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Summary: The Hippo signaling pathway is an important regulator of organ growth and differentiation, and its deregulation contributes to the development of cancer. The activity of its downstream targets YAP/TAZ depends on adherens junctions. Plakophilin 4 (PKP4) is a cell-type specific adherens junction protein expressed in the proliferating cells of the epidermis. Here, we show that PKP4 diminishes proliferation as well as differentiation. Depletion of PKP4 increased proliferation but at the same time induced premature epidermal differentiation. PKP4 interacted with several Hippo pathway components, including the transcriptional co-activators YAP/TAZ, and promoted nuclear YAP localization and target gene expression. In differentiated keratinocytes, PKP4 recruited LATS and YAP to cell junctions where YAP is transcriptionally inactive. YAP depletion, on the other hand, reduced PKP4 levels and keratinocyte adhesion indicative of a feedback mechanism controlling adhesion, proliferation, and differentiation by balancing YAP functions.

Summary: Protein activities and interactions are determined by their subcellular localization. Elucidating the network of protein-protein interactions at a spatial resolution is essential for understanding the complexity of protein functions, their regulation, and cellular processes. Here, we present a protocol to determine the subcellular localization of protein interactions in non-transformed murine keratinocytes. We describe steps for nucleus/cytoplasm fractionation, immunoprecipitation from these fractions, and immunoblotting. We then detail binding quantification.For complete details on the use and execution of this protocol, please refer to Müller et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Summary: Plakophilin 3 (PKP3) is a component of desmosomes and is frequently overexpressed in cancer. Using keratinocytes either lacking or overexpressing PKP3, we identify a signaling axis from ERK to the retinoblastoma (RB) protein and the E2F1 transcription factor that is controlled by PKP3. RB and E2F1 are key components controlling G1/S transition in the cell cycle. We show that PKP3 stimulates the activity of ERK and its target RSK1. This inhibits expression of the transcription factor RUNX3, a positive regulator of the CDK inhibitor CDKN1A/p21, which is also downregulated by PKP3. Elevated CDKN1A prevents RB phosphorylation and E2F1 target gene expression, leading to delayed S phase entry and reduced proliferation in PKP3-depleted cells. Elevated PKP3 expression not only increases ERK activity but also captures phosphorylated RB (phospho-RB) in the cytoplasm to promote E2F1 activity and cell-cycle progression. These data identify a mechanism by which PKP3 promotes proliferation and acts as an oncogene.

Codon degeneracy of amino acid sequences permits an additional “mRNP code” layer underlying the genetic code that is related to RNA processing. In pre-mRNA splicing, splice site usage is determined by both intrinsic strength and sequence context providing RNA binding sites for splicing regulatory proteins. In this study, we systematically examined modification of splicing regulatory properties in the neighborhood of a GT site, i.e. potential splice site, without altering the encoded amino acids.We quantified the splicing regulatory properties of the neighborhood around a potential splice site by its Splice Site HEXplorer Weight (SSHW) based on the HEXplorer score algorithm. To systematically modify GT site neighborhoods, either minimizing or maximizing their SSHW, we designed the novel stochastic optimization algorithm ModCon that applies a genetic algorithm with stochastic crossover, insertion and random mutation elements supplemented by a heuristic sliding window approach.To assess the achievable range in SSHW in human splice donors without altering the encoded amino acids, we applied ModCon to a set of 1000 randomly selected Ensembl annotated human splice donor sites, achieving substantial and accurate changes in SSHW. Using ModCon optimization, we successfully switched splice donor usage in a splice site competition reporter containing coding sequences from FANCA, FANCB or BRCA2, while retaining their amino acid coding information.The ModCon algorithm and its R package implementation can assist in reporter design by either introducing novel splice sites, silencing accidental, undesired splice sites, and by generally modifying the entire mRNP code while maintaining the genetic code.

Samples from the secondary clarifier effluent of a waste water treatment plant (serving 98500 inhabitants) were analyzed to determine the microplastics (MP) emission.The samples were collected using a stainless steel centrifugal pump and filtered through a 10 μm stainless steel cartridge filter. Microplastics particles (MPPs) and microplastics fibers (MPFs) were recovered by chemical and physical sample purification. To remove natural organic matter, the samples were first subjected to oxidative treatment with H2O2 and NaClO. Inorganic materials were subsequently removed by density separation in ZnCl2 (ρ = 1.9 g/cm3) using a centrifuge. Special centrifuge tubes were developed for this purpose. Sample analysis was performed on a Si filter by Raman micro-spectroscopy. Particles with a diameter (dp) ≥ 10 μm were analyzed.The results were differentiated by dry and wet weather samples. On average, 5900 MPPs m−3 were identified in the effluent on wet weather days compared to 3000 MPPs m−3 on dry weather days. Most of the MPPs detected were in the 30 μm

Toxoplasma gondii is a parasite of significant public health importance. We attempted to detect T. gondii contamination and assess advantages and disadvantages of contamination indicators through surveilling soil, wildlife, cats (Felis catus), and cows (Bos taurus) on a farm in Tennessee, U.S. in 2016 and 2017. Twenty-two soil samples were collected from the farm and subjected to oocyst flotation, DNA extraction, and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) targeting 18S ribosomal RNA (18S rRNA) gene to detect and identify T. gondii. Three samples (13.6%) were positive for the parasite; however, T. gondii DNA was not consistently detected from repeated tests. Blood samples were collected from small mammals, cats, and mesopredators live-trapped on the farm, and serum from 30 of the farm's cows were obtained. Serological testing by the modified agglutination test (MAT; cutoff 1:50) found 2.5% (1/40) of small mammals, 52.9% (9/17) of raccoons (Procyon lotor), and 50% (1/2) of domestic cats were seropositive for T. gondii antibodies. No antibodies were found in 16 opossums (Didelphis virginiana), two skunks (Mephitis mephitis), and 30 cows. Small mammal tissue samples were subjected to PCR-RFLP detection. Four out of 29 (13.7%) tissue samples were positive for T. gondii; however, T. gondii DNA was not consistently detected during repeated PCR-RFLP testing. Our results indicate the ability to detect T. gondii varies greatly by contamination indicator. We found detection of soil oocysts to be challenging, and results suggest limited utility of the method performed. The ability to detect T. gondii in animals was highly variable among species. Our research emphasizes the importance of a holistic approach when surveilling for T. gondii to compensate for shortcomings of each contamination indicator. Future research should be conducted to further investigate the most effective T. gondii surveillance methods and species with increased sample sizes at other agricultural facilities.