Switchable stiffness scanning microscope probe

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2005.Includes bibliographical references (p. 77-80).Atomic Force Microscopy (AFM) has rapidly gained widespread utilization as an imaging device and micro/nano-manipulator during recent years. This thesis investigates the new concept of a dual stiffness scanning probe with respect to biological applications and determines the resulting requirements for the scanning of soft bio samples, such as low-pressure contact. On this basis, an in-plane AFM probe that is specifically tailored to the needs of biological applications is developed. It features a variable stiffness, which makes the stiffness of the probe adjustable to the surface hardness of the sample, and a very low overall stiffness, which is needed in order to achieve high resolution imaging. The switchable stiffness probe allows the scanning of biological samples with varying surface hardness without changing probes during scanning, and therefore prevents a loss of positional information, as is unavoidable with conventional devices. For the integration of the components into a MEMS device, the conventional cantilever-type design of AFM probes has been abandoned in favor of an in-plane design. The new design has an advantage in that it facilitates a high-density array of AFM probes and allows for easy surface micromachining of the integrated device. It also enables the future integration of micro-fluidic channels for reagent delivery and nanopipetting. For the scanning of nano-scale trenches and grooves, a multi-walled carbon nanotube, embedded in a nanopellet, is planned as a high-aspect-ratio tip. The variable stiffness is accomplished in a mechanical way by engaging or disengaging auxiliary beams to the compliant beam structure by means of electrostatically actuated clutches.(cont.) For actuation, an electrostatic combdrive is considered to move the probe tip up and down. The vertical displacement of the tip can be measured by a capacitive sensor, which can easily be integrated into the system. A scaled-up proof-of-concept model is manufactured with surface-micromachining processes. The clutch performance is successfully tested and the dual stiffness concept is verified by measuring the stiffness of the device with the clutches engaged and disengaged.by Clemens T. Mueller-Falcke.S.M

CCAAT/Enhancer-Binding Protein Homologous (CHOP) Protein Promotes Carcinogenesis in the DEN-Induced Hepatocellular Carcinoma Model

Background and Aims C/EBP homologous protein (CHOP) plays pro-apoptotic roles in the integrated stress response. Recently, a tumor suppressive role for CHOP was demonstrated in lung cancer via regulation of tumor metabolism. To explore the role of CHOP in hepatocarcinogenesis, we induced hepatocellular carcinoma (HCC) in wild type (wt) and CHOP knockout (KO) mice using the carcinogen N-diethylnitrosamine (DEN). Results: Analysis of tumor development showed reduced tumor load, with markedly smaller tumor nodules in the CHOP KO animals, suggesting oncogenic roles of CHOP in carcinogen-induced HCC. In wt tumors, CHOP was exclusively expressed in tumor tissue, with minimal expression in normal parenchyma. Analysis of human adenocarcinomas of various origins demonstrated scattered expression of CHOP in the tumors, pointing to relevance in human pathology. Characterization of pathways that may contribute to preferential expression of CHOP in the tumor identified ATF6 as a potential candidate. ATF6, a key member of the endoplasmic reticulum stress signaling machinery, exhibited a similar pattern of expression as CHOP and strong activation in wt but not CHOP KO tumors. Because HCC is induced by chronic inflammation, we assessed whether CHOP deficiency affects tumor-immune system crosstalk. We found that the number of macrophages and levels of IFNγ and CCL4 mRNA were markedly reduced in tumors from CHOP KO relative to wt mice, suggesting a role for CHOP in modulating tumor microenvironment and macrophage recruitment to the tumor. Conclusion: Our data highlights a role for CHOP as a positive regulator of carcinogen-induced HCC progression through a complex mechanism that involves the immune system and modulation of stress signaling pathways

Severe portal and systemic acidosis during CO2-laparoscopy compared to helium or gasless laparoscopy and laparotomy in a rodent model: an experimental study

Background and aims: This experimental study assesses the influence of different gases and insufflation pressures on the portal, central-venous and peripheral-arterial pH during experimental laparoscopy. Methods: Firstly, 36 male WAG/Rij rats were randomized into six groups (n = 6) spontaneously breathing during anaesthesia: laparoscopy using carbon dioxide or helium at 6 and 12 mmHg, gasless laparoscopy and laparotomy. 45 and 90 min after setup, blood was sampled from the portal vein, vena cava and the common femoral artery with immediate blood gas analysis. Secondly, 12 animals were mechanically ventilated at physiological arterial pH during 90 min of laparotomy (n = 6) or carbon dioxide laparoscopy at 12 mmHg (n = 6) with respective blood gas analyses. Results: Over time, in spontaneously breathing rats, carbon dioxide laparoscopy caused significant insufflation pressure-dependent portal acidosis (pH at 6 mmHg, 6.99 [6.95-7.04] at 45 min and 6.95 [6.94-6.96] at 90 min, pH at 12 mmHg, 6.89 [6.82-6.90] at 45 min and 6.84 [6.81-6.87] at 90 min; p 0.05). Central-venous and peripheral-arterial acidosis was significant but less severely reduced during carbon dioxide laparoscopy. Laparotomy, helium laparoscopy and gasless laparoscopy showed no comparable acidosis in all vessels. Portal and central-venous acidosis during carbon dioxide laparoscopy at 12 mmHg was not reversible by mechanical hyperventilation maintaining a physiological arterial pH (pH portal 6.85 [6.84-6.90] (p = 0.004), central-venous 6.93 [6.90-6.99] (p = 0.004), peripheral-arterial 7.29 [7.29-7.31] (p = 0.220) at 90 min; Wilcoxon-Mann-Whitney test). Conclusion: Carbon dioxide laparoscopy led to insufflation pressure-dependent severe portal and less severe central-venous acidosis not reversible by mechanical hyperventilation. Keywords: Acidosis; Blood gases; Insufflation gas; Insufflation pressure; Laparoscop

Estimating damages from price-fixing: the value of transaction data

We use a unique private data set of about 340,000 invoice positions from 36 smaller and larger customers of German cement producers to study the value of such transaction data for an estimation of cartel damages. In particular, we investigate, first, how structural break analysis can be used to identify the exact end of the cartel agreement and, second, how an application of before-and-after approaches to estimate the price overcharge can benefit from such rich data sets. We conclude that transaction data allows such a detailed assessment of the cartel and its impact on direct customers that its regular application in private antitrust cases is desired as long as data collection and preparation procedures are not prohibitively expensive

Spin-Imbalance in a One-Dimensional Fermi Gas

Superconductivity and magnetism generally do not coexist. Changing the relative number of up and down spin electrons disrupts the basic mechanism of superconductivity, where atoms of opposite momentum and spin form Cooper pairs. Nearly forty years ago Fulde and Ferrell and Larkin and Ovchinnikov proposed an exotic pairing mechanism (FFLO) where magnetism is accommodated by formation of pairs with finite momentum. Despite intense theoretical and experimental efforts, however, polarized superconductivity remains largely elusive. Here we report experimental measurements of density profiles of a two spin mixture of ultracold 6Li atoms trapped in an array of one dimensional (1D) tubes, a system analogous to electrons in 1D wires. At finite spin imbalance, the system phase separates with an inverted phase profile in comparison to the three-dimensional case. In 1D we find a partially polarized core surrounded by wings composed of either a completely paired BCS superfluid or a fully polarized Fermi gas, depending on the degree of polarization. Our observations are in quantitative agreement with theoretical calculations in which the partially polarized phase is found to be a 1D analogue of the FFLO state. This study demonstrates how ultracold atomic gases in 1D may be used to create non-trivial new phases of matter, and also paves the way for direct observation and further study of the FFLO phase.Comment: 30 pages, 7 figure

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics.

Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives

In-depth profiling of COVID-19 risk factors and preventive measures in healthcare workers

PURPOSE To determine risk factors for coronavirus disease 2019 (COVID-19) in healthcare workers (HCWs), characterize symptoms, and evaluate preventive measures against SARS-CoV-2 spread in hospitals. METHODS In a cross-sectional study conducted between May 27 and August 12, 2020, after the first wave of the COVID-19 pandemic, we obtained serological, epidemiological, occupational as well as COVID-19-related data at a~quaternary care, multicenter hospital~in Munich, Germany. RESULTS 7554 HCWs participated, 2.2% of whom tested positive for anti-SARS-CoV-2 antibodies. Multivariate analysis revealed increased COVID-19 risk for nurses (3.1% seropositivity, 95% CI 2.5-3.9%, p = 0.012), staff working on COVID-19 units (4.6% seropositivity, 95% CI 3.2-6.5%, p = 0.032), males (2.4% seropositivity, 95% CI 1.8-3.2%, p = 0.019), and HCWs reporting high-risk exposures to infected patients (5.5% seropositivity, 95% CI 4.0-7.5%, p = 0.0022) or outside of work (12.0% seropositivity, 95% CI 8.0-17.4%, p < 0.0001). Smoking was a protective factor (1.1% seropositivity, 95% CI 0.7-1.8% p = 0.00018) and the symptom taste disorder was strongly associated with COVID-19 (29.8% seropositivity, 95% CI 24.3-35.8%, p < 0.0001). An unbiased decision tree identified subgroups with different risk profiles. Working from home as a preventive measure did not protect against SARS-CoV-2 infection. A PCR-testing strategy focused on symptoms and high-risk exposures detected all larger COVID-19 outbreaks. CONCLUSION Awareness of the identified COVID-19 risk factors and successful surveillance strategies are key to protecting HCWs against SARS-CoV-2, especially in settings with limited vaccination capacities or reduced vaccine efficacy

Spatial Modes of Laser-Induced Mass Transfer in Micro-Gaps

We have observed the concentric deposition patterns of small molecules transferred by means of laser-induced forward transfer (LIFT). The patterns comprised different parts whose presence changed with the experimental constraints in a mode-like fashion. In experiments, we studied this previously unknown phenomenon and derived model assumptions for its emergence. We identified aerosol micro-flow and geometric confinement as the mechanism behind the mass transfer and the cause of the concentric patterns. We validated our model using a simulation

The structural basis of rubisco phase separation in the pyrenoid

Approximately one-third of global CO2 fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO2-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle

Association of toll-interacting protein gene polymorphisms with atopic dermatitis

BACKGROUND: Atopic dermatitis (AD) is a common inflammatory skin disorder, affecting up to 15% of children in industrialized countries. Toll-interacting protein (TOLLIP) is an inhibitory adaptor protein within the toll-like receptor (TLR) pathway, a part of the innate immune system that recognizes structurally conserved molecular patterns of microbial pathogens, leading to an inflammatory immune response. METHODS: In order to detect a possible role of TOLLIP variation in the pathogenesis of AD, we screened the entire coding sequence of the TOLLIP gene by SSCP in 50 AD patients. We identified an amino acid exchange in exon 6 (Ala222Ser) and a synonymous variation in exon 4 (Pro139Pro). Subsequently, these two variations and four additional non-coding polymorphisms (-526 C/G, two polymorphisms in intron 1 and one in the 3'UTR) were genotyped in 317 AD patients and 224 healthy controls. RESULTS: The -526G allele showed borderline association with AD in our cohort (p = 0.012; significance level after correction for multiple testing 0.0102). Haplotype analysis did not yield additional information. Evaluation of mRNA expression by quantitative real-time polymerase chain reaction in six probands with the CC and six with the GG genotype at the -526 C/G locus did not reveal significant differences between genotypes. CONCLUSION: Variation in the TOLLIP gene may play a role in the pathogenesis of AD. Yet, replication studies in other cohorts and populations are warranted to confirm these association results