A Nonlinear Photochromic Reaction Based on Sensitizer-Free Triplet-Triplet Annihilation in a Perylene-Substituted Rhodamine Spirolactam.

Nonlinear photochromic reactions that work with weak incoherent light are important for molecular operations with high spatial resolution and multiple photofunctions based on single molecules. However, nonlinear photochromic compounds generally require complex molecular design, restricting accessibility in various fields. Herein, we report nonlinear photochromic properties in a perylene-substituted rhodamine spirolactam derivative (Rh-Pe), which is synthesized from rhodamine B in facile procedures.

Homo-trimeric structure of the ribonuclease for rRNA processing, FAU-1, from Pyrococcus furiosus.

Crystal structure of a ribonuclease for ribosomal RNA processing, FAU-1, from Pyrococcus furiosus was determined with the resolution of 2.57 Å in a homo-trimeric form. The monomer structure consists of two domains: N-terminal and C-terminal domains.

HIV-1 RNAs whose transcription initiates from the third deoxyguanosine of GGG tract in the 5' long terminal repeat serve as a dominant genome for efficient provirus DNA formation.

Unspliced HIV-1 RNAs function as messenger RNAs for Gag or Gag-Pol polyproteins and progeny genomes packaged into virus particles. Recently, it has been reported that fate of the RNAs might be primarily determined, depending on transcriptional initiation sites among three consecutive deoxyguanosine residues (GGG tract) downstream of TATA-box in the 5' long terminal repeat (LTR). Although HIV-1 RNA transcription starts mostly from the first deoxyguanosine of the GGG tract and often from the second or third deoxyguanosine, RNAs beginning with one guanosine (G1-form RNAs), whose transcription initiates from the third deoxyguanosine, were predominant in HIV-1 particles.

Crystal structure of adenylosuccinate lyase from the thermophilic bacterium Thermus thermophilus HB8.

Adenylosuccinate lyase (PurB) catalyzes two distinct reactions in the purine nucleotide biosynthetic pathway using the same active site. The ability to recognize two different sets of substrates is of structural and evolutionary interest. In the present study, the crystal structure of PurB from the thermophilic bacterium Thermus thermophilus HB8 (TtPurB) was determined at a resolution of 2.

Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins.

XenoAptamers are DNA fragments containing additional letters (unnatural bases, UBs) that bind specifically to their target proteins with high affinities (sub-nanomolar values). One of the UBs is the highly hydrophobic 7-(2-thienyl)imidazo[4,5-]pyridine (Ds), which significantly increases XenoAptamers' affinities to targets. Originally, Ds was developed as a third base pair with a complementary UB, 2-nitro-4-propynylpyrrole (Px), for replication, and thus it can be used for aptamer generation by an evolutional engineering method involving PCR amplification.

Expression analysis of box C/D snoRNAs with SNPs between C57BL/6 and MSM/Ms strains in male mouse.

MSM/Ms mouse derived from the Japanese wild mouse has unique characteristics compared to the widely used C57BL/6 mouse. To examine the usefulness of the MSM/Ms mouse for the comparative genomic analysis, expression of small RNAs were analyzed by the large-scale sequence analysis for two strains of mouse, C57BL/6 and MSM/Ms. As a trial, expression of box C/D snoRNAs, which are the most abundant small RNAs in the cell, were analyzed.

An automated screening model for aortic emergencies using convolutional neural networks and cropped computed tomography angiography images of the aorta.

Purpose: Patients with aortic emergencies, such as aortic dissection and rupture, are at risk of rapid deterioration, necessitating prompt diagnosis. This study introduces a novel automated screening model for computed tomography angiography (CTA) of patients with aortic emergencies, utilizing deep convolutional neural network (DCNN) algorithms.

Methods: Our model (Model A) initially predicted the positions of the aorta in the original axial CTA images and extracted the sections containing the aorta from these images.

Convergent evolution of nitrogen-adding enzymes in the purine nucleotide biosynthetic pathway, based on structural analysis of adenylosuccinate synthetase (PurA).

Adenylosuccinate synthetase (PurA) is an enzyme responsible for the nitrogen addition to inosine monophosphate (IMP) by aspartate in the purine nucleotide biosynthetic pathway. And after which the fumarate is removed by adenylosuccinate lyase (PurB), leaving an amino group. There are two other enzymes that catalyze aspartate addition reactions similar to PurA, one in the purine nucleotide biosynthetic pathway (SAICAR synthetase, PurC) and the other in the arginine biosynthetic pathway (argininosuccinate sythetase, ArgG).

Linguistic representation of vowels in speech imagery EEG.

Speech imagery recognition from electroencephalograms (EEGs) could potentially become a strong contender among non-invasive brain-computer interfaces (BCIs). In this report, first we extract language representations as the difference of line-spectra of phones by statistically analyzing many EEG signals from the Broca area. Then we extract vowels by using iterative search from hand-labeled short-syllable data.

Non-coding RNAs and functional RNA elements in Thermus thermophilus.

To complete the ThermusQ database, small non-coding RNAs (ncRNAs) and functional RNA elements found in Thermus thermophilus were summarized with annotations. The well-known three ncRNAs, M1 RNA, tmRNA and SRP RNA, were annotated as ttj8_nc001 to ttj8_nc003, and 10 novel RNAs were annotated as ttj8_nc004 to ttj8_nc013. Antisense RNAs for some ORFs were annotated as ttj8_EST00001 to ttj8_EST00006.

Interaction between a fluoroquinolone derivative KG022 and RNAs: Effect of base pairs 3' adjacent to the bulged residues.

RNA-targeted small molecules are a promising modality in drug discovery. Recently, we found that a fluoroquinolone derivative, KG022, can bind to RNAs with bulged C or G. To clarify the RNA specificity of KG022, we analyzed the effect of the base pair located at the 3'side of the bulged residue.

-Allosteric Regulation of HIV-1 Reverse Transcriptase by Integrase.

Reverse transcriptase (RT) and integrase (IN) are encoded tandemly in the genes of retroviruses. We reported recently that HIV-1 RT and IN need to be supplied as the precursor intermediates, in which RT and IN are in fusion form (RTIN) to exert efficient reverse transcription in the context of HIV-1 replication. The mechanism underlying RTIN's effect, however, remains to be elucidated.

[Integrase and reversetranscriptase: New insights into the HIV genome replication system in line.].

Reverse transcriptase (RT) and integrase (IN) are retrovirus enzymes to convert virus genomic RNA into provirus DNA state in host cells. The RT and IN encoded tandemly in the pol gene, are translated as a fused form and incorporated into the virus particles. Recently, we discovered the potential role of HIV-1 IN to regulate the reverse transcription through the fused state with RT (RT-IN).

Chronological characterization of sperm morpho-functional damage and recovery after testicular heat stress in Nellore bulls.

Heat stress (HS) affects spermatogenesis and sperm maturation, decreasing sperm quality. Yet sperm morpho-functional changes caused by HS in Nellore bulls are not fully elucidated. This study aimed to show the chronological effects on sperm quality of HS during spermatogenesis and sperm maturation until recovery of the seminiferous epithelium in Nellore bulls.

Free-Energy Profile Analysis of the Catalytic Reaction of Glycinamide Ribonucleotide Synthetase.

The second step in the de novo biosynthetic pathway of purine is catalyzed by PurD, which consumes an ATP molecule to produce glycinamide ribonucleotide (GAR) from glycine and phosphoribosylamine (PRA). PurD initially reacts with ATP to produce an intermediate, glycyl-phosphate, which then reacts with PRA to produce GAR. The structure of the glycyl-phosphate intermediate bound to PurD has not been determined.

Dye-Conjugated Spinach RNA by Genetic Alphabet Expansion.

Light-emitting systems using an RNA aptamer-dye pair, such as Spinach RNA, are an attractive method for imaging and tracing RNA expression in vitro and in vivo. We present an alternative Spinach method by genetic alphabet expansion using an unnatural base pair system, in which a dye-conjugated unnatural base substrate is site-specifically incorporated at a specific position in Spinach RNA by transcription involving the third base pair. The incorporation position was predicted by molecular dynamics simulations.

Sperm function and oxidative status: Effect on fertility in Bos taurus and Bos indicus bulls when semen is used for fixed-time artificial insemination.

Semen quality is one of the criteria used for the selection of bulls with relatively greater fertility. In addition, bull fertility depends on the integrity and function of all sperm structures. The aim of this study, therefore, was to determine associations when there was conducting of conventional and functional techniques for the evaluation of sperm samples from bulls with known fertility history as determined when semen from these bulls was used for fixed-time artificial insemination programs.

Amelioration of Alzheimer's Disease by Gut-Pancreas-Liver-Brain Interaction in an App Knock-In Mouse Model.

In this study, we observed disease progression, changes in the gut microbiota, and interactions among the brain, liver, pancreas, and intestine in a mouse model of Alzheimer's disease (AD), in addition to attempting to inhibit disease progression through the dietary supplementation of L-arginine and limonoids. Wild-type mice (WC) and AD mice were fed a normal diet (AC), a diet supplemented with L-arginine and limonoids (ALA), or a diet containing only limonoids (AL) for 12-64 weeks. The normal diet-fed WC and AC mice showed a decrease in the diversity of the gut microbiota, with an increase in the Firmicutes/Bacteroidetes ratio, and bacterial translocation.

T-hairpin structure found in the RNA element involved in piRNA biogenesis.

PIWI-interacting RNAs (piRNAs) repress transposons to protect the germline genome from DNA damage caused by transposon transposition. In , the () mRNA is consumed to produce piRNA in its 3'-UTR. A element located within the 3'-UTR, , is necessary for piRNA biogenesis.

Interaction between a fluoroquinolone derivative and RNAs with a single bulge.

Interaction analysis between small molecules and RNA as well as structure determination of RNA-small molecule complexes will be the clues to search for compounds that bind to specific mRNA or non-coding RNA in drug discovery. In this study, the RNA-binding ability of a fluoroquinolone derivative, KG022, was examined against single-residue bulge-containing hairpin RNAs as RNA models. Nuclear magnetic resonance analysis indicated that KG022 interacts with the RNAs in the vicinity of the bulge residue, with preferring C and G as the bulge residues.

Hydroxy-selenomethionine as an organic source of selenium in the diet improves boar reproductive performance in artificial insemination programs.

This study aimed to compare different selenium (Se) sources in the diet on boar's semen quality and fertility. For this, 28 boars aged 8 to 28 mo were fed with the following dietary treatments for 95 d: 0.3 mg Se/kg as sodium selenite (SS; n = 14) and 0.

Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes.

For the last 20 years, it has been common lore that the free energy of RNA duplexes formed from canonical Watson-Crick base pairs (bps) can be largely approximated with dinucleotide bp parameters and a few simple corrective constants that are duplex independent. Additionally, the standard benchmark set of duplexes used to generate the parameters were GC-rich in the shorter duplexes and AU-rich in the longer duplexes, and the length of the majority of the duplexes ranged between 6 and 8 bps. We were curious if other models would generate similar results and whether adding longer duplexes of 17 bps would affect the conclusions.