Biology subjects

Soma, M.

Publications and source records attributed to Soma, M..

6 recordsLinked to original sources

bioRxiv2026

Proximity Labeling-Assisted Flow Cytometry Improves Fluorescence Contrast in Extracellular Vesicle-Enriched Fractions

Extracellular vesicles (EVs) are potential sources of circulating biomarkers, but disease-associated EVs are often scarce and their nanoscale dimensions limit analysis by conventional flow cytometry. To improve the detection of disease-associated EV signals using widely available instruments, we developed a workflow combining preparation of serum EV-enriched fractions by size-exclusion chromatography, CHL1-initiated enzyme-mediated activation of radical sources (EMARS) proximity labeling, and conventional flow cytometry. EMARS deposits fluorescein on molecules proximal to antibody-bound CHL1, thereby increasing target-initiated fluorescence. In a representative comparison, EMARS increased the signal-to-background ratio from 1.21 with conventional antibody labeling to 6.28. Because unlabeled EVs and debris interfered with analysis, we used an AI-assisted procedure to explore FITC-H cutoffs for retained P1 events. ChatGPT compared 65 candidate cutoffs across statistical and event-retention metrics and recommended 1000; the authors reviewed the complete results before adopting this value. At this data-selected cutoff, mean fluorescence intensity was higher in interstitial lung disease (ILD) than in non-ILD samples among 28 evaluable samples (P = 0.002; area under the receiver operating characteristic curve [AUC] = 0.846); neither value was adjusted for cutoff selection. Post hoc nested leave-oneout cross-validation (LOOCV), in which cutoff selection was repeated within each outer fold, yielded an AUC of 0.716 with 29 of 34 samples evaluable. The association with ILD requires validation in independent cohorts, but these exploratory findings suggest that proximity labeling may enhance measurable fluorescence contrast in serum EV-enriched fractions and support further evaluation of disease-associated EV signals using conventional flow cytometers.

biochemistry↗

bioRxiv2025

Age-related decline of synaptic plasticity is regulated by neuro-androgen and neuro-estrogen in normal aging of hippocampus

We revealed a good relationship between age-dependent decrease in the hippocampal dendritic spine density and age-dependent decrease in hippocampal androgen and estrogen levels with normal aging of male rats. Approximately 25% decrease in the spine density was observed in hippocampal CA1 region by going from 3 month-old (3m; young adult) to 24 month-old (24m; aged). We found a significant age-induced decrease in hippocampal neuro-androgen levels by going from 3m to 24 m using mass-spectrometric analysis. The hippocampal levels of testosterone (T) and dihydrotestosterone (DHT) dramatically decreased from 17 nM T and 7 nM DHT at 3 m to 17/100 nM T and 7/15 nM DHT at 24 m. On the other hand, hippocampal estradiol (E2) was moderately decreased with aging, from 8 nM at 3 m to 2 nM at 24m. Comprehensive analysis of mRNAs of hippocampal steroidogenic enzymes and receptors showed an age-dependent decrease in their expression levels by approximately 50% (P450(17)), 25% (17-hydroxysteroid dehydrogenase) and 0% (5-reductase and P450arom). Androgen receptor AR was moderately decreased but estrogen receptor ER was not decreased with aging. The 25% decrease in the spine density with aging may be due to a balance between considerably decreased T and DHT levels (spine decrease factor) and remained moderately high E2 level (spine increase factor) in the 24m hippocampus. Aged hippocampus still has moderate capacity of sex-steroid synthesis and their functions. Interestingly, DHT-supplementation and T-supplementation recovered the spine density at 24m.

neuroscience↗

bioRxiv2025

Rethinking synthesis and function of neuro-estrogen and neuro-androgen in the hippocampus: some methodological problems and possible solutions

Local synthesis and action of neuro-estrogen and neuro-androgen (including neuro-estradiol (nE2) and neuro-testosterone (nT) have become recognized as key mechanisms in modulation of neural plasticity and cognitive performance, in addition to the contribution of circulating sex steroids. However, still several methodological problems are left to be solved in order to get an better understanding of functions of neural sex steroids in the brain. Here we describe and discuss important improvements in the methods for determination of accurate concentrations of nE2 and nT in rat hippocampus (Section 1), and in methods for analysis of the dendritic spine density in castrated male rat hippocampus (Section 2). The improvements are discussed in order to solve the following two problems. One problem is that the previously reported nE2 concentrations in the hippocampus were widely distributed between [~]3 pg/g tissue and [~]2 ng/g tissue (i.e., between [~]11 pM and [~]7 nM) (Section 1). The other problem is that the degree of decrease in hippocampal spine density by castration in male rat hippocamps was strongly dependent on surgical skills of operators (surgeons) (Section 2).

neuroscience↗

bioRxiv2024

Inhibition of PDE5 induces rapid non-genomic increase in hippocampal dendritic spines via specific kinases

Cyclic guanosine monophosphate (cGMP) is a typical neuromodulator that is used in neuronal synapses. Inhibitor of phosphodiesterase 5 (PDE5) could regulates signaling pathways by elevating cGMP levels. In the current study, we found that the treatments with tadalafil, a PDE5 inhibitor, for 2 h rapidly and non-genomically increased the total density of dendritic spines, using confocal imaging of Lucifer Yellow-injected hippocampal CA1 pyramidal neurons. Since inhibition of PDE5 elevates cGMP levels at synapses, we analyzed downstream nongenomic signaling. We analyzed the involvement of kinase signaling, because rapid postsynaptic modulation often involves kinase networks as observed from many investigations of synaptic functions. Upon co-treatments of PKG inhibitor (KT5823) with tadalafil, the spine increase was considerably blocked. In addition, co-treatments of GSK-3 inhibitor (I8) also blocked the spine increase induced by tadalafil. However, inhibitors of other representative synaptic kinases, including LIMK, Erk/MAPK, PKA, PKC and PI3K, did not suppress the tadalafil-induced spine increases. PDE5 inhibitors have attracted attention on their recovery effects from pathological damages, including memory improvement from cognitive impairment by Stroke, Amyloid beta accumulation and tau phosphorylation. The current finding of tadalafil function about rapid modulation of neural plasticity may add new elemental steps of anti-aging capacity against cognitive decline.

neuroscience↗

bioRxiv2024

Song preferences in female Java Sparrows: Familiarity or Complexity?

Songs play an important role in mate choice for many bird species. Females of some species prefer mates with song characteristics such as complexity, or with specific temporal or note features. In some species, females also prefer familiar songs, or songs that are acoustically similar to those of their fathers. These different aspects of songs may provide distinct information about the birds that produced those songs. For example, perceived familiarity may be a signal of local adaptation, locally relevant information or learned behaviours, or genetic compatibility, while song complexity may be a signal of overall genetic quality or ability to provide parental care. As a result, multiple axes of variation could influence female song preferences. We examined female preference for song familiarity and complexity using the Java sparrow (Lonchura oryzivora) as a model species. Females were presented with two pairs of song stimuli. In one pair one song was from the females father or from a social relative with an acoustically similar song and the other was unfamiliar. In the other pair the songs differed in two aspects of complexity: note repertoire and linearity. Females preferred their fathers songs over unfamiliar songs, but we did not find strong evidence that females generalized this preference to other socially related individuals. Females also preferred complex songs, specifically those with larger note repertoires and lower linearity. Our results suggest that female song preference in Java sparrows is multi-faceted, and females may obtain multiple kinds of information from male song.

animal behavior and cognition↗

bioRxiv2023

Java sparrow song conforms to Mezerath's Law but not Zipf's Law of Abbreviation

Linguistic laws, which describe common statistical patterns in human language, are often studied in animal communication systems. Despite good evidence for adherence to these laws in non-human primate communication, there is still a paucity of data on other taxa. Birdsong is often used as a model for human language development due to similarities in vocal learning processes. Investigating whether birdsong also adheres to linguistic laws may provide further value or help determine the limitations of such comparisons. Here, we looked for patterns consistent with Menzeraths law, the tendency for longer sequences to be made up of smaller constituent parts, and Zipfs Law of Abbreviation, the tendency for more frequently used elements to be shorter in length, in the songs of Java sparrows (Padda oryzivora). We found that songs conformed to Menzeraths law at both the population and individual level; longer sequences were made up of shorter notes. This pattern was achieved through note type selection rather than the shortening of existing note types. Adherence to Menzeraths law may reflect species-specific constraints on song durations. We found no evidence to support adherence to Zipfs Law of Abbreviation, either at population or individual level; more frequently used notes were not shorter in length. However, as repertoire size in Java sparrows is small, we expect our power to detect Zipfs Law of Abbreviation to be weak. Whilst there may be some limitations in applying linguistic laws derived from human language to birdsong, especially Zipfs Law of Abbreviation, these laws may still provide insights into animal and human communication systems.

animal behavior and cognition↗