Unearthing New ccr Genes and Staphylococcal Cassette Chromosome Elements in Staphylococci Through Genome Mining.

Staphylococcal cassette chromosome mec (SCCmec) typing is crucial for investigating methicillin-resistant Staphylococcus aureus (MRSA), relying primarily on the combination of ccr and mec gene complexes. To date, 19 ccr genes and 10 ccr gene complexes have been identified, forming 15 SCCmec types. With the vast release of bacterial genome sequences, mining the database for novel ccr gene complexes and SCC/SCCmec elements could enhance MRSA epidemiological studies. In this study, we identified 12 novel ccr genes (6 ccrA, 3 ccrB, and 3 ccrC) through mining of the National Center for Biotechnology Information (NCBI) database, forming 12 novel ccr gene complexes and 10 novel SCC elements. Overexpression of 5 groups of novel Ccr recombinases (CcrA9B3, CcrA10B1, CcrC3, CcrC4, and CcrC5) in a mutant MRSA strain lacking the ccr gene and extrachromosomal circular intermediate (ciSCC) production significantly promoted ciSCC production, demonstrating their biological activity. This discovery provides an opportunity to advance MRSA epidemiological research and develop database-based bacterial typing methods.

Photonic stepped-frequency radar with 150-m unambiguous detection and centimeter range resolution.

Photonic stepped-frequency radars based on optical frequency-shifting modulation have shown attractive properties such as wide bandwidth, centimeter range resolution, inherent frequency-time linearity with low spectrum spurs, and reduced system complexity. However, existing approaches typically exhibit meter- or centimeter-level radar range ambiguity, inversely proportional to the frequency step, due to the large frequency shift determined by acousto-optic or electro-optic (EO) modulators. Here, we overcome this limitation by injecting a narrowband, stepped-frequency signal into an optical frequency-shifting fiber cavity to achieve, for the first time, to our knowledge, a broadband photonic stepped-frequency radar with 150-m unambiguous detection and centimeter range resolution, surpassing the reported photonic- and electronic-based counterparts. The demonstrated approach effectively resolves the trade-off between ambiguity range and shifting frequency while maintaining the signal quality and bandwidth, bringing its practicality into reach for outdoor applications.

Periodontal disease increases the severity of chronic obstructive pulmonary disease: a Mendelian randomization study.

BACKGROUND: Recent research suggests that periodontitis can increase the risk of chronic obstructive pulmonary disease (COPD). In this study, we performed two-sample Mendelian randomization (MR) and investigated the causal effect of periodontitis (PD) on the genetic prediction of COPD. The study aimed to estimate how exposures affected outcomes. METHODS: Published data from the Gene-Lifestyle Interaction in the Dental Endpoints (GLIDE) Consortium's genome-wide association studies (GWAS) for periodontitis (17,353 cases and 28,210 controls) and COPD (16,488 cases and 169,688 controls) from European ancestry were utilized. This study employed a two-sample MR analysis approach and applied several complementary methods, including weighted median, inverse variance weighted (IVW), and MR-Egger regression. Multivariable Mendelian randomization (MVMR) analysis was further conducted to mitigate the influence of smoking on COPD. RESULTS: We chose five single-nucleotide polymorphisms (SNPs) as instrumental variables for periodontitis. A strong genetically predicted causal link between periodontitis and COPD, that is, periodontitis as an independent risk factor for COPD was detected. PD (OR = 1.102951, 95% CI: 1.005-1.211, p = 0.039) MR-Egger regression and weighted median analysis results were coincident with those of the IVW method. According to the sensitivity analysis, horizontal pleiotropy's effect on causal estimations seemed unlikely. However, reverse MR analysis revealed no significant genetic causal association between COPD and periodontitis. IVW (OR = 1.048 > 1, 95%CI: 0.973-1.128, p = 0.2082) MR Egger (OR = 0.826, 95%CI:0.658-1.037, p = 0.1104) and weighted median (OR = 1.043, 95%CI: 0.941-1.156, p = 0.4239). The results of multivariable Mendelian randomization (MVMR) analysis, after adjusting for the confounding effect of smoking, suggest a potential causal relationship between periodontitis and COPD (P = 0.035). CONCLUSION: In this study, periodontitis was found to be independent of COPD and a significant risk factor, providing new insights into periodontitis-mediated mechanisms underlying COPD development.

Overcoming pancreatic cancer immune resistance by codelivery of CCR2 antagonist using a STING-activating gemcitabine-based nanocarrier.

STING agonist has recently gained much attention for cancer treatment, but the therapeutic potential of STING agonist is hampered by STING-associated tumor immune resistance. In this work, guided by both bioinformatics and computer modeling, we rationally designed a "one stone hits two birds" nanoparticle-based strategy to simultaneously activate STING innate immune response while eliminating STING-associated immune resistance for the treatment of pancreatic ductal adenocarcinoma (PDAC). We discovered that the ultra-small sized micellar system based on gemcitabine-conjugated polymer (PGEM), which showed superior capacity of penetration in pancreatic tumor spheroid model and orthotopic tumor model, could serve as a novel "STING agonist". The activation of STING signaling in dendritic cells (DCs) by PGEM increased both innate nature killer (NK) and adaptive anti-tumor T cell response. However, activation of STING signaling by PGEM in tumor cells also drove the induction of chemokines CCL2 and CCL7, resulting in immune resistance by recruiting tumor associated macrophage (TAM) and myeloid-derived suppressor cells (MDSCs). Through the combination of computer modeling and experimental screening, we developed a dual delivery modality by incorporating a CCR2 (the receptor shared by both CCL2 and CCL7) antagonist PF-6309 (PF) into PGEM micellar system. Our studies demonstrated that PGEM/PF formulation significantly reduced pancreatic tumor burden and induced potent anti-tumor immunity through reversing the CCL2/CCL7-mediated immunosuppression. Moreover, PGEM/PF sensitized PDAC tumors to anti-PD-1 therapy, leading to complete suppression/eradication of the tumors. Our work has shed light to the multi-faceted role of STING activation and provided a novel immunotherapy regimen to maximize the benefit of STING activation for PDAC treatment. In addition, this work paved a new way for bioinformatics and computer modeling-guided rational design of nanomedicine.

Norepinephrine promotes glioma cell migration through up-regulating the expression of Twist1.

BACKGROUND: Glioma cells are characterized by high migration ability, resulting in aggressive growth of the tumors and poor prognosis of patients. It has been reported that the stress-induced hormone norepinephrine (NE) contributes to tumor progression through mediating a number of important biological processes in various cancers. However, the role of NE in the regulation of glioma migration is still unclear. Epithelial-to-mesenchymal transition (EMT) is one of the most important steps for tumor migration and metastasis. Twist1, as a key regulator of EMT, has been found to be elevated during glioma migration. But it is still unknown whether Twist1 is involved in the effect of NE on the migration of glioma cells. METHODS: Wound healing assay and transwell assay were conducted to evaluate the migration of glioma cells upon different treatments. The mesenchymal-like phenotype and the expression of Twist1 after NE treatment were assessed by cell diameters, real-time PCR, western blot and immunofluorescence staining. The gain-and loss-of-function experiments were carried out to investigate the biological function of Twist1 in the migration induced by NE. Finally, the clinical significance of Twist1 was explored among three public glioma datasets. RESULTS: In this study, our finding revealed a facilitative effect of NE on glioma cell migration in a ß-adrenergic receptor (ADRB)-dependent way. Mechanistically, NE induced mesenchymal-like phenotype and the expression of Twist1. Twist1 overexpression promoted glioma cells migration, while knockdown of Twist1 abolished the discrepancy in the migration ability between NE treated glioma cells and control cells. In addition, the clinical analysis demonstrated that Twist1 was up-regulated in malignant gliomas and recurrent gliomas, and predicted a poor prognosis of glioma patients. CONCLUSIONS: NE enhanced the migration ability of glioma cells through elevating the expression of Twist1. Our finding may provide potential therapeutic target for protecting patients with glioma from the detrimental effects of stress biology on the tumor progression.

Repair of ATAAD with a 3D-printing assisted pre-windowed coated stent: A case report.

Acute type A aortic dissection (ATAAD) is a life-threatening vascular disease. We report a case of ATAAD treated with interventional therapy using 3D-printing assisted pre-windowing coated stent combined with in situ window-opening technology. There were few complications and the patient experienced an uneventful recovery.

Periodontal ligament cells derived small extracellular vesicles are involved in orthodontic tooth movement.

OBJECTIVES: Small extracellular vesicles (EVs) from human periodontal ligament cells (hPDLCs) are closely associated with periodontal homeostasis. Far less is known about EVs association with orthodontic tooth movement (OTM). This study aimed to explore the role of small EVs originated from hPDLCs during OTM. MATERIALS AND METHODS: Adult C57BL/6 mice were used. Springs were bonded to the upper first molars of mice for 7 days to induce OTM in vivo. To block small EVs release, GW4869 was intraperitoneally injected and the efficacy of small EVs inhibition in periodontal ligament was verified by transmission electron microscope (TEM). Tooth movement distance and osteoclastic activity were studied. In vitro, hPDLCs were isolated and administered compressive force in the EV-free culture media. The cell morphologies and CD63 expression of hPDLCs were studied. Small EVs were purified and characterized using a scanning electron microscope, TEM, western blot, and nanoparticle tracking analysis. The expression of proteins in the small EVs was further processed and validated using a human immuno-regulated cytokines array and an enzyme-linked immunosorbent assay (ELISA). RESULTS: The small EV depletion significantly decreased the distance and osteoclastic activity of OTM in the mice. The hPDLCs displayed different morphologies under force compression and CD63 expression level decreased verified by western blot and immunofluorescence staining. Small EVs purified from supernatants of the hPDLCs showed features with <200 nm diameter, the positive EVs marker CD63, and the negative Golgi body marker GM130. The number of small EVs particles increased in hPDLCs suffering force stimuli. According to the proteome array, the level of soluble intercellular adhesion molecule-1 (sICAM-1) displayed the most significant fold change in small EVs under compressive force and this was further confirmed using an ELISA. LIMITATIONS: Further mechanism studies are warranted to validate the hPDLC-originated small EVs function in OTM through proteins delivery. CONCLUSIONS: The notable decrease in the OTM distance after small EV blocking and the significant alteration of the sICAM-1 level in the hPDLC-originated small EVs under compression provide a new vista into small EV-related OTM biology.

A cysteine-triggered fluorogenic donor base on native chemical ligation for tracking H2S delivery in vivo.

A hydrogen sulfide (H2S) donor is a fundamental molecular tool used as an exogenous source in biological studies and therapies. However, finding a controllable and visual fluorescent H2S donor is difficult. We report a new H2S donor, HSD560, the H2S release of which is triggered by cysteine. Importantly, the H2S generation is accompanied with enhanced green fluorescence, which could be utilized to track H2S release in cells using microscopy. H2S release from HSD560 undergoes a non-enzymatic native chemical ligation (NCL) process, which provides an accurate match with activated fluorescence and localization of H2S in zebrafish.

Perilla Leaf Extract Attenuates Asthma Airway Inflammation by Blocking the Syk Pathway.

Perilla frutescens (L.) Britton is a classic herbal plant used widely against asthma in China. But its mechanism of beneficial effect remains undermined. In the study, the antiallergic asthma effects of Perilla leaf extract (PLE) were investigated, and the underlying mechanism was also explored. Results showed that PLE treatment significantly attenuated airway inflammation in OVA-induced asthma mice, by ameliorating lung pathological changes, inhibiting recruitment of inflammatory cells in lung tissues and bronchoalveolar lavage fluid (BALF), decreasing the production of inflammatory cytokines in the BALF, and reducing the level of immunoglobulin in serum. PLE treatment suppressed inflammatory response in antigen-induced rat basophilic leukemia 2H3 (RBL-2H3) cells as well as in OVA-induced human peripheral blood mononuclear cells (PBMCs). Furthermore, PLE markedly inhibited the expression and phosphorylation of Syk, NF-κB, PKC, and cPLA2 both in vivo and in vitro. By cotreating with inhibitors (BAY61-3606, Rottlerin, BAY11-7082, and arachidonyl trifluoromethyl ketone) in vitro, results revealed that PLE's antiallergic inflammatory effects were associated with the inhibition of Syk and its downstream signals NF-κB, PKC, and cPLA2. Collectively, the present results suggested that PLE could attenuate allergic inflammation, and its mechanism might be partly mediated through inhibiting the Syk pathway.

Chondroprotective and anti-inflammatory effects of amurensin H by regulating TLR4/Syk/NF-κB signals.

The low-grade, chronic inflammation initiated by TLR4-triggered innate immune responses has a central role on early osteoarthritis. Amurensin H is a resveratrol dimer with anti-inflammatory and anti-apoptotic effects, while its effects on TLR-4 signals to inhibit osteoarthritis are still unclear. In the present study, treatment with amurensin H for 2 weeks in monosodium iodoacetate-induced mice significantly slows down cartilage degeneration and inflammation using macroscopic evaluation, haematoxylin and eosin (HE) staining and micro-magnetic resonance imaging. In IL-1ß-stimulated rat chondrocytes, amurensin H suppresses the production of inflammatory mediators including nitric oxide, IL-6, IL-17, PGE2 and TNF-α using Greiss and ELISA assay. Amurensin H inhibits matrix degradation via decreasing levels of MMP-9 and MMP-13 using Western blot assay, promotes synthesis of type II collagen and glycosaminoglycan using immunostaining and safranin O staining, respectively. Amurensin H inhibits intracellular and mitochondrial reactive oxygen species (ROS) generation, and mitochondrial membrane depolarization using DCFH-DA, MitoSOX Red and JC-1 assay as well. IL-1ß stimulates TLR4 activation and Syk phosphorylation in chondrocytes, while amurensin H inhibits TLR4/Syk signals and downstream p65 phosphorylation and translocation in a time and dose-dependent manner. Together, these results suggest that amurensin H exerts chondroprotective effects by attenuating oxidative stress, inflammation and matrix degradation via the TLR4/Syk/NF-κB pathway.

Si3N4-chip-based versatile photonic RF waveform generator with a wide tuning range of repetition rate.

In this Letter, we demonstrate a ${{\rm Si}_3}{{\rm N}_4}$Si3N4-chip-based photonic approach to generate versatile radio frequency (RF) waveforms with a large tuning range of repetition rates. The amplitude and phase of the RF-phase-modulated signal are spectrally manipulated to synthesize Fourier coefficients of the desired RF waveforms by controlling the resonance conditions and frequencies of ${{\rm Si}_3}{{\rm N}_4}$Si3N4 optical ring resonators. Full-duty-cycle triangular, square, and sawtooth waveforms with widely tunable repetition rates from 1 to 13 GHz were experimentally generated.

Population genetics, diversity and forensic characteristics of Tai-Kadai-speaking Bouyei revealed by insertion/deletions markers.

China, inhabited by over 1.3 billion people and known for its genetic, cultural and linguistic diversity, is considered to be indispensable for understanding the association between language families and genetic diversity. In order to get a better understanding of the genetic diversity and forensic characteristics of Tai-Kadai-speaking populations in Southwest China, we genotyped 30 insertion/deletion (InDel) markers and amelogenin in 205 individuals from Tai-Kadai-speaking Bouyei people using the Qiagen Investigator DIPplex amplification kit. We carried out a comprehensive population genetic relationship investigation among 14,303 individuals from 84 worldwide populations based on allele frequency correlation and 4907 genotypes of 30 InDels from 36 populations distributed in all continental or major subregions and seven linguistic phyla in China. Forensic parameters observed show highly polymorphic and informative features for Asians, although the DIPplex kit was developed focusing on Europeans, and indicate that this amplification system is appropriate to forensic personal identification and parentage testing. Patterns of InDel variations revealed by principal components analysis, multidimensional scaling plots, phylogenetic relationship exploration, model-based clustering as well as four pairwise genetic distances (Fst, Nei, Cavalli-Sforza and Reynolds) demonstrate significant genetic differentiation at the continental scale and genetic uniformity in Asia except for Tibeto-Burman and Turkic-speaking populations. Additionally, Tai-Kadai speakers, including Bouyei, Zhuang and Dong, share more genetic ancestry components than with other language speakers, and in general they are genetically very similar to Hmong-Mien-speaking populations. The dataset of Bouyei people generated in the present study is valuable for forensic identification and parentage tests in China.

Importance of Trp139 in the product specificity of a maltooligosaccharide-forming amylase from Bacillus stearothermophilus STB04.

The maltooligosaccharide-forming amylase from Bacillus stearothermophilus STB04 (Bst-MFA) randomly cleaves the α-1,4 glycosidic linkages of starch to produce predominantly maltopentaose and maltohexaose. The three-dimensional co-crystal structure of Bst-MFA with acarbose highlighted the stacking interactions between Trp139 and the substrate in subsites - 5 and - 6. Interactions like this are thought to play a critical role in maltopentaose/maltohexaose production. A site-directed mutagenesis approach was used to test this hypothesis. Replacement of Trp139 by alanine, leucine, or tyrosine dramatically increased maltopentaose production and reduced maltohexaose production. Oligosaccharide degradation indicated that these mutants also enhance productive binding of the substrate aglycone, leading to a high maltopentaose yield. Therefore, the aromatic stacking between Trp139 and substrate is suggested to control product specificity and the oligosaccharide cleavage pattern.

Genetic structure and forensic characterisation of 19 X-chromosomal STR loci in Guizhou Sui population.

Background: Guizhou Sui people are an officially recognised ethnic group living in southwest China, but have seldom been studied genetically.Aim: To investigate the polymorphisms of 19 X-chromosome STR loci in a typical Sui population and enrich the East Asian X-STR reference database for forensic DNA analysis.Subjects and methods: A total of 400 Sui individuals (195 males and 205 females) were genotyped at 19 X-STR loci using the AGCU X19 STR Kit. The allele frequencies and forensic parameters were calculated and illustrated and the data of Guizhou Sui were merged with 18 other nationwide populations to explore genetic polymorphisms and population relationships.Results: A total of 215 alleles were observed with corresponding frequencies ranging from 0.0017-0.6512 in Sui using male and female pooled allele frequencies. Large values were observed, at least 0.9999999933, in combined powers of discrimination of Sui males and females, as well as the four mean paternity exclusion chances (MECs). The phylogenetic analysis among 19 populations showed that Sui have close genetic affinities with other Tai-Kadai populations, as well as the Sinitic populations living in southern China.Conclusions: The AGCU X-19 STRs are highly polymorphic and informative in Guizhou Sui people. The genetic relationships between Sui and other populations in China are generally consistent with the language classification and geographical distance.

Forensic genetic polymorphisms and population structure of the Guizhou Bouyei people based on 19 X-STR loci.

Background: Guizhou province is located in southwest China with abundant genetic, linguistic and cultural diversity. The Bouyei is one of the 18 officially recognised minority groups in Guizhou, accounting for about 97% of the total Bouyei population in China. However, the genetic history and forensic characterisation of the Bouyei people is largely unknown due to a lack of genetic data.Aim: We aim to investigate genetic polymorphisms and forensic characterisation of the Guizhou Bouyei population, as well as the relationships between the Bouyei and other East Asian populations.Subjects and methods: We genotyped 19 X-STRs in 188 males and 165 females of Guizhou Bouyei using the AGCU X19 STR Kit. We estimated allele frequencies, forensic parameters and genetic distances between the Bouyei and other East Asian populations. We presented the genetic distances in a phylogenetic tree, an MDS plot and a PCA plot.Results: In Guizhou Bouyei individuals, we observed 216 alleles with corresponding frequencies ranging from 0.0019 to 0.6757. All of the six combined powers of PDm, PDf, MEC Krüger, MEC Kishida, MEC Desmarais and MEC Desmarais in allele diversity and haplotype diversity are larger than 0.99999995. We found genetic affinities among the Bouyei people and their geographical neighbouring populations in Guizhou, such as the Sui, Miao and Han.Conclusions: The highly polymorphic and informative forensic parameters of the 19 X-STRs in Bouyei people show the powerful potential of those markers in forensic identification and parentage tests. The genetic relationships of the Bouyei with other East Asian populations correspond well with geographic affiliations as well as linguistic classifications.

A Water-Soluble, Green-Light Triggered, and Photo-Calibrated Nitric Oxide Donor for Biological Applications.

Nitric oxide (NO) is a versatile endogenous molecule, involved in various physiological processes and implicated in the progression of many pathological conditions. Therefore, NO donors are valuable tools in NO related basic and applied applications. The traditional spontaneous NO donors are limited in scenarios where flux, localization, and dose of NO could be monitored. This has promoted the development of novel NO donors, whose NO release is not only under control, but also self-calibrated. Herein, we reported a phototriggered and photocalibrated NO donor (NOD565) with an N-nitroso group on a rhodamine dye. NOD565 is nonfluorescent and could release NO efficiently upon irradiation by green light. A bright rhodamine dye is generated as a side-product and its fluorescence can be used to monitor the NO release. The potentials of NOD565 in practical applications are showcased in in vitro studies, e.g., platelet aggregation inhibition and fungi growth suppression.

Identification and characterization of SNJ2, the first temperate pleolipovirus integrating into the genome of the SNJ1-lysogenic archaeal strain.

Proviral regions have been identified in the genomes of many haloarchaea, but only a few archaeal halophilic temperate viruses have been studied. Here, we report a new virus, SNJ2, originating from archaeal strain Natrinema sp. J7-1. We demonstrate that this temperate virus coexists with SNJ1 virus and is dependent on SNJ1 for efficient production. Here, we show that SNJ1 is an icosahedral membrane-containing virus, whereas SNJ2 is a pleomorphic one. Instead of producing progeny virions and forming plaques, SNJ2 integrates into the host tRNA(Met) gene. The virion contains a discontinuous, circular, double-stranded DNA genome of 16 992 bp, in which both nicks and single-stranded regions are present preceded by a 'GCCCA' motif. Among 25 putative SNJ2 open reading frames (ORFs), five of them form a cluster of conserved ORFs homologous to archaeal pleolipoviruses isolated from hypersaline environments. Two structural protein encoding genes in the conserved cluster were verified in SNJ2. Furthermore, SNJ2-like proviruses containing the conserved gene cluster were identified in the chromosomes of archaea belonging to 10 different genera. Comparison of SNJ2 and these proviruses suggests that they employ a similar integration strategy into a tRNA gene.

Photocalibrated NO Release from N-Nitrosated Napthalimides upon One-Photon or Two-Photon Irradiation.

NO donors are routinely used as the exogenous source in in vitro studies. However, the kinetics or the dose of NO release from the existing donors is not readily monitored. This complicates the elucidation of the involvement of NO in a biological response. We report herein a series of NO donors (NOD545a-g), whose NO release is triggered by UV light at 365 nm or a two-photon laser at 740 nm, and importantly, their NO release is accompanied by a drastic fluorescence turn-on, which has been harnessed to follow the kinetics and dose of NO release in a real-time fashion with spectroscopic methods or microscopic methods in in vitro studies. These merits have rendered NOD545a-g useful molecular tools in NO biology.

[Drug glucuronidation and disposition in brain].

UDP-glucuronosyltransferase (UGT), a kind of phase II drug-metabolizing enzyme, catalyzes the conjugation of glucuronic acid and drugs. UGTs are widely expressed in brain, but at a relatively low level compared to that in liver. Brain UGTs are inducible or inhibitable, which influences the drug distribution in the central nervous system. UGTs, cytochrome P450 (CYPs) and transporters act together to effect pharmacokinetics of drugs in brain. Several drugs have the capacity to cross the blood brain barrier after glucuronidation and certain drugs may be subject to direct glucuronidate in brain by the function of UGTs. The brain UGTs' isoforms, localization, induction, inhibition, and interaction with CYP and transporters are introduced in this review. The process of drug glucuronidation and distribution in brain is summarized for five drugs. A deep insight into the process of drug metabolism and distribution in brain may provide a valuable reference for drug design for the central nervous system.

Simultaneous quantification of Hg²âº and MeHg⁺ in aqueous media with a single fluorescent probe by multiplexing in the time domain.

Development of a molecular probe for selective detection of MeHg(+) in the presence of Hg(2+) is a mission impossible to accomplish. Speciation analysis of two substrates with a single kinetic trace exploiting their differential reactivity toward a single probe, i.e., multiplexing in the time domain, is a cost-effective and powerful alternative. We have developed such a probe (Hg410) for simultaneously quantification of Hg(2+) and MeHg(+) in aqueous media. Hg410 is designed via the "covalent-assembly" approach, displays a zero background, and bears a very concise molecular construct. It has harnessed proximity-based catalysis to achieve high reactivity toward Hg(2+) and MeHg(+). An unprecedentedly low detection limit of ca. 4.6 pM and 160 pM was measured for Hg(2+) and MeHg(+), respectively.