Evolution of snow algae, from cosmopolitans to endemics, revealed by DNA analysis of ancient ice.

Recent studies of microbial biogeography have revealed the global distribution of cosmopolitans and dispersal of regional endemics, but little is known about how these processes are affected by microbial evolution. Here, we compared DNA sequences from snow/glacier algae found in an 8000-year-old ice from a glacier in central Asia with those from modern snow samples collected at 34 snow samples from globally distributed sites at the poles and mid-latitudes, to determine the evolutionary relationship between cosmopolitan and endemic phylotypes of snow algae. We further applied a coalescent theory-based demographic model to the DNA sequences.

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.

The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete.

Transcriptomic exploration of the Coleopteran wings reveals insight into the evolution of novel structures associated with the beetle elytron.

The acquisition of novel traits is central to organismal evolution, yet the molecular mechanisms underlying this process are elusive. The beetle forewings (elytra) are evolutionarily modified to serve as a protective shield, providing a unique opportunity to study these mechanisms. In the past, the orthologs of genes within the wing gene network from Drosophila studies served as the starting point when studying the evolution of elytra (candidate genes).

Short-term ex vivo tissue culture models help study human lung infectionsA review.

Most studies on human lung infection have been performed using animal models, formalin or other fixed tissues, and in vitro cultures of established cell lines. However, the experimental data and results obtained from these studies may not completely represent the complicated molecular events that take place in intact human lung tissue in vivo. The newly developed ex vivo short-term tissue culture model can mimic the in vivo microenvironment of humans and allow investigations of different cell types that closely interact with each other in intact human lung tissues.

Polycarcin V induces DNA-damage response and enables the profiling of DNA-binding proteins.

To maintain genomic integrity and avoid diseases, the DNA-damage response (DDR) not only detects and repairs DNA lesions, but also contributes to the resistance to DNA-damaging chemotherapeutics. Targeting the DDR plays a significant role in drug discovery using the principle of synthetic lethality. The incomplete current knowledge of the DDR encouraged us to develop new strategies to identify and study its components and pathways.

Biomimetic Total Synthesis and the Biological Evaluation of Natural Product (-)-Fargesone A as a Novel FXR Agonist.

Farnesoid X receptor (FXR), a member of the nuclear receptor superfamily, plays an important role in maintaining or reversing metabolic homeostasis during the development of liver diseases. However, developing FXR modulators to intervene in FXR-related diseases is still an unmet clinical need. Therefore, it is significant to develop novel small-molecule agonists for drug discovery targeting FXR.

Natural Product 2-Oxokolavenol Is a Novel FXR Agonist.

Acetaminophen (APAP) toxicity is a common cause of hepatic failure, and the development of effective therapy is still urgently needed. Farnesoid X receptor (FXR), a member of the nuclear receptor superfamily, has been identified as a master gene for regulating enterohepatic metabolic homeostasis and has proven to be a promising drug target for various liver diseases. Through high-throughput chemical screening, the natural product 2-oxokolavenol was identified as a novel and selective FXR agonist.

Melanogenesis and the Targeted Therapy of Melanoma.

Pigment production is a unique character of melanocytes. Numerous factors are linked with melanin production, including genetics, ultraviolet radiation (UVR) and inflammation. Understanding the mechanism of melanogenesis is crucial to identify new preventive and therapeutic strategies in the treatment of melanoma.

The effect of adenomyosis types on clinical outcomes of IVF embryo transfer after ultra-long GnRH agonist protocol.

Research Question: What is the effect of adenomyosis types on IVF and embryo transfer (IVF-ET) after ultra-long gonadotrophin-releasing hormone (GnRH) agonist protocol?

Design: Patients who underwent the first cycle of IVF-ET with ultra-long GnRH agonist protocol were included in this retrospective cohort study. They were divided into three groups: (A) 428 patients with diffuse adenomyosis; (B) 718 patients with focal adenomyosis; and (C) 519 patients with tubal infertility. Reproduction outcomes were analysed.

The UBE2C/CDH1/DEPTOR axis is an oncogene and tumor suppressor cascade in lung cancer cells.

Ubiquitin-conjugating enzyme E2C (UBE2C) mediates ubiquitylation chain formation via the K11 linkage. While previous in vitro studies showed that UBE2C plays a growth-promoting role in cancer cell lines, the underlying mechanism remains elusive. Still unknown is whether and how UBE2C plays a promoting role in vivo.

The Sag-Shoc2 axis regulates conversion of mPanINs to cystic lesions in Kras pancreatic tumor model.

SAG/RBX2 is an E3 ligase, whereas SHOC2 is a RAS-RAF positive regulator. In this study, we address how Sag-Shoc2 crosstalk regulates pancreatic tumorigenesis induced by Kras. Sag deletion increases the size of pancreas and causes the conversion of murine pancreatic intraepithelial neoplasms (mPanINs) to neoplastic cystic lesions with a mechanism involving Shoc2 accumulation, suggesting that Sag determines the pathological process via targeting Shoc2.

The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan.

Accurate genotype imputation requires large-scale reference panel datasets. When conducting genotype imputation on the Japanese population, researchers can use such datasets under collaborative studies or controlled access conditions in public databases. We developed the NBDC-DDBJ imputation server, which securely provides users with a web user interface to execute genotype imputation on the server.

Multi-color live-cell STED nanoscopy of mitochondria with a gentle inner membrane stain.

Capturing mitochondria's intricate and dynamic structure poses a daunting challenge for optical nanoscopy. Different labeling strategies have been demonstrated for live-cell stimulated emission depletion (STED) microscopy of mitochondria, but orthogonal strategies are yet to be established, and image acquisition has suffered either from photodamage to the organelles or from rapid photobleaching. Therefore, live-cell nanoscopy of mitochondria has been largely restricted to two-dimensional (2D) single-color recordings of cancer cells.

Radiation-assisted strategies provide new perspectives to improve the nanoparticle delivery to tumor.

Nanoparticles (NPs), with advantages in tumor targeting, have been extensively developed for anticancer treatment. However, the delivery efficacy of NPs tends to be heterogeneous in clinical research. Surprisingly, a traditional cancer treatment, radiotherapy (radiation), has been observed with the potential to improve the delivery of NPs by influencing the features of the tumor microenvironment, which provides new perspectives to overcome the barriers in the NPs delivery.

TogoVar: A comprehensive Japanese genetic variation database.

TogoVar ( https://togovar.org ) is a database that integrates allele frequencies derived from Japanese populations and provides annotations for variant interpretation. First, a scheme to reanalyze individual-level genome sequence data deposited in the Japanese Genotype-phenotype Archive (JGA), a controlled-access database, was established to make allele frequencies publicly available.

Piwil2 (Mili) sustains neurogenesis and prevents cellular senescence in the postnatal hippocampus.

Adult neural progenitor cells (aNPCs) ensure lifelong neurogenesis in the mammalian hippocampus. Proper regulation of aNPC fate has thus important implications for brain plasticity and healthy aging. Piwi proteins and the small noncoding RNAs interacting with them (piRNAs) have been proposed to control memory and anxiety, but the mechanism remains elusive.

LncRNA-WAKMAR2 regulates expression of CLDN1 to affect skin barrier through recruiting c-Fos.

Background: Chronic actinic dermatitis (CAD) is an immune-mediated photo-allergic skin disease. In the clinic, the treatment of this disease is hampered by the lack of proper understanding of the skin barrier dysfunction mechanism.

Objective: To illuminate the mechanism of skin barrier dysfunction in CAD.

An Optical Approach for Cell Pellet Detection.

Cell-based screening methods are increasingly used in diagnostics and drug development. As a result, various research groups from around the world have been working on this topic to develop methods and algorithms that increase the degree of automation of various measurement techniques. The field of computer vision is becoming increasingly important and has therefore a significant influence on the development of various processes in modern laboratories.

Post-translational modifications: emerging regulators manipulating jasmonate biosynthesis and signaling.

Jasmonate (JA) is one of the key phytohormones essential for plant development and defense processes. The core JA biosynthetic and signaling pathways have been well-characterized. Notably, post-translational modifications (PTMs), which affect the protein structures and functions, have emerged as critical mechanisms to modulate JA output at different spatiotemporal levels.

Essential Oils from the Leaves, Stem, and Roots of Druce in Vietnam: Determination of Chemical Composition, and In Vitro, In Vivo, and In Silico Studies on Anti-Inflammatory Activity.

Druce, a flowering plant, is used for treating cancer and inflammatory diseases. In this study, we determined the chemical composition of the EOs extracted from the leaves (LBEO), stem (SBEO), and roots (RBEO) of and analyzed their anti-inflammation potential. Overall, 30 compounds representing 99.

Gallium-Based Nanoplatform for Combating Multidrug-Resistant and Postoperative Inflammation in Endophthalmitis Secondary to Cataract Surgery.

Postcataract endophthalmitis (PCE), a devastating complication following cataract surgeries, is one of the most crucial diseases causing irreversible eye blindness. (PA), a multiple-drug-resistance (MDR) pathogen, always leads to uncontrolled infection and severe inflammation in PCE that can be difficult to treat by antibiotics. Therefore, it is urgent to develop new feasible strategies composed of both antibacterial and anti-inflammatory capabilities.

The ProteomeXchange consortium at 10 years: 2023 update.

Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.

Evaluating a Novel Gas Sensor for Ambient Monitoring in Automated Life Science Laboratories.

Air pollution and leakages of hazardous and toxic gases and chemicals are among the dangers that frequently occur at automated chemical and life science laboratories. This type of accident needs to be processed as soon as possible to avoid the harmful side effects that can happen when a human is exposed. Nitrogen oxides and volatile organic compounds are among the most prominent indoor air pollutants, which greatly affect the lifestyles in these places.