Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
Project description:Our histological findings showed that vermillion is present in the lip of Japanese macaque. In addition, the immunostaining pattern of K10 and SPRR3 of the lip of Japanese macaque is similar to that of a human. Thus, the transcriptome analysis of Japanese monkey can provide several unique genes specific to vermillion keratinocytes, which is required to develop a human lip/vermillion in vitro model.
Project description:Maternal overnutrition increases inflammatory and metabolic disease risk in postnatal offspring. This constitutes a major public health concern due to the increasing prevalence of these diseases yet the mechanisms remain unclear. Here, using nonhuman primate models, we show that maternal Western-style diet (mWSD) exposure is associated with persistent pro-inflammatory phenotypes at the transcriptional, metabolic, and functional levels in bone marrow-derived macrophages (BMDMs) from 3-year-old juvenile offspring and in hematopoietic stem and progenitor cells (HSPCs) from fetal and juvenile bone marrow and fetal liver. mWSD exposure is also associated with increased oleic acid in fetal and juvenile bone marrow and fetal liver. ATAC-seq profiling of HSPCs and BMDMs from mWSD-exposed juveniles supports a model in which HSPCs transmit pro-inflammatory memory to myeloid cells beginning in utero. These findings demonstrate that maternal diet alters long-term immune cell developmental programming in HSPCs with proposed consequences for chronic diseases featuring altered immune/inflammatory activation across the lifespan.
Project description:CTCF ChIP-Seq experiment was performed to map and compare potential evolutionary changes of CTCF binding, chimpanzee and macaque iAstrocytes.
Project description:H3K4me3 ChIP-Seq experiment was performed to map and compare potential evolutionary changes in active promoters of human, chimpanzee and macaque iAstrocytes.
Project description:While genome sequencing has identified numerous non-coding alterations between primate species, which of these are regulatory and potentially relevant to the evolution of the human brain is unclear. Here, we annotate cis-regulatory elements (CREs) in the human, rhesus macaque and chimpanzee genome using ChIP-sequencing in different anatomical parts of the adult brain. We find high similarity in the genomic positioning of CREs between rhesus macaque and humans, suggesting that the majority of these elements were already present in a common ancestor 25 million years ago. Most of the observed regulatory changes between humans and rhesus macaque occurred prior to the ancestral separation of humans and chimpanzee, leaving a modest set of regulatory elements with predicted human-specificity. Our data refine previous predictions and hypotheses on the consequences of genomic changes between primate species, and allow the identification of regulatory alterations relevant to the evolution of the brain. ChIP-Sequencing for H3K27ac on 8 distinct brain regions from human (three biological replicates per brain region), chimpanzee (two biological replicates per brain region) and rhesus macaque (three biological replicates per brain region).
Project description:Many known miRNAs in fish come from zebrafish and fugu whose genome sequence data are available. The Japanese flounder undergoes typical metamorphosis which is characterized by major morphological, functional, and behavioral changes during growth due to this metamorphosis from larva to juvenile. Metamorphosis is a biological process by which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's body structure through cell growth and differentiation. Here, the high-throughput sequencing was adopted to identify the miRNAs during metamorphosis in the Japanese flounder. We found abundant microRNAs during metamorphosis in the Japanese flounder.
Project description:H3K27ac ChIP-Seq experiment was performed to map and compare potential evolutionary changes in active promoters and enhancer elements of human, chimpanzee and macaque iAstrocytes.