Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini

Translation initiation generally occurs at AUG codons in eukaryotes, although it has been shown that non-AUG or non-canonical translation initiation can also occur. However, the evidence for noncanonical translation initiation sites (TISs) is largely indirect and based on ribosome profiling (Ribo-seq) studies. Here, using a strategy specifically designed to enrich N termini of proteins, we demonstrate that many human proteins are translated at noncanonical TISs. The large majority of TISs that mapped to 5' untranslated regions were noncanonical and led to N-terminal extension of annotated proteins or translation of upstream small open reading frames (uORF). It has been controversial whether the amino acid corresponding to the start codon is incorporated at the TIS or methionine is still incorporated. We found that methionine was incorporated at almost all noncanonical TISs identified in this study. Comparison of the TISs determined through mass spectrometry with ribosome profiling data revealed that about two-thirds of the novel annotations were indeed supported by the available ribosome profiling data. Sequence conservation across species and a higher abundance of noncanonical TISs than canonical ones in some cases suggests that the noncanonical TISs can have biological functions. Overall, this study provides evidence of protein translation initiation at noncanonical TISs and argues that further studies are required for elucidation of functional implications of such noncanonical translation initiation

Identification of novel transcripts and peptides in developing murine lens.

We previously investigated the transcriptome and proteome profiles of the murine ocular lens at six developmental time points including two embryonic (E15 and E18) and four postnatal time points (P0, P3, P6, and P9). Here, we extend our analyses to identify novel transcripts and peptides in developing  mouse lens. We identified a total of 9,707 novel transcripts and 325 novel fusion genes in developing mouse lens. Additionally, we identified 13,281 novel alternative splicing (AS) events in mouse lens including 6,990 exon skipping (ES), 2,447 alternative 3' splice site (A3SS), 1,900 alternative 5' splice site (A5SS), 1,771 mutually exclusive exons (MXE), and 173 intron retention (IR). Finally, we integrated our OMIC (Transcriptome and Proteome) datasets identifying 20 novel peptides in mouse lens. All 20 peptides were validated through matching MS/MS spectra of synthetic peptides. To the best of our knowledge, this is the first report integrating OMIC datasets to identify novel peptides in developing murine lens

Phosphotyrosine profiling of human cerebrospinal fluid

Additional file 3: Figure S1. A relative abundance of the tyrosine phosphorylated peptides in the CSF samples

Plasmodium sporozoite phospholipid scramblase interacts with mammalian carbamoyl-phosphate synthetase 1 to infect hepatocytes

After inoculation by the bite of an infected mosquito, Plasmodium sporozoites enter the blood stream and infect the liver, where each infected cell produces thousands of merozoites. These in turn, infect red blood cells and cause malaria symptoms. To initiate a productive infection, sporozoites must exit the circulation by traversing the blood lining of the liver vessels after which they infect hepatocytes with unique specificity. We screened a phage display library for peptides that structurally mimic (mimotope) a sporozoite ligand for hepatocyte recognition. We identified HP1 (hepatocyte-binding peptide 1) that mimics a ~50 kDa sporozoite ligand (identified as phospholipid scramblase). Further, we show that HP1 interacts with a ~160 kDa hepatocyte membrane putative receptor (identified as carbamoyl-phosphate synthetase 1). Importantly, immunization of mice with the HP1 peptide partially protects them from infection by the rodent parasite P. berghei. Moreover, an antibody to the HP1 mimotope inhibits human parasite P. falciparum infection of human hepatocytes in culture. The sporozoite ligand for hepatocyte invasion is a potential novel pre-erythrocytic vaccine candidate. © 2021, The Author(s).1

Effects of Murine Dermal Cells on the Regulation of Hair Growth Is Dependent on the Cell Number and Post-Natal Age of Newborn Mice

Dermal cells from neonatal mice can initiate the formation of hair follicles (HFs) when combined with adult mouse epidermal cells and transplanted subcutaneously into athymic mice. In the present study, the effects of dermal cells on HF formation were tested in terms of total cell number and the time course of cell harvest. Results demonstrated that the number of dermal cells is critical to the formation of HF. Furthermore, hair forming ability is rapidly decreasing as the neonatal mice age. To examine potential differences in gene expression, cDNA array was performed. Results demonstrate that numerous molecules which are directly involved in receptor and signaling correlated with decreased hair inductivity in early time points after delivery. It is reported that bone morphogenic protein (BMP)-6 and Wnt3a treatment increased hair inductivity of dermal papilla cells. But in our study, no changes were observed in the expression levels of BMP-6 and Wnt3a. However, several Wnt related genes demonstrate increased or decreased expression levels. Thus, our results suggest that co-ordinated regulation of these molecules will be important in hair neogenesis within our model system

Design and performance of closed cycle sample cooling stage for angle resolved photoemission spectroscopy capable of reaching temperatures below 2 K

We have designed, constructed, and tested a unique cold finger suitable for angle resolved photoemission spectroscopy. This design is based on in situ helium reliquification and utilizes pulse tube cryocooler. The pulse tube can be removed for baking without breaking Ultra High Vacuum (UHV). This design also allows the use of non-UHV heater that can be replaced without the need to vent the system. The cold finger has minimal vibration, operates over a temperature range of 1.7 K–400 K, and has no measurable residual magnetization. In continuous mode, it can maintain a sample temperature of 2.6 K, while in single shot mode (by pumping on liquid helium), it can reach temperatures down to 1.8 K for a period of several hours

In-rich InGaN/GaN quantum wells grown by metal-organic chemical vapor deposition

Growth mechanism of In-rich InGaN/GaN quantum wells (QWs) was investigated. First, we examined the initial stage of InN growth on GaN template considering strain-relieving mechanisms such as defect generation, islanding, and alloy formation at 730 degrees C. It was found that, instead of formation of InN layer, defective In-rich InGaN layer with thickness fluctuations was formed to relieve large lattice mismatch over 10% between InN and GaN. By introducing growth interruption (GI) before GaN capping at the same temperature, however, atomically flat InGaN/GaN interfaces were observed, and the quality of In-rich InGaN layer was greatly improved. We found that decomposition and mass transport processes during GI in InGaN layer are responsible for this phenomenon. There exists severe decomposition in InGaN layer during GI, and a 1-nm-thick InGaN layer remained after GI due to stronger bond strength near the InGaN/GaN interface. It was observed that the mass transport processes actively occurred during GI in InGaN layer above 730 degrees C so that defect annihilation in InGaN layer was greatly enhanced. Finally, based on these experimental results, we propose the growth mechanism of In-rich InGaN/GaN QWs using GI.open9