The Largest Subunit of Human TFIIIC Complex, TFIIIC220, a Lysine Acetyltransferase Targets Histone H3K18

TFIIIC is a multi-subunit complex required for tRNA transcription by RNA polymerase III. Human TFIIIC holo-complex possesses lysine acetyltransferase activity that aids in relieving chromatin-mediated repression for RNA polymerase III-mediated transcription and chromatin assembly. Here we have characterized the acetyltransferase activity of the largest and DNA-binding subunit of TFIIIC complex, TFIIIC220. Purified recombinant human TFIIIC220 acetylated core histones H3, H4 and H2A in vitro. Moreover, we have identified the putative catalytic domain of TFIIIC220 that efficiently acetylates core histones in vitro. Mutating critical residues of the putative acetyl-CoA binding 'P loop' drastically reduced the catalytic activity of the acetyltransferase domain. Further analysis showed that the knockdown of TFIIIC220 in mammalian cell lines dramatically reduces global H3K18 acetylation level, which was rescued by overexpression of the putative acetyltransferase domain of human TFIIIC220. Our findings indicated a possibility of a crucial role for TFIIIC220 in maintaining acetylation homeostasis in the cell.

Nanofibrous PAN-PDMS Films-Based High-Performance Triboelectric Artificial Whisker for Self-Powered Obstacle Detection

Avoiding collisions is a key necessity for any autonomous mobile robot, and obstacle mapping enables them to maneuver in an uncharted area. In this era of the Internet of Things, with the emerging need for a multitude of sensors, adopting self-powered technologies is more practically viable than batteries for powering the same. Herein, with the fabrication of a triboelectric artificial whisker (TAW), a self-powered obstacle detection is demonstrated via tactile perception. The mechanical contact with the obstacle gives rise to an electrical signal from the TAW owing to the embedded triboelectric sensor. In addition, the triboelectric nanogenerator (TENG) based on electrospun polyacrylonitrile (PAN) nanofibers and polydimethylsiloxane film, which facilitates this self-powered artificial sensation, generates an output voltage of 720 V and current density of 5 mA m-2 with 1.7 W m-2 of maximum power delivery from a force of 10 N. The electro-spinning aided enhancement in contact area of the PAN is responsible for the remarkable improvement in the performance of the TENG, 3.4 times enhancement in power density, when compared to the nonsurface-modified ones. In addition, the TENG is able to charge commercial capacitors up to appreciable values and demonstrates powering different electronic gadgets such as calculators and thermometers.

Scientific characterization methods for better utilization of cattle dung and urine: a concise review

Cattle are usually raised for food, manure, leather, therapeutic, and draught purposes. Biowastes from cattle, such as dung and urine, harbor a diverse group of crucial compounds, metabolites/chemicals, and microorganisms that may benefit humans for agriculture, nutrition, therapeutics, industrial, and other utility products. Several bioactive compounds have been identified in cattle dung and urine, which possess unique properties and may vary based on agro-climatic zones and feeding practices. Therefore, cattle dung and urine have great significance, and a balanced nutritional diet may be a key to improved quality of these products/by-products. This review primarily focuses on the scientific aspects of biochemical and microbial characterization of cattle biowastes. Various methods including genomics for analyzing cattle dung and gas chromatography-mass spectroscopy for cattle urine have been reviewed. The presented information might open doors for the further characterization of cattle resources for heterogeneous applications in the production of utility items and addressing research gaps. Methods for cattle's dung and urine characterization.

Anti-oxidative property of xylolipid produced by Lactococcus lactis LNH70 and its potential use as fruit juice preservative

In the present study, 20 lactic acid bacteria (LAB) were isolated from different fruit juices, milk, and milk products. Based on preliminary screening methods like emulsification index, oil displacement method, hemolysis, and reduction in surface tension, strain LNH70 was selected for further studies. Further, it was evaluated for preliminary probiotic characteristics, identified by 16 s rRNA sequencing as Lactococcus lactis, submitted to NCBI, and an accession number was obtained (MH174454). In addition, LNH70 was found to tolerate over wide range of temperatures (10-45 °C), pH (3-10), NaCl (up to 9%), bile (0.7%), and phenol (0.1%) concentrations. Further, optimization studies at flask level revealed that lactose as carbon source, peptone as organic nitrogen, and inorganic nitrogen (ammonium sulfate) enhanced biosurfactant production. Chemical composition of purified biosurfactant obtained from LNH70 was characterized by various physico-chemical analytical techniques and identified as xylolipid. Xylolipid biosurfactant exhibited anti-adhesion activity against food borne pathogens in in vitro conditions. Its anti-oxidative property by 1, 1-diphenyl-2-picrylhydrazyl (DPPH), 2, 2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid (ABTS), and ferric reducing antioxidant power (FRAP) radical scavenging activity was found in range of 60.76 ± 0.5 to 83.50 ± 0.73%. Furthermore, xylolipid (0.05, 0.1, 0.3 mg/mL) when used for its potential as orange and pineapple juices preservation revealed miniature changes in the physico-chemical parameters evaluated in this study. However, the microbial population slightly lowered when xylolipid was used at 0.3 mg/mL after 5th day. Hence, this study supports the potential use of biosurfactant from L. lactis for its application as food preservative.

Bacterial Outer Membrane Polysaccharide Export (OPX) Proteins Occupy Three Structural Classes with Selective β-Barrel Porin Requirements for Polymer Secretion

Secretion of high-molecular-weight polysaccharides across the bacterial envelope is ubiquitous, as it enhances prokaryotic survival in (a)biotic settings. Such polymers are often assembled by Wzx/Wzy- or ABC transporter-dependent schemes implicating outer membrane (OM) polysaccharide export (OPX) proteins in cell-surface polymer translocation. In the social predatory bacterium Myxococcus xanthus, the exopolysaccharide (EPS) pathway WzaX, major spore coat (MASC) pathway WzaS, and biosurfactant polysaccharide (BPS) pathway WzaB were herein found to be truncated OPX homologues of Escherichia coli Wza lacking OM-spanning α-helices. Comparative genomics across all bacteria (>91,000 OPX proteins identified and analyzed), complemented with cryo-electron tomography cell-envelope analyses, revealed such "truncated" WzaX/S/B architecture to be the most common among three defined OPX-protein structural classes independent of periplasm thickness. Fold recognition and deep learning revealed the conserved M. xanthus proteins MXAN_7418/3226/1916 (encoded beside wzaX/S/B, respectively) to be integral OM β-barrels, with structural homology to the poly-N-acetyl-d-glucosamine synthase-dependent pathway porin PgaA. Such bacterial porins were identified near numerous genes for all three OPX protein classes. Interior MXAN_7418/3226/1916 β-barrel electrostatics were found to match properties of their associated polymers. With MXAN_3226 essential for MASC export, and MXAN_7418 herein shown to mediate EPS translocation, we have designated this new secretion machinery component "Wzp" (i.e., Wz porin), with the final step of M. xanthus EPS/MASC/BPS secretion across the OM now proposed to be mediated by WzpX/S/B (i.e., MXAN_7418/3226/1916). Importantly, these data support a novel and widespread secretion paradigm for polysaccharide biosynthesis pathways in which those containing OPX components that cannot span the OM instead utilize β-barrel porins to mediate polysaccharide transport across the OM. IMPORTANCE Diverse bacteria assemble and secrete polysaccharides that alter their physiologies through modulation of motility, biofilm formation, and host immune system evasion. Most such pathways require outer membrane (OM) polysaccharide export (OPX) proteins for sugar-polymer transport to the cell surface. In the prototypic Escherichia coli Group-1-capsule biosynthesis system, eight copies of this canonical OPX protein cross the OM with an α-helix, forming a polysaccharide-export pore. Herein, we instead reveal that most OPX proteins across all bacteria lack this α-helix, raising questions as to the manner by which most secreted polysaccharides actually exit cells. In the model developmental bacterium Myxococcus xanthus, we show this process to depend on OPX-coupled OM-spanning β-barrel porins, with similar porins encoded near numerous OPX genes in diverse bacteria. Knowledge of the terminal polysaccharide secretion step will enable development of antimicrobial compounds targeted to blocking polymer export from outside the cell, thus bypassing any requirements for antimicrobial compound uptake by the cell.

Expression based biomarkers and models to classify early and late-stage samples of Papillary Thyroid Carcinoma

INTRODUCTION

Recently, the rise in the incidences of thyroid cancer worldwide renders it to be the sixth most common cancer among women. Commonly, Fine Needle Aspiration biopsy predominantly facilitates the diagnosis of the nature of thyroid nodules. However, it is inconsiderable in determining the tumor's state, i.e., benign or malignant. This study aims to identify the key RNA transcripts that can segregate the early and late-stage samples of Thyroid Carcinoma (THCA) using RNA expression profiles.

MATERIALS AND METHODS

In this study, we used the THCA RNA-Seq dataset of The Cancer Genome Atlas, consisting of 500 cancer and 58 normal (adjacent non-tumorous) samples obtained from the Genomics Data Commons (GDC) data portal. This dataset was dissected to identify key RNA expression features using various feature selection techniques. Subsequently, samples were classified based on selected features employing different machine learning algorithms.

RESULTS

Single gene ranking based on the Area Under the Receiver Operating Characteristics (AUROC) curve identified the DCN transcript that can classify the early-stage samples from late-stage samples with 0.66 AUROC. To further improve the performance, we identified a panel of 36 RNA transcripts that achieved F1 score of 0.75 with 0.73 AUROC (95% CI: 0.62-0.84) on the validation dataset. Moreover, prediction models based on 18-features from this panel correctly predicted 75% of the samples of the external validation dataset. In addition, the multiclass model classified normal, early, and late-stage samples with AUROC of 0.95 (95% CI: 0.84-1), 0.76 (95% CI: 0.66-0.85) and 0.72 (95% CI: 0.61-0.83) on the validation dataset. Besides, a five protein-coding transcripts panel was also recognized, which segregated cancer and normal samples in the validation dataset with F1 score of 0.97 and 0.99 AUROC (95% CI: 0.91-1).

CONCLUSION

We identified 36 important RNA transcripts whose expression segregated early and late-stage samples with reasonable accuracy. The models and dataset used in this study are available from the webserver CancerTSP (http://webs.iiitd.edu.in/raghava/cancertsp/).