Entosis: the core mechanism and crosstalk with other cell death programs.

Cell death pathways play critical roles in organism development and homeostasis as well as in the pathogenesis of various diseases. While studies over the last decade have elucidated numerous different forms of cell death that can eliminate cells in various contexts, how certain mechanisms impact physiology is still not well understood. Moreover, recent studies have shown that multiple forms cell death can occur in a cell population, with different forms of death eliminating individual cells. Here, we aim to describe the known molecular mechanisms of entosis, a non-apoptotic cell engulfment process, and discuss signaling mechanisms that control its induction as well as its possible crosstalk with other cell death mechanisms.

Pan-cancer mutational signature analysis of 111,711 targeted sequenced tumors using SATS.

Tumor mutational signatures have the potential to inform cancer diagnosis and treatment. However, their detection in targeted sequenced tumors is hampered by sparse mutations and variability in targeted gene panels. Here we present SATS, a scalable mutational signature analyzer addressing these challenges by leveraging tumor mutational burdens from targeted gene panels. Through analyzing simulated data, pseudo-targeted sequencing data generated by down-sampling whole exome and genome data, and samples with matched whole genome sequencing and targeted sequencing, we showed that SATS can accurately detect common mutational signatures and estimate signature burdens. Applying SATS to 111,711 targeted sequenced tumors from the AACR Project GENIE, we generated a pan-cancer catalogue of mutational signatures tailored to targeted sequencing, enabling estimation of signature burdens within individual tumors. Integrating signatures with clinical data, we demonstrated SATS's clinical utility, including identifying signatures enriched in early-onset hypermutated colorectal cancers and signatures associated with cancer prognosis and immunotherapy response.

Nitrated Polycyclic Aromatic Hydrocarbon (Nitro-PAH) Signatures and Somatic Mutations in Diesel Exhaust-Exposed Bladder Tumors.

BACKGROUND: Diesel exhaust is a complex mixture, including polycyclic aromatic hydrocarbons (PAH) and nitrated PAHs (nitro-PAH), many of which are potent mutagens and possible bladder carcinogens. To explore the association between diesel exposure and bladder carcinogenesis, we examined the relationship between exposure and somatic mutations and mutational signatures in bladder tumors. METHODS: Targeted sequencing was conducted in bladder tumors from the New England Bladder Cancer Study. Using data on 797 cases and 1,418 controls, two-stage polytomous logistic regression was used to evaluate etiologic heterogeneity between bladder cancer subtypes and quantitative, lifetime estimates of respirable elemental carbon (REC), a surrogate for diesel exposure. Poisson regression was used to evaluate associations between REC and mutational signatures. RESULTS: We observed significant heterogeneity in the diesel-bladder cancer risk relationship, with a strong positive association among cases with high-grade, nonmuscle invasive TP53-mutated tumors compared with controls [ORTop Tertile vs.Unexposed, 4.8; 95% confidence interval (CI), 2.2-10.5; Ptrend < 0.001; Pheterogeneity = 0.002]. In muscle-invasive tumors, we observed a positive association between diesel exposure and the nitro-PAH signatures of 1,6-dintropyrene (RR, 1.93; 95% CI, 1.28-2.92) and 3-nitrobenzoic acid (RR, 1.97; 95% CI, 1.33-2.92). CONCLUSIONS: The relationship between diesel exhaust and bladder cancer was heterogeneous based on the presence of TP53 mutations in tumors, further supporting the link between PAH exposure and TP53 mutations in carcinogenesis. Future studies that can identify nitro-PAH signatures in exposed tumors are warranted to add human data supporting the link between diesel and bladder cancer. IMPACT: This study provides additional insight into the etiology and possible mechanisms related to diesel exhaust-induced bladder cancer.

CD20/TNFR1 dual-targeting antibody enhances lysosome rupture-mediated cell death in B cell lymphoma.

Obinutuzumab is a therapeutic antibody for B cell non-Hodgkin's Lymphoma (BNHL), which is a glyco-engineered anti-CD20 antibody with enhanced antibody-dependent cellular cytotoxicity (ADCC) and causes binding-induced direct cell death (DCD) through lysosome membrane permeabilization (LMP). Tumour necrosis factor receptor 1 (TNFR1), a pro-inflammatory death receptor, also evokes cell death, partly through lysosomal rupture. As both obinutuzumab- and TNFR1-induced cell deaths are mediated by LMP and combining TNFR1 and obinutuzumab can amplify LMP-mediated cell death, we made dual-targeting antibody for CD20 and TNFR1 to enhance DCD of obinutuzumab.Obinutuzumab treatment-induced CD20 and TNFR1 colocalisation, and TNFR1-overexpressing cells showed increased obinutuzumab-induced DCD. Two targeting modes, anti-CD20/TNFR1 bispecific antibodies (bsAbs), and obinutuzumab-TNFα fusion proteins (OBI-TNFαWT and OBI-TNFαMUT), were designed to cluster CD20 and TNFR1 on the plasma membrane. OBI-TNFαWT and OBI-TNFαMUT showed significantly enhanced LMP, DCD, and ADCC compared with that induced by obinutuzumab. TNFR1 expression is upregulated in many BNHL subtypes compared to that in normal B cells; OBI-TNFαMUT specifically increased DCD and ADCC in a B cell lymphoma cell line overexpressing TNFR1. Further, OBI-TNFαMUT blocked NF-κB activation in the presence of TNF-α, implying that it can antagonise the proliferative role of TNF-α in cancers.Our study suggests that dual targeting of CD20 and TNFR1 can be a new therapeutic strategy for improving BNHL treatment. The OBI-TNFαMUT fusion protein enhances DCD and ADCC and prevents the proliferating effect of TNFα signalling; therefore, it may provide precision treatment for patients with BNHL, especially those with upregulated TNFR1 expression.

Purification and Detection of Ubiquitinated Plant Proteins Using Tandem Ubiquitin Binding Entities.

The timing and amplitude of plant signaling are frequently regulated through posttranslational modification of key signaling sectors, which facilitates rapid and flexible responses. Protein ubiquitination can serve as a degradation marker, influence subcellular localization, alter protein-protein interactions, and affect protein activity. Identification of polyubiquitinated proteins has been challenging due to their rapid degradation by the proteasome or removal of modifications by deubiquitination enzymes (DUBs). Tandem ubiquitin binding entities (TUBEs) are based on ubiquitin-associated domains and protect against both proteasomal degradation and DUBs. Here, we provide a protocol for purification of ubiquitinated plant proteins using TUBEs after transient expression in Nicotiana benthamiana. This protocol can also be applied to other plants to purify multiple ubiquitinated proteins or track ubiquitination of a target protein. This methodology provides an effective method for identification of ubiquitin ligase substrates and can be coupled with TUBEs targeting specific ubiquitination linkages.

Magnetoresponsive Artificial Cilia Self-Assembled with Magnetic Micro/Nanoparticles.

Biological cilia have exquisitely organized dynamic ultrafine structures with submicron diameters and exceptional aspect ratios, which are self-assembled with ciliary proteins. However, the construction of artificial cilia with size and dynamic functions comparable to biological cilia remains highly challenging. Here, we propose a self-assembly technique that generates magnetoresponsive artificial cilia with a highly ordered 3D structural arrangement using vapor-phase magnetic particles of varying sizes and shapes. We demonstrate that both monodispersed Fe3O4 nanoparticles and Fe microparticles can be assembled layer-by-layer vertically in patterned magnetic fields, generating both "nanoscale" or "microscale" artificial cilia, respectively. The resulting cilia display several structural features, such as diameters of single particle resolution, controllable diameters and lengths spanning from nanometers to micrometers, and accurate positioning. We further demonstrate that both the magnetic nanocilia and microcilia can dynamically and immediately actuate in response to modulated magnetic fields while providing different stroke ranges and actuation torques. Our strategy provides new possibilities for constructing artificial nano- and microcilia with controlled 3D morphology and dynamic field responsiveness using magnetic particles of varied sizes and shapes.

Self-Assembled Artificial Nanocilia Actuators.

Self-assembly of nanoparticles (NPs) is a powerful route to constructing higher-order structures. However, the programmed self-assembly of NPs into non-close-packed, 3D, shape-morphing nanocilia arrays remains elusive, whereas dynamically actuated nanometer cilia are universal in living systems. Here, a programmable self-assembly strategy is presented that can direct magnetic NPs into a highly ordered responsive artificial nanocilia actuator with exquisite nanometer 3D structural arrangements. The self-assembled artificial NP cilia can maintain their structural integrity through the interplay of interparticle interactions. Interestingly, the nanocilia can exhibit a field-responsive actuation motion through "rolling and sliding" between assembled NPs rather than bending the entire ciliary beam. It is demonstrated that oleic acid coated over the NPs acts as a lubricating bearing and enables the rolling/sliding-based actuation of the cilia.

SUITOR: Selecting the number of mutational signatures through cross-validation.

For de novo mutational signature analysis, the critical first step is to decide how many signatures should be expected in a cancer genomics study. An incorrect number could mislead downstream analyses. Here we present SUITOR (Selecting the nUmber of mutatIonal signaTures thrOugh cRoss-validation), an unsupervised cross-validation method that requires little assumptions and no numerical approximations to select the optimal number of signatures without overfitting the data. In vitro studies and in silico simulations demonstrated that SUITOR can correctly identify signatures, some of which were missed by other widely used methods. Applied to 2,540 whole-genome sequenced tumors across 22 cancer types, SUITOR selected signatures with the smallest prediction errors and almost all signatures of breast cancer selected by SUITOR were validated in an independent breast cancer study. SUITOR is a powerful tool to select the optimal number of mutational signatures, facilitating downstream analyses with etiological or therapeutic importance.

Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients.

Recent genomic studies suggest that Asian breast cancer (BC) may have distinct somatic features; however, most comparisons of BC genomic features across populations did not account for differences in age, subtype, and sequencing methods. In this study, we analyzed whole-exome sequencing (WES) data to characterize somatic copy number alterations (SCNAs) and mutation profiles in 98 Hong Kong BC (HKBC) patients and compared with those from The Cancer Genome Atlas of European ancestry (TCGA-EA, N = 686), which had similar distributions of age at diagnosis and PAM50 subtypes as in HKBC. We developed a two-sample Poisson model to compare driver gene selection pressure, which reflects the effect sizes of cancer driver genes, while accounting for differences in sample size, sequencing platforms, depths, and mutation calling methods. We found that somatic mutation and SCNA profiles were overall very similar between HKBC and TCGA-EA. The selection pressure for small insertions and deletions (indels) in GATA3 (false discovery rate (FDR) corrected p < 0.01) and single-nucleotide variants (SNVs) in TP53 (nominal p = 0.02, FDR corrected p = 0.28) was lower in HKBC than in TCGA-EA. Among the 13 signatures of single-base substitutions (SBS) that are common in BC, we found a suggestively higher contribution of SBS18 and a lower contribution of SBS1 in HKBC than in TCGA-EA, while the two APOBEC-induced signatures showed similar prevalence. Our results suggest that the genomic landscape of BC was largely very similar between HKBC and TCGA-EA, despite suggestive differences in some driver genes and mutational signatures that warrant future investigations in large and diverse Asian populations.

Plasma Membrane Localized GCaMP-MS4A12 by Orai1 Co-Expression Shows Thapsigargin- and Ca2+-Dependent Fluorescence Increases.

Uniquely expressed in the colon, MS4A12 exhibits store-operated Ca2+ entry (SOCE) activity. However, compared to MS4A1 (CD20), a Ca2+ channel and ideal target for successful leukaemia immunotherapy, MS4A12 has rarely been studied. In this study, we investigated the involvement of MS4A12 in Ca2+ influx and expression changes in MS4A12 in human colonic malignancy. Fluorescence of GCaMP-fused MS4A12 (GCaMP-M12) was evaluated to analyse MS4A12 activity in Ca2+ influx. Plasma membrane expression of GCaMP-M12 was achieved by homo- or hetero-complex formation with no-tagged MS4A12 (nt-M12) or Orai1, respectively. GCaMP-M12 fluorescence in plasma membrane increased only after thapsigargin-induced depletion of endoplasmic reticulum Ca2+ stores, and this fluorescence was inhibited by typical SOCE inhibitors and siRNA for Orai1. Furthermore, GCaMP-MS4A12 and Orai1 co-transfection elicited greater plasma membrane fluorescence than GCaMP-M12 co-transfected with nt-M12. Interestingly, the fluorescence of GCaMP-M12 was decreased by STIM1 over-expression, while increased by siRNA for STIM1 in the presence of thapsigargin and extracellular Ca2+. Moreover, immunoprecipitation assay revealed that Orai1 co-expression decreased protein interactions between MS4A12 and STIM1. In human colon tissue, MS4A12 was expressed in the apical region of the colonic epithelium, although its expression was dramatically decreased in colon cancer tissues. In conclusion, we propose that MS4A12 contributes to SOCE through complex formation with Orai1, but does not cooperate with STIM1. Additionally, we discovered that MS4A12 is expressed in the apical membrane of the colonic epithelium and that its expression is decreased with cancer progression.

Targeted Deep Sequencing of Bladder Tumors Reveals Novel Associations between Cancer Gene Mutations and Mutational Signatures with Major Risk Factors.

PURPOSE: Exome- and whole-genome sequencing of muscle-invasive bladder cancer has revealed important insights into the molecular landscape; however, there are few studies of non-muscle-invasive bladder cancer with detailed risk factor information. EXPERIMENTAL DESIGN: We examined the relationship between smoking and other bladder cancer risk factors and somatic mutations and mutational signatures in bladder tumors. Targeted sequencing of frequently mutated genes in bladder cancer was conducted in 322 formalin-fixed paraffin-embedded bladder tumors from a population-based case-control study. Logistic regression was used to calculate odds ratios (OR) and 95% confidence intervals (CI), evaluating mutations and risk factors. We used SignatureEstimation to extract four known single base substitution mutational signatures and Poisson regression to calculate risk ratios (RR) and 95% CIs, evaluating signatures and risk factors. RESULTS: Non-silent KDM6A mutations were more common in females than males (OR = 1.83; 95% CI, 1.05-3.19). There was striking heterogeneity in the relationship between smoking status and established single base substitution signatures: current smoking status was associated with greater ERCC2-Signature mutations compared with former (P = 0.024) and never smoking (RR = 1.40; 95% CI, 1.09-1.80; P = 0.008), former smoking was associated with greater APOBEC-Signature13 mutations (P = 0.05), and never smoking was associated with greater APOBEC-Signature2 mutations (RR = 1.54; 95% CI, 1.17-2.01; P = 0.002). There was evidence that smoking duration (the component most strongly associated with bladder cancer risk) was associated with ERCC2-Signature mutations and APOBEC-Signature13 mutations among current (P trend = 0.005) and former smokers (P = 0.0004), respectively. CONCLUSIONS: These data quantify the contribution of bladder cancer risk factors to mutational burden and suggest different signature enrichments among never, former, and current smokers.

A semiparametric kernel independence test with application to mutational signatures.

Cancers arise owing to somatic mutations, and the characteristic combinations of somatic mutations form mutational signatures. Despite many mutational signatures being identified, mutational processes underlying a number of mutational signatures remain unknown, which hinders the identification of interventions that may reduce somatic mutation burdens and prevent the development of cancer. We demonstrate that the unknown cause of a mutational signature can be inferred by the associated signatures with known etiology. However, existing association tests are not statistically powerful due to excess zeros in mutational signatures data. To address this limitation, we propose a semiparametric kernel independence test (SKIT). The SKIT statistic is defined as the integrated squared distance between mixed probability distributions and is decomposed into four disjoint components to pinpoint the source of dependency. We derive the asymptotic null distribution and prove the asymptotic convergence of power. Due to slow convergence to the asymptotic null distribution, a bootstrap method is employed to compute p-values. Simulation studies demonstrate that when zeros are prevalent, SKIT is more resilient to power loss than existing tests and robust to random errors. We applied SKIT to The Cancer Genome Atlas (TCGA) mutational signatures data for over 9,000 tumors across 32 cancer types, and identified a novel association between signature 17 curated in the Catalogue Of Somatic Mutations In Cancer (COSMIC) and apolipoprotein B mRNA editing enzyme (APOBEC) signatures in gastrointestinal cancers. It indicates that APOBEC activity is likely associated with the unknown cause of signature 17.

Integrative molecular characterisation of gallbladder cancer reveals micro-environment-associated subtypes.

BACKGROUND & AIMS: Gallbladder cancer (GBC) is the most common type of biliary tract cancer, but the molecular mechanisms involved in gallbladder carcinogenesis remain poorly understood. In this study, we applied integrative genomics approaches to characterise GBC and explore molecular subtypes associated with patient survival. METHODS: We profiled the mutational landscape of GBC tumours (whole-exome sequencing on 92, targeted sequencing on 98, in total 190 patients). In a subset (n = 45), we interrogated the matched transcriptomes, DNA methylomes, and somatic copy number alterations. We explored molecular subtypes identified through clustering tumours by genes whose expression was associated with survival in 47 tumours and validated subtypes on 34 publicly available GBC cases. RESULTS: Exome analysis revealed TP53 was the most mutated gene. The overall mutation rate was low (median 0.82 Mut/Mb). APOBEC-mediated mutational signatures were more common in tumours with higher mutational burden. Aflatoxin-related signatures tended to be highly clonal (present in ≥50% of cancer cells). Transcriptome-wide survival association analysis revealed a 95-gene signature that stratified all GBC patients into 3 subtypes that suggested an association with overall survival post-resection. The 2 poor-survival subtypes were associated with adverse clinicopathologic features (advanced stage, pN1, pM1), immunosuppressive micro-environments (myeloid-derived suppressor cell accumulation, extensive desmoplasia, hypoxia) and T cell dysfunction, whereas the good-survival subtype showed the opposite features. CONCLUSION: These data suggest that the tumour micro-environment and immune profiles could play an important role in gallbladder carcinogenesis and should be evaluated in future clinical studies, along with mutational profiles. LAY SUMMARY: Gallbladder cancer is highly fatal, and its causes are poorly understood. We evaluated gallbladder tumours to see if there were differences between tumours in genetic information such as DNA and RNA. We found evidence of aflatoxin exposure in these tumours, and immune cells surrounding the tumours were associated with survival.

Efficacy of Acupuncture Treatment to Prevent Cerebral Vasospasm After Subarachnoid Hemorrhage: A Double-Blind, Randomized Placebo-Controlled Trial.

Objectives: To investigate the efficacy of acupuncture in preventing cerebral vasospasm following aneurysmal subarachnoid hemorrhage (SAH) and explore its underlying mechanism. Design: A randomized, double-blinded, and placebo-controlled trial. Setting/Location: Subjects were recruited from Kyung Hee University Hospital at Gangdong, Seoul, Korea Subjects: A total of 50 patients admitted with acute SAH. Interventions: The study group received acupuncture treatments (n = 25), while the control group underwent mock transcutaneous electrical nerve stimulation and sham acupuncture (n = 25) six times/week for 2 weeks. Outcome measures: The primary outcome was the incidence of delayed ischemic neurologic deficit (DIND), and secondary measurements included angiographic vasospasm, vasospasm-related infarction, modified Rankin Scale score, and plasma nitric oxide (NO) and endothelin-1 (ET-1) levels. Results: The study group treated with acupuncture showed a lower incidence of DIND (9.1%) than the control group (20.8%); however, this difference in the incidence of DIND was not statistically significant. The study group demonstrated better clinical outcomes, especially in functional recovery. Significant alterations in plasma NO and ET-1 levels after the 2-week intervention were observed only in the study group. Conclusions: Their study shows that acupuncture treatment improved functional recovery after SAH and could potentially prevent cerebral vasospasm. These effects could be attributed to the recovery of endothelial dysfunction by acupuncture through modulating the plasma NO and ET-1 levels. The study protocol has been registered on www.clinicaltrials.gov (NCT02275949).

Evaluation of a Novel Trocar-Site Closure Device in Laparoscopic Surgery.

BACKGROUND AND OBJECTIVES: We evaluated the effectiveness and safety of EZ-CloseTM compared to those of hand suture for trocar-site closure according to obesity. METHODS: Fifty-four cases of laparoscopic colorectal surgery were enrolled. For the same patient, the right port site was closed using EZ-CloseTM and left port site was closed by hand suture among cases with port-site diameter ≥10 mm. Cases switched to use of a conventional fascial closure device or with closure time 120 s were considered failures. Closure time was analyzed according to body mass index (BMI) and abdominal wall thickness (AWT). RESULTS: The mean closure time was significantly shorter with EZ-CloseTM than with hand suture (87.9 ± 21.0 vs. 128.0 ± 59.0 s, p < 0.001). The number of failure cases was significantly lower with EZ-CloseTM than with hand suture (7 vs. 27, p < 0.001). The closure time of EZ-CloseTM was significantly shorter than that of hand suture in patients with BMI ≥ 25 and < 27 kg/m2 (n = 15, 85.9 ± 19.8 vs. 135.6 ± 67.9 s, p < 0.014) and ≥ 27 kg/m2 (n = 13, 85.1 ± 18.4 vs. 150.2 ± 70.6 s, p < 0.010). With respect to AWT, the closure time of EZ-CloseTM was significantly shorter than that of hand suture in patients with AWT ≥ 20 and < 26 mm (n = 12, 81.1 ± 11.5 vs. 142.3 ± 83.7 s, p = 0.023) and ≥ 26 mm (n = 17, 85.6 ± 22.6 vs. 160.2 ± 55.5, p < 0.001). No infection and herniation were detected in both trocar sites during the follow-up period (median 20.4 months). CONCLUSION: EZ-CloseTM could provide time efficiency in trocar-site closure, especially in obese patients.

Regulation of reactive oxygen species during plant immunity through phosphorylation and ubiquitination of RBOHD.

Production of reactive oxygen species (ROS) is critical for successful activation of immune responses against pathogen infection. The plant NADPH oxidase RBOHD is a primary player in ROS production during innate immunity. However, how RBOHD is negatively regulated remains elusive. Here we show that RBOHD is regulated by C-terminal phosphorylation and ubiquitination. Genetic and biochemical analyses reveal that the PBL13 receptor-like cytoplasmic kinase phosphorylates RBOHD's C-terminus and two phosphorylated residues (S862 and T912) affect RBOHD activity and stability, respectively. Using protein array technology, we identified an E3 ubiquitin ligase PIRE (PBL13 interacting RING domain E3 ligase) that interacts with both PBL13 and RBOHD. Mimicking phosphorylation of RBOHD (T912D) results in enhanced ubiquitination and decreased protein abundance. PIRE and PBL13 mutants display higher RBOHD protein accumulation, increased ROS production, and are more resistant to bacterial infection. Thus, our study reveals an intricate post-translational network that negatively regulates the abundance of a conserved NADPH oxidase.

Mutations in the HPV16 genome induced by APOBEC3 are associated with viral clearance.

HPV16 causes half of cervical cancers worldwide; for unknown reasons, most infections resolve within two years. Here, we analyze the viral genomes of 5,328 HPV16-positive case-control samples to investigate mutational signatures and the role of human APOBEC3-induced mutations in viral clearance and cervical carcinogenesis. We identify four de novo mutational signatures, one of which matches the COSMIC APOBEC-associated signature 2. The viral genomes of the precancer/cancer cases are less likely to contain within-host somatic HPV16 APOBEC3-induced mutations (Fisher's exact test, P = 6.2 x 10-14), and have a 30% lower nonsynonymous APOBEC3 mutation burden compared to controls. We replicate the low prevalence of HPV16 APOBEC3-induced mutations in 1,749 additional cases. APOBEC3 mutations also historically contribute to the evolution of HPV16 lineages. We demonstrate that cervical infections with a greater burden of somatic HPV16 APOBEC3-induced mutations are more likely to be benign or subsequently clear, suggesting they may reduce persistence, and thus progression, within the host.

A test of homogeneity of distributions when observations are subject to measurement errors.

When the observed data are contaminated with errors, the standard two-sample testing approaches that ignore measurement errors may produce misleading results, including a higher type-I error rate than the nominal level. To tackle this inconsistency, a nonparametric test is proposed for testing equality of two distributions when the observed contaminated data follow the classical additive measurement error model. The proposed test takes into account the presence of errors in the observed data, and the test statistic is defined in terms of the (deconvoluted) characteristic functions of the latent variables. Proposed method is applicable to a wide range of scenarios as no parametric restrictions are imposed either on the distribution of the underlying latent variables or on the distribution of the measurement errors. Asymptotic null distribution of the test statistic is derived, which is given by an integral of a squared Gaussian process with a complicated covariance structure. For data-based calibration of the test, a new nonparametric Bootstrap method is developed under the two-sample measurement error framework and its validity is established. Finite sample performance of the proposed test is investigated through simulation studies, and the results show superior performance of the proposed method than the standard tests that exhibit inconsistent behavior. Finally, the proposed method was applied to real data sets from the National Health and Nutrition Examination Survey. An R package MEtest is available through CRAN.

Micropipette Resonator Enabling Targeted Aspiration and Mass Measurement of Single Particles and Cells.

This paper reports micropipette resonators, mechanical resonator-integrated micropipettes, which enable selective aspiration and mass measurement of particles or cells suspended in liquids with two orthogonal vibration modes. A custom pipette pulling system is built to provide power-modulated linear heating on a rotating glass capillary to make an asymmetric cross section with extended uniformity.A glass capillary is stretched with the custom puller, cut within the pulled region, polished, mounted on a machined metallic jig, and then coated with a metal. As a result, a doubly clamped tube resonator-integrated micropipette is made. For simultaneous frequency readouts of two orthogonal modes, an optical pickup, originally developed for optical data storage, is configured closely above and properly aligned to the micropipette resonator and two digital phase-locked loops are employed. For mass responsivity calibration, frequency shifts of the micropipette resonator are measured with various liquids and glass microparticles. Buoyant masses of unicellular organisms, Paramecium aurelia, freely swimming in a culture dish are successfully measured with two orthogonal modes.

The MAP4 Kinase SIK1 Ensures Robust Extracellular ROS Burst and Antibacterial Immunity in Plants.

Microbial patterns are recognized by cell-surface receptors to initiate pattern-triggered immunity (PTI) in plants. Receptor-like cytoplasmic kinases (RLCKs), such as BIK1, and calcium-dependent protein kinases (CPKs) are engaged during PTI to activate the NADPH oxidase RBOHD for reactive oxygen species (ROS) production. It is unknown whether protein kinases besides CPKs and RLCKs participate in RBOHD regulation. We screened mutants in all ten Arabidopsis MAP4 kinases (MAP4Ks) and identified the conserved MAP4K SIK1 as a positive regulator of PTI. sik1 mutants were compromised in their ability to elicit the ROS burst in response to microbial features and exhibited compromised PTI to bacterial infection. SIK1 directly interacts with, phosphorylates, and stabilizes BIK1 in a kinase activity-dependent manner. Furthermore, SIK1 directly interacts with and phosphorylates RBOHD upon flagellin perception. Thus, SIK1 positively regulates immunity by stabilizing BIK1 and activating RBOHD to promote the extracellular ROS burst.