A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication.

When DNA is unwound during replication, it becomes overtwisted and forms positive supercoils in front of the translocating DNA polymerase. Unless removed or dissipated, this superhelical tension can impede replication elongation. Topoisomerases, including gyrase and topoisomerase IV in bacteria, are required to relax positive supercoils ahead of DNA polymerase but may not be sufficient for replication. Here, we find that GapR, a chromosome structuring protein in Caulobacter crescentus, is required to complete DNA replication. GapR associates in vivo with positively supercoiled chromosomal DNA, and our biochemical and structural studies demonstrate that GapR forms a dimer-of-dimers that fully encircles overtwisted DNA. Further, we show that GapR stimulates gyrase and topo IV to relax positive supercoils, thereby enabling DNA replication. Analogous chromosome structuring proteins that locate to the overtwisted DNA in front of replication forks may be present in other organisms, similarly helping to recruit and stimulate topoisomerases during DNA replication.

c-di-GMP Arms an Anti-σ to Control Progression of Multicellular Differentiation in Streptomyces.

Streptomyces are our primary source of antibiotics, produced concomitantly with the transition from vegetative growth to sporulation in a complex developmental life cycle. We previously showed that the signaling molecule c-di-GMP binds BldD, a master repressor, to control initiation of development. Here we demonstrate that c-di-GMP also intervenes later in development to control differentiation of the reproductive hyphae into spores by arming a novel anti-σ (RsiG) to bind and sequester a sporulation-specific σ factor (σWhiG). We present the structure of the RsiG-(c-di-GMP)2-σWhiG complex, revealing an unusual, partially intercalated c-di-GMP dimer bound at the RsiG-σWhiG interface. RsiG binds c-di-GMP in the absence of σWhiG, employing a novel E(X)3S(X)2R(X)3Q(X)3D motif repeated on each helix of a coiled coil. Further studies demonstrate that c-di-GMP is essential for RsiG to inhibit σWhiG. These findings reveal a newly described control mechanism for σ-anti-σ complex formation and establish c-di-GMP as the central integrator of Streptomyces development.

Application of multiple sgRNAs boosts efficiency of CRISPR/Cas9-mediated gene targeting in Arabidopsis.

BACKGROUND: Precise gene targeting (GT) is a powerful tool for heritable precision genome engineering, enabling knock-in or replacement of the endogenous sequence via homologous recombination. We recently established a CRISPR/Cas9-mediated approach for heritable GT in Arabidopsis thaliana (Arabidopsis) and rice and reported that the double-strand breaks (DSBs) frequency of Cas9 influences the GT efficiency. However, the relationship between DSBs and GT at the same locus was not examined. Furthermore, it has never been investigated whether an increase in the number of copies of sgRNAs or the use of multiple sgRNAs would improve the efficiency of GT. RESULTS: Here, we achieved precise GT at endogenous loci Embryo Defective 2410 (EMB2410) and Repressor of Silencing 1 (ROS1) using the sequential transformation strategy and the combination of sgRNAs. We show that increasing of sgRNAs copy number elevates both DSBs and GT efficiency. On the other hand, application of multiple sgRNAs does not always enhance GT efficiency. Our results also suggested that some inefficient sgRNAs would play a role as a helper to facilitate other sgRNAs DSBs activity. CONCLUSIONS: The results of this study clearly show that DSB efficiency, rather than mutation pattern, is one of the most important key factors determining GT efficiency. This study provides new insights into the relationship between sgRNAs, DSBs, and GTs and the molecular mechanisms of CRISPR/Cas9-mediated GTs in plants.

Discovery of crucial cytokines associated with deep vein thrombus formation by protein array analysis.

BACKGROUND: Expanding the number of biomarkers is imperative for studying the etiology and improving venous thromboembolism prediction. In this study, we aimed to identify promising biomarkers or targeted therapies to improve the detection accuracy of early-stage deep vein thrombosis (DVT) or reduce complications. METHODS: Quantibody Human Cytokine Antibody Array 440 (QAH-CAA-440) was used to screen novel serum-based biomarkers for DVT/non-lower extremity DVT (NDVT). Differentially expressed proteins in DVT were analyzed using bioinformatics methods and validated using a customized array. Diagnostic accuracy was calculated using receiver operating characteristics, and machine learning was applied to establish a biomarker model for evaluating the identified targets. Twelve targets were selected for validation. RESULTS: Cytokine profiling was conducted using a QAH-CAA-440 (RayBiotech, USA) quantimeter array. Cross-tabulation analysis with Venn diagrams identified common differential factors, leading to the selection of 12 cytokines for validation based on their clinical significance. These 12 biomarkers were consistent with the results of previous array analysis: FGF-6 (AUC = 0.956), Galectin-3 (AUC = 0.942), EDA-A2 (AUC = 0.933), CHI3L1 (AUC = 0.911), IL-1 F9 (AUC = 0.898), Dkk-4 (AUC = 0.88), IG-H3 (AUC = 0.876), IGFBP (AUC = 0.858), Gas-1 (AUC = 0.858), Layilin (AUC = 0.849), ULBP-2 (AUC = 0.813)and FGF-9 (AUC = 0.773). These cytokines are expected to serve as biomarkers, targets, or therapeutic targets to differentiate DVT from NDVT. CONCLUSIONS: EDA-A2, FGF-6, Dkk-4, IL-1 F9, Galentin-3, Layilin, Big-h3, CHI3L1, ULBP-2, Gas-1, IGFBP-5, and FGF-9 are promising targets for DVT diagnosis and treatment.

Evaluation of quality consistency between dispensing granules and traditional decoction of Bombyx batryticatus based on peptidomics and in silico simulations.

The application of traditional Chinese medicine dispensing granules is becoming increasingly prevalent. However, the consistency of dispensing granules with traditional decoction remains controversial. In this study, the consistency of peptide composition and pharmacodynamics between dispensing granules and traditional decoction of Bombyx batryticatus (BB) were assessed. A peptidomics method based on LC-tandem mass spectrometry technology was used to evaluate peptide composition similarity between BB traditional decoction and dispensing granules. The results revealed notable differences in peptide sequences between the two dosage forms, with only 8.55% of peptides shared between them. To evaluate the potential pharmacodynamic effects of the two dosage forms on epilepsy, virtual screening was used to identify potential active peptides, including blood-brain barrier permeability, toxicity prediction, and molecular docking. BB traditional decoction demonstrated a higher number and greater abundance of potential active peptides than BB dispensing granules, suggesting that BB traditional decoction may have a more favorable effect in treating epilepsy compared with BB dispensing granules. Moreover, molecular docking and molecular dynamics simulation studies confirmed the mechanism of action of active peptides to γ-aminobutyric acid transporter 1 (GAT-1). This study provides a scientific basis for the evaluation of quality consistency between BB traditional decoction and dispensing granules.

Circumlimbal suture and laser burns: Comparison between two different chronic glaucoma models. / çŽ¯è§’è†œç¼˜ç¼åˆä¸Žæ¿€å ‰å ‰å‡æ¨¡åž‹ï¼šä¸¤ç§æ ¢æ€§é«˜çœ¼åŽ‹æ¨¡åž‹çš„æ¯”è¾ƒï¼ˆè‹±æ–‡ï¼‰.

OBJECTIVES: Glaucoma is a multifactorial optic neuropathy with a high rate of irreversible visual loss, and its pathogenesis is complex and still unclear. Elevated intraocular pressure (IOP) is well recognized as the sole modifiable risk factor for the development of glaucoma in the majority of cases. This study aims to compare 2 different methods of inducing chronic ocular hypertension by circumlimbal suture or by laser burns in degree and lasting time of the IOP, different status of the retina and retinal ganglion cells (RGCs), and changes of the microstructure of neurons. METHODS: The chronic ocular hypertension models were induced by 2 different ways. One kind of the models was built by unilateral circumlimbal suture (10/0) implantation (suture group), another kind of model was built by laser burns at trabecular meshwork and episcleral veins (laser group). The untreated contralateral eye served as the control group. Changes in IOP were observed and regularly monitored in the 2 groups of rats. HE staining was applied to observe the retinal and optic nerve pathology. Transmission electron microscope (TEM) was used to observe the mitochondrial morphology. RGCs were specifically labeled with Brn3b antibody and counted. The expression of caspase-3 was detected by Western blotting to clarify the apoptosis of RGCs. RESULTS: Compared with the control group, IOP were significantly increased in the suture group and the laser group (both P<0.05). The suture group induced a 1.5-fold elevation of IOP, and sustained for 8 weeks. The laser group induced a 2-fold elevation of IOP for 12 weeks. Both methods could cause RGCs loss (both P<0.05), which were verified by pathology and immune staining of Brn3b. The expressions of caspase-3 were also increased (both P<0.05). The mitochondrial morphology became more fragment, which changed from long shape to round and small one under TEM in 2 models. For comparison, the pathology changes of retinal structure in suture group were not obviously than those in the laser group. CONCLUSIONS: Circumlimbal suture can build an effective model of chronic elevated IOP and induce glaucomatous pathologic changes similar to those in the laser photocoagulation, but the pathologic changes are milder than those in laser photocoagulation. Compare with translimbal laser photocoagulation, equipment and skill demand for circumlimbal suture is less.

Insights into the molecular mechanisms of CRISPR/Cas9-mediated gene targeting at multiple loci in Arabidopsis.

Homologous recombination-mediated gene targeting (GT) enables precise sequence knockin or sequence replacement, and thus is a powerful tool for heritable precision genome engineering. We recently established a clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9)-mediated approach for heritable GT in Arabidopsis (Arabidopsis thaliana), but its broad utility was not tested, and the underlying molecular mechanism was unclear. Here, we achieved precise GT at 14 out of 27 tested endogenous target loci using the sequential transformation approach and obtained vector-free GT plants by backcrossing. Thus, the sequential transformation GT method provides a broadly applicable technology for precise genome manipulation. We show that our approach generates heritable GT in the egg cell or early embryo of T1 Arabidopsis plants. Analysis of imprecise GT events suggested that single-stranded transfer DNA (T-DNA)/VirD2 complexes produced during the Agrobacterium (Agrobacterium tumefaciens) transformation process may serve as the donor templates for homologous recombination-mediated repair in the GT process. This study provides new insights into the molecular mechanisms of CRISPR/Cas9-mediated GT in Arabidopsis.

An integrated model for predicting pupils' acceptance of artificially intelligent robots as teachers.

Artificially intelligent robots as teachers (AI teachers) have attracted extensive attention due to their potential to relieve the challenge of global teacher shortage and realize universal elementary education by 2030. Despite mass production of service robots and discussions about their educational applications, the study of full-fledged AI teachers and children's attitudes towards them is quite preliminary. Here, we report a new AI teacher and an integrated model to assess how pupils accept and use it. Participants included students from Chinese elementary schools via convenience sampling. Questionnaires (n = 665), descriptive statistics and structural equation modeling based on software SPSS Statistics 23.0 and Amos 26.0 were carried out in data collection and analysis. This study first developed an AI teacher by coding a lesson design, course contents and Power Point with script language. Based on the popular Technology Acceptance Model and Task-Technology Fit Theory, this study identified key determinants of the acceptance, including robot use anxiety (RUA), perceived usefulness (PU), perceived ease of use (PEOU) and robot instructional task difficulty (RITD). Moreover, this study found that pupils' attitudes towards the AI teacher, which could be predicted by PU, PEOU and RITD, were generally positive. It is also found that the relationship between RITD and acceptance was mediated by RUA, PEOU and PU. This study holds significance for stakeholders to develop independent AI teachers for students.

Lipidomic profiling in the Strong Heart Study identified American Indians at risk of chronic kidney disease.

Dyslipidemia associates with and usually precedes the onset of chronic kidney disease (CKD), but a comprehensive assessment of molecular lipid species associated with risk of CKD is lacking. Here, we sought to identify fasting plasma lipids associated with risk of CKD among American Indians in the Strong Heart Family Study, a large-scale community-dwelling of individuals, followed by replication in Mexican Americans from the San Antonio Family Heart Study and Caucasians from the Australian Diabetes, Obesity and Lifestyle Study. We also performed repeated measurement analysis to examine the temporal relationship between the change in the lipidome and change in kidney function between baseline and follow-up of about five years apart. Network analysis was conducted to identify differential lipid classes associated with risk of CKD. In the discovery cohort, we found that higher baseline level of multiple lipid species, including glycerophospholipids, glycerolipids and sphingolipids, was significantly associated with increased risk of CKD, independent of age, sex, body mass index, diabetes and hypertension. Many lipid species were replicated in at least one external cohort at the individual lipid species and/or the class level. Longitudinal change in the plasma lipidome was significantly associated with change in the estimated glomerular filtration rate after adjusting for covariates, baseline lipids and the baseline rate. Network analysis identified distinct lipidomic signatures differentiating high from low-risk groups. Thus, our results demonstrated that disturbed lipid metabolism precedes the onset of CKD. These findings shed light on the mechanisms linking dyslipidemia to CKD and provide potential novel biomarkers for identifying individuals with early impaired kidney function at preclinical stages.

Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs in Trypanosoma brucei.

Most mitochondrial mRNAs are transcribed as polycistronic precursors that are cleaved by endonucleases to produce mature mRNA transcripts. However, recent studies have shown that mitochondrial transcripts in the kinetoplastid protozoan, Trypanosoma brucei, are transcribed individually. Also unlike most mitochondrial mRNAs, the 5' end of these transcripts harbor a triphosphate that is hydrolyzed. This modification is carried out by a putative Nudix hydrolase called MERS1. The Nudix motif in MERS1 is degenerate, lacking a conserved glutamic acid, thus it is unclear how it may bind its substrates and whether it contains a Nudix fold. To obtain insight into this unusual hydrolase, we determined structures of apo, GTP-bound and RNA-bound T. brucei MERS1 to 2.30 Å, 2.45 Å, and 2.60 Å, respectively. The MERS1 structure has a unique fold that indeed contains a Nudix motif. The nucleotide bound structures combined with binding studies reveal that MERS1 shows preference for RNA sequences with a central guanine repeat which it binds in a single-stranded conformation. The apo MERS1 structure indicates that a significant portion of its nucleotide binding site folds upon substrate binding. Finally, a potential interaction region for a binding partner, MERS2, that activates MERS1 was identified. The MERS2-like peptide inserts a glutamate near the missing Nudix acidic residue in the RNA binding pocket, suggesting how the enzyme may be activated. Thus, the combined studies reveal insight into the structure and enzyme properties of MERS1 and its substrate-binding activities.

Bone marrow-derived mesenchymal stem cells attenuate myocardial ischemia-reperfusion injury via upregulation of splenic regulatory T cells.

BACKGROUND: Myocardial ischemia-reperfusion injury (MIRI) is the main pathological manifestation of cardiovascular diseases such as myocardial infarction. The potential therapeutic effects of bone marrow-derived mesenchymal stem cells (BM-MSCs) and the participation of regulatory T cells (Tregs) in MIRI remains to be defined. METHODS: We used the experimental acute MIRI that was induced in mice by left ascending coronary ischemia, which were subsequently randomized to receive immunoglobulin G (IgG) or anti-CD25 antibody PC61 with or without intravenously injected BM-MSCs. The splenectomized mice underwent prior to experimental MIRI followed by intravenous administration of BM-MSCs. At 72 h post-MIRI, the hearts and spleens were harvested and subjected to cytometric and histologic analyses. RESULTS: CD25+Foxp3+ regulatory T cells were significantly elevated after MIRI in the hearts and spleens of mice receiving IgG + BM-MSCs and PC61 + BM-MSCs compared to the respective control mice (all p < 0.01). This was accompanied by upregulation of interleukin 10 and transforming growth factor ß1 and downregulation of creatinine kinase and lactate dehydrogenase in the serum. The post-MIRI mice receiving BM-MSCs showed attenuated inflammation and cellular apoptosis in the heart. Meanwhile, splenectomy compromised all therapeutic effects of BM-MSCs. CONCLUSION: Administration of BM-MSCs effectively alleviates MIRI in mice through inducing Treg activation, particularly in the spleen.

Case report: an unusual unilateral pterygium - a secondary pterygium caused by parasitosis in the scleral fistula.

BACKGROUND: Ocular parasitosis can cause eye damage, which contribute to eye symptoms such as burning, itching and even blindness. It is uncommon to see the parasitosis lying in the sclera layer, neither it causing pterygium. Here, we present an unusual case of a secondary pterygium caused by intrascleral worm. CASE PRESENTATION: A 52-year-old women complained about discomfort in right eye for 6 years. Slit-lamp examination indicated a thickened triangular layers of conjunctiva extending from the nasal edge to the cornea. The diagnosis was pterygium in the right eye. To our surprise, after scleral of nasal side exposed, we could see a tiny fistula right in the sclera which lied right under the pterygium, with an alive and motile worm inside. An intrascleral fistula was noted. Then the worm was removed by forceps from the fistula, which was creamy white, thread-like and 1 cm long. DISCUSSION AND CONCLUSIONS: As far as we known, it is the first case of an intrascleral worm hidden beneath the conjunctiva which caused the secondary pterygium. It is hard to know the etiology of the secondary pterygium which caused by parasitosis in the scleral fistula untill excision surgery. It is hard to imagine the worm was living in the sclera of the patient for a long-time.

Structural basis of O-GlcNAc recognition by mammalian 14-3-3 proteins.

O-GlcNAc is an intracellular posttranslational modification that governs myriad cell biological processes and is dysregulated in human diseases. Despite this broad pathophysiological significance, the biochemical effects of most O-GlcNAcylation events remain uncharacterized. One prevalent hypothesis is that O-GlcNAc moieties may be recognized by "reader" proteins to effect downstream signaling. However, no general O-GlcNAc readers have been identified, leaving a considerable gap in the field. To elucidate O-GlcNAc signaling mechanisms, we devised a biochemical screen for candidate O-GlcNAc reader proteins. We identified several human proteins, including 14-3-3 isoforms, that bind O-GlcNAc directly and selectively. We demonstrate that 14-3-3 proteins bind O-GlcNAc moieties in human cells, and we present the structures of 14-3-3ß/α and γ bound to glycopeptides, providing biophysical insights into O-GlcNAc-mediated protein-protein interactions. Because 14-3-3 proteins also bind to phospho-serine and phospho-threonine, they may integrate information from O-GlcNAc and O-phosphate signaling pathways to regulate numerous physiological functions.

Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance.

DNA methylation is an epigenetic mark important for genome stability and gene expression. In Arabidopsis thaliana, the 5-methylcytosine DNA glycosylase/demethylase DEMETER (DME) controls active DNA demethylation during the reproductive stage; however, the lethality of loss-of-function dme mutations has made it difficult to assess DME function in vegetative tissues. Here, we edited DME using clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated protein 9 and created three weak dme mutants that produced a few viable seeds. We also performed central cell-specific complementation in a strong dme mutant and combined this line with mutations in the other three Arabidopsis demethylase genes to generate the dme ros1 dml2 dml3 (drdd) quadruple mutant. A DNA methylome analysis showed that DME is required for DNA demethylation at hundreds of genomic regions in vegetative tissues. A transcriptome analysis of the drdd mutant revealed that DME and the other three demethylases are important for plant responses to biotic and abiotic stresses in vegetative tissues. Despite the limited role of DME in regulating DNA methylation in vegetative tissues, the dme mutants showed increased susceptibility to bacterial and fungal pathogens. Our study highlights the important functions of DME in vegetative tissues and provides valuable genetic tools for future investigations of DNA demethylation in plants.

Covalent organic frameworks bearing pillar[6]arene-reduced Au nanoparticles for the catalytic reduction of nitroaromatics.

While tremendous advancements in 2D materials anchoring Au nanoparticles have been made, it is an urgent challenge to explore a green and facile approach for obtaining small-size Au nanoparticles. The rise of 2D covalent organic framework (COF) presents more-promising candidates for constructing excellent sites for loading metal nanoparticles. In this study, a novel 2D heterogeneous hybrid nanomaterial (P6-Au-COF) based on COF and pillar[6]arene (P6) reduced Au nanoparticles (P6-Au) is prepared by a simple and green procedure. The Au nanoparticles with an average small diameter of 2-3 nm are homogeneously dispersed on the surface of the COF. The P6-Au-COF hybrid material shows highly catalytic performance for the reduction of nitrophenol isomers when compared with commercial Pd/C catalyst and other reported materials. The P6-Au-COF hybrid material exhibits durable recyclablility and stability during the catalytic reaction. Considering the outstanding merits of the heterogeneous 2D catalyst of P6-Au-COF as well as the simple and green preparation, this research might not only present enormous opportunities for stabilized, high-performance and sustainable catalysts, but be applied in other frontier study of sustainable functionalized nanocomposites and advanced materials.

The crystal structure of the RsbN-σBldN complex from Streptomyces venezuelae defines a new structural class of anti-σ factor.

Streptomyces are filamentous bacteria with a complex developmental life cycle characterized by the formation of spore-forming aerial hyphae. Transcription of the chaplin and rodlin genes, which are essential for aerial hyphae production, is directed by the extracytoplasmic function (ECF) σ factor BldN, which is in turn controlled by an anti-σ factor, RsbN. RsbN shows no sequence similarity to known anti-σ factors and binds and inhibits BldN in an unknown manner. Here we describe the 2.23 Å structure of the RsbN-BldN complex. The structure shows that BldN harbors σ2 and σ4 domains that are individually similar to other ECF σ domains, which bind -10 and -35 promoter regions, respectively. The anti-σ RsbN consists of three helices, with α3 forming a long helix embraced between BldN σ2 and σ4 while RsbN α1-α2 dock against σ4 in a manner that would block -35 DNA binding. RsbN binding also freezes BldN in a conformation inactive for simultaneous -10 and -35 promoter interaction and RNAP binding. Strikingly, RsbN is structurally distinct from previously solved anti-σ proteins. Thus, these data characterize the molecular determinants controlling a central Streptomyces developmental switch and reveal RsbN to be the founding member of a new structural class of anti-σ factor.

A case report and literature review of vaginal bleeding in prepubertal girl.

Vaginal bleeding in the prepubertal girl is an uncommon condition with complex aetiological factors. We report a case of a 6-year-old girl brought to hospital when vaginal bleeding was noticed after defecation. Various common causes were excluded by genital and auxiliary examinations. Serial vaginoscopy revealed increasing petechiae within the non-oestrogenised cervix and vaginal wall. The aetiology of these petechiae was considered to result from ruptured small blood vessels or submucosal capillaries due to an increase in abdominal pressure. CONCLUSION: This case report and review of literature has shed new light on the aetiology of prepubertal bleeding, which details challenging clinical characteristics of use to gynaecologists in the evaluation of related conditions and formulation of appropriate treatment regimens.

Risk factors and clinical characteristics of recurrent ectopic pregnancy: A case-control study.

OBJECTIVE: To compare signs and symptoms between patients with recurrent ectopic pregnancies (REP) and primary ectopic pregnancies (PEP) and to identify potential risk factors of REP. MATERIALS AND METHODS: Data from 2014 to 2016 were analyzed. The study included 81 women each diagnosed with REP and PEP with no recurrence of ectopic pregnancy (EP) before January 2019. Information, including historical factors and findings at presentation of both group were collected. Data were compared between the two groups. Associations between REP and the risk factors were analyzed by logistic regression. RESULTS: The findings revealed that compared to the patients in the PEP group, REP patients had significantly lower education (P = 0.001), higher proportion of previous infertility (P < 0.001) and different methods of PEP treatment (P = 0.001). Clinical data of the last operation revealed significantly higher occurrences of pelvic and peritubal adhesions (P < 0.05). Further multiple regression analysis showed that lower educational background (odds ratio [OR] = 4.183 95% confidence interval [CI] 1.311-13.344 P = 0.016), nulliparity (OR = 12.312 95% CI 3.382-44.824 P < 0.001), history of salpingotomy (OR = 7.129 95% CI 1.022-49.748 P < 0.05) and abortion (OR for one abortion = 21.576, P = 0.001; OR for two abortions =36.794, P < 0.001; OR for three abortions or more = 119.013, P < 0.001) were significant risk factors for REP. CONCLUSION: Active education on contraception is required for patients with lower educational level and history of abortion. Different plans should be formulated for patients with EP. For EP patients wanting fertility, the risk between fertility preservation and REP needs to be evaluated as reproductive function cannot be pursued blindly while ignoring the risk of recurrence.