Biology subjects

Marti, S.

Publications and source records attributed to Marti, S..

8 recordsLinked to original sources

bioRxiv2023

Adeno-associated virus (AAV2) can replicate its DNA by a rolling hairpin or rolling circle mechanism, depending on the helper virus.

Adeno-associated virus type 2 (AAV2) is a small, non-pathogenic, helper virus-dependent parvovirus with a single-stranded (ss) DNA genome of approximately 4.7 kb. AAV2 DNA replication requires the presence of a helper virus such as adenovirus type 5 (AdV5) or herpes simplex virus type 1 (HSV-1) and is generally assumed to occur as a strand-displacement rolling hairpin (RHR) mechanism initiated at the AAV2 3 inverted terminal repeat (ITR). We have recently shown that AAV2 replication supported by HSV-1 leads to the formation of double-stranded head-to-tail concatemers, which provides evidence for a rolling circle replication (RCR) mechanism. We have revisited AAV2 DNA replication and specifically compared the formation of AAV2 replication intermediates in presence of either HSV-1 or AdV5 as the helper virus. The results confirmed that the AAV2 DNA replication mechanism is helper virus-dependent and follows a strand-displacement RHR mechanism when AdV5 is the helper virus and primarily an RCR mechanism when HSV-1 is the helper virus. We also demonstrate that recombination plays a negligible role in AAV2 genome replication. Interestingly, the formation of high molecular weight AAV2 DNA concatemers in presence of HSV-1 as the helper virus was dependent on an intact HSV-1 DNA polymerase. ImportanceAAV is a small helper virus-dependent, non-pathogenic parvovirus. The AAV genome replication mechanism was extensively studied in presence of AdV as the helper virus and described to proceed using RHR. Surprisingly, HSV-1 co-infection facilitates RCR of the AAV2 DNA. We directly compared AdV5 and HSV-1 supported AAV2 DNA replication and show that AAV2 can adapt its replication mechanism to the helper virus. Detailed understanding of the AAV replication mechanism expands our knowledge of virus biology and can contribute to increase gene therapy vector production.

molecular biology↗

bioRxiv2021

Orthogonal neural codes for phonetic features in the infant brain

Creating invariant representations from an ever-changing speech signal is a major challenge for the human brain. Such an ability is particularly crucial for preverbal infants who must discover the phonological, lexical and syntactic regularities of an extremely inconsistent signal in order to acquire language. Within visual perception, an efficient neural solution to overcome signal variability consists in factorizing the input into orthogonal and relevant low-dimensional components. In this study we asked whether a similar neural strategy grounded on phonetic features is recruited in speech perception. Using a 256-channel electroencephalographic system, we recorded the neural responses of 3-month-old infants to 120 natural consonant-vowel syllables with varying acoustic and phonetic profiles. To characterize the specificity and granularity of the elicited representations, we employed a hierarchical generalization approach based on multivariate pattern analyses. We identified two stages of processing. At first, the features of manner and place of articulation were decodable as stable and independent dimensions of neural responsivity. Subsequently, phonetic features were integrated into phoneme-identity (i.e. consonant) neural codes. The latter remained distinct from the representation of the vowel, accounting for the different weights attributed to consonants and vowels in lexical and syntactic computations. This study reveals that, despite the paucity of articulatory motor plans and productive skills, the preverbal brain is already equipped with a structured phonetic space which provides a combinatorial code for speech analysis. The early availability of a stable and orthogonal neural code for phonetic features might account for the rapid pace of language acquisition during the first year. SIGNIFICANCE STATEMENTFor adults to comprehend spoken language, and for infants to acquire their native tongue, it is fundamental to perceive speech as a sequence of stable and invariant segments despite its extreme acoustic variability. We show that the brain can achieve such a critical task thanks to a factorized representational system which breaks down the speech input into minimal and orthogonal components: the phonetic features. These elementary representations are robust to signal variability and are flexibly recombined into phoneme-identity percepts in a secondary processing phase. In contradiction with previous accounts questioning the availability of authentic phonetic representations in early infancy, we show that this neural strategy is implemented from the very first stages of language development.

neuroscience↗

bioRxiv2020

An abstract language of thought for spatial sequences in humans

How does the human brain store sequences of spatial locations? The standard view is that each consecutive item occupies a distinct slot in working memory. Here, we formulate and test the alternative hypothesis that the human brain compresses the whole sequence using an abstract, language-like code that captures the numerical and geometrical regularities of the sequence at multiple nested levels. We exposed participants to spatial sequences of fixed length but variable regularity, and asked them to remember the sequence in order to detect deviants, while their brain activity was recorded using magneto-encephalography. Using multivariate decoders, each successive location could be decoded from brain signals, and upcoming locations were anticipated prior to their actual onset. Crucially, sequences with lower complexity, defined as the minimal description length provided by the formal language, and whose memory representation was therefore predicted to be more compressed, led to lower error rates and to increased anticipations. Furthermore, neural codes specific to the numerical and geometrical primitives of the postulated language could be detected, both in isolation and within the sequences. These results suggest that the human brain detects sequence regularities at multiple nested levels and uses them to compress long sequences in working memory.

neuroscience↗

bioRxiv2019

Establishment of primary transgenic human airway epithelial cell cultures to study respiratory virus-host interactions

Primary human airway epithelial cell (hAEC) cultures represent a universal platform to propagate respiratory viruses and characterize their host interactions in authentic target cells. To further elucidate specific interactions between human respiratory viruses and important host factors in airway epithelium, it is important to make hAEC cultures amenable to genetic modification. However, the short and finite lifespan of primary cells in cell culture creates a bottleneck for the genetic modification of these cultures. In the current study, we show that the incorporation of the Rho-associated protein kinase (ROCK) inhibitor (Y-27632) during cell propagation extends the life span of primary human cells in vitro and thereby facilitates the incorporation of lentivirus-based expression systems. Using fluorescent reporters for FACS-based sorting, we generated homogenously fluorescent hAEC cultures that differentiate normally after lentiviral transduction. As proof-of-principle, we demonstrate that host gene expression can be modulated post-differentiation via inducible short hairpin (sh)RNA-mediated knockdown. Importantly, functional characterization of these transgenic hAEC cultures with exogenous poly(I:C), as a proxy for virus infection, demonstrates that such modifications do not influence the host innate immune response. Moreover, the propagation kinetics of both human coronavirus 229E (HCoV-229E) and human respiratory syncytial virus (RSV) were not affected. Combined, these results validate our newly established protocol for the genetic modification of hAEC cultures thereby unlocking a unique potential for detailed molecular characterization of virus - host interactions in human respiratory epithelium.

microbiology↗

bioRxiv2018

Probing the limits of activity-silent non-conscious working memory

Two types of working memory (WM) have recently been proposed: conscious active WM, depending on sustained neural activity, and activity-silent WM, requiring neither conscious awareness nor accompanying neural activity. However, whether both states support identical forms of information processing is unknown. Theory predicts that activity-silent states are confined to passive storage and cannot operate on stored information. To determine whether an explicit reactivation is required prior to the manipulation of information in WM, we evaluated whether participants could mentally rotate brief visual stimuli of variable subjective visibility. Behaviorally, even for unseen targets, subjects reported the rotated location above chance after several seconds. As predicted, however, such blindsight performance was accompanied by neural signatures of conscious reactivation at the time of mental rotation, including a sustained desynchronization in alpha/beta frequency and a decodable representation of participants guess and response. Our findings challenge the concept of genuine non-conscious \"working\" memory, argue that activity-silent states merely support passive short-term memory, and provide a cautionary note for purely behavioral studies of non-conscious information processing.

neuroscience↗

bioRxiv2018

Posttranscriptional regulation of intestinal epithelial cell repair by RNA binding protein IMP1

RNA binding proteins, such as IMP1, are emerging as essential regulators of intestinal development and cancer. IMP1 hypomorphic mice exhibit severe intestinal growth defects, yet its role in adult intestinal epithelium is unclear. We employed ribosome profiling to test the effect of IMP1 loss on the \"translatome\" in colon cancer cell lines. In parallel, we evaluated mice with intestinal epithelial-specific Imp1 deletion (Imp1{Delta}IEC) following irradiation or colitis models. Ribosome-profiling revealed translation efficiency changes for multiple pathways important for intestinal homeostasis, including autophagy, in IMP1 knockout cells. We found increased autophagy flux in Imp1{Delta}IEC mice, reinforced through in silico and biochemical analyses revealing direct binding of IMP1 to autophagy transcripts MAP1LC3B and ATG3. We found that Imp1{Delta}IEC mice exhibit enhanced recovery following irradiation, which is attenuated with genetic deletion of autophagy gene Atg7. Finally, we demonstrated that IMP1 is upregulated in Crohns disease patients and Imp1 loss lessened colitis severity in mice. These studies demonstrate that IMP1 acts as a posttranscriptional regulator of gut epithelial repair post-irradiation and colitis, in part through modulation of autophagy.

physiology↗

bioRxiv2018

A method for RNA structure prediction shows evidence for structure in lncRNAs

To compare the secondary structures of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure at single-nucleotide resolution using sequence information, and the Dynamic Time Warping (DTW) method to align profiles of different lengths. We applied CROSSalign to investigate the structural conservation of long non-coding RNAs such as XIST and HOTAIR as well as ssRNA viruses including HIV. In a pool of sequences with the same secondary structure CROSSalign accurately recognizes repeat A of XIST and domain D2 of HOTAIR and outperforms other methods based on covariance modelling. CROSSalign can be applied to perform pair-wise comparisons and is able to find homologues between thousands of matches identifying the exact regions of similarity between profiles of different lengths. The algorithm is freely available at the webpage http://service.tartaglialab.com//new_submission/CROSSalign.

bioinformatics↗

bioRxiv2016

A theory of working memory without consciousness or sustained activity

Working memory and conscious perception are thought to share similar brain mechanisms, yet recent reports of non-conscious working memory challenge this view. Combining visual masking with magnetoencephalography, we demonstrate the reality of non-conscious working memory and dissect its neural mechanisms. In a spatial delayed-response task, participants reported the location of a subjectively unseen target above chance-level after a long delay. Conscious perception and conscious working memory were characterized by similar signatures: a sustained desynchronization in the alpha/beta band over frontal cortex, and a decodable representation of target location in posterior sensors. During non-conscious working memory, such activity vanished. Our findings contradict models that identify working memory with sustained neural firing, but are compatible with recent proposals of activity-silent working memory. We present a theoretical framework and simulations showing how slowly decaying synaptic changes allow cell assemblies to go dormant during the delay, yet be retrieved above chance-level after several seconds.

neuroscience↗