Age-associated aberrations of the cumulus-oocyte interaction and in the zona pellucida structure reduce fertility in female mice.

One of the major age-related declines in female reproductive function is the reduced quantity and quality of oocytes. Here we demonstrate that structural changes in the zona pellucida (ZP) were associated with decreased fertilization rates from 34- to 38-week-old female mice, equivalent to the mid-reproductive of human females. In middle-aged mouse ovaries, the decline in the number of transzonal projections was accompanied by a decrease in cumulus cell-oocyte interactions, resulting in a deterioration of the oocyte quality.

Structure and engineering of Brevibacillus laterosporus Cas9.

The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets complementary to an RNA guide, and is widely used as a powerful genome-editing tool. Here, we report the crystal structure of Brevibacillus laterosporus Cas9 (BlCas9, also known as BlatCas9), in complex with a guide RNA and its target DNA at 2.4-Å resolution.

An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis.

SpCas9 and AsCas12a are widely utilized as genome-editing tools in human cells. However, their relatively large size poses a limitation for delivery by cargo-size-limited adeno-associated virus (AAV) vectors. The type V-F Cas12f from Acidibacillus sulfuroxidans is exceptionally compact (422 amino acids) and has been harnessed as a compact genome-editing tool.

Integrating Both Parallax and Latency Compensation into Video See-through Head-mounted Display.

This work introduces a perspective-corrected video see-through mixed-reality head-mounted display with edge-preserving occlusion and low-latency capabilities. To realize the consistent spatial and temporal composition of a captured real world containing virtual objects, we perform three essential tasks: 1) to reconstruct captured images so as to match the user's view; 2) to occlude virtual objects with nearer real objects, to provide users with correct depth cues; and 3) to reproject the virtual and captured scenes to be matched and to keep up with users' head motions. Captured image reconstruction and occlusion-mask generation require dense and accurate depth maps.

A framework to efficiently describe and share reproducible DNA materials and construction protocols.

DNA constructs and their annotated sequence maps have been rapidly accumulating with the advancement of DNA cloning, synthesis, and assembly methods. Such resources have also been utilized in designing and building new DNA materials. However, as commonly seen in the life sciences, no framework exists to describe reproducible DNA construction processes.

Engineered Campylobacter jejuni Cas9 variant with enhanced activity and broader targeting range.

The RNA-guided DNA endonuclease Cas9 is a versatile genome-editing tool. However, the molecular weight of the commonly used Streptococcus pyogenes Cas9 is relatively large. Consequently, its gene cannot be efficiently packaged into an adeno-associated virus vector, thereby limiting its applications for therapeutic genome editing.

CRISPR/Cas9-mediated base-editing enables a chain reaction through sequential repair of sgRNA scaffold mutations.

Cell behavior is controlled by complex gene regulatory networks. Although studies have uncovered diverse roles of individual genes, it has been challenging to record or control sequential genetic events in living cells. In this study, we designed two cellular chain reaction systems that enable sequential sgRNA activation in mammalian cells using a nickase Cas9 tethering of a cytosine nucleotide deaminase (nCas9-CDA).

Rubicon prevents autophagic degradation of GATA4 to promote Sertoli cell function.

Autophagy degrades unnecessary proteins or damaged organelles to maintain cellular function. Therefore, autophagy has a preventive role against various diseases including hepatic disorders, neurodegenerative diseases, and cancer. Although autophagy in germ cells or Sertoli cells is known to be required for spermatogenesis and male fertility, it remains poorly understood how autophagy participates in spermatogenesis.

Publisher Correction: Base editors for simultaneous introduction of C-to-T and A-to-G mutations.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Base editors for simultaneous introduction of C-to-T and A-to-G mutations.

We describe base editors that combine both cytosine and adenine base-editing functions. A codon-optimized fusion of the cytosine deaminase PmCDA1, the adenosine deaminase TadA and a Cas9 nickase (Target-ACEmax) showed a high median simultaneous C-to-T and A-to-G editing activity at 47 genomic targets. On-target as well as DNA and RNA off-target activities of Target-ACEmax were similar to those of existing single-function base editors.

Complete Genome Sequence of sp. Strain KH172YL63, Isolated from Deep-Sea Sediment.

sp. strain KH172YL63 is a Gram-positive bacterium isolated from the deep-sea floor surface sediment at 3,308 m below sea level in the Nankai Trough in Japan. Here, we report the complete genome sequence of sp.

DNA barcodes evolve for high-resolution cell lineage tracing.

Mammalian development involves continuous dynamic processes in which cells propagate, differentiate, orchestrate, and decease to produce high-order functions. Although accurate cell lineage information can provide a strong foundation to understand such complex processes, the cell lineages involved in development of the whole mammalian body remain largely unclear, except for in early embryogenesis, which is observable under a microscope. With CRISPR genome editing, the concept of 'evolving DNA barcodes' has rapidly emerged for large-scale, high-resolution cell lineage tracing, where cell-embedded DNA barcodes continuously accumulate random mutations that are inherited from mother to daughter cells.

DNA event recorders send past information of cells to the time of observation.

While current omics and single cell technologies have enabled measurements of high-resolution molecular snapshots of cells at a large scale, these technologies all require destruction of samples and prevent us from analyzing dynamic changes in molecular profiles, phenotypes, and behaviors of individual cells in a complex system. One possible direction to overcome this issue is the development of a cell-embedded 'event recorder' system, whereby molecular and phenotypic information of a cell(s) can be obtained at the time of observation with their past event information stored in 'heritable polymers' of the same cell. This concept has been demonstrated by many synthetic cellular circuits that monitor and transmit a certain set of environmental and intracellular signals into DNA, and have now been further accelerated by recent CRISPR-related technologies.

Complete Genome Sequence of sp. Strain KH172YL61, Isolated from Deep-Sea Sediments in the Nankai Trough, Japan.

sp. strain KH172YL61 is a Gram-negative bacterium isolated from deep-sea sediment in the Nankai Trough in Japan. Here, we report the complete genome sequence of this strain, which has a genome size of 3.

Fast and global detection of periodic sequence repeats in large genomic resources.

Periodically repeating DNA and protein elements are involved in various important biological events including genomic evolution, gene regulation, protein complex formation, and immunity. Notably, the currently used genome editing tools such as ZFNs, TALENs, and CRISPRs are also all associated with periodically repeating biomolecules of natural organisms. Despite the biological importance of periodically repeating sequences and the expectation that new genome editing modules could be discovered from such periodical repeats, no software that globally detects such structured elements in large genomic resources in a high-throughput and unsupervised manner has been developed.

Engineered CRISPR-Cas9 nuclease with expanded targeting space.

The RNA-guided endonuclease Cas9 cleaves its target DNA and is a powerful genome-editing tool. However, the widely used Cas9 enzyme (SpCas9) requires an NGG protospacer adjacent motif (PAM) for target recognition, thereby restricting the targetable genomic loci. Here, we report a rationally engineered SpCas9 variant (SpCas9-NG) that can recognize relaxed NG PAMs.

[Application of one step RT-PCR assay for detection of flavivirus RNA in mosquitoes].

The conditions of one step RT-PCR method for detection of virus RNA in field-collected mosquitoes, and preservation period of infected mosquitoes for one step RT-PCR were examined. We compared several virus RNA extraction methods with artificially contaminated mosquito pools with dengue virus (DV), Japanese encephalitis virus (JEV), and yellow fever virus (YFV) with a known amount of plaque forming unit (PFU) to establish the condition of one step RT-PCR. In this study, most effective RNA extraction method was ISOGEN-LS extraction combined with supernatant of centrifuged mosquito homogenates.

Sum-frequency-generation system for differential absorption lidar measurement of atmospheric nitrogen dioxide.

A sum-frequency-generation system for differential absorption lidar measurement of atmospheric nitrogen dioxide in the lower troposphere was developed. The system uses a combination of a pair of KD*P crystals and a tunable dye laser with LDS 765 dye pumped by the second harmonic of a Nd:YAG laser to generate lambdaon and lambdaoff alternatively. Compared with the conventional system that uses Coumarin 445 dye pumped by the third harmonic, the output energy and long-term stability were improved.