The Making and Breaking of Serine-ADP-Ribosylation in the DNA Damage Response

ADP-ribosylation is a widespread posttranslational modification that is of particular therapeutic relevance due to its involvement in DNA repair. In response to DNA damage, PARP1 and 2 are the main enzymes that catalyze ADP-ribosylation at damage sites. Recently, serine was identified as the primary amino acid acceptor of the ADP-ribosyl moiety following DNA damage and appears to act as seed for chain elongation in this context. Serine-ADP-ribosylation strictly depends on HPF1, an auxiliary factor of PARP1/2, which facilitates this modification by completing the PARP1/2 active site. The signal is terminated by initial poly(ADP-ribose) chain degradation, primarily carried out by PARG, while another enzyme, (ADP-ribosyl)hydrolase 3 (ARH3), specifically cleaves the terminal seryl-ADP-ribosyl bond, thus completing the chain degradation initiated by PARG. This review summarizes recent findings in the field of serine-ADP-ribosylation, its mechanisms, possible functions and potential for therapeutic targeting through HPF1 and ARH3 inhibition.

First record of straight-needle pteropod Creseis acicula Rang, 1828 bloom in the Çanakkale Strait (NE Aegean Sea, Turkey)

Pteropods are marine pelagic calcifier mollusks sensitive to chemical changes in seawater due to their highly soluble aragonite shells. Increased acidity (reduced pH) of seawater causes difficulties in precipitating their shells and/or results in their dissolution, which is related to increased atmospheric CO2 concentrations and warming of seawater. They are therefore indicators of environmental changes. In this paper, we present the first record of the straight-needle pteropod Creseis acicula Rang, 1828 bloom in the surface waters of the Ҫanakkale Strait, Turkey (NE Aegean Sea), encountered in July 2020, when the highest sea surface temperatures and pH levels since 2007 were recorded. In coastal zones, such as the Ҫanakkale Strait, anthropogenic activity contributes significantly to environmental changes. Consequently, the increase in pH at elevated temperatures indicates an auxiliary factor (i.e. anthropogenic activity) that triggered the C. acicula bloom, rather than global atmospheric CO2 levels.

Dental Pulp Stem Cell Polarization: Effects of Biophysical Factors

Dental pulp stem cells (DPSCs) have the potential to polarize, differentiate, and form tubular dentin under certain conditions. However, the factors that initiate and regulate DPSC polarization and its underlying mechanism remain unclear. Identification of the factors that control DPSC polarization is a prerequisite for tubular dentin regeneration. We recently developed a unique bioinspired 3-dimensional platform that is capable of deciphering the factors that initiate and modulate cell polarization. The bioinspired platform has a simple background and confines a single cell on each microisland of the platform; therefore, it is an effective tool to study DPSC polarization at the single-cell level. In this work, we explored the effects of biophysical factors (surface topography, microisland area, geometry, tubular size, and gravity) on single DPSC polarization. Our results demonstrated that nanofibrous architecture, microisland area, tubular size, and gravity participated in regulating DPSC polarization by influencing the formation of the DPSC process and relocation of the Golgi apparatus. Among these factors, nanofibrous architecture, tubular size, and appropriate microisland area were indispensable for initiating DPSC polarization, whereas gravity served as an auxiliary factor to the process of DPSC polarization. Meanwhile, microisland geometry had a limited effect on DPSC polarization. Collectively, this work provides information on DPSC polarization and paves the way for the development of new biomaterials for tubular dentin regeneration.

GRP78 binds SARS-CoV-2 Spike protein and ACE2 and GRP78 depleting antibody blocks viral entry and infection in vitro

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the current COVID-19 global pandemic, utilizes the host receptor angiotensin-converting enzyme 2 (ACE2) for viral entry. However, other host factors may also play major roles in viral infection. Here we report that the stress-inducible molecular chaperone GRP78 can form a complex with the SARS-CoV-2 Spike protein and ACE2 intracellularly and on the cell surface, and that the substrate binding domain of GRP78 is critical for this function. Knock-down of GRP78 by siRNA dramatically reduced cell surface ACE2 expression. Treatment of lung epithelial cells with a humanized monoclonal antibody (hMAb159), selected for its ability to cause GRP78 endocytosis and its safe clinical profile in preclinical models, reduces cell surface ACE2 expression, SARS-CoV-2 Spike-driven viral entry, and significantly inhibits SARS-CoV-2 infection in vitro. Our data suggest that GRP78 is an important host auxiliary factor for SARS-CoV-2 entry and infection and a potential target to combat this novel pathogen and other viruses that utilize GRP78.

The viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape

SUMMARYWhile viral infections are known to hijack the transcription and translation of the host cell, the extent to which encoded viral proteins coordinate these perturbations remains unclear. Here we demonstrate that the oncoviral proteins Tax and HBZ interact with specific components of the spliceosome machinery, including the U2 auxiliary factor large subunit (U2AF2), and the complementary factor for APOBEC-1 (A1CF), respectively. Tax and HBZ perturb the splicing landscape in T-cells by altering cassette exons in opposing manners, with Tax inducing exon inclusion while HBZ induces exon exclusion. Among Tax- and HBZ-dependent splicing changes, we identify events that are also altered in Adult T cell leukemia (ATL) patients, and in well-known cancer census genes. Our interactome mapping approach, applicable to other viral oncogenes, has identified spliceosome perturbation as a novel mechanism coordinately used by Tax and HBZ to reprogram the transcriptome.HighlightsTax and HBZ interact with RNA-binding proteins as well as transcription factorsHTLV-1 encoded proteins Tax and HBZ alter the splicing landscape in T-cellsTax and HBZ expression affect alternative splicing of 33 and 63 cancer genes, respectivelyOpposing roles for Tax and HBZ in deregulation of gene expressionGraphical abstract

THEORETICAL RESEARCHES OF A CAR WHEEL WITH A TRACTION COMPENSATOR

he rolling process of the wheel drive is accompanied by the loading of the wheel drive by the force of gravity, which leads to compression and stretching of the tire during its deformation. The article deals with the study of the mechanical system “automobile wheel-spring compensator of traction force”, using the theorem on the change of kinetic energy of this system, the general equation of dynamics, as well as the Lagrange equation of the second kind. The purpose of the study is to improve the design and technological scheme of rolling the wheel drive, converting the energy of the wheel drive into the rotational motion of the wheel-elastic traction compensator, which is an auxiliary factor to this technology. The scientific and practical significance of the work lies in the fact that for the first time a technology was proposed in which the share of rotational motion energy of a mechanical system “automobile wheel-spring traction compensator” was introduced during rotation of a wheel drive, which significantly increases traction. The research methodology was to establish a mathematical relationship between the force created by the “car wheel-spring traction compensator” and the additional path that the wheel travels. The result is the developed geometry of the wheel drive in the damping cycle “automotive wheel-spring traction compensator” failure of the bearing surface. The value of the study, the results of this work will contribute to the automotive industry. A model for increasing the traction capabilities of the vehicle is proposed.

U2AF65-Dependent SF3B1 Function in SMN Alternative Splicing

Splicing factor 3b subunit 1 (SF3B1) is an essential protein in spliceosomes and mutated frequently in many cancers. While roles of SF3B1 in single intron splicing and roles of its cancer-linked mutant in aberrant splicing have been identified to some extent, regulatory functions of wild-type SF3B1 in alternative splicing (AS) are not well-understood yet. Here, we applied RNA sequencing (RNA-seq) to analyze genome-wide AS in SF3B1 knockdown (KD) cells and to identify a large number of skipped exons (SEs), with a considerable number of alternative 5′ splice-site selection, alternative 3′ splice-site selection, mutually exclusive exons (MXE), and retention of introns (RI). Among altered SEs by SF3B1 KD, survival motor neuron 2 (SMN2) pre-mRNA exon 7 splicing was a regulatory target of SF3B1. RT-PCR analysis of SMN exon 7 splicing in SF3B1 KD or overexpressed HCT116, SH-SY5Y, HEK293T, and spinal muscular atrophy (SMA) patient cells validated the results. A deletion mutation demonstrated that the U2 snRNP auxiliary factor 65 kDa (U2AF65) interaction domain of SF3B1 was required for its function in SMN exon 7 splicing. In addition, mutations to lower the score of the polypyrimidine tract (PPT) of exon 7, resulting in lower affinity for U2AF65, were not able to support SF3B1 function, suggesting the importance of U2AF65 in SF3B1 function. Furthermore, the PPT of exon 7 with higher affinity to U2AF65 than exon 8 showed significantly stronger interactions with SF3B1. Collectively, our results revealed SF3B1 function in SMN alternative splicing.

Experimental Study and Percolation Analysis on Seepage Characteristics of Fractured Coal and Sandstone Based on Real-Time Micro-CT

Sandstone and coal are the two most common types of reservoirs in nature. The permeability of sandstone in oil-bearing formations controls its oil and gas production; the permeability of the coal seam containing gas has a crucial influence on the gas drainage efficiency. One of the main factors affecting rock permeability is the spatial distribution and connectivity of pores and fissures in the rock. In this paper, a small-sized sample with a diameter of 5 mm and a height of 10 mm was used for the test. The rock samples under different stress states were scanned in real-time during the seepage testing. Based on 2D images, a 3D digital sample was reconstructed. We extracted the pores and fissures from the 3D digital sample, studied the size and distribution of the largest cluster in the sample, and revealed the influence of confining pressure and seepage pressure on the percolation probability and permeability of the sample. The research results show that brittle sandstone and plastic coal, two types of rocks with completely different properties of mechanics, have obvious differences in the spatial distribution of the largest clusters. Under the same stress state, in brittle sandstone-like rocks, the connectivity of the fissures is the primary factor affecting permeability, and the pores are the auxiliary factor; for plastic rocks such as coal, the situation is just the opposite, pores are the primary factor affecting permeability, and fissures are the auxiliary factor. The research results answer the question: Hydraulic fracturing technology can increase the oil and gas production of sandstone reservoirs but cannot increase the drainage efficiency of coalbed methane.