SCPLPA: An miRNA-disease association prediction model based on spatial consistency projection and label propagation algorithm.

Identifying the association between miRNA and diseases is helpful for disease prevention, diagnosis and treatment. It is of great significance to use computational methods to predict potential human miRNA disease associations. Considering the shortcomings of existing computational methods, such as low prediction accuracy and weak generalization, we propose a new method called SCPLPA to predict miRNA-disease associations. First, a heterogeneous disease similarity network was constructed using the disease semantic similarity network and the disease Gaussian interaction spectrum kernel similarity network, while a heterogeneous miRNA similarity network was constructed using the miRNA functional similarity network and the miRNA Gaussian interaction spectrum kernel similarity network. Then, the estimated miRNA-disease association scores were evaluated by integrating the outcomes obtained by implementing label propagation algorithms in the heterogeneous disease similarity network and the heterogeneous miRNA similarity network. Finally, the spatial consistency projection algorithm of the network was used to extract miRNA disease association features to predict unverified associations between miRNA and diseases. SCPLPA was compared with four classical methods (MDHGI, NSEMDA, RFMDA and SNMFMDA), and the results of multiple evaluation metrics showed that SCPLPA exhibited the most outstanding predictive performance. Case studies have shown that SCPLPA can effectively identify miRNAs associated with colon neoplasms and kidney neoplasms. In summary, our proposed SCPLPA algorithm is easy to implement and can effectively predict miRNA disease associations, making it a reliable auxiliary tool for biomedical research.

Profiling DNA Cargos in Single Extracellular Vesicles via Hydrogel-Based Droplet Digital Multiple Displacement Amplification.

Due to the substantial heterogeneity among extracellular vesicle (EV) subpopulations, single-EV analysis has the potential to elucidate the mechanisms behind EV biogenesis and shed light on the myriad functions, leading to the development of novel diagnostics and therapeutics. While many studies have been devoted to reveal between-EV variations in surface proteins and RNAs, DNA cargos (EV-DNA) have received little attention. Here, we report a hydrogel-based droplet digital multiple displacement amplification approach for the comprehensive analysis of EV-DNA at the single-EV level. Single EVs are dispersed in thousands of hydrogel droplets and lysed for DNA amplification and identification. The droplet microfluidics strategy empowers the assay with single-molecule sensitivity and capability for absolute quantification of DNA-containing EVs. In particular, our findings indicate that 5-40% EVs are associated with DNA, depending on the cell of origin. Large EVs exhibit a higher proportion of DNA-containing EVs and a more substantial presence of intraluminal DNA, compared to small EVs. These DNA-containing EVs carry multiple DNA fragments on average. Furthermore, both double-stranded DNA and single-stranded DNA were able to be detected at the single-EV level. Utilizing this method, the abundance, distribution, and biophysical properties of EV-DNA in various EV populations are evaluated. The DNA level within EVs provides insight into the status of the originating cells and offers valuable information on the outcomes of anticancer treatments. The utilization of single-EV analysis for EV-DNA holds significant promise for early cancer detection and treatment response monitoring.

3D Printing of Metals with sub-10 µm Resolution.

The ability to manufacture 3D metallic architectures with microscale resolution is greatly pursued because of their diverse applications in microelectromechanical systems (MEMS) including microelectronics, mechanical metamaterials, and biomedical devices. However, the well-developed photolithography and emerging metal additive manufacturing technologies have limited abilities in manufacturing micro-scaled metallic structures with freeform 3D geometries. Here, for the first time, the high-fidelity fabrication of arbitrary metallic motifs with sub-10 µm resolution is achieved by employing an embedded-writing embedded-sintering (EWES) process. A paraffin wax-based supporting matrix with high thermal stability is developed, which permits the printed silver nanoparticle ink to be pre-sintered at 175 °C to form metallic green bodies. Via carefully regulating the matrix components, the printing resolution is tuned down to ≈7 µm. The green bodies are then embedded in a supporting salt bath and further sintered to realize freeform 3D silver motifs with great structure fidelity. 3D printing of various micro-scaled silver architectures is demonstrated such as micro-spring arrays, BCC lattices, horn antenna, and rotatable windmills. This method can be extended to the high-fidelity 3D printing of other metals and metal oxides which require high-temperature sintering, providing the pathways toward the design and fabrication of 3D MEMS with complex geometries and functions.

Association between risk of preterm birth and long-term and short-term exposure to ambient carbon monoxide during pregnancy in chongqing, China: a study from 2016-2020.

BACKGROUND: Preterm birth (PTB) is an important predictor of perinatal morbidity and mortality. Previous researches have reported a correlation between air pollution and an increased risk of preterm birth. However, the specific relationship between short-term and long-term exposure to carbon monoxide (CO) and preterm birth remains less explored. METHODS: A population-based study was conducted among 515,498 pregnant women in Chongqing, China, to assess short-term and long-term effects of CO on preterm and very preterm births. Generalized additive models (GAM) were applied to evaluate short-term effects, and exposure-response correlation curves were plotted after adjusting for confounding factors. Hazard ratios (HR) and 95% confidence intervals (CI) were calculated using COX proportional hazard models to estimate the long-term effect. RESULTS: The daily incidence of preterm and very preterm birth was 5.99% and 0.41%, respectively. A positive association between a 100 µg/m³ increase in CO and PTB was observed at lag 0-3 days and 12-21 days, with a maximum relative risk (RR) of 1.021(95%CI: 1.001-1.043). The exposure-response curves (lag 0 day) revealed a rapid increase in PTB due to CO. Regarding long-term exposure, positive associations were found between a 100 µg/m3 CO increase for each trimester(Model 2 for trimester 1: HR = 1.054, 95%CI: 1.048-1.060; Model 2 for trimester 2: HR = 1.066, 95%CI: 1.060-1.073; Model 2 for trimester 3: HR = 1.007, 95%CI: 1.001-1.013; Model 2 for entire pregnancy: HR = 1.080, 95%CI: 1.073-1.088) and higher HRs of very preterm birth. Multiplicative interactions between air pollution and CO on the risk of preterm and very preterm birth were detected (P- interaction<0.05). CONCLUSIONS: Our findings suggest that short-term exposure to low levels of CO may have protective effects against preterm birth, while long-term exposure to low concentrations of CO may reduce the risk of both preterm and very preterm birth. Moreover, our study indicated that very preterm birth is more susceptible to the influence of long-term exposure to CO during pregnancy, with acute CO exposure exhibiting a greater impact on preterm birth. It is imperative for pregnant women to minimize exposure to ambient air pollutants.

KATZNCP: a miRNA-disease association prediction model integrating KATZ algorithm and network consistency projection.

BACKGROUND: Clinical studies have shown that miRNAs are closely related to human health. The study of potential associations between miRNAs and diseases will contribute to a profound understanding of the mechanism of disease development, as well as human disease prevention and treatment. MiRNA-disease associations predicted by computational methods are the best complement to biological experiments. RESULTS: In this research, a federated computational model KATZNCP was proposed on the basis of the KATZ algorithm and network consistency projection to infer the potential miRNA-disease associations. In KATZNCP, a heterogeneous network was initially constructed by integrating the known miRNA-disease association, integrated miRNA similarities, and integrated disease similarities; then, the KATZ algorithm was implemented in the heterogeneous network to obtain the estimated miRNA-disease prediction scores. Finally, the precise scores were obtained by the network consistency projection method as the final prediction results. KATZNCP achieved the reliable predictive performance in leave-one-out cross-validation (LOOCV) with an AUC value of 0.9325, which was better than the state-of-the-art comparable algorithms. Furthermore, case studies of lung neoplasms and esophageal neoplasms demonstrated the excellent predictive performance of KATZNCP. CONCLUSION: A new computational model KATZNCP was proposed for predicting potential miRNA-drug associations based on KATZ and network consistency projections, which can effectively predict the potential miRNA-disease interactions. Therefore, KATZNCP can be used to provide guidance for future experiments.

Three tyrosine kinase inhibitors cause cardiotoxicity by inducing endoplasmic reticulum stress and inflammation in cardiomyocytes.

BACKGROUND: Tyrosine kinase inhibitors (TKIs) are anti-cancer therapeutics often prescribed for long-term treatment. Many of these treatments cause cardiotoxicity with limited cure. We aim to clarify molecular mechanisms of TKI-induced cardiotoxicity so as to find potential targets for treating the adverse cardiac complications. METHODS: Eight TKIs with different levels of cardiotoxicity reported are selected. Phenotypic and transcriptomic responses of human cardiomyocytes to TKIs at varying doses and times are profiled and analyzed. Stress responses and signaling pathways that modulate cardiotoxicity induced by three TKIs are validated in cardiomyocytes and rat hearts. RESULTS: Toxicity rank of the eight TKIs determined by measuring their effects on cell viability, contractility, and respiration is largely consistent with that derived from database or literature, indicating that human cardiomyocytes are a good cellular model for studying cardiotoxicity. When transcriptomes are measured for selected TKI treatments with different levels of toxicity in human cardiomyocytes, the data are classified into 7 clusters with mainly single-drug clusters. Drug-specific effects on the transcriptome dominate over dose-, time- or toxicity-dependent effects. Two clusters with three TKIs (afatinib, ponatinib, and sorafenib) have the top enriched pathway as the endoplasmic reticulum stress (ERS). All three TKIs induce ERS in rat primary cardiomyocytes and ponatinib activates the IRE1α-XBP1s axis downstream of ERS in the hearts of rats underwent a 7-day course of drug treatment. To look for potential triggers of ERS, we find that the three TKIs induce transient reactive oxygen species followed by lipid peroxidation. Inhibiting either PERK or IRE1α downstream of ERS blocks TKI-induced cardiac damages, represented by the induction of cardiac fetal and pro-inflammatory genes without causing more cell death. CONCLUSIONS: Our data contain rich information about phenotypic and transcriptional responses of human cardiomyocytes to eight TKIs, uncovering potential molecular mechanisms in modulating cardiotoxicity. ER stress is activated by multiple TKIs and leads to cardiotoxicity through promoting expression of pro-inflammatory factors and cardiac fetal genes. ER stress-induced inflammation is a promising therapeutic target to mitigate ponatinib- and sorafenib-induced cardiotoxicity.

Inhibitory effects of circulating natural autoantibodies to CD47-derived peptides on OSCC cells.

OBJECTIVES: Natural autoantibodies serve as an important anti-tumorigenic component in the body. This study was thus designed to investigate whether circulating natural IgG autoantibodies against a cluster of differentiation 47 (CD47) could exert inhibitory effects on oral squamous cell carcinoma (OSCC). SUBJECTS AND METHODS: The expression levels of 13 tumor-targeted genes in three OSCC cell lines were analyzed by qPCR, and CD47 expression in OSCC tissues was also verified with IHC staining. An in-house ELISA was performed to analyze circulating anti-CD47 IgG levels in control subjects, oral benign tumor, and OSCC patients, and to detect anti-CD47 IgG-abundant plasma. Three OSCC cell lines were treated with anti-CD47 IgG-abundant and -deficient plasma, respectively, followed by the analysis of cell proliferation, apoptosis, and invasion/metastasis. RESULTS: The CD47 gene showed the highest expression among 13 genes detected in three OSCC cell lines; its expression was significantly higher in OSCC tissues than adjacent tissues. Plasma anti-CD47 IgG levels showed the differences between control subjects, oral benign tumor, and OSCC patients. Anti-CD47 IgG-abundant plasma could evidently reduce cell viability via suppressing p-AKT expression and inducing cell apoptosis and inhibit the invasion of all three OSCC cell lines. CONCLUSIONS: Natural autoantibodies against CD47 may be a potential agent for OSCC immunotherapy.

Significance of CD80 as a Prognostic and Immunotherapeutic Biomarker in Lung Adenocarcinoma.

Lung adenocarcinoma (LUAD) is the primary cause of death among pulmonary cancer patients. Upregulation of CD80 may interact with cytotoxic T lymphocyte antigen 4 (CTLA4) to promote tumor progression and provide a potential target for biological antitumor therapy. However, the role of CD80 in LUAD is still unclear. To investigate the function of CD80 in LUAD, we collected transcriptomic data from 594 lung samples from The Cancer Genome Atlas of America (TCGA) database, along with the corresponding clinical information. We systematically explored the role of CD80 in LUAD using bioinformatics methods, including GO enrichment analysis, KEGG pathway analysis, Gene Set Enrichment Analysis (GSEA), co-expression analysis, and the CIBERSORT algorithm. Finally, we investigated the differences between the two subgroups of CD80 expression in terms of some drug sensitivity, using the pRRophetic package to screen small molecular drugs for therapeutic use. A predictive model based on CD80 for LUAD patients was successfully constructed. In addition, we discovered that the CD80-based prediction model was an independent prognostic factor. Co-expression analysis revealed 10 CD80-related genes, including oncogenes and immune-related genes. Functional analysis showed that the differentially expressed genes in patients with high CD80 expression were mainly located in immune-related signaling pathways. CD80 expression was also associated with immune cell infiltration and immune checkpoints. Highly expressing patients were more sensitive to several drugs, such as rapamycin, paclitaxel, crizotinib, and bortezomib. Finally, we found evidence that 15 different small molecular drugs may benefit the treatment of LUAD patients. This study found that elevated CD80 pairs could improve the prognosis of LUAD patients. CD80 is likely to be a potential as a prognostic and therapeutic target. The future use of small molecular drugs in combination with immune checkpoint blockade to enhance antitumor therapy and improve prognosis for LUAD patients is promising.

Highly Stable Two-Dimensional Cluster-Based Ni/Co-Organic Layers for High-Performance Supercapacitors.

Basic requirements for advanced and practical supercapacitors need electrode materials with strong stability, high surface area, well-defined porosity, and enhanced capability of ion insertion and electron transfer. It is worth mentioning that the two-dimensional cluster-based Ni/Co-organic layer (Ni0.7Co0.3-CMOL) inherits high stability from the Kagóme lattice and shows excellent pseudocapacitance behavior. As an optimized atomic composition, this crystalline CMOL exhibits excellent performance and stability both in 1.0 M KOH and All-Solid-State Flexible Asymmetric Supercapacitor (ASCs). The specific capacitance values are 1211 and 394 F g-1 and the energy density is 54.67 Wh kg-1 at 1 A g-1. Good cycling stability is characterized by its capacitance retention, maintained at 92.4% after 5000 cycles in a three-electrode system and 90% after 2000 cycles at 20 A g-1 for assembled All-Solid-State Flexible ASCs. An in situ XRD technique was used in the three-electrode system, which showed that there was no signal of crystalline substance that affected the cyclic stability of the material while charging and discharging. These superior results prove that Ni0.7Co0.3-CMOL is a promising candidate for supercapacitor applications.

A comparison between ultrasound-guided AIIS injection and radiography in the diagnosis of subspine impingement in patients with FAI.

BACKGROUND: Subspine impingement (SSI) does not have effective diagnostic criteria, especially in patients who also have femoroacetabular impingement (FAI). The classification of anterior inferior iliac spine (AIIS) morphology via three-dimensional CT is controversial. PURPOSE: To propose a method for ultrasound-guided AIIS injection as a way to diagnose SSI and evaluate the accuracy of radiography methods, including 3-D CT and MRI, as well as intraoperative findings. METHODS: Patients diagnosed with FAI between September 2020 and December 2021 were evaluated in this prospective study. Those who met the criteria were included in the ultrasound-guided AIIS injection test. Whether the pain was relieved after injection was recorded in the radiology report. Patients who experienced significant relief of the anterior groin pain (more than 50%) after the AIIS injection were considered positive responders. Among these patients, radiography materials, including AIIS morphology as measured by 3-D CT as well as superior capsular oedema on MRI, were compared. The presence of congestion or bruising on the capsule side of the labrum corresponding to the AIIS during hip arthroscopy was recorded. RESULTS: A total of 73 patients with FAI underwent the ultrasound-guided AIIS injection test. Prevalence rates of 13.70% (10/73), 58.90% (43/73), 23.29% (17/73) and 4.11% (3/73) were recorded for Type I, Type IIA, Type IIB and Type III AIISs, respectively. Thirty-six patients had positive responses to injection, and 37 patients had negative responses to injection. None of the patients with Type I, 23 (53.49%) patients with Type IIA, 11 (64.71%) patients with Type IIB and 2 (66.7%) patients with Type III AIISs had positive responses to the injection. A total of 57.14% of patients with Type II or Type III AIIS had positive responses to the injection. The proportions of patients with superior capsular oedema on MRI in the Type I, Type IIA, Type IIB, and Type III AIIS groups was 0, 30.23, 29.41 and 0%, respectively. Among non-Type I AIIS patients, those who reported positive responses to the injection had a higher incidence of superior capsular oedema (38.89% vs. 14.81%, P = 0.036), but they had no significant differences in the proportion of congestion or bruising of the labrum (47.22% vs. 37.04%, P = 0.419). The results showed that no pairs of methods-ultrasound-guided injection, MRI, and intraoperative findings-achieved good consistency (κ = 0.222, κ = 0.098 and κ = - 0.116). CONCLUSIONS: Radiographic methods including 3-D CT and MRI as well as the intraoperative findings of the labrum cannot be considered an accurate and reliable basis for the diagnosis and treatment of SSI in FAI patients. It is suggested that ultrasound-guided AIIS injections be combined with radiography to better diagnose SSI. LEVEL OF EVIDENCE: IV, case series.

Anterior tibial subluxation measured under a modified protocol is positively correlated with posterior tibial slope: a comparative study of MRI measurement methods.

PURPOSE: Anatomic factors, such as posterior tibial slope (PTS) and anterior tibial subluxation (ATS) obtained by quantitative measurement, have been proposed as predictors for clinical outcomes of anterior cruciate ligament (ACL) reconstruction. However, the correlation between PTS and ATS is controversial, and the method for quantitative ATS measurement remains unsettled. This study aimed to identify the correlation between PTS and ATS in patients with injured and intact ACLs and compare the two ATS measuring protocols. METHODS: This study included 128 ACL-injured and 176 ACL-intact patients with no concomitant ligament injuries. PTS and ATS were measured on sagittal MRI. ATS was measured using two measuring protocols, including the modified protocol using the longitudinal tibial axis (axis protocol) and the established protocol using a line perpendicular to the tibial plateau (plateau protocol). Correlation analyses between PTS and ATS and between PTS and the difference in the ATS value measured under the two protocols (ATSdiff) were performed. The difference between the two ATS measuring protocols was further analyzed by trigonometric analysis. Intra- and interobserver reliability tests were performed for the axis protocol. RESULTS: Under the axis protocol, ATS was positively correlated with PTS in both the ACL-injured and ACL-intact groups (p < 0.001). Under the plateau protocol, no correlation was observed in the ACL-injured group. In the ACL-intact group, no correlation was observed for lateral ATS, and a negative correlation was observed for medial ATS (p = 0.001). ATSdiff was positively correlated with PTS (p < 0.001), indicating that the two protocols varied greatly in those with a steep PTS. Trigonometric analysis showed that a steep PTS influenced the measurement of ATS under the plateau protocol but not the axis protocol. Intra- and interobserver reliability tests showed good-to-excellent strength of reliability for the ATS measurement under the axis protocol. CONCLUSION: ATS measured under the axis protocol was positively correlated with PTS, indicating that a steep PTS was associated with a worse anatomic tibiofemoral relationship. The axis protocol for ATS measurement is a promising method for clinical use since it is not influenced by PTS and reflects the global position of the tibia. LEVEL OF EVIDENCE: III.

[Para-Bombay phenotype due to bi-allelic heterozygous base deletions of FUT1 gene].

OBJECTIVE: To explore the genetic mechanism underlying a case with para-Bombay phenotype. METHODS: The ABO and Lewis phenotype were identified with serological methods. The coding regions of exons 6 and 7 of the ABO and FUT1 genes were amplified with PCR and directly sequenced. Haploid sequence analysis was carried out on the variant sites of the FUT1 gene. RESULTS: Serological analysis confirmed that the proband has a rare para-Bombay phenotype. Direct sequencing revealed that he was a B.01/O.01.02 heterozygote for the ABO gene, and had heterozygous deletion for the 768 and 881-882 sites of the FUT1 gene. Further haploid analysis showed that the c.881_882delTT deletion has occurred in one haploid while c.768delC was present in the other haploid. The proband was therefore determined as a FUT1*01N.13/01N.20 heterozygote, which have resulted in frameshift in polypeptide chain p.Phe294Cysfs*40 and p.Val257Phefs*23, respectively. CONCLUSION: A rare bi-allelic heterozygous deletion of para-Bombay phenotype has been identified in a blood donor. The c.881_882delTT and c.768delC deletions may decrease the activity of α-1,2-fucosyltransferase.

Composable Microfluidic Plates (cPlate): A Simple and Scalable Fluid Manipulation System for Multiplexed Enzyme-Linked Immunosorbent Assay (ELISA).

Enzyme-linked immunosorbent assay (ELISA) is the gold standard method for protein biomarkers. However, scaling up ELISA for multiplexed biomarker analysis is not a trivial task due to the lengthy procedures for fluid manipulation and high reagent/sample consumption. Herein, we present a highly scalable multiplexed ELISA that achieves a similar level of performance to commercial single-target ELISA kits as well as shorter assay time, less consumption, and simpler procedures. This ELISA is enabled by a novel microscale fluid manipulation method, composable microfluidic plates (cPlate), which are comprised of miniaturized 96-well plates and their corresponding channel plates. By assembling and disassembling the plates, all of the fluid manipulations for 96 independent ELISA reactions can be achieved simultaneously without any external fluid manipulation equipment. Simultaneous quantification of four protein biomarkers in serum samples is demonstrated with the cPlate system, achieving high sensitivity and specificity (∼ pg/mL), short assay time (∼1 h), low consumption (∼5 µL/well), high scalability, and ease of use. This platform is further applied to probe the levels of three protein biomarkers related to vascular dysfunction under pulmonary nanoparticle exposure in rat's plasma. Because of the low cost, portability, and instrument-free nature of the cPlate system, it will have great potential for multiplexed point-of-care testing in resource-limited regions.

A case of hyperhaemolysis syndrome in a pregnant Chinese woman with ß-thalassemia during perinatal transfusion.

OBJECTIVES: To report a case of hyperhaemolysis syndrome (HHS) that occurred during perinatal blood transfusion in a pregnant Chinese woman with ß-thalassemia to deepen the understanding of HHS and the risk of transfusion therapy for patients with thalassemia. BACKGROUND: Most HHS cases occur in people with sickle cell disease. So far, no cases of HHS have been reported in the Chinese population. Here, we report a pregnant Chinese women with ß-thalassemia experiencing HHS. METHODS: The patient received ABO- and RhD-matched red blood cell transfusion from six blood donors in four perinatal transfusions. Haemoglobinuria and lower haemoglobin levels compared to those before transfusion were observed after each transfusion, and the lactate dehydrogenase was consistently elevated. The blood samples were collected at different time points during the hospitalisation for direct antiglobulin test (DAT), antibody screening test and acid elution test. The antigens of six blood donors were identified, and the cross-matching tests were repeated using the blood sample of the patient with specific irregular antibodies after the last transfusion. RESULTS: The DAT of the patient was negative for anti-IgG and positive (1+) for anti-C3d, and no red blood cell antibodies were detected in the eluent before, between and after transfusions. Before and between transfusions, blood samples were negative for red blood cell irregular antibodies, whereas IgM anti-P1 and IgG anti-Jka were detected in blood samples the next day after the last transfusion. In the six donors, two were negative for P1 and Jka , one was positive for P1 and negative for Jka , and three were negative for P1 and positive for Jka . The tentative cross-matching tests using the indirect antiglobulin method in saline showed that only agglutination occurred in the blood samples of the patient collected after last transfusion and the three Jka -positive blood donors. DISCUSSION: The clinical manifestations and laboratory test results suggested that HHS occurred in this patient with ß-thalassemia after each transfusion. Clinicians should be aware that HHS can occur with compatible blood transfusion.

Mineralization of the herbicide swep by a two-strain consortium and characterization of a new amidase for hydrolyzing swep.

BACKGROUND: Swep is an excellent carbamate herbicide that kills weeds by interfering with metabolic processes and inhibiting cell division at the growth point. Due to the large amount of use, swep residues in soil and water not only cause environmental pollution but also accumulate through the food chain, ultimately pose a threat to human health. This herbicide is degraded in soil mainly by microbial activity, but no studies on the biotransformation of swep have been reported. RESULTS: In this study, a consortium consisting of two bacterial strains, Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34, was enriched from a contaminated soil sample and shown to be capable of mineralizing swep. Swep was first transformed by Comamonas sp. SWP-3 to the intermediate 3,4-dichloroaniline (3,4-DCA), after which 3,4-DCA was mineralized by Alicycliphilus sp. PH-34. An amidase gene, designated as ppa, responsible for the transformation of swep into 3,4-DCA was cloned from strain SWP-3. The expressed Ppa protein efficiently hydrolyzed swep and a number of other structural analogues, such as propanil, chlorpropham and propham. Ppa shared less than 50% identity with previously reported arylamidases and displayed maximal activity at 30 °C and pH 8.6. Gly449 and Val266 were confirmed by sequential error prone PCR to be the key catalytic sites for Ppa in the conversion of swep. CONCLUSIONS: These results provide additional microbial resources for the potential remediation of swep-contaminated sites and add new insights into the catalytic mechanism of amidase in the hydrolysis of swep.

In Situ Monitoring of Fluid Shear Stress Enhanced Adherence of Bacteria to Cancer Cells on Microfluidic Chip.

Mechanosensing mechanisms for surface recognition by bacteria play an important role in inflammation and phagocytosis. Here, we describe a set of DNA probes for revealing microbe adherence to cancer cells under fluid shear stress. DNA probes modified with a biotin group, an azido group, and hexadecanoic acid were indiscriminately anchored to the cell surface, acting as indicators for the membrane proteins, cell-surface carbohydrate, and phospholipids. When cancer cells were exposed to bacteria in fluid, enhanced accumulation of membrane proteins was indicated by the strong fluorescence aggregation, meanwhile the weakened accumulation of cell-surface carbohydrate and phospholipids indication was indicated by attenuated fluorescence. Further research demonstrates that this mechanosensing strategy was applicable to different bacterial-cancer cell interactions. This study not only uncovered new cellular mechanotransduction mechanisms, but also provided a versatile method that enabled in situ and dynamic indication of cancer cell responses to mechanical stimuli.

Shear Stress-Enhanced Internalization of Cell Membrane Proteins Indicated by a Hairpin-Type DNA Probe.

Shear stress is an important mechanical stimulus that plays a critical role in modulating cell functions. In this study, we investigated the regulating effects of shear stress on the internalization of cell membrane proteins in a microfluidic chip. A hairpin-type DNA probe was developed and indiscriminately anchored to the cell surface, acting as an indicator for the membrane proteins. When cells were exposed to shear stress generated from fluid cell medium containing external proteins, strong fluorescence was emanated from intracellular regions. With intensive investigation, results revealed that shear stress could enhance the specific cell endocytosis pathway and promote membrane protein internalization. This process was indicated by the enhanced intracellular fluorescence, generated from the internalized and mitochondria accumulated DNA probes. This study not only uncovered new cellular mechanotransduction mechanisms but also provided a versatile method that enabled in situ and dynamic indication of cell responses to mechanical stimuli.

Phagocytic intracellular digestion in amphioxus (Branchiostoma).

The digestive methods employed by amphioxus (Branchiostoma)-both intracellular phagocytic digestion and extracellular digestion-have been discussed since 1937. Recent studies also show that epithelial cells lining the Branchiostoma digestive tract can express many immune genes. Here, in Branchiostoma belcheri, using a special tissue fixation method, we show that some epithelial cells, especially those lining the large diverticulum protruding from the gut tube, phagocytize food particles directly, and Branchiostoma can rely on this kind of phagocytic intracellular digestion to obtain energy throughout all stages of its life. Gene expression profiles suggest that diverticulum epithelial cells have functional features of both digestive cells and phagocytes. In starved Branchiostoma, these cells accumulate endogenous digestive and hydrolytic enzymes, whereas, when sated, they express many kinds of immune genes in response to stimulation by phagocytized food particles. We also found that the distal hindgut epithelium can phagocytize food particles, but not as many. These results illustrate phagocytic intercellular digestion in Branchiostoma, explain why Branchiostoma digestive tract epithelial cells express typical immune genes and suggest that the main physiological function of the Branchiostoma diverticulum is different from that of the vertebrate liver.