Biology subjects

Gil, G.

Publications and source records attributed to Gil, G..

4 recordsLinked to original sources

bioRxiv2025

Multi-fiber array-based photometry system for multi-regional functional mapping in the mouse brain

Mesoscopic functional brain mapping is essential to better understanding of various brain functions and dysfunctions. However, accessing distributed neural circuits in mammalian brain regions remains a significant challenge. While fiber photometry is a versatile optical approach, existing methods often suffer from invasiveness and scalability. Here we present an affordable multi-fiber array (MFA)-based photometry system to monitor neural signals across multiple regions. Our system comprises a custom-designed MFA utilizing 50-{micro}m diameter optical fibers and off-the-shelf optical components. To demonstrate the systems versatility, we monitored GABAergic population activity using jGCaMP8s across multiple brain regions in head-fixed, awake mice. By combining with pupillometry, we identified state-dependent, region-specific GABAergic dynamics. Our MFA-based photometry system opens new avenues for investigating state-dependent neural dynamics at the mesoscopic level. To facilitate wider adoption, all codes and resources are publicly available on GitHub (https://github.com/Sakata-Lab/MFA).

neuroscience↗

bioRxiv2024

Evolutionary history and rhizosphere microbial community composition in domesticated hops (Humulus lupulus L.)

Humulus lupulus L., commonly known as hops, is a perennial crop grown worldwide and is well known for its pharmacological, commercial, and most importantly brewing applications. For hundreds of years, hops have undergone intense artificial selection with over 250 cultivated varieties being developed worldwide, all displaying differences in key characteristics such as bitter acid concentrations, flavor and aroma profiles, changes in photoperiod, growth, and pathogen/pest resistances. Previous studies have individually explored differences between cultivars, aiming to identify markers that can quickly and cost-effectively differentiate between cultivars. However, little is known about their evolutionary history and the variability in their associated rhizospheric microbial communities. Coupling phenotypic, genomic, and soil metagenomic data, our study aims to explore the global population structure and domestication history of 98 hops cultivars. Additionally, we assessed differences in growth rates, rates of viral infection, usage of dissolvable nitrogen, and soil microbial community compositions between US and non-US based cultivars. Contrary to previous studies, our study revealed that worldwide hop cultivars cluster into four primary subpopulations; Central European, English, and American ancestry as previously reported, and one new group, the Nobles, revealing further substructure amongst Central European cultivars. Modeling the evolutionary history of domesticated hops reveals an early divergence of the common ancestors of modern US cultivars around 2800 ybp, and more recent divergences with gene flow across English, Central European, and Noble cultivars, reconciled with key events in human history and migrations. Furthermore, cultivars of US origin were shown to overall outperform non-US cultivars in both growth rates and usage of dissolvable nitrogen and display novel microbial composition.

evolutionary biology↗

bioRxiv2024

The minimal number of genes needed to identify a tumor

We demonstrate that the global state of a Gene Regulatory Network [1] may be labeled by a few genes in spite of the fact that there are thousands of genes participating in it. For example, the expression values of only 3 genes are enough to discriminate between a tissue sample coming from a normal lung or a lung adenocarcinoma. We follow a pragmatic procedure, dependent on the sample set, but which is expected to become exact for large enough sets of samples. The proof relies on a scheme for the construction of perfect classification panels of genes [2], inspired by rough set theory [3].

cancer biology↗

bioRxiv2023

A bird's eye view to the homeostatic, Alzheimer and Glioblastoma attractors

Available data for white matter of the brain allows to locate the normal (homeostatic), Glioblastoma and Alzheimers disease attractors in gene expression space and to identify paths related to transitions like carcinogenesis or Alzheimers disease onset. A predefined path for aging is also apparent, which is consistent with the hypothesis of programmatic aging. In addition, reasonable assumptions about the relative strengths of attractors allow to draw a schematic landscape of fitness: a Wrights diagram. These simple diagrams reproduce known relations between aging, Glioblastoma and Alzheimers disease, and rise interesting questions like the possible connection between programmatic aging and Glioblastoma in this tissue. We anticipate that similar multiple diagrams in other tissues could be useful in the understanding of the biology of apparently unrelated diseases or disorders, and in the discovery of unexpected clues for their treatment. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/568350v3_ufig1.gif" ALT="Figure 1"> View larger version (9K): org.highwire.dtl.DTLVardef@1e2ba82org.highwire.dtl.DTLVardef@42c55dorg.highwire.dtl.DTLVardef@1ab84cforg.highwire.dtl.DTLVardef@19c32e4_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefAging, carcinogenesis and Alzheimers disease onset in white matter of the brain are shown as paths or directions in gene-expression space, a simple view that allows the analysis of their mutual relations and to rise interesting questions such as whether programmatic aging could be related to avoiding the Glioblastoma. HighlightsO_LINormal homeostatic, Glioblastoma and Alzheimers disease attractors are apparent in gene-expression space C_LIO_LIThe relative disposition of paths for carcinogenesis and Alzheimers disease onset reproduce known relations between these diseases C_LIO_LIThe observed corridor for aging is consistent with programmatic aging C_LIO_LIAvoiding the fall into the huge basin of the Glioblastoma could be the subject of selection pressure C_LIO_LIAged normal samples could be captured by the weak Alzheimers disease attractor C_LI

biophysics↗