Cdc42-dependent modulation of rigidity sensing and cell spreading in tumor repopulating cells

Recently, a robust mechanical method has been established to isolate a small subpopulation of highly tumorigenic tumor repopulating cells (TRCs) from parental melanoma cells. In order to characterize the molecular and mechanical properties of TRCs, we utilized the tension gauge tether (TGT) single-molecule platform and investigated force requirements during early cell spreading events. TRCs required the peak single molecular tension of around 40 pN through integrins for initial adhesion like the parental control cells, but unlike the control cells, they did not spread and formed very few mature focal adhesions (FAs). Single molecule resolution RNA quantification of three Rho GTPases showed that downregulation of Cdc42, but not Rac1, is responsible for the unusual biophysical features of TRCs and that a threshold level of Cdc42 transcripts per unit cell area is required to initiate cell spreading. Cdc42 overexpression rescued TRC spreading through FA formation and restored the sensitivity to tension cues such that TRCs, like parental control cells, increase cell spreading with increasing single-molecular tension cues. Our single molecule studies identified an unusual biophysical feature of suppressed spreading of TRCs that may enable us to distinguish TRC population from a pool of heterogeneous tumor cell population

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

AN ANALYSIS OF RGD CELL ADHESION MOTIF USING QUARTZ CRYSTAL MICROBALANCE TO UNDERSTAND THE LOADING RATE OF CELL LIGAND INTERACTION

It is now well accepted that mechanical environment partly defines the cellular behavior. The understanding of cell interactions with mechanical microenvironment is the most crucial step to control cell functions in disease and development. Living cells utilize cell surface receptors to interact with the ligands present in mechanical environments. Over the last few decades, several dominant techniques such as AFM, optical tweezers, magnetic tweezers, biomembranes force probes etc. have been extensively used to characterize the ligand-receptor interactions at the molecular level. These studies provided a plethora of information regarding molecular force loading and unloading features. However, these rupture forces have been shown to be strongly dependent on the rate of force application. Yet, it remains poorly understood what is the rate at which cells apply forces via ligand-receptor interactions that consequently defines rupture force relevant to living cells. Our goal is to create a bulk sensor that can detect the rate of cellular force application during early stages of cell adhesion and spreading. We hypothesize that using a quartz crystal microbalance (QCM), an ultra-sensitive piezoelectric device, can provide us with changes to the resonant frequency of the device due to the cellular probing (force application) of the QCM surface, and from the frequency shift we can isolate a mass change on the surface, calculate the coupling coefficient of the cells with their interaction with the substrate. A self-assembled monolayer (SAM) will be functionalized on top of the quartz crystal bonded with gold, the top component of which is the cyclo-RGD that interacts with the αv β3 integrins on cell membrane, henceforth we’ll study the ligand-receptor interaction. The loading rate was quantified through the experiment for variable cell numbers and loading rate and peak force generated on the surface due to ligand-receptor interaction was calculated. The loading rate found was the mean of all cells applying force cumulatively on the surface

A Defected Structure Shaped CPW-Fed Wideband Microstrip Antenna for Wireless Applications

A coplanar waveguide- (CPW-) fed compact wideband defected structure shaped microstrip antenna is proposed for wireless applications. Defected structure is produced by cutting the U shape antenna in the form of two-sided T shape. The proposed antenna consists of two-sided T shape strip as compared to usual monopole patch antenna for minimizing the height of the antenna. The large space around the radiator is fully utilized as the ground is on the same plane as of radiator. Microstrip line feed is used to excite the proposed antenna placed on an FR4 substrate (dielectric constant εr=4.4). The antenna is practically fabricated and simulated. Simulated results of the proposed antenna have been obtained by using Ansoft High-Frequency Structure Simulator (HFSS) software. These results are compared with measured results by using network analyzer. Measured result shows good agreement with the simulated results. It is observed that the proposed antenna shows a wideband from 2.96 GHz to 7.95 GHz with three bands at f1=3.23 GHz, f2=4.93 GHz, and f3=7.04 GHz

A CPW-Fed Structure Shaped Substrate Wideband Microstrip Antenna for Wireless Applications

Abstract A structure shaped substrate wideband microstrip patch antenna fed by coplanar waveguide (CPW) is proposed for wireless applications. Structure shaped substrate is produced by cutting the rectangle shape substrate in the form of a semicircular disc. The radiating patch of proposed antenna is taken in the form of U-shape. The ground plane is extended towards both sides of radiator for reducing the size of the antenna. The proposed antenna is simulated by Ansoft's High Frequency Structure Simulator (HFSS). A good agreement is observed between simulated and measured results. The prototype is taken with dimensions 24 mm × 24 mm ×1.6 mm that achieves wide bandwidth, constant group delay and good radiation patterns over the entire operating bandwidth from 3.4 to 9.4 GHz (6.0 GHz) with 93.7% impedance bandwidth at 6.4 GHz center frequency. Thus, the proposed antenna is applicable for C band applications

Reduced Cell–ECM Interactions in the EpiSC Colony Center Cause Heterogeneous Differentiation

Mechanoregulation of cell–extracellular matrix (ECM) interactions are crucial for dictating pluripotent stem cell differentiation. However, not all pluripotent cells respond homogeneously which results in heterogeneous cell populations. When cells, such as mouse epiblast stem cells (EpiSCs), are cultured in clusters, the heterogeneity effect during differentiation is even more pronounced. While past studies implicated variations in signaling pathways to be the root cause of heterogeneity, the biophysical aspects of differentiation have not been thoroughly considered. Here, we demonstrate that the heterogeneity of EpiSC differentiation arises from differences in the colony size and varying degrees of interactions between cells within the colonies and the ECM. Confocal imaging demonstrates that cells in the colony periphery established good contact with the surface while the cells in the colony center were separated by an average of 1–2 µm from the surface. Traction force measurements of the cells within the EpiSC colonies show that peripheral cells generate large tractions while the colony center cells do not. A finite element modeling of EpiSC colonies shows that tractions generated by the cells at the colony periphery lift off the colony center preventing the colony center from undergoing differentiation. Together, our results demonstrate a biophysical regulation of heterogeneous EpiSC colony differentiation

COL2A1 Is a Novel Biomarker of Melanoma Tumor Repopulating Cells

Soft 3D-fibrin-gel selected tumor repopulating cells (TRCs) from the B16F1 melanoma cell line exhibit extraordinary self-renewal and tumor-regeneration capabilities. However, their biomarkers and gene regulatory features remain largely unknown. Here, we utilized the next-generation sequencing-based RNA sequencing (RNA-seq) technique to discover novel biomarkers and active gene regulatory features of TRCs. Systems biology analysis of RNA-seq data identified differentially expressed gene clusters, including the cell adhesion cluster, which subsequently identified highly specific and novel biomarkers, such as Col2a1, Ncam1, F11r, and Negr1. We validated the expression of these genes by real-time qPCR. The expression level of Col2a1 was found to be relatively low in TRCs but twenty-fold higher compared to the parental control cell line, thus making the biomarker very specific for TRCs. We validated the COL2A1 protein by immunofluorescence microscopy, showing a higher expression of COL2A1 in TRCs compared to parental control cells. KEGG pathway analysis showed the JAK/STAT, hypoxia, and Akt signaling pathways to be active in TRCs. Besides, the aerobic glycolysis pathway was found to be very active, indicating a typical Warburg Effect on highly tumorigenic cells. Together, our study revealed highly specific biomarkers and active cell signaling pathways of melanoma TRCs that can potentially target and neutralize TRCs

Estimation of tuberculosis incidence at subnational level using three methods to monitor progress towards ending TB in India, 2015–2020

Objectives We verified subnational (state/union territory (UT)/district) claims of achievements in reducing tuberculosis (TB) incidence in 2020 compared with 2015, in India.Design A community-based survey, analysis of programme data and anti-TB drug sales and utilisation data.Setting National TB Elimination Program and private TB treatment settings in 73 districts that had filed a claim to the Central TB Division of India for progress towards TB-free status.Participants Each district was divided into survey units (SU) and one village/ward was randomly selected from each SU. All household members in the selected village were interviewed. Sputum from participants with a history of anti-TB therapy (ATT), those currently experiencing chest symptoms or on ATT were tested using Xpert/Rif/TrueNat. The survey continued until 30 Mycobacterium tuberculosis cases were identified in a district.Outcome measures We calculated a direct estimate of TB incidence based on incident cases identified in the survey. We calculated an under-reporting factor by matching these cases within the TB notification system. The TB notification adjusted for this factor was the estimate by the indirect method. We also calculated TB incidence from drug sale data in the private sector and drug utilisation data in the public sector. We compared the three estimates of TB incidence in 2020 with TB incidence in 2015.Results The estimated direct incidence ranged from 19 (Purba Medinipur, West Bengal) to 1457 (Jaintia Hills, Meghalaya) per 100 000 population. Indirect estimates of incidence ranged between 19 (Diu, Dadra and Nagar Haveli) and 788 (Dumka, Jharkhand) per 100 000 population. The incidence using drug sale data ranged from 19 per 100 000 population in Diu, Dadra and Nagar Haveli to 651 per 100 000 population in Centenary, Maharashtra.Conclusion TB incidence in 1 state, 2 UTs and 35 districts had declined by at least 20% since 2015. Two districts in India were declared TB free in 2020

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press