Biology subjects

Zinchenko, A.

Publications and source records attributed to Zinchenko, A..

4 recordsLinked to original sources

bioRxiv2026

The Attentional Thief: How Self-Paced Visual Exploration Compresses Subjective Time

Social media users often feel that time vanishes while scrolling, but real feeds confound novelty, rewards, social signals, and self-paced control, leaving the driver of this distortion unclear. We tested whether self-paced visual exploration is sufficient to compress subjective time by comparing active scrolling with passive, yoked viewing and a static baseline. Twenty-three adults viewed sequences of natural images under three within-subject conditions: Scrolling (self-paced mouse clicks), Watching (a passive, yoked replay of their own scrolling sequence), and a Baseline (a static image). Participants estimated the elapsed duration of each block. Subjective duration was most compressed under Scrolling (48% of elapsed time), followed by Watching (51%) and Baseline (65%). Two sources separated these effects. Adding back the empty inter-image fixations brought the image-rich conditions to within seconds of the Baseline, showing that observers barely counted the blank gaps; the Scrolling-Watching difference, by contrast, was independent of these shared gaps, isolating self-paced control as a second source of compression. Electrophysiology linked that control to anticipatory neural states and the timing of early visual responses, with no amplified encoding of individual images. The results favor an attention-weighted account of timing, on which subjective duration tracks how much attention reaches the clock, a resource that a self-paced stream and its uncounted gaps both draw away.

neuroscience↗

bioRxiv2023

Rapid quantitative assessment of small molecule leakage from microdroplets by flow cytometry and improvement of fluorophore retention in biochemical assays

Microdroplets are compartments made in the laboratory that allow the miniaturisation of chemical and biological experiments to the femto- to picolitre scale, replacing the classical test tube with a droplet. Ideally containment of the contents of individual droplets would be perfect, but in reality this situation rarely occurs. Instead the leaking of molecules even from intact droplets presents a challenge to the success of miniaturisation and must be assessed on a case-by-case basis. We now present a new method for quantitative determination of leakage: a sheath fluid-free flow cytometer (Guava EasyCyte) is used to directly determine the fluorescence of water-in-oil droplets as a function of time. We validate this method by demonstrating that this assessment of leakage provides a framework for experimental improvements that reduce the leakage of two widely used fluorophores. A 40-fold better retention compared to current protocols is achieved for resorufin with an optimized mix (oil: FC-70, surfactant: 0.1% w/w AZ900C, additive: 1% BSA) to maintain useful retention for up to 130 hours. Likewise leakage of the fluorophore methylumbelliferone is reduced by 75-fold. The availability of a method to quantitate leakage quickly for a variety of experimental conditions will facilitate future applications of droplet-based experiments (e.g. in directed evolution or diagnostics), aid miniaturisation of lab-scale assays into this format, and improve the degrees of freedom in setting up such ultrahigh-throughput experiments.

bioengineering↗

bioRxiv2023

Electrophysiological signatures of temporal context in the bisection task

Despite relatively accurate time judgment, subjective time is susceptible to various contexts, such as sample spacing and frequency. Several electroencephalographic (EEG) components have been linked to timing, including the contingent negative variation (CNV), offset P2, and late positive component of timing (LPCt). However, the specific role of these components in the contextual modulation of perceived time remains unclear. In this study, we conducted two temporal bisection experiments, where participants had to judge if a test duration was close to a short or long standard. Unbeknownst to participants, the sample spacing (Experiment 1) and frequency (Experiment 2) were altered to create short and long contexts while keeping the test range and standards the same in different sessions. The results showed that the bisection threshold shifted toward the ensemble mean and that CNV and LPCt were sensitive to context modulation. Compared to the long context, the CNV climbing rate increased in the short context, and the amplitude and latency of the LPCt were reduced. These findings suggest the CNV represents an expectancy wave for upcoming decision-making, while LPCt reflects the decision-making process, both influenced by the temporal context.

neuroscience↗

bioRxiv2018

High-Throughput, Lysis-free Screening for sulfatase Activity Using Escherichia coli Autodisplay in Microdroplets

Directed evolution of enzymes toward improved catalytic performance has become a powerful tool in protein engineering. To be effective, a directed evolution campaign requires the use of high-throughput screening. In this study we describe the development of a high-throughput lysis-free procedure to screen for improved sulfatase activity by combining microdroplet-based single-variant activity sorting with E. coli autodisplay. For the first step in a 4-step screening procedure we quantitatively screened >105 variants of the homodimeric arylsulfatase from Silicibacter pomeroyi (SpAS1), displayed on the E. coli cell surface, for improved sulfatase activity using fluorescence activated droplet sorting. Display of the sulfatase variants on living E. coli cells ensured the continuous linkage of genotype and phenotype during droplet sorting and allowed for direct recovery by simple regrowth of the sorted cells. The use of autodisplay on living cells simplified and reduced the degree of liquid handling during all steps in the screening procedure to the single event of simply mixing substrate and cells. The percentage of apparent improved variants was enriched >10-fold as a result of droplet sorting. We ultimately identified 25 SpAS1-variants with improved performance toward 4-nitrophenyl sulfate (up to 6.2-fold) and/or fluorescein disulfate (up to 30-fold). In SpAS1 variants with improved performance toward the bulky fluorescein disulfate, many of the beneficial mutations occur in residues that form hydrogen bonds between -helices in the C-terminal oligomerization region, suggesting a non-trivial, previously unknown role for the dimer interface in shaping the substrate binding site of SpAS1.\n\nTable of contents graphic\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC=\"FIGDIR/small/479162v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@1f9211aorg.highwire.dtl.DTLVardef@ec3b2dorg.highwire.dtl.DTLVardef@1214667org.highwire.dtl.DTLVardef@1952a50_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗