Comparison of miRNA transcriptome of exosomes in three categories of somatic cells with derived iPSCs

Somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) through epigenetic manipulation. While the essential role of miRNA in reprogramming and maintaining pluripotency is well studied, little is known about the functions of miRNA from exosomes in this context. To fill this research gap,we comprehensively obtained the 17 sets of cellular mRNA transcriptomic data with 3.93 × 1010 bp raw reads and 18 sets of exosomal miRNA transcriptomic data with 2.83 × 107 bp raw reads from three categories of human somatic cells: peripheral blood mononuclear cells (PBMCs), skin fibroblasts(SFs) and urine cells (UCs), along with their derived iPSCs. Additionally, differentially expressed molecules of each category were identified and used to perform gene set enrichment analysis. Our study provides sets of comparative transcriptomic data of cellular mRNA and exosomal miRNA from three categories of human tissue with three individual biological controls in studies of iPSCs generation, which will contribute to a better understanding of donor cell variation in functional epigenetic regulation and differentiation bias in iPSCs.

Single-atom vibrational spectroscopy with chemical-bonding sensitivity

Correlation of lattice vibrational properties with local atomic configurations in materials is essential for elucidating functionalities that involve phonon transport in solids. Recent developments in vibrational spectroscopy in a scanning transmission electron microscope have enabled direct measurements of local phonon modes at defects and interfaces by combining high spatial and energy resolution. However, pushing the ultimate limit of vibrational spectroscopy in a scanning transmission electron microscope to reveal the impact of chemical bonding on local phonon modes requires extreme sensitivity of the experiment at the chemical-bond level. Here we demonstrate that, with improved instrument stability and sensitivity, the specific vibrational signals of the same substitutional impurity and the neighbouring carbon atoms in monolayer graphene with different chemical-bonding configurations are clearly resolved, complementary with density functional theory calculations. The present work opens the door to the direct observation of local phonon modes with chemical-bonding sensitivity, and provides more insights into the defect-induced physics in graphene.

Photoperiod controls plant seed size in a CONSTANS-dependent manner

Photoperiodic plants perceive changes in day length as seasonal cues to orchestrate their vegetative and reproductive growth. Although it is known that the floral transition of photoperiod-sensitive plants is tightly controlled by day length, how photoperiod affects their post-flowering development remains to be clearly defined, as do the underlying mechanisms. Here we demonstrate that photoperiod plays a prominent role in seed development. We found that long-day (LD) and short-day (SD) plants produce larger seeds under LD and SD conditions, respectively; however, seed size remains unchanged when CONSTANS (CO), the central regulatory gene of the photoperiodic response pathway, is mutated in Arabidopsis and soybean. We further found that CO directly represses the transcription of AP2 (a known regulatory gene of seed development) under LD conditions in Arabidopsis and SD conditions in soybean, thereby controlling seed size in a photoperiod-dependent manner, and that these effects are exerted through regulation of the proliferation of seed coat epidermal cells. Collectively, our findings reveal that a crucial regulatory cascade involving CO-AP2 modulates photoperiod-mediated seed development in plants and provide new insights into how plants with different photoperiod response types perceive seasonal changes that enable them to optimize their reproductive growth.

Eight soybean reference genome resources from varying latitudes and agronomic traits

Comparative analysis of multiple reference genomes representing diverse genetic backgrounds is critical for understanding the role of key alleles important in domestication and genetic breeding of important crops such as soybean. To enrich the genetic resources for soybean, we describe the generation, technical assessment, and preliminary genomic variation analysis of eight de novo reference-grade soybean genome assemblies from wild and cultivated accessions. These resources represent soybeans cultured at different latitudes and exhibiting different agronomical traits. Of these eight soybeans, five are from new accessions that have not been sequenced before. We demonstrate the usage of these genomes to identify small and large genomic variations affecting known genes as well as screening for genic PAV regions for identifying candidates for further functional studies.

SerpinA3N deficiency deteriorates impairments of learning and memory in mice following hippocampal stab injury

Traumatic brain injury is a global leading cause of disability and death, which puts patients at high risk for developing dementia. Early intervention is believed as the key to minimize the development of brain damages that could aggravate the symptoms. Here, we report that the serine protease inhibitor SerpinA3N is upregulated in hippocampal neurons in the early stage of hippocampal stab injury (HSI), while its deficiency causes a greater degree of neuronal apoptosis and severer impairments of spatial learning and memory in mice after HSI. We further show that MMP2 is a key substrate of SerpinA3N, and MMP2 specific inhibitor (ARP100) can protect against neuronal apoptosis and cognitive dysfunction in mice after HSI. These findings demonstrate a critical role for SerpinA3N in neuroprotection, suggesting that SerpinA3N and MMP2 inhibitors might be a novel therapeutic agents for neurotrauma.

Low sample volume origami-paper-based graphene-modified aptasensors for label-free electrochemical detection of cancer biomarker-EGFR

In this work, an electrochemical paper-based aptasensor was fabricated for label-free and ultrasensitive detection of epidermal growth factor receptor (EGFR) by employing anti-EGFR aptamers as the bio-recognition element. The device used the concept of paper-folding, or origami, to serve as a valve between sample introduction and detection, so reducing sampling volumes and improving operation convenience. Amino-functionalized graphene (NH₂-GO)/thionine (THI)/gold particle (AuNP) nanocomposites were used to modify the working electrode not only to generate the electrochemical signals, but also to provide an environment conducive to aptamer immobilization. Electrochemical characterization revealed that the formation of an insulating aptamer-antigen immunocomplex would hinder electron transfer from the sample medium to the working electrode, thus resulting in a lower signal. The experimental results showed that the proposed aptasensor exhibited a linear range from 0.05 to 200 ngmL^-1 (R ² = 0.989) and a detection limit of 5 pgmL^-1 for EGFR. The analytical reliability of the proposed paper-based aptasensor was further investigated by analyzing serum samples, showing good agreement with the gold-standard enzyme-linked immunosorbent assay.

N-Phenylquinazolin-2-amine Yhhu4952 as a novel promotor for oligodendrocyte differentiation and myelination

Oligodendrocytes are a type of glial cells that ensheath multiple neuronal axons and form myelin. Under pathological conditions, such as multiple sclerosis (MS), inflammatory damage to myelin and oligodendrocytes leads to demyelination. Although the demyelinated regions can partially resolve functional deficits through remyelination, however, as the disease progresses, remyelination typically becomes incomplete and ultimately fails. One possible explanation for this failure is the activation of the Notch pathway in MS lesions, which impedes oligodendrocyte precursor cells (OPCs) at maturation. This leads to a potential target for remyelination. Here, we have identified a compound Yhhu4952 that promoted the maturation of cultured OPCs in a dose-dependent and time-dependent manner. Neonatal rats showed a significant increase in the expression of myelin basic protein (MBP) and the prevalence of mature oligodendrocytes in the corpus callosum after Yhhu4952 treatment. The compound was also effective in promoting remyelination in cuprizone-induced demyelination model and improving severity scores in experimental autoimmune encephalomyelitis (EAE) model. Mechanism studies revealed that Yhhu4952 promotes OPC differentiation through the inhibition of the Jagged1-Notch1 pathway. These findings suggest Yhhu4952 is potentially useful for proceeding oligodendrocyte differentiation and remyelination.