincidentally, and exploring correlation or association in most situations does not answer scientific questions rich in causality. Causal discovery (also called causal inference) infers causal interactions between objects from observational data. Reported causal discovery methods and single-cell datasets make applying causal discovery to single cells a promising direction. However, evaluating and choosing causal discovery methods and developing and performing proper workflow remain challenges. We report the workflow and platform CausalCell (http://www.gaemons.net/causalcell/causalDiscovery/) for performing single-cell causal discovery. The workflow/platform is developed upon benchmarking four kinds of causal discovery methods and is examined by analyzing multiple single-cell RNA-sequencing (scRNA-seq) datasets. Our results suggest that different situations need different methods and the constraint-based PC algorithm with kernel-based conditional independence tests work best in most situations. Related issues are discussed and tips for best practices are given. Inferred causal interactions in single cells provide valuable clues for investigating molecular interactions and gene regulations, identifying critical diagnostic and therapeutic targets, and designing experimental and clinical interventions.

The KdmB-EcoA-RpdA-SntB chromatin complex binds regulatory genes and coordinates fungal development with mycotoxin synthesis.

Chromatin complexes control a vast number of epigenetic developmental processes. Filamentous fungi present an important clade of microbes with poor understanding of underlying epigenetic mechanisms. Here, we describe a chromatin binding complex in the fungus Aspergillus nidulans composing of a H3K4 histone demethylase KdmB, a cohesin acetyltransferase (EcoA), a histone deacetylase (RpdA) and a histone reader/E3 ligase protein (SntB). In vitro and in vivo evidence demonstrate that this KERS complex is assembled from the EcoA-KdmB and SntB-RpdA heterodimers. KdmB and SntB play opposing roles in regulating the cellular levels and stability of EcoA, as KdmB prevents SntB-mediated degradation of EcoA. The KERS complex is recruited to transcription initiation start sites at active core promoters exerting promoter-specific transcriptional effects. Interestingly, deletion of any one of the KERS subunits results in a common negative effect on morphogenesis and production of secondary metabolites, molecules important for niche securement in filamentous fungi. Consequently, the entire mycotoxin sterigmatocystin gene cluster is downregulated and asexual development is reduced in the four KERS mutants. The elucidation of the recruitment of epigenetic regulators to chromatin via the KERS complex provides the first mechanistic, chromatin-based understanding of how development is connected with small molecule synthesis in fungi.

Pt Atoms/Clusters on Ni-phytate-sensitized Carbon Nitride for Enhanced NIR-light-driven Overall Water Splitting beyond 800†nm.

Near-infrared (NIR) light-driven overall water splitting beyond 800 nm remains a high-priority target yet great challenge. Here we report that efficient utilization of photogenerated electrons in a photosensitized system prepared by site-selective photodeposition of platinum single atoms/clusters (Pt-SACs) on Ni-phytate (PA-Ni)-sensitized polymeric carbon nitride (PCN). The optimal catalyst presents simultaneous hydrogen (H2 ) and oxygen (O2 ) evolution with an H2 evolution amount of 1.4 µmol at λ>800 nm for 24 hours, which its activity was approximately 140 times higher than that of a system without Pt-SAC modification (PA-Ni1.1 @PCN). This work represents the first NIR-light responsive photosensitized system for overall water splitting, and may open an avenue for precisely manipulating cocatalyst positions at the atomic level to improve NIR-light-driven overall water splitting via photosensitization.

Terrigenous organic carbon drives methane dynamics in cascade reservoirs in the upper Yangtze China.

Methane (CH4) emissions from freshwaters to the atmosphere have a profound impact on global atmospheric greenhouse gas (GHG) concentrations. Anthropogenic footprints such as dam construction and reservoir operation significantly changed the fate and transport of CH4 in freshwaters. The source of particulate organic carbon (POC) in reservoirs is a critical factor controlling CH4 production and emissions. However, little is known of how reservoir operation mediates the transport of POC and regulates CH4 accumulation in cascade hydroelectric reservoirs. Here, spatial and temporal variations in POC and CH4 were explored in the Xiluodu (XLD) and Xiangjiaba (XJB) reservoirs which are deep valley cascade reservoirs located in the main channel of the upper Yangtze River. Based on the δ13C-POC and N/C mole ratio of particulate organic matter, the results of multi-endmember stable isotope mixing models by a Bayesian model showed that terrigenous POC and autochthonous POC accounted for approximately 55% ± 18% and 43% ± 19% (SD, n = 179) of POC, respectively. Together with other hydrological and environmental parameters, we found that the input of terrigenous POC was dominantly influenced by water level variations and flow regulation due to reservoir operation. The cumulative effect of POC caused by cascade dams was not apparent. Terrigenous POC were more likely to drive CH4 accumulation in our study. Evident low level of CH4 in both reservoirs were likely affected by low sedimentation of POC and microbial CH4 oxidation. We hope our study could provide a conceptual framework for further modeling of CH4 dynamics in cascade reservoirs.

Mobility in China, 2020: a tale of four phases.

2020 was an unprecedented year, with rapid and drastic changes in human mobility due to the COVID-19 pandemic. To understand the variation in commuting patterns among the Chinese population across stable and unstable periods, we used nationwide mobility data from 318 million mobile phone users in China to examine the extreme fluctuations of population movements in 2020, ranging from the Lunar New Year travel season (chunyun), to the exceptional calm of COVID-19 lockdown, and then to the recovery period. We observed that cross-city movements, which increased substantially in chunyun and then dropped sharply during the lockdown, are primarily dependent on travel distance and the socio-economic development of cities. Following the Lunar New Year holiday, national mobility remained low until mid-February, and COVID-19 interventions delayed more than 72.89 million people returning to large cities. Mobility network analysis revealed clusters of highly connected cities, conforming to the social-economic division of urban agglomerations in China. While the mass migration back to large cities was delayed, smaller cities connected more densely to form new clusters. During the recovery period after travel restrictions were lifted, the netflows of over 55% city pairs reversed in direction compared to before the lockdown. These findings offer the most comprehensive picture of Chinese mobility at fine resolution across various scenarios in China and are of critical importance for decision making regarding future public-health-emergency response, transportation planning and regional economic development, among others.

Transcription in fungal conidia before dormancy produces phenotypically variable conidia that maximize survival in different environments.

Fungi produce millions of clonal asexual conidia (spores) that remain dormant until favourable conditions occur. Conidia contain abundant stable messenger RNAs but the mechanisms underlying the production of these transcripts and their composition and functions are unknown. Here, we report that the conidia of three filamentous fungal species (Aspergillus nidulans, Aspergillus fumigatus, Talaromyces marneffei) are transcriptionally active and can synthesize mRNAs. We find that transcription in fully developed conidia is modulated in response to changes in the environment until conidia leave the developmental structure. Environment-specific transcriptional responses can alter conidial content (mRNAs, proteins and secondary metabolites) and change gene expression when dormancy is broken. Conidial transcription affects the fitness and capabilities of fungal cells after germination, including stress and antifungal drug (azole) resistance, mycotoxin and secondary metabolite production and virulence. The transcriptional variation that we characterize in fungal conidia explains how genetically identical conidia mature into phenotypically variable conidia. We find that fungal conidia prepare for the future by synthesizing and storing transcripts according to environmental conditions present before dormancy.

Human Biological Monitoring of Mercury Through Hair Samples in China.

Mercury (Hg) is a global pollutant that affects environmental and human health. Considering the high toxicity of Hg, it is required to assess the exposure of Hg in human body for appropriate risk management. In this review paper, we summarized data obtained through regional and small-scaled human biomonitoring (HBM) program for Hg in hair samples in China, which can deliver scientific data to make decisions on environmental health policy. Besides, the major conclusions got from this study and perspectives for future works through these HBM program in China were presented. To better understand the current situation of hair Hg levels in China, a well-coordinated and designed national HBM program is urgently needed considering the requirements of the Minamata Convention on Mercury for effectiveness evaluation.

Universal plasmids to facilitate gene deletion and gene tagging in filamentous fungi.

Gene manipulation is an important routine technique and its efficiency is often a rate-limiting step in research. To facilitate gene manipulation in filamentous fungi, we adapted the S. cerevisiae Gene Deletion and Gene Tagging plasmid collections to include additional selectable markers that make the useful resources applicable to other fungi. Three markers for auxotrophic selection in Aspergillus and related species (the riboB, pyroA and pyrG genes of Aspergillus fumigatus) and a dominant selectable marker for glufosinate resistance (the Bar gene from Streptomyces hygroscopicus) were introduced to the collections. A total of fifty-six plasmids were constructed for all combinations between the four new markers and thirteen epitope tags (viz., 3xHA, 13xMYC, 3xFLAG, FLAG, MYC, T7, HIS, Strep, S, HSV, VSV-G, V5 and GFP). The selectable marker and epitope tag cassettes are positioned between two universal sequences in the plasmids, and therefore, can be amplified by PCR using the same pair of primers. With these plasmids, we have also established a simple and efficient procedure for making gene deletion and gene tagging transformation DNA constructs. The procedure, along with the universal flanking sequences, allows quick and easy interchange of selectable marker and epitope cassettes in transformation DNA constructs for different selection and/or tagging. To demonstrate utility and efficiency of the system, we simultaneously performed C-terminal tagging of HapB - a subunit of the highly conserved Aspergillus nidulans CCAAT binding complex that plays important transcriptional regulatory roles - using ten different epitopes in order to identify those neutral to HapB function in vivo. It is expected that the expanded plasmid collections coupled with the simple construction strategy would facilitate gene manipulation in many fungal species.

Danshenol A inhibits TNF-α-induced expression of intercellular adhesion molecule-1 (ICAM-1) mediated by NOX4 in endothelial cells.

ICAM-1 overexpression and subsequent adhesion of leukocytes to endothelial cells play critical roles in the early stage of atherosclerosis. Danshenol A (DA) is an abietane-type diterpenoid isolated from traditional Chinese herb Salvia miltiorrhiza Bunge. The mechanisms under its regulation of adhesion of molecular expression are explored. Here, the effect of DA on TNF-α-induced ICAM-1 expression was investigated in endothelial cells. TNF-α-induced ICAM-1 expression and subsequent adhesion of monocytes, as well as elevated reactive oxygen species (ROS) generation and NOX4 expression were all significantly reversed by DA, siNOX4 and NOX4 inhibitor GKT137831. Furthermore, TNF-α-induced ICAM-1 expression, which was increased via IKKß/IκBα-mediated activation of NF-κB p65, was also inhibited by DA. Interestingly, NOX4 overexpression suppressed the ICAM-1 expression, and this finding may be ascribed to the activation of Nrf-2. Additionally, NF-κB inhibitor PDTC, siNOX4, or DA can decrease the TNF-α-induced ICAM-1 expression and suppress the adhesion of monocytes. In all, DA inhibited TNF-α-induced ICAM-1 expression and subsequent monocyte adhesion to endothelial cells through the NOX4-dependent IKKß/NF-κB pathway. Besides, NOX4 played dual role in regulating ICAM-1 expression via diverse signal pathway. This novel bioactivity will make DA a good candidate to be further explored for therapeutic or preventive application for atherosclerosis.

Chemical constituents and biological research on plants in the genus Curcuma.

Curcuma, a valuable genus in the family Zingiberaceae, includes approximately 110 species. These plants are native to Southeast Asia and are extensively cultivated in India, China, Sri Lanka, Indonesia, Peru, Australia, and the West Indies. The plants have long been used in folk medicine to treat stomach ailments, stimulate digestion, and protect the digestive organs, including the intestines, stomach, and liver. In recent years, substantial progress has been achieved in investigations regarding the chemical and pharmacological properties, as well as in clinical trials of certain Curcuma species. This review comprehensively summarizes the current knowledge on the chemistry and briefly discusses the biological activities of Curcuma species. A total of 720 compounds, including 102 diphenylalkanoids, 19 phenylpropene derivatives, 529 terpenoids, 15 flavonoids, 7 steroids, 3 alkaloids, and 44 compounds of other types isolated or identified from 32 species, have been phytochemically investigated. The biological activities of plant extracts and pure compounds are classified into 15 groups in detail, with emphasis on anti-inflammatory and antitumor activities.

Isocryptotanshinone, a STAT3 inhibitor, induces apoptosis and pro-death autophagy in A549 lung cancer cells.

Signal transducer and activator of transcription 3 (STAT3) is a potential drug target for chemotherapy. Cryptotanshinone (CTS) was identified as a potent STAT3 inhibitor, while the effect of other tanshinones remains unknown. In this study, the influence of eight tanshinones on STAT3 activity was initially screened and isocryptotanshinone (ICTS) significantly inhibited STAT3 activity in a dual luciferase assay. ICTS inhibited the constitutive and inducible phosphorylation of STAT3 at Y705 without affecting the phosphorylation of STAT3 at S727 in A549 lung cancer cells. Furthermore, ICTS inhibited the nuclear translocation of STAT3. Compared with CTS, ICTS exhibited a stronger inhibitory effect on STAT3 phosphorylation and on A549 cytotoxicity. ICTS induced autophagy as evidenced by the accumulation of autophagic vacuoles and the increased expression of LC3 protein and autophagosomes. ICTS-induced cell death was partially reversed by the autophagy inhibitor chloroquine. The docking assay predicted that both ICTS and CTS bind the SH2 domain of STAT3. ICTS formed hydrogen bonds and pi-pi interaction with the nearby amino acid residues of Lys591, Arg609, and Ser636. These findings suggested that ICTS, a natural compound, is a potent STAT3 inhibitor. ICTS induced apoptosis and pro-death autophagy in A549 cells.

The human Nox4: gene, structure, physiological function and pathological significance.

Increased generation of reactive oxygen species (ROS) has been implicated in the pathogenesis of a variety of diseases such as cardiovascular diseases and cancer. NADPH oxidase (Nox), a multicomponent enzyme, has been identified as one of the key sources of ROS. Nox4, one of the seven members of Nox family (Nox1, Nox2, Nox3, Nox4, Nox5, Duox1 and Duox2), has been extensively investigated in recent years. Its unique structures result in the constitutive generation of hydrogen peroxide (H2O2) as the main product. As a key oxygen sensor, Nox4-derived H2O2 plays diverse roles in cell proliferation, migration and death. Increased expression of Nox4 in cancer has been observed, which participates in metastasis, angiogenesis and apoptosis. Expression of Nox4 in endothelial cells actively mediated endothelial activation, dysfunction and injury, which contributes to the development of atherosclerosis, hypertension, cardiac hypertrophy and among others. This article explores the experimental studies related to the gene, structure, physiological function and pathological significance of Nox4. As Nox4 might serve as a potential target for the therapy of cardiovascular diseases and cancer, the Nox4 inhibitor is also discussed in this article.

A new cytoplasmic monoheme cytochrome c from Acidithiobacillus ferrooxidans involved in sulfur oxidation.

Acidithiobacillus ferrooxidans can obtain energy from the oxidation of various reduced inorganic sulfur compounds (RISCs, e.g., sulfur) and ferrous iron in bioleaching so has multiple branched respiratory pathways with a diverse range of electron transporters, especially cytochrome c proteins. A cytochrome c family gene, afe1130, which has never been reported before, was found by screening the whole genome of A. ferrooxidans. Here we report the differential gene transcription, bioinformatics analysis, and molecular modeling of the protein encoded by the afe1130 gene (AFE1130). The differential transcription of the target afe1130 gene versus the reference rrs gene in the A. ferrooxidans, respectively, on the culture conditions of sulfur and ferrous energy sources was performed through quantitative reverse transcription polymerase chain reaction (qRT-PCR) with a SYBR green-based assay according to the standard curves method. The qRT-PCR results showed that the afe1130 gene in sulfur culture condition was obviously more transcribed than that in ferrous culture condition. Bioinformatics analysis indicated that the AFE1130 was affiliated to the subclass ID of class I of cytochrome c and located in cytoplasm. Molecular modeling results exhibited that the AFE1130 protein consisted of 5 alpha-helices harboring one heme c group covalently bonded by Cys13 and Cys16 and ligated by His17 and Met62 and owned a big raised hydrophobic surface responsible for attaching to inner cytomembrane. So the AFE1130 in A. ferrooxidans plays a role in the RISCs oxidation in bioleaching in cytoplasm bound to inner membrane.

HdrC2 from Acidithiobacillus ferrooxidans owns two iron-sulfur binding motifs but binds only one variable cluster between [4Fe-4S] and [3Fe-4S].

The heterodisulfide reductase complex HdrABC from Acidithiobacillus ferrooxidans was suggested to own novel features that act in reverse to convert the sulfane sulfur of GS( n )H species (n > 1) into sulfite in sulfur oxidation. The HdrC subunit is potentially encoded by two different highly upregulated genes sharing only 29 % identity in A. ferrooxidans grown in sulfur-containing medium, which were named as HdrC1 and HdrC2, respectively and had been confirmed to contain iron-sulfur cluster by expression and characterization, especially the HdrC1 which had been showed to bind only one [4Fe-4S] cluster by mutations. However, the mutations of the HdrC2 remain to be done and the detailed binding information of it is still unclear. Here, we report the expression, mutations, and molecular modeling of the HdrC2 from A. ferrooxidans. This HdrC2 had two identical motifs (Cx(2)Cx(2)Cx(3)C) containing total of eight cysteine residues potentially for iron-sulfur cluster binding. This purified HdrC2 was exhibited to contain one variable cluster converted between [4Fe-4S] and [3Fe-4S] according to different conditions by the UV-scanning and EPR spectra. The site-directed mutagenesis results of these eight residues further confirmed that the HdrC2 in reduction with Fe(2+) condition loaded only one [4Fe-4S](+) with spin S = 1/2 ligated by the residues of Cys73, Cys109, Cys112, and Cys115; the HdrC2 in natural aeration condition lost the Fe atom ligated by the residue of Cys73 and loaded only one [3Fe-4S](0) with spin S = 0; the HdrC2 in oxidation condition loaded only one [3Fe-4S](+) with spin S = 1/2. Molecular modeling results were also in line with the experiment results.