β1A Integrin Is a Master Regulator of Invadosome Organization and Function

Use of patterned surfaces, reverse genetics, and time-controlled photoinactivation showed that β1 but not β3 integrins are required for invadosome formation, self-assembly, and stabilization into a ring structure. The activation state of β1 as well as its phosphorylation by protein kinase C on Ser785 control these process and link to the degradative function

MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets

Advances in proteomic technologies continue to substantially accelerate capability for generating experimental data on protein levels, states, and activities in biological samples. For example, studies on receptor tyrosine kinase signaling networks can now capture the phosphorylation state of hundreds to thousands of proteins across multiple conditions. However, little is known about the function of many of these protein modifications, or the enzymes responsible for modifying them. To address this challenge, we have developed an approach that enhances the power of clustering techniques to infer functional and regulatory meaning of protein states in cell signaling networks. We have created a new computational framework for applying clustering to biological data in order to overcome the typical dependence on specific a priori assumptions and expert knowledge concerning the technical aspects of clustering. Multiple clustering analysis methodology (‘MCAM’) employs an array of diverse data transformations, distance metrics, set sizes, and clustering algorithms, in a combinatorial fashion, to create a suite of clustering sets. These sets are then evaluated based on their ability to produce biological insights through statistical enrichment of metadata relating to knowledge concerning protein functions, kinase substrates, and sequence motifs. We applied MCAM to a set of dynamic phosphorylation measurements of the ERRB network to explore the relationships between algorithmic parameters and the biological meaning that could be inferred and report on interesting biological predictions. Further, we applied MCAM to multiple phosphoproteomic datasets for the ERBB network, which allowed us to compare independent and incomplete overlapping measurements of phosphorylation sites in the network. We report specific and global differences of the ERBB network stimulated with different ligands and with changes in HER2 expression. Overall, we offer MCAM as a broadly-applicable approach for analysis of proteomic data which may help increase the current understanding of molecular networks in a variety of biological problems.National Institutes of Health (U.S.) (NIH-U54-CA112967 )National Institutes of Health (U.S.) (NIH-R01-CA096504

Chemical methods for reusing of devasted permanent grassland

Doświadczenia przeprowadzono w latach 2003-2005. Oceniano różne dawki herbicydów zawierających w swoim składzie substancję aktywną glifosat. Herbicydy aplikowano wiosną, w dawkach 720, 1440 i 2160 g*ha-1 (s. a. glifosatu). Wyższa dawka glifosatu bardzo dobrze eliminowała następujące gatunki: Alopecurus pratensis, Arhenatherum elatius, Dactylis glomerata, Poa pratensis, Artemisia vulgaris, Cirsium arvense, Daucus carota, Galium molugo, Glechoma hederaceum, Plantago spp., Ranunculus arvensis, Urtica dioica, Veronica spp., Achillea millefolium, Arctium minus, Heracleum sphondylium, Taraxacum officinale. Natomiast Roundup 360 SL w dawce 6,0 l*ha-1 (Standard I) bardzo dobrze zwalczał zarówno gatunki jednoliścienne (trawy) jak również chwasty wieloletnie dwuliścienne.The experiment was carried out in 2003-2005. There was tested herbicides including glyphosate as a active substans. It was used on permanent grassland with high denisty of perennial weeds. The herbicides was applied in spring at dose 720, 1440 and 2160 g*ha-1 active substans (glyphosate). The glyphosate, at the high dose, efficiently controled Alopecurus pratensis, Arhenatherum elatius, Dactylis glomerata, Poa pratensis and broad leaves weeds annual and perennial (Artemisia vulgaris, Cirsium arvense, Daucus carota, Galium molugo, Glechoma hederaceum, Plantago spp., Ranunculus arvensis, Urtica dioica, Veronica spp., Achillea millefolium, Arctium minus, Heracleum sphondylium, Taraxacum officinale. Standard I herbicide Roundup 360 SL in the rate of 6,0 l*ha-1 eliminated grasses and majority broad-leaveds weeds

Comparison of Manual versus Automated SARS-CoV-2 Rapid Antigen Testing in Asymptomatic Individuals

The SARS-CoV-2 pandemic has infected more than 770 M people and killed more than 6.9 M persons worldwide. In the USA, as of August 2023, it has infected more than 103 M people while causing more than 1.1 M deaths. During a pandemic, it is necessary to rapidly identify those individuals infected with the virus so that disease transmission can be stopped. We examined the sensitivity of the Quidel Rapid Antigen test on the manual Sofia 2 platform and the Beckman-Coulter antigen test on the automated DxI-800 system for use in screening asymptomatic individuals at the University of Arizona from March through May 2021. A total of 378 asymptomatic subjects along with 176 validation sets of samples in 23 independent experiments were assessed in side-by-side antigen testing using both assays. Nasal swabs and saliva were used as viral sources. Manual testing (Quidel) was compared with automated testing (Beckman) methods for cost and efficiency. Limit dilution of viral antigen spiked samples was performed to determine sensitivity to antigen load by the tests. The results between the two tests were found to be concordant. Both tests were comparable in terms of detecting low numbers of positive subjects in the asymptomatic population. A concordance of 98% was observed between the two tests. Experiments also demonstrated that saliva specimens were an acceptable viral source and produced comparable results for each test. Overall, the two methods were interchangeable

Long-Term Biobanking of Intact Tissue from Lipoaspirate

Autologous fat grafting has now been extensively and successfully performed for more than two decades. Although most adipose grafts and adipose-derived MSC therapies are done with fresh tissue, cryopreservation of tissue allows for much greater flexibility of use. Over the course of five years, 194 cryopreserved adipose samples were thawed and then returned to the collecting physician for subsequent autologous applications. Samples were stored with a mean cryogenic storage time of 9.5 months, with some samples being stored as long as 44 months. The volumes of tissue stored varied from 12 cc to as large as 960 cc. Upon thawing, the volume of recovered whole adipose tissue averaged 67% of the original amount stored for all samples, while the samples that were stored for longer than one year averaged 71%. Recovery was not found to be a function of length of time in cryopreservation. No significant relationship was found between tissue recovery and patient age. While an average recovery of 67% of volume frozen indicates that the use of banked and thawed tissue requires a larger amount of sample to be taken from the patient initially, an experienced clinician easily accomplishes this requirement. As cryopreservation of adipose tissue becomes more commonplace, physicians will find it helpful to know the amount and quality of tissue that will be available after thawing procedures

Analysis of High-Throughput Processing Methods for Peripheral Blood Cell Isolation

12 month embargo; published online: 13 June 2022This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]