Review of: The inhibitor of cyclin-dependent kinase 4a/alternative reading frame (INK4a/ARF) locus encoded proteins p16INK4a and p19ARF repress cyclin D1 transcription through distinct cis elements

Commentary of the article: D’Amico M., Wu K., Fu M., Rao M., Albanese C., Russell R. G., Lian H., Bregman D., White M. A., Pestell R. G. Cancer Research 2004 Jun 15; 64(12): 4122–4130

Fixed point actions and on-shell tree-level Symanzik improvement

In this paper it is argued that the properties of the fixed point action of a renormalization group transformation can be used to implement the on-shell tree-level Symanzik improvement of lattice actions to any given order in the expansion in the lattice spacing, in a way which does not involve any perturbative calculations. In particular, a well-known technique for the lowest order improvement of SU(N) lattice gauge theories is revisited from the point of view of fixed point actions, which allows to shed light on some subtle points.Comment: 14 pages, LaTeX, 1 TeX figur

A combinatorial approach to gene expression analysis: DNA microarrays.

The microarray technology is based on analytical tools that parallelize the quantitative and qualitative analysis of nucleic acids, proteins and tissue sections one of its more recent evolutions-. By miniaturizing the size of the reaction and sensing area, microarrays allow to assess at the activity of thousands of genes in a given tissue or cell line at once in a rapid and quantitative way, and to carry out serial comparative tests in multiple samples. These tools, that stem from the innovations resulting from the technological improvements and knowledge arising from the genome sequencing projects, can be considered as a combinatorial technique that can rapidly provide significant information about complex cellular pathways and processes within one or few ‘‘mass scale’’ and comprehensive testing of a biological sample’s composition

Augmenting Large Language Models with Audio Generation Capabilities

Chatbots or conversational agent interfaces utilize large language models (LLMs) to provide text responses to user queries. However, such chatbots are not capable of receiving audio input and providing generated audio as a response. This disclosure describes techniques to augment a LLM with an interface to an audio generation model. The LLM is fine-tuned to train it to leverage an API to access the audio generation model when input queries request query response in audio form. The trained LLM performs reasoning tasks and generates prompts for the audio generation model. The user-provided audio input and the LLM-generated prompts are fed to the audio generation model which generates audio. The output audio is analyzed to determine attributes as textual description. The LLM can perform multiple rounds of reasoning, prompt generation, and calling the audio generation model based on previously generated audio and associated textual descriptions. The ultimate audio output as generated by the audio generation model is provided as a response to the user query

Interaction of rat liver glucocorticoid receptor with heparin.

When rat liver cytosol containing [3H]dexamethasone-glucocorticoid receptor complex is exposed to immobilized heparin (Sepharose-heparin; Seph-hep) the steroid receptor complex binds to the substituted Sepharose avidly [Kd = 3.5 (+/- 1.7) X 10(-10) M], and 80-90% of the receptor present is adsorbed to the solid phase after 40 min at 0 degree C. The binding is enhanced by Mn2+ (10 mM) and Mg2+, whereas Ca2+ and Sr2+ are ineffective. Sodium molybdate (10 mM) does not influence the reaction but enhances receptor stability. Moreover, binding of the receptor to Seph-hep is dependent on the ionic strength of the medium, because binding is totally reversed by 300 mM KCl. The bound [3H]dexamethasone-receptor complex can be recovered from Seph-hep with solutions (4 mg/mL) of heparin (95% release), dextran sulfate (88%), and chondroitin sulfate (63%); total calf liver RNA is less effective (9%), whereas dextran, D-glucosamine, N-acetyl-D-glucosamine, D-glucuronic acid, and sheared calf thymus DNA are totally ineffective (less than 3%). Both "native" and temperature "transformed" forms of the glucocorticoid receptor interact with immobilized heparin. These results strongly suggest that the receptor site that binds heparin is distinct from that binding DNA. An immediate application of this newly found ability of the glucocorticoid receptor to interact with heparin is the use of Seph-hep for affinity chromatography purification of the glucocorticoid receptor. A purification of 10-fold, with a recovery of 55-65%, can be achieved by using either 4 mg/mL heparin or 300 mM KCl to elute [3H]dexamethasone-receptor bound to the resin

Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells

<p>Abstract</p> <p>Background</p> <p>Microarray experiments enable simultaneous measurement of the expression levels of virtually all transcripts present in cells, thereby providing a ‘molecular picture’ of the cell state. On the other hand, the genomic responses to a pharmacological or hormonal stimulus are dynamic molecular processes, where time influences gene activity and expression. The potential use of the statistical analysis of microarray data in time series has not been fully exploited so far, due to the fact that only few methods are available which take into proper account temporal relationships between samples.</p> <p>Results</p> <p>We compared here four different methods to analyze data derived from a time course mRNA expression profiling experiment which consisted in the study of the effects of estrogen on hormone-responsive human breast cancer cells. Gene expression was monitored with the innovative Illumina BeadArray platform, which includes an average of 30-40 replicates for each probe sequence randomly distributed on the chip surface. We present and discuss the results obtained by applying to these datasets different statistical methods for serial gene expression analysis. The influence of the normalization algorithm applied on data and of different parameter or threshold choices for the selection of differentially expressed transcripts has also been evaluated. In most cases, the selection was found fairly robust with respect to changes in parameters and type of normalization. We then identified which genes showed an expression profile significantly affected by the hormonal treatment over time. The final list of differentially expressed genes underwent cluster analysis of functional type, to identify groups of genes with similar regulation dynamics.</p> <p>Conclusions</p> <p>Several methods for processing time series gene expression data are presented, including evaluation of benefits and drawbacks of the different methods applied. The resulting protocol for data analysis was applied to characterization of the gene expression changes induced by estrogen in human breast cancer ZR-75.1 cells over an entire cell cycle.</p

Identification of hypoxia-inducible factor 1 ancillary sequence and its function in vascular endothelial growth factor gene induction by hypoxia and nitric oxide.

Transcription of hypoxia-inducible genes is regulated by hypoxia response elements (HREs) located in either the promoter or enhancer regions. Analysis of these elements reveals the presence of one or more binding sites for hypoxia-inducible factor 1 (HIF-1). Hypoxia-inducible genes include vascular endothelial growth factor (VEGF), erythropoietin, and glycolytic enzyme genes. Site-directed mutational analysis of the VEGF gene promoter revealed that an HIF-1 binding site (HBS) and its downstream HIF-1 ancillary sequence (HAS) within the HRE are required as cis-elements for the transcriptional activation of VEGF by either hypoxia or nitric oxide (NO). The core sequences of the HBS and the HAS were determined as TACGTG and CAGGT, respectively. These elements form an imperfect inverted repeat, and the spacing between these motifs is crucial for activity of the promoter. Gel shift assays demonstrate that as yet unknown protein complexes constitutively bind to the HAS regardless of the presence of these stimuli in several cell lines, in contrast with hypoxia- or NO-induced activation of HIF-1 binding to the HBS. A common structure of the HRE, which consists of the HBS and the HAS, is seen among several hypoxia-inducible genes, suggesting the presence of a novel mechanism mediated by the HAS for the regulation of these genes

Identification of proteins associated with ligand-activated estrogen receptor alpha in human breast cancer cell nuclei by tandem affinity purification and nanoLC-MS/MS.

Estrogen receptor a (ER-a) is a key mediator of estrogen actions in breast cancer (BC) cells. Understanding the effects of ligand-activated ER-a in target cells requires identification of the molecular partners acting in concert with this nuclear receptor to transduce the hormonal signal. We applied tandem affinity purification (TAP), glycerol gradient centrifugation and MS analysis to isolate and identify proteins interacting with ligand-activated ER-a in MCF-7 cell nuclei. This led to the identification of 264 ER-associated proteins, whose functions highlight the hinge role of ER-a in the coordination of multiple hormone-regulated nuclear processes in BC cells