Matthew M. Parks's research while affiliated with Weill Cornell Medical College and other places

... Of note, enhanced ribosome biogenesis facilitates the transition of cells from an epithelial to a mesenchymal state, a process known as epithelial-mesenchymal transition (EMT). This EMT-associated ribosome biogenesis is accompanied by a pronounced increase in Rictor's localization in the endoplasmic reticulum (ER), indicating also a regulatory role of mTORC2 in ribosome biogenesis [87]. ...

... We are interested in understanding the evolution of rRNA genes due to the uneven distribution of crossing over, which evolves co-ordinately within but independently between species [25]. Here, we have undertaken the functional characterization of unusual ribosomal gene sequences from Oryza species that showed great diversity but are absent in the present genomic sequence. ...

... While both Etv2 and Sox17-Erg activated a generic endothelial gene program seen by Cdh5 expression or marker gene expression (Hpgd and Igfbp3), Etv2 directed the targeted fibroblasts to an immature endothelial fate seen by the activation and maintained expression levels of Vegfr3 (Fig. 5g). The expression of Vegfr3 was of particular note because it is normally expressed in developing coronary vessels and lymphatic vessels and its expression is shut off in properly matured adult coronary vessels [18][19][20] . Sox17-Erg, however, directly targeted a differentiated arterial fate as seen by the gradual decrease in Cdk1 expression and increase of Gja5, both of which mimic what has been observed in the development of pre-artery and arterial vessels 10,21,22 (Fig. 5g). ...

... Although in this case we cannot rule out that this is intraspecific variation and not a manifestation of HGT, these data demonstrate the power and importance of concerted evolution for the evolutionary dynamics of 16S rRNA. In fact, this variability at the 16S rRNA level has been described previously and its significance appears to be biologically relevant 53 ; but see 54 . In particular, transcriptional upregulation of a variant referred to as rssh 16S rRNA (referred to here as variant B) is associated with a general stress response, activation of starvation related gene pathways and increased antibiotic resistance 53 . ...

... Naturally, such methods are sensitive to the parametric specification. Parks, Raphael, and Lawrence [28] proposed to estimate the local FDR using a kernel density estimator based on the internal negative controls but did not provide theoretical justifications of their method. Other authors suggested heuristic approaches that use the internal negative controls to estimate the FDR [34,42]. ...

... The WGBS data was mapped to a reference genome modified to include a representative copy of the rDNA since the rDNA clusters present on chromosomes 13, 14, 15, 21 and 22 in humans are not included in the genome assembly 5,9 . The sequencing depth of these data (~14x), is sufficient to produce high resolution quantitation of DNA methylation when considering groups of genomic features, or mapping to a consensus for a multi-copy genomic element, such as the rDNA (Table S2). ...

... Differences in stem cell index were determined using the Wilcoxon test and Kruskal-Wallis test for glioma and nontumor tissue and for different clinical features (Parks, 2018). The tumor samples were divided into a high stem cell index group (high) and low stem cell index group (low) according to the median value. ...

... Interestingly, the spliceosome is one of the members of RNPs. Moreover, growing evidence strongly identi es an essential link between the EMT program and Ribonucleoprotein (RNP) biogenesis 32,33 , which leads to tumor cell migration, invasion, and eventual metastasis. Previous studies shows that high expression of DLAT is associated with metastasis in liver and colon cancer, predicting a poor prognosis 34,35 . ...

... Ribosomes were isolated from the E. coli strain MRE600, which does not produce RNase I due to a missense mutation in the rna gene 38 . Several hundred grams of log-phase cells were commercially produced and purchased. ...

... Table 2). This is substantially less frequent than what was observed in pre-translocation bacterial and human ribosomes (28,65). Importantly, spontaneous transitions of pre-translocation ribosomes in complex with tRNAs are fast and occur on the subsecond time scale (28,29,(66)(67)(68). ...