DNA Mismatch Repair in Eukaryotes and Bacteria

DNA mismatch repair (MMR) corrects mismatched base pairs mainly caused by DNA replication errors. The fundamental mechanisms and proteins involved in the early reactions of MMR are highly conserved in almost all organisms ranging from bacteria to human. The significance of this repair system is also indicated by the fact that defects in MMR cause human hereditary nonpolyposis colon cancers as well as sporadic tumors. To date, 2 types of MMRs are known: the human type and Escherichia coli type. The basic features of the former system are expected to be universal among the vast majority of organisms including most bacteria. Here, I review the molecular mechanisms of eukaryotic and bacterial MMR, emphasizing on the similarities between them

Structure and Function of the Small MutS-Related Domain

MutS family proteins are widely distributed in almost all organisms from bacteria to human and play central roles in various DNA transactions such as DNA mismatch repair and recombinational events. The small MutS-related (Smr) domain was originally found in the C-terminal domain of an antirecombination protein, MutS2, a member of the MutS family. MutS2 is thought to suppress homologous recombination by endonucleolytic resolution of early intermediates in the process. The endonuclease activity of MutS2 is derived from the Smr domain. Interestingly, sequences homologous to the Smr domain are abundant in a variety of proteins other than MutS2 and can be classified into 3 subfamilies. Recently, the tertiary structures and endonuclease activities of all 3 Smr subfamilies were reported. In this paper, we review the biochemical characteristics and structures of the Smr domains as well as cellular functions of the Smr-containing proteins

Filmy Cloud Removal on Satellite Imagery with Multispectral Conditional Generative Adversarial Nets

In this paper, we propose a method for cloud removal from visible light RGB satellite images by extending the conditional Generative Adversarial Networks (cGANs) from RGB images to multispectral images. Satellite images have been widely utilized for various purposes, such as natural environment monitoring (pollution, forest or rivers), transportation improvement and prompt emergency response to disasters. However, the obscurity caused by clouds makes it unstable to monitor the situation on the ground with the visible light camera. Images captured by a longer wavelength are introduced to reduce the effects of clouds. Synthetic Aperture Radar (SAR) is such an example that improves visibility even the clouds exist. On the other hand, the spatial resolution decreases as the wavelength increases. Furthermore, the images captured by long wavelengths differs considerably from those captured by visible light in terms of their appearance. Therefore, we propose a network that can remove clouds and generate visible light images from the multispectral images taken as inputs. This is achieved by extending the input channels of cGANs to be compatible with multispectral images. The networks are trained to output images that are close to the ground truth using the images synthesized with clouds over the ground truth as inputs. In the available dataset, the proportion of images of the forest or the sea is very high, which will introduce bias in the training dataset if uniformly sampled from the original dataset. Thus, we utilize the t-Distributed Stochastic Neighbor Embedding (t-SNE) to improve the problem of bias in the training dataset. Finally, we confirm the feasibility of the proposed network on the dataset of four bands images, which include three visible light bands and one near-infrared (NIR) band

Inactivation of the DNA Repair Genes mutS, mutL or the Anti-Recombination Gene mutS2 Leads to Activation of Vitamin B1 Biosynthesis Genes

Oxidative stress generates harmful reactive oxygen species (ROS) that attack biomolecules including DNA. In living cells, there are several mechanisms for detoxifying ROS and repairing oxidatively-damaged DNA. In this study, transcriptomic analyses clarified that disruption of DNA repair genes mutS and mutL, or the anti-recombination gene mutS2, in Thermus thermophilus HB8, induces the biosynthesis pathway for vitamin B1, which can serve as an ROS scavenger. In addition, disruption of mutS, mutL, or mutS2 resulted in an increased rate of oxidative stress-induced mutagenesis. Co-immunoprecipitation and pull-down experiments revealed previously-unknown interactions of MutS2 with MutS and MutL, indicating that these proteins cooperatively participate in the repair of oxidatively damaged DNA. These results suggested that bacterial cells sense the accumulation of oxidative DNA damage or absence of DNA repair activity, and signal the information to the transcriptional regulation machinery for an ROS-detoxifying system

Femtoscopic study of coupled-channel baryon-baryon interactions with S=−2S=-2

Particles and Nuclei International Conference - PANIC2021, 5 - 10 September, 2021, OnlineThe correlation functions of pΞ− and ΛΛ pairs from pp and pA collisions are studied in the coupled-channel framework using the NΞ-ΛΛ coupled-channel baryon-baryon potentials obtained in the lattice QCD calculation at almost physical quark masses. The pΞ− correlation function is calculated to be significantly enhanced from the pure Coulomb case, while the ΛΛ correlation function is slightly enhanced from that of the pure fermion quantum statistics. These features reflect the large and small scattering lengths in the pΞ− and ΛΛ channels in magnitude, and agree with the observed data by the ALICE collaboration. The agreement confirms the S = −2 baryon-baryon potentials from lattice QCD

Analysis of a nuclease activity of catalytic domain of Thermus thermophilus MutS2 by high-accuracy mass spectrometry

Electrospray ionization with Fourier-transform ion cyclotron resonance mass spectrometry (ESI–FT ICR MS) is a powerful tool for analyzing the precise structural features of biopolymers, including oligonucleotides. Here, we described the detailed characterization of a newly discovered nuclease activity of the C-terminal domain of Thermus thermophilus MutS2 (ttMutS2). Using this method, the length, nucleotide content and nature of the 5′- and 3′-termini of the product oligonucleotides were accurately identified. It is revealed that the C-terminal domain of ttMutS2 incised the phosphate backbone of oligodeoxynucleotides non-sequence-specifically at the 3′ side of the phosphates. The simultaneous identification of the innumerable fragments was achieved by the extremely high-accuracy of ESI–FT ICR MS