Probabilistic modeling of ambient noise in single-cell omics data

Droplet-based single-cell omics, including single-cell RNA sequencing (scRNAseq), single cell CRISPR perturbations (e.g., CROP-seq) and single-cell protein and transcriptomic profiling (e.g., CITE-seq) hold great promise for comprehensive cell profiling and genetic screening at the single cell resolution, yet these technologies suffer from substantial noise, among which ambient signals present in the cell suspension may be the predominant source. Current efforts to address this issue are highly specific to a certain technology, while a universal model to describe the noise across these technologies may reveal this common source thereby improving the denoising accuracy. To this end, we explicitly examined these unexpected signals and observed a predictable pattern in multiple datasets across different technologies. Based on the finding, we developed single cell Ambient Remover (scAR) which uses probabilistic deep learning to deconvolute the observed signals into native and ambient composition. scAR provides an efficient and universal solution to count denoising for multiple types of single-cell omics data, including single cell CRISPR screens, CITE-seq and scRNAseq. It will facilitate the application of single-cell omics technologies.

Pathological Diagnosis and Genomic Characterization of ICP4 Gene of lnfectious Laryngotracheitis Virus (ILTV) Isolates in Clinically Infected Chicken in Tamil Nadu, India

Background: Infectious laryngotracheitis (ILT) is an economically important viral respiratory disease in poultry. Recently, re-emergence of Infectious laryngotracheitis virus (ILTV) has been reported in several countries including India. The current study aimed to evaluate the poultry flocks of Tamil Nadu with circulating GaHV-1 and to elucidate the origin of the virus involved in the outbreak. Methods: In this study, a molecular based survey on the overall occurrence of natural cases of Infectious laryngo-tracheitis in poultry flocks from Tamil Nadu, India were performed. Pathological findings in respiratory and secondary lymphoid organs like caecal tonsils and harderian gland was carried out. The PCR technique targeting Infected Cell Protein-4 (ICP4) gene along with molecular characterization was performed. Result: The overall prevalence rate in the outbreak was 42.86% with highest incidence in layer flocks (62.85%) than the broiler flocks (22.85%). The highest susceptible age groups were between 20-30 weeks old. Tracheal pathology revealed epithelial sloughing, syncytial cell formation, eosinophilic intranuclear inclusion bodies and heterophilic exudation microscopically. Partial genome sequencing and phylogenetic analysis of ICP4 gene revealed high genetic homology between field isolates and the virulent strains from Turkey, Germany, China and Brazil. In the present study, along with pathological findings, a rapid and sensitive PCR assay was used for detection of ILT virus specific ICP4 gene in commercial poultry farms in the region.

Yeast Protein as an Easily Accessible Food Source

In recent years, the awareness and willingness of consumers to consume healthy food has grown significantly. In order to meet these needs, scientists are looking for innovative methods of food production, which is a source of easily digestible protein with a balanced amino acid composition. Yeast protein biomass (single cell protein, SPC) is a bioavailable product which is obtained when primarily using as a culture medium inexpensive various waste substrates including agricultural and industrial wastes. With the growing population, yeast protein seems to be an attractive alternative to traditional protein sources such as plants and meat. Moreover, yeast protein biomass also contains trace minerals and vitamins including B-group. Thus, using yeast in the production of protein provides both valuable nutrients and enhances purification of wastes. In conclusion, nutritional yeast protein biomass may be the best option for human and animal nutrition with a low environmental footprint. The rapidly evolving SCP production technology and discoveries from the world of biotechnology can make a huge difference in the future for the key improvement of hunger problems and the possibility of improving world food security. On the market of growing demand for cheap and environmentally clean SPC protein with practically unlimited scale of production, it may soon become one of the ingredients of our food. The review article presents the possibilities of protein production by yeast groups with the use of various substrates as well as the safety of yeast protein used as food.

The catalytic activity of TCPTP is auto-regulated by its intrinsically disordered tail and activated by Integrin alpha-1

T-Cell Protein Tyrosine Phosphatase (TCPTP, PTPN2) is a non-receptor type protein tyrosine phosphatase that is ubiquitously expressed in human cells. TCPTP is a critical component of a variety of key signaling pathways that are directly associated with the formation of cancer and inflammation. Thus, understanding the molecular mechanism of TCPTP activation and regulation is essential for the development of TCPTP therapeutics. Under basal conditions, TCPTP is largely inactive, although how this is achieved is poorly understood. By combining biomolecular nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and chemical cross-linking coupled with mass spectrometry, we show that the C-terminal intrinsically disordered tail of TCPTP functions as an intramolecular autoinhibitory element that controls the TCPTP catalytic activity. Activation of TCPTP is achieved by cellular competition, i.e., the intrinsically disordered cytosolic tail of Integrin-α1 displaces the TCPTP autoinhibitory tail, allowing for the full activation of TCPTP. This work not only defines the mechanism by which TCPTP is regulated but also reveals that the intrinsically disordered tails of two of the most closely related PTPs (PTP1B and TCPTP) autoregulate the activity of their cognate PTPs via completely different mechanisms.

Co-production of amino acid-rich xylooligosaccharide and single-cell protein from paper mulberry by autohydrolysis and fermentation technologies

Background Autohydrolysis is an extensively investigated pretreatment method due to its environmental friendliness. During autohydrolysis, most xylan from hemicellulose can be converted into xylooligosaccharides (XOS), and cellulose in the autohydrolyzed residues can be transformed into glucose after enzymatic hydrolysis. Both of these are value-added biochemicals in the biorefining process. In this work, paper mulberry (PM), which contains abundant protein, was utilized as a raw material to coproduce XOS and single-cell protein (SCP) through autohydrolysis and fermentation technologies. Results The results showed that 8.3 g of XOS and 1.8 g of amino acids could be recovered in the autohydrolysate (based on 100 g raw material) after autohydrolysis (170 °C, 1 h). Moreover, 5.7 g of low-DP XOS along with 1.8 g of amino acids could be further obtained from the autohydrolysate after hydrolysis with endo-β-1-4-xylanase. In addition, 20.1 g of fermentable monosaccharides was recovered after hydrolyzing the autohydrolyzed PM with cellulase, which can be used to produce 4.8 g of SCP after fermentation with Candida utilis. Conclusion As a valuable application of PM, a novel process is proposed to coproduce amino acid-rich XOS and SCP through autohydrolysis. The carbohydrate of PM is effectively converted to high value-added products.

Angio-Associated Migratory Cell Protein (AAMP) Regulates the Hippo/YAP Pathway and Mitochondrial Functionality to Drive Osteosarcoma Metastasis

Background: Osteosarcoma (OS) is the prevalent form of primary bone cancer among adolescents, but the 5-year overall survival rate for patients with a metastatic or recurrent OS is under 20%. Angio-associated migratory cell protein (AAMP) is known to be a key regulator of cellular migration, yet its role in the context of OS metastasis has yet to be firmly established.Methods: Bioinformatics analyses were used to explore the association between AAMP and YAP expression and the prognosis of OS patients, and to evaluate differences in AAMP expression in patients with primary OS, recurrent OS, and pulmonary metastatic OS. Immunohistochemical (IHC) staining was additionally performed to compare AAMP levels in primary OS and pulmonary metastatic OS patient samples. Lentiviral transduction was further used to establish OS cell lines in which AAMP or YAP had been stably knocked down or overexpressed. OS cell migration and invasion were assessed using wound healing and Transwell assays. Proteins associated with the mitochondria, the epithelial-mesenchymal transition (EMT), YAP, and its target proteins were assessed in OS cell lines via Western blotting. OS cell lamellipodia were detected via phalloidin staining. Mitochondrial morphological characteristics were assessed via transmission electron microscopy following the knockdown of AAMP. An ATP kit was employed to measure ATP levels in OS cells in which AAMP had been knocked down. Animal model studies were used to confirm indices associated with OS cell lung metastasis following AAMP knockdown. Results: Patients with metastatic OS exhibit higher levels of AAMP expression that are correlated with poorer patient prognosis. Knocking down AAMP suppressed the migratory, invasive, and EMT activity of analyzed OS cell lines. AAMP was found to regulate CFL1 and thereby control OS cell protrusion. AAMP knockdown was further found to promote OS cell mitochondrial dysfunction and decreased intracellular ATP production, with these AAMP knockdown cells exhibiting impaired migratory and invasive activity as a consequence of YAP inhibition. Consistently, the knockdown of AAMP suppressed the in vivo metastasis of OS cells. Conclusions: Together, these data highlight a model wherein AAMP can promote OS cell migratory and invasive activity by regulating YAP and mitochondrial functionality. The AAMP/CFL1/YAP signaling pathway may thus represent a viable therapeutic target for efforts aimed at suppressing the metastatic progression of OS.

An ultra-sensitive and easy-to-use multiplexed single-cell proteomic analysis

Proteins analysis from an average cell population often overlooks the cellular heterogeneity of expressed effector molecules, and knowledge about the regulations of key biological processes may remain obscure. Therefore, the necessity of single-cell proteomics (SCP) technologies arises. Without microfluidic chip, expensive ultrasonic equipment, or reformed liquid chromatogram (LC) system, we established an Ultra-sensitive and Easy-to-use multiplexed Single-Cell Proteomic workflow (UE-SCP). Specifically, the flexible sorting system ensured outstanding cell activity, high accuracy, remarkable efficiency, and robustness during single-cell isolation. Multiplex isobaric labeling realized the high-throughput analysis in trapped ion mobility spectrometry coupled with quadrupole time-of-flight mass spectrometry (timsTOF MS). Using this pipeline, we achieved single-cell protein quantities to a depth of over 2,000 protein groups in two human cell lines, Hela and HEK-293T. A small batch experiment can identify and quantify more than 3200 protein groups in 32 single cells, while a large batch experiment can identify and quantify about 4000 protein groups in 96 single cells. All the 128 single cells from different cell lines could been unsupervised clustered based on their proteomes. After the integration of data quality control, data cleaning, and data analysis, we are confident that our UE-SCP platform will be easy-to-marketing popularization and will promote biological applications of single-cell proteomics.