Structural basis for self-cleavage prevention by tag:anti-tag pairing complementarity in type VI Cas13 CRISPR systems.

Bacteria and archaea apply CRISPR-Cas surveillance complexes to defend against foreign invaders. These invading genetic elements are captured and integrated into the CRISPR array as spacer elements, guiding sequence-specific DNA/RNA targeting and cleavage. Recently, in vivo studies have shown that target RNAs with extended complementarity with repeat sequences flanking the target element (tag:anti-tag pairing) can dramatically reduce RNA cleavage by the type VI-A Cas13a system. Here, we report the cryo-EM structure of Leptotrichia shahii LshCas13acrRNA in complex with target RNA harboring tag:anti-tag pairing complementarity, with the observed conformational changes providing a molecular explanation for inactivation of the composite HEPN domain cleavage activity. These structural insights, together with in vitro biochemical and in vivo cell-based assays on key mutants, define the molecular principles underlying Cas13a's capacity to target and discriminate between self and non-self RNA targets. Our studies illuminate approaches to regulate Cas13a's cleavage activity, thereby influencing Cas13a-mediated biotechnological applications.

Transdermal microarrayed electroporation for enhanced cancer immunotherapy based on DNA vaccination.

Despite the tremendous clinical potential of nucleic acid-based vaccines, their efficacy to induce therapeutic immune response has been limited by the lack of efficient local gene delivery techniques in the human body. In this study, we develop a hydrogel-based organic electronic device (µEPO) for both transdermal delivery of nucleic acids and in vivo microarrayed cell electroporation, which is specifically oriented toward one-step transfection of DNAs in subcutaneous antigen-presenting cells (APCs) for cancer immunotherapy. The µEPO device contains an array of microneedle-shaped electrodes with pre-encapsulated dry DNAs. Upon a pressurized contact with skin tissue, the electrodes are rehydrated, electrically triggered to release DNAs, and then electroporate nearby cells, which can achieve in vivo transfection of more than 50% of the cells in the epidermal and upper dermal layer. As a proof-of-concept, the µEPO technique is employed to facilitate transdermal delivery of neoantigen genes to activate antigen-specific immune response for enhanced cancer immunotherapy based on a DNA vaccination strategy. In an ovalbumin (OVA) cancer vaccine model, we show that high-efficiency transdermal transfection of APCs with OVA-DNAs induces robust cellular and humoral immune responses, including antigen presentation and generation of IFN-γ+ cytotoxic T lymphocytes with a more than 10-fold dose sparing over existing intramuscular injection (IM) approach, and effectively inhibits tumor growth in rodent animals.

Association between high-flow nasal cannula use and mortality in patients with sepsis-induced acute lung injury: a retrospective propensity score-matched cohort study.

BACKGROUND: High-flow nasal cannula (HFNC) has emerged as a promising noninvasive method for delivering oxygen to critically ill patients, particularly those with sepsis and acute lung injury. However, uncertainties persist regarding its therapeutic benefits in this specific patient population. METHODS: This retrospective study utilized a propensity score-matched cohort from the Medical Information Mart in Intensive Care-IV (MIMIC-IV) database to explore the correlation between HFNC utilization and mortality in patients with sepsis-induced acute lung injury. The primary outcome was 28-day all-cause mortality. RESULTS: In the propensity score-matched cohort, the 28-day all-cause mortality rate was 18.63% (95 out of 510) in the HFNC use group, compared to 31.18% (159 out of 510) in the non-HFNC group. The use of HFNC was associated with a lower 28-day all-cause mortality rate (hazard ratio [HR] = 0.53; 95% confidence interval [CI] = 0.41-0.69; P < 0.001). HFNC use was also associated with lower ICU mortality (odds ratio [OR] = 0.52; 95% CI = 0.38-0.71; P < 0.001) and lower in-hospital mortality (OR = 0.51; 95% CI = 0.38-0.68; P < 0.001). Additionally, HFNC use was found to be associated with a statistically significant increase in both the ICU and overall hospitalization length. CONCLUSIONS: These findings indicate that HFNC may be beneficial for reducing mortality rates among sepsis-induced acute lung injury patients; however, it is also associated with longer hospital stays.

Molecular insight into the potential functional role of pseudoenzyme GFOD1 via interaction with NKIRAS2.

The glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family includes a variety of oxidoreductases with a wide range of substrates that utilize NAD or NADP as redox cofactor. Human contains two members of this family, namely glucose-fructose oxidoreductase domain-containing protein 1 and 2 (GFOD1 and GFOD2). While GFOD1 exhibits low tissue specificity, it is notably expressed in the brain, potentially linked to psychiatric disorders and severe diseases. Nevertheless, the specific function, cofactor preference, and enzymatic activity of GFOD1 remain largely unknown. In this work, we find that GFOD1 does not bind to either NAD or NADP. Crystal structure analysis unveils that GFOD1 exists as a typical homodimer resembling other family members, but lacks essential residues required for cofactor binding, suggesting that it may function as a pseudoenzyme. Exploration of GFOD1-interacting partners in proteomic database identifies NK-κB inhibitor-interacting Ras-like 2 (NKIRAS2) as one potential candidate. Co-immunoprecipitation (co-IP) analysis indicates that GFOD1 interacts with both GTP- and GDP-bound forms of NKIRAS2. The predicted structural model of the GFOD1-NKIRAS2 complex is validated in cells using point mutants and shows that GFOD1 selectively recognizes the interswitch region of NKIRAS2. These findings reveal the distinct structural properties of GFOD1 and shed light on its potential functional role in cellular processes.

Quantitative Analysis of the Cu Element Enhanced by AgNPs in a Single Microsized Suspended Particle Based on Optical Trapping-LIBS and Machine Learning.

Extremely severe and persistent particulate pollution caused by industrialization and urbanization impacts air quality, regional and global climates, and human health. The unstable and complex spectral signal of laser-induced breakdown spectroscopy (LIBS) with minimal feature information and interference signals considerably influences the accuracy of qualitative and quantitative analysis. In response to overcome this phenomenon, in this work, quantitative analysis of Cu element enhanced by silver nanoparticles (AgNPs) in a single microsized suspended particle was proposed herein using optical trapping-LIBS and machine learning method was proposed. Initially, the optimal AgNPs enhancement conditions were optimized. The LIBS spectra of 15 polluted black carbon samples were collected and various spectral pretreatment methods were compared to optimize the LIBS spectra. Variable selection methods include variable importance measurement (VIM), variable importance projection (VIP), VIM-successive projections algorithm (VIM-SPA), VIM-genetic algorithm (VIM-GA), and VIM-mutual information (VIM-MI). Finally, several hybrid variable selection methods were implemented in random forest (RF) calibration models. In particular, a wavelet transform (WT)-VIM-SPA-RF calibration model has constructed under the WT spectral pretreatment method and the selected and optimized input variables (VIM-SPA). Results elucidate that the WT-VIM-SPA-RF calibration model (R2P = 0.9858, MREP = 0.0396) have the best prediction performance than the WT-RF and Raw-RF models in predicting the Cu level in a single microsized black carbon particle. Compared to the WT-RF and Raw-RF models, MREP values decreased by 37% and 62%, respectively. The values of RSD, RPD, and RER of this calibration model are 2.8%, 8.39%, and 17.79%, respectively. The aforementioned results demonstrate that the WT-VIM-SPA-RF calibration model with accuracy, stability, and robustness is a promising approach for improving the quantitative accuracy of the Cu level in carbon black particles.

Microfluidic Separation and Enrichment of Escherichia coli by Size Using Viscoelastic Flows.

Here, we achieve the separation and enrichment of Escherichia coli clusters from its singlets in a viscoelastic microfluidic device. E. coli, an important prokaryotic model organism and a widely used microbial factory, can aggregate in clusters, leading to biofilm development that can be detrimental to human health and industrial processes. The ability to obtain high-purity populations of E. coli clusters is of significance for biological, biomedical, and industrial applications. In this study, polystyrene particles of two different sizes, 1 and 4.8 µm, are used to mimic E. coli singlets and clusters, respectively. Experimental results show that particles migrate toward the channel center in a size-dependent manner, due to the combined effects of inertial and elastic forces; 4.8 and 1 µm particles are found to have lateral equilibrium positions closer to the channel centerline and sidewalls, respectively. The size-dependent separation performance of the microdevice is demonstrated to be affected by three main factors: channel length, the ratio of sheath to sample flow rate, and poly(ethylene oxide) (PEO) concentration. Further, the separation of E. coli singlets and clusters is achieved at the outlets, and the separation efficiency is evaluated in terms of purity and enrichment factor.

Inertial Separation of Particles Assisted by Symmetrical Sheath Flows in a Straight Microchannel.

Over the past two decades, inertial microfluidics, which works at an intermediate range of Reynolds number (∼1 < Re < ∼100), has been widely used for particle separation due to its high-throughput and label-free features. This work proposes a novel method for continuous separation of particles by size using inertial microfluidics, with the assistance of symmetrical sheath flows in a straight microchannel. Here, larger particles (>3 µm) are arranged close to the channel sidewalls, while smaller particles (<2 µm) remain flowing along the channel centerline. This conclusion is supported by experimental data with particles of different sizes ranging from 0.79 to 10.5 µm. Symmetrical Newtonian sheath flows are injected on both sides of particle mixtures into a straight rectangular microchannel with an aspect ratio (AR = height/width) of 2.5. Results show that the separation performance of the developed microfluidic device is affected by three main factors: channel length, total flow rate, and flow rate ratio of sheath to sample. Besides, separation of platelets from whole blood is demonstrated. The developed microfluidic platform owns the advantages of low fabrication cost, simple experiment setup, versatile selections of particle candidates, and stable operations. This systematic study provides a new perspective for particle separation, which is expected to find applications across various fields spanning physics, biology, biomedicine, and industry.

Assessing the causal effect of genetically predicted metabolites and metabolic pathways on stroke.

BACKGROUND: Stroke is a common neurological disorder that disproportionately affects middle-aged and elderly individuals, leading to significant disability and mortality. Recently, human blood metabolites have been discovered to be useful in unraveling the underlying biological mechanisms of neurological disorders. Therefore, we aimed to evaluate the causal relationship between human blood metabolites and susceptibility to stroke. METHODS: Summary data from genome-wide association studies (GWASs) of serum metabolites and stroke and its subtypes were obtained separately. A total of 486 serum metabolites were used as the exposure. Simultaneously, 11 different stroke phenotypes were set as the outcomes, including any stroke (AS), any ischemic stroke (AIS), large artery stroke (LAS), cardioembolic stroke (CES), small vessel stroke (SVS), lacunar stroke (LS), white matter hyperintensities (WMH), intracerebral hemorrhage (ICH), subarachnoid hemorrhage (SAH), transient ischemic attack (TIA), and brain microbleeds (BMB). A two-sample Mendelian randomization (MR) study was conducted to investigate the causal effects of serum metabolites on stroke and its subtypes. The inverse variance-weighted MR analyses were conducted as causal estimates, accompanied by a series of sensitivity analyses to evaluate the robustness of the results. Furthermore, a reverse MR analysis was conducted to assess the potential for reverse causation. Additionally, metabolic pathway analysis was performed using the web-based MetOrigin. RESULTS: After correcting for the false discovery rate (FDR), MR analysis results revealed remarkable causative associations with 25 metabolites. Further sensitivity analyses confirmed that only four causative associations involving three specific metabolites passed all sensitivity tests, namely ADpSGEGDFXAEGGGVR* for AS (OR: 1.599, 95% CI 1.283-1.993, p = 2.92 × 10-5) and AIS (OR: 1.776, 95% CI 1.380-2.285, p = 8.05 × 10-6), 1-linoleoylglycerophosph-oethanolamine* for LAS (OR: 0.198, 95% CI 0.091-0.428, p = 3.92 × 10-5), and gamma-glutamylmethionine* for SAH (OR: 3.251, 95% CI 1.876-5.635, p = 2.66 × 10-5), thereby demonstrating a high degree of stability. Moreover, eight causative associations involving seven other metabolites passed both sensitivity tests and were considered robust. The association result of one metabolite (glutamate for LAS) was considered non-robust. As for the remaining metabolites, we speculate that they may potentially possess underlying causal relationships. Notably, no common metabolites emerged from the reverse MR analysis. Moreover, after FDR correction, metabolic pathway analysis identified 40 significant pathways across 11 stroke phenotypes. CONCLUSIONS: The identified metabolites and their associated metabolic pathways are promising circulating metabolic biomarkers, holding potential for their application in stroke screening and preventive strategies within clinical settings.

Crown Ether-Based Ion Transporters in Bilayer Membranes.

Bilayer membranes that enhance the stability of the cell are essential for cell survival, separating and protecting the interior of the cell from its external environment. Membrane-based channel proteins are crucial for sustaining cellular activities. However, dysfunction of these proteins would induce serial channelopathies, which could be substituted by artificial ion channel analogs. Crown ethers (CEs) are widely studied in the area of artificial ion channels owing to their intrinsic host-guest interaction with different kinds of organic and inorganic ions. Other advantages such as lower price, chemical stability, and easier modification also make CE a research hotspot in the field of synthetic transmembrane nanopores. And numerous CEs-based membrane-active synthetic ion channels were designed and fabricated in the past decades. Herein, the recent progress of CEs-based synthetic ion transporters has been comprehensively summarized in this review, including their design principles, functional mechanisms, controllable properties, and biomedical applications. Furthermore, this review has been concluded by discussing the future opportunities and challenges facing this research field. It is anticipated that this review could offer some inspiration for the future fabrication of novel CEs-derived ion transporters with more advanced structures, properties, and practical applications.

Discovery of novel 2-(4-(benzyloxy)-5-(hydroxyl) phenyl) benzothiazole derivatives as multifunctional MAO-B inhibitors for the treatment of Parkinson's disease.

To discover novel multifunctional agents for the treatment of Parkinson's disease, a series of 2-(4-(benzyloxy)-5-(hydroxyl) phenyl) benzothiazole derivatives was designed, synthesized and evaluated. The results revealed that representative compound 3h possessed potent and selective MAO-B inhibitory activity (IC50 = 0.062 µM), and its inhibitory mode was competitive and reversible. Additionally, 3h also displayed excellent anti-oxidative effect (ORAC = 2.27 Trolox equivalent), significant metal chelating ability and appropriate BBB permeability. Moreover, 3h exhibited good neuroprotective effect and anti-neuroinflammtory ability. These results indicated that compound 3h was a promising candidate for further development against PD.

Multi-element Quantitative Analysis of Single Micro-sized Suspended Particles in Air with High Accuracy Based on Random Forest and Variable Selection Strategies.

The chemical compositions of atmospheric particles have been studied for several decades, and the traditional techniques for particle analysis usually require time-consuming sample preparation. Within this study, simultaneous quantitative detection of multiple metallic species (Zn, Cu, and Ni) in single micro-sized suspended particles was investigated by combining random forest (RF) and variable selection strategies. Laser-induced breakdown spectra of 15 polluted black carbon samples were applied for establishing the RF model, and the movmean smoothing spectral pretreatment method and variable selection methods [variable importance measurement (VIM), genetic algorithm (GA), and variable importance projection (VIP)] were proposed. Finally, the optimized RF calibration model with the evaluation indicators of mean relative error (MRE), root-mean-square error (RMSE), and coefficient of determination (R2) was constructed based on the optimal input variables and model parameters. Compared with the univariate regression method, the VIP-RF (Zn) and VIM-RF (Cu and Ni) models showed a better correlation relationship (Rp2 = 0.9662 for Zn, Rp2 = 0.9596 for Cu, and Rp2 = 0.9548 for Ni). For Zn, Cu, and Ni, the values of RMSEP (RMSE of prediction) decreased by 116.44, 68.94, and 102.10 ppm, while the values of MREP (MRE of prediction) decreased by 67, 55, and 48%, respectively. The values of ratio of prediction to deviation (RPD) of VIP-RF (Zn), VIM-RF (Cu), and VIM-RF (Ni) models were 5.4, 5.0, and 4.7, respectively. The performance of this combined approach displays a notable accuracy improvement in the quantitative analysis of single particles, suggesting that it is a promising tool for real-time air particulate matter pollution monitoring and control in the future.

Microfibrillar-associated protein 5 regulates osteogenic differentiation by modulating the Wnt/ß-catenin and AMPK signaling pathways.

BACKGROUND: Dysfunctional osteogenesis of bone marrow mesenchymal stem cells (BMSCs) plays an important role in osteoporosis occurrence and development. However, the molecular mechanisms of osteogenic differentiation remain unclear. This study explored whether microfibrillar-associated protein 5 (MFAP5) regulated BMSCs osteogenic differentiation. METHODS: We used shRNA or cDNA to knock down or overexpress MFAP5 in C3H10 and MC3T3-E1 cells. AR-S- and ALP-staining were performed to quantify cellular osteogenic differentiation. The mRNA levels of the classical osteogenic differentiation biomarkers Runx2, Col1α1, and OCN were quantified by qRT-PCR. Finally, we employed Western blotting to measure the levels of Wnt/ß-catenin and AMPK signaling proteins. RESULTS: At days 0, 3, 7, and 14 after osteogenic induction, AR-S- and ALP-staining was lighter in MFAP5 knockdown compared to control cells, as were the levels of Runx2, Col1α1 and OCN. During osteogenesis, the levels of ß-catenin, p-GSK-3ß, AMPK, and p-AMPK were upregulated, while that of GSK-3ß was downregulated, indicating that Wnt/ß-catenin and AMPK signaling were activated. The relevant molecules were expressed at lower levels in the knockdown than control group; the opposite was seen for overexpressing cell lines. CONCLUSIONS: MFAP5 regulates osteogenesis via Wnt/ß­catenin- and AMPK-signaling; MFAP5 may serve as a therapeutic target in patients with osteoporosis.

Novel Method Based on Hollow Laser Trapping-LIBS-Machine Learning for Simultaneous Quantitative Analysis of Multiple Metal Elements in a Single Microsized Particle in Air.

Elemental identification of individual microsized aerosol particles is an important topic in air pollution studies. However, simultaneous and quantitative analysis of multiple constituents in a single aerosol particle with the noncontact in situ manner is still a challenging task. In this work, we explore the laser trapping-LIBS-machine learning to analyze four elements (Zn, Ni, Cu, and Cr) absorbed in a single micro-carbon black particle in air. By employing a hollow laser beam for trapping, the particle can be restricted in a range as small as ∼1.72 µm, which is much smaller than the focal diameter of the flat-topped LIBS exciting laser (∼20 µm). Therefore, the particle can be entirely and homogeneously radiated, and the LIBS spectrum with a high signal-to-noise ratio (SNR) is correspondingly achieved. Then, two types of calibration models, i.e., the univariate method (calibration curve) and the multivariate calibration method (random forests (RF) regression), are employed for data processing. The results indicate that the RF calibration model shows a better prediction performance. The mean relative error (MRE), relative standard deviation (RSD), and root-mean-squared error (RMSE) are reduced from 0.1854, 363.7, and 434.7 to 0.0866, 179.8, and 216.2 ppm, respectively. Finally, simultaneous and quantitative determination of the four metal contents with high accuracy is realized based on the RF model. The method proposed in this work has the potential for online single aerosol particle analysis and further provides a theoretical basis and technical support for the precise prevention and control of composite air pollution.

A novel hybrid filter/wrapper method for feature selection in archaeological ceramics classification by laser-induced breakdown spectroscopy.

Laser-induced breakdown spectroscopy (LIBS) has been appreciated as a valuable analytical tool in the cultural heritage field owing to its unique technological superiority, particularly in combination with chemometric methods. Feature selection (FS) as an indispensable pre-processing step in data optimization, for eliminating the redundant or irrelevant features from high-dimensional data to enhance the predictive capacity and result comprehensibility of multivariate classification based on LIBS technology. In this paper, a novel hybrid filter/wrapper method based on the MI-DBS algorithm was proposed to enhance the qualitative analysis performance of the LIBS technique. The proposed method combines the advantages of the mutual information (MI) algorithm based filter method and bi-directional selection (DBS) algorithm based wrapper method. The MI algorithm is the first to remove the redundant or uncorrelated features so that a simplified input subset can be established. Then, the DBS algorithm is used to further select the retained features and hence to seek an optimal feature subset with good predictive performance. To benefit the above feature selection process, the wavelet transform denoising (WTD) method was used to reduce the noise from LIBS spectra. LIBS experiments were performed using 35 archaeological ceramic samples. Besides, the proposed hybrid filter/wrapper method was implemented through a random forest (RF) based nonlinear multivariate classification method. Through a comparison between several other feature selection methods and the proposed method, it has been seen that the proposed method is the best regarding the predictive performance and number of the selected features. Finally, the MI-DBS algorithm is used to seek the optimal features from the full spectrum (220-720 nm); the corresponding sensitivity, specificity and accuracy acquired through the RF classifier for the test set were 0.9722, 0.9956 and 0.9850. It is shown from the general results that the MI-DBS algorithm is more effective in terms of improving the model performance and decreasing the redundant or uncorrelated features and computational time and serves as a good alternative for FS in multivariate classification.

Molecular basis for the function of the αß heterodimer of human NAD-dependent isocitrate dehydrogenase.

Mammalian mitochondrial NAD-dependent isocitrate dehydrogenase (NAD-IDH) catalyzes the decarboxylation of isocitrate into α-ketoglutarate in the tricarboxylic acid cycle. It exists as the α2ßγ heterotetramer composed of the αß and αγ heterodimers. Different from the αγ heterodimer that can be allosterically activated by CIT and ADP, the αß heterodimer cannot be allosterically regulated by the activators; however, the molecular mechanism is unclear. We report here the crystal structures of the αß heterodimer of human NAD-IDH with the α subunit in apo form and in Ca2+-bound, NAD-bound, and NADH-bound forms. Structural analyses and comparisons reveal that the αß heterodimer has a similar yet more compact overall structure compared with the αγ heterodimer and contains a pseudo-allosteric site that is structurally different from the allosteric site. In particular, the ß3-α3 and ß12-α8 loops of the ß subunit at the pseudo-allosteric site adopt significantly different conformations from those of the γ subunit at the allosteric site and hence impede the binding of the activators, explaining why the αß heterodimer cannot be allosterically regulated by the activators. The structural data also show that NADH can compete with NAD to bind to the active site and inhibits the activity of the αß heterodimer. These findings together with the biochemical data reveal the molecular basis for the function of the αß heterodimer of human NAD-IDH.

Multiscale experimental study on the effects of different weight-bearing levels during moderate treadmill exercise on bone quality in growing female rats.

BACKGROUND: Bone tissue displays a hierarchical organization. Mechanical environments influence bone mass and structure. This study aimed to explore the effects of different mechanical stimuli on growing bone properties at macro-micro-nano scales. METHODS: Sixty five-week-old female Wistar rats were treadmill exercised at moderate intensity with the speed of 12 m/min, and then randomly divided into five groups according to weight-bearing level. After 8 weeks of experiment, femurs were harvested to perform multiscale tests. RESULTS: Bone formation was significantly increased by weight-bearing exercise, whereas bone resorption was not significantly inhibited. Trabecular and cortical bone mineral densities showed no significant increase by weight-bearing exercise. The microstructure of trabecular bone was significantly improved by 12% weight-bearing exercise. However, similar positive effects were not observed with further increase in weight-bearing levels. The nanomechanical properties of trabecular bone were not significantly changed by weight-bearing exercise. The macrostrength of whole femur and the nanomechanical properties of cortical bone significantly decreased in the 19% and 26% weight-bearing exercise groups. CONCLUSION: When rats ran on the treadmill at moderate intensity during growth period, additional 12% weight-bearing level could significantly increase bone formation, improve microstructure of trabecular bone, as well as maintain the structure and mechanical properties of cortical bone. Excessive weight-bearing level caused no positive effects on the trabecular bone microstructure and properties of cortical bone at all scales. In addition, increased weight-bearing level exerted no significant influence on trabecular and cortical bone mineral densities.

Structural basis for the functional role of the Shu complex in homologous recombination.

The Shu complex, a conserved regulator consisting of Csm2, Psy3, Shu1 and Shu2 in budding yeast, plays an important role in the assembly of the Rad51-ssDNA filament in homologous recombination. However, the molecular basis for the assembly of the Shu complex and its functional role in DNA repair is still elusive. Here, we report the crystal structure of the yeast Shu complex, revealing that Csm2, Psy3, Shu1 and Shu2 interact with each other in sequence to form a V-shape overall structure. Shu1 adopts a structure resembling the ATPase core domain of Rad51 and represents a new Rad51 paralog. Shu2 assumes a novel structural fold consisting of a conserved zinc-finger containing SWIM domain and a small insertion domain. The functional roles of the key residues are validated using mutagenesis and in vitro pull-down and in vivo yeast growth studies. Structural analysis together with available biological data identifies two potential DNA-binding sites, one of which might be responsible for binding the ssDNA region of the 3'-overhang DNA and the other for the dsDNA region. Collectively, these findings reveal the molecular basis for the assembly of the Shu complex and shed new insight on its functional role in homologous recombination.

Hemodynamic shear flow regulates biophysical characteristics and functions of circulating breast tumor cells reminiscent of brain metastasis.

Tumor cells disseminate to distant organs mainly through blood circulation, where they experience considerable levels of fluid shear flow. However, its influence on circulating tumor cells remains less understood. This study elucidates the effects of hemodynamic shear flow on biophysical properties and functions of breast circulating tumor cells with metastatic preference to brain. Only a small subpopulation of tumor cells are able to survive in shear flow with enhanced anti-apoptosis ability. Compared to untreated cells, surviving tumor cells spread more on soft substrates that mimic brain tissue but less on stiff substrates. They exhibit much lower expression of F-actin and cell stiffness but generate significantly higher cellular contractility. In addition, hemodynamic shear flow upregulates the stemness genes and considerably changes the expression of the genes related to brain metastasis. The enhanced cell spreading on soft substrates, reduced stiffness, elevated cellular contractility, and upregulation of the stemness and brain metastasis genes in tumor cells after shear flow treatment may be related to breast cancer metastasis in soft brain tissues. Our findings thus provide the first piece of evidence that hemodynamic shear flow regulates biophysical properties and functions of circulating tumor cells that are associated with brain metastasis, suggesting that tumor cells surviving in blood shear flow may better reflect the characteristics of organ preference in metastasis.

Multiscale investigation on the effects of additional weight bearing in combination with low-magnitude high-frequency vibration on bone quality of growing female rats.

This study aimed to explore the effects of additional weight bearing in combination with low-magnitude high-frequency vibration (LMHFV; 45 Hz, 0.3 g) on bone quality. One hundred twenty rats were randomly divided into ten groups; namely, sedentary (SED), additional weight bearing in which the rat wears a backpack whose weight is x% of the body weight (WBx; x = 5, 12, 19, 26), basic vibration (V), and additional weight bearing in combination with LMHFV in which the rat wears a backpack whose weight is x% of the body weight (Vx; x = 5, 12, 19, 26). The experiment was conducted for 12 weeks, 7 days per week, and 15 min per day. A three-point bending mechanical test, micro computed tomography, and a nanoindentation test were used. Serum samples were analyzed chemically. Failure load in V19 rats was significantly lower than that in SED rats (P < 0.05). Vx (x = 5, 12, 19, 26) rats showed poor microarchitectures. The content of tartrate-resistant acid phosphatase 5b was significantly higher in Vx (x = 5, 12, 19, 26) rats than that in SED rats (P < 0.05). V26 rats demonstrated comparatively better nanomechanical properties of materials than the other vibrational groups. Additional weight bearing in combination with LMHFV negatively affected the macromechanical properties and microarchitecture of bone. Heavy additional weight bearing, such as 26% of body weight, in combination with LMHFV was able to improve the nanomechanical properties of growing bone material compared with LMHFV. A combined mechanical stimulation was used, which may provide useful information to understand the mechanism of this mechanical stimulation on bone.

Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi.

TET proteins play a vital role in active DNA demethylation in mammals and thus have important functions in many essential cellular processes. The chemistry for the conversion of 5mC to 5hmC, 5fC and 5caC catalysed by TET proteins is similar to that of T to 5hmU, 5fU and 5caU catalysed by thymine-7-hydroxylase (T7H) in the nucleotide anabolism in fungi. Here, we report the crystal structures and biochemical properties of Neurospora crassa T7H. T7H can bind the substrates only in the presence of cosubstrate, and binding of different substrates does not induce notable conformational changes. T7H exhibits comparable binding affinity for T and 5hmU, but 3-fold lower affinity for 5fU. Residues Phe292, Tyr217 and Arg190 play critical roles in substrate binding and catalysis, and the interactions of the C5 modification group of substrates with the cosubstrate and enzyme contribute to the slightly varied binding affinity and activity towards different substrates. After the catalysis, the products are released and new cosubstrate and substrate are reloaded to conduct the next oxidation reaction. Our data reveal the molecular basis for substrate specificity and catalytic mechanism of T7H and provide new insights into the molecular mechanism of substrate recognition and catalysis of TET proteins.