Biology subjects

Pollak, B.

Publications and source records attributed to Pollak, B..

6 recordsLinked to original sources

bioRxiv2025

Pigs' brain responses to stroking after long-term positive human interactions: An fMRI exploratory study

Positive interactions with humans can induce pleasurable experiences in animals, but their underlying neurobiology mechanisms are unknown. We investigated the brain responses (Functional Magnetic Resonance Imaging) to stroking by a human in 20 pigs under general anaesthesia. Ten pigs received positive human contacts over 9 weeks post-weaning (POS) and 10 pigs did not (CTL). Images from CTL pigs showed peaks of activation in the primary somatosensory cortex, caudate nucleus, anterior prefrontal cortex, and dorsal anterior cingulate cortex during stroking. Greater peaks of activation in the anterior prefrontal, ventral anterior cingulate, primary somatosensory and somatosensory association cortices were observed in POS pigs; whereas greater peaks of activation in the amygdala were observed in CTL pigs. Therefore, stroking is perceived and possibly elicited positive emotions in anesthetised pigs, and it may be perceived as more pleasant by experienced pigs than naive pigs, which may rather perceive it as a novel stimulus. Highlights- The brain of anaesthetised pigs can perceive tactile stimuli - Stroking by humans is a pleasurable experience for pigs - Experience with positive contacts enhances signs of positive perception of stroking

neuroscience↗

bioRxiv2023

Antisense transcription interferes with heterologous expression of a codon-optimised mNeonGreen fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii.

Although over 30 years have passed since Chlamydomonas reinhardtii chloroplast transformation was first achieved, robust genetic engineering of the chloroplast still remains a challenging task. The glass-bead transformation method has enabled simple and accessible chloroplast transformation of the C. reinhardtii TN72 strain, allowing generation of marker-free transplastomic strains for low-cost experimentation. However, lack of functional in vivo fluorescent reporters limit research and widespread development of chloroplast engineering. Here, we developed a chloroplast codon-optimised mNeonGreen fluorescent reporter, which can be detected in vivo through fluorescence microscopy and fluorometry, by context-aware construct engineering, leading up to a [~]6-fold increase in fluorescence. We found evidence for chloroplast post-transcriptional regulation of gene expression derived from formation of antisense pairing of mRNAs due to transcriptional readthrough of the convergent adjacent gene, which was validated through detection of the double-stranded RNA. In addition, engineering approaches were used to modulate transcriptional readthrough, allowing a better understanding of context effects that are relevant for heterologous expression. Finally, we characterised a suite of regulatory parts for transgene expression in a sense-transcriptional context regarding to the selectable marker, achieving up to [~]2-fold increase in mNeonGreen fluorescence levels regarding to the control, with the use of PrrnS, 5atpA and 3rbcL endogenous regulatory sequences from the chloroplast of C. reinhardtii. This work provides new tools for studying basic aspects of the molecular biology in the chloroplast in C. reinhardtii, as well as evidence for fundamental processes of gene regulation that may enable developing rules for more efficient chloroplast engineering.

plant biology↗

bioRxiv2022

Viroscope: plant viral diagnosis from NGS data using biologically-informed genome assembly coverage

Next-generation sequencing (NGS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care NGS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particularly in cases of low sequencing coverage. Lack of standardized metrics and harmonized detection thresholds confound the problem further, impeding the adoption and implementation of these solutions in real-world applications. In this work, we tackle these issues and propose biologically-informed viral genome assembly coverage as a method to improve diagnostic certainty. We use the identification of viral replicases, an essential function of viral life cycles, to define genome coverage thresholds in which biological functions can be described. We validate the analysis pipeline, Viroscope, using field samples, synthetic and published datasets and demonstrate that it provides sensitive and specific viral detection. Furthermore, we developed Viroscope.io a web-service to provide on-demand NGS data viral diagnosis to facilitate adoption and implementation by phytosanitary agencies to enable precise viral diagnosis.

microbiology↗

bioRxiv2021

Bacterial small RNAs and host epigenetic effectors of a transgenerational memory of pathogens in C. elegans.

The inheritance of memories is adaptive for survival. Microbes interact with all organisms challenging their immunity and triggering behavioral adaptations. Some of these behaviors induced by bacteria can be inherited although the mechanisms of action are largely unexplored. In this work, we use C. elegans and its bacteria to study the transgenerational RNA dynamics of an interspecies crosstalk leading to a heritable behavior. Heritable responses to bacterial pathogens in the nematode include avoidance and pathogen-induced diapause (PIDF), a state of suspended animation to evade the pathogen threat. We identify a small RNA RsmY, involved in quorum sensing from P. aeruginosa as required for initiation of PIDF. Histone methyltransferase SET-18/SMYD3 is also needed for PIDF initiation in C. elegans. In contrast, SET-25/EHMT2 is necessary for the maintenance of the memory of pathogen exposure in the transgenerational lineage. This work can be a starting point to understanding microbiome-induced inheritance of acquired traits.

microbiology↗

bioRxiv2019

Universal Loop assembly (uLoop): open, efficient, and species-agnostic DNA fabrication

Standardised Type IIS DNA assembly methods are becoming essential for biological engineering and research. Although a common syntax has been proposed to enable higher interoperability between DNA libraries, Golden Gate (GG)-based assembly systems remain specific to target organisms. Furthermore, these GG assembly systems become laborious and unnecessarily complicated beyond the assembly of 4 transcriptional units. Here, we describe \"universal Loop\" (uLoop) assembly, a simple system based on Loop assembly that enables hierarchical fabrication of large DNA constructs (> 30 kb) for any organism of choice. uLoop comprises two sets of four plasmids that are iteratively used as odd and even levels to compile DNA elements in an exponential manner (4n-1). The elements required for transformation/maintenance in target organisms are also assembled as standardised parts, enabling customisation of host-specific plasmids. Thus, this species-agnostic method decouples efficiency of assembly from the stability of vectors in the target organism. As a proof-of-concept, we show the engineering of multi-gene expression vectors in diatoms, yeast, plants and bacteria. These resources will become available through the OpenMTA for unrestricted sharing and open-access.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC=\"FIGDIR/small/744854v2_ufig.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@c36f4forg.highwire.dtl.DTLVardef@c0b007org.highwire.dtl.DTLVardef@64c810org.highwire.dtl.DTLVardef@8a94b0_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2018

Loop Assembly: a simple and open system for recursive fabrication of DNA circuits

High efficiency methods for DNA assembly are based on sequence overlap between fragments or Type IIS restriction endonuclease cleavage and ligation. These have enabled routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customisation, elaborate vector sets and serial manipulations for the different stages of assembly. We present Loop assembly, based on a recursive approach to DNA fabrication. Alternate use of two Type IIS restriction endonucleases and corresponding vector sets allows efficient and parallel assembly of large DNA circuits. Plasmids containing standard Level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly provides a simple generalised solution for DNA construction with standardised parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.

synthetic biology↗