Biology subjects

Nag, S.

Publications and source records attributed to Nag, S..

26 records · Page 2Linked to original sources

bioRxiv2022

Cardiac myosin filaments are directly regulated by calcium

Contraction of cardiac and skeletal muscle is initiated by calcium (Ca2+) binding to regulatory proteins on actin-containing thin filaments. During muscle contraction, structural changes in Ca2+-dependent thin filament allow the binding of myosin motors to drive muscle contraction1. The dynamic switching between the resting off states and the active on states of myosin is also critical in regulating muscle contractility2-4. However, the molecular switch on the myosin-containing thick filament that drives this process is not understood. Here we show that cardiac thick filaments are directly Ca2+-regulated. We find that Ca2+ progressively moves the myosin heads from ordered off states close to the thick filament backbone to disordered on states closer to the thin filaments. This Ca2+-dependent structural shift of myosin is accompanied by a biochemically defined transition from the inactive super-relaxed state(s) to the active disordered relaxed state(s)3. Furthermore, we find that this Ca2+-mediated molecular switching is an intrinsic property of cardiac myosin but only when assembled into thick filaments. This novel concept of Ca2+ as a regulatory modulator of the thick filament provides a fresh perspective on cardiac muscle regulation, which may be particularly valuable for devising restorative treatments for pathologies altering the Ca2+ sensitivity of the sarcomere.

biophysics↗

bioRxiv2021

Visual search for upright bigrams predicts reading fluency in children

Fluent reading is an important milestone in education, but we lack a clear understanding of why children vary so widely in attaining this milestone. Language-related factors such as rapid automatized naming (RAN) and phonological awareness have been identified as important factors that influence reading fluency. Of theoretical interest is also, however, whether aspects of visual processing influence reading fluency. To investigate this issue, we tested primary school children (n = 68) on four tasks: two reading fluency tasks (word reading and passage reading), a RAN task to measure naming speed, and a visual search task using letters and bigrams to measure visual processing. As expected, the RAN score was strongly correlated with reading fluency. In addition, visual processing of bigrams was correlated with reading fluency. Importantly, this association was specific to upright but not inverted bigrams, and to bigrams with normal but not large letter spacing. Thus, reading fluency in children is accompanied by specialized changes in upright bigram processing. We propose that bigram processing during visual search could complement existing measures of language processing to understand individual differences in reading fluency.

neuroscience↗

bioRxiv2020

TWO CLASSES OF MYOSIN INHIBITORS, BLEBBISTATIN AND MAVACAMTEN, STABILIZE β-CARDIAC MYOSIN IN DIFFERENT STRUCTURAL AND FUNCTIONAL STATES

In addition to a conventional relaxed state, a fraction of myosins in the cardiac muscle exists in a newly-discovered low-energy consuming super-relaxed (SRX) state, which is kept as a reserve pool that may be engaged under sustained increased cardiac demand. The conventional and the super-relaxed states are widely assumed to correspond respectively to a structure where myosin heads are in an open configuration, free to interact with actin, and a closed configuration, inhibiting binding to actin. Disruption of the SRX population in different heart diseases, such as hypertrophic cardiomyopathy, results in unwarranted muscle contraction, and stabilizing them using myosin inhibitors is budding as an attractive therapeutic strategy. Here we examine the structure-function relationships of two myosin ATPase inhibitors, mavacamten, and blebbistatin, and found that binding of mavacamten to myosin at a site different than blebbistatin populates myosin into the SRX state. Blebbistatin, and para-nitroblebbistatin, binding to a distal pocket to the myosin lever arm near the nucleotide-binding site, does not affect the usual myosin SRX state but instead appears to render myosin into a new, perhaps non-functional, ultra-relaxed state. X-ray scattering-based rigid body modeling shows that both mavacamten and para-nitroblebbistatin induce novel conformations that diverge significantly from the hypothetical open and closed states and furthermore, mavacamten treatment causes a greater compaction than para-nitroblebbistatin. Taken together, we conclude that mavacamten and blebbistatin stabilize myosin in different structural states, and such states may give rise to different functional energy-sparing SRX states.

biochemistry↗

bioRxiv2020

A colony-level optimisation model provides a potential mechanism for the evolution of novel castes in eusocial ant colonies

Ant species often have multiple morphologically distinct castes within a single colony. Given that most of these castes are involved in non-reproductive tasks, and since such individuals thus never reproduce, the question of how ant castes can evolve is a non-trivial one. Over the years, several models have been proposed in order to explain the evolution of castes in ant colonies. Here, we attempt to answer this question using an economics-based approach, developing an optimization model that implements adaptation and selection at the colony level. We argue that due to the nature of ant colonies, selection is shifted to the group level, and, due to this, individual ants are sheltered from negative selection. We show that our framework can explain the evolution of novel castes in ant colonies, and discuss the novelty of our model with regard to previous models that have been proposed. We also show that our model is consistent with several empirical observations of ant colonies.

evolutionary biology↗

bioRxiv2020

CONSERVED INTERACTIONS IN CARDIAC SYNTHETIC THICK FILAMENTS DIFFERENTLY AFFECT MYOSIN SUPER-RELAXED STATE IN HEALTHY, DISEASE AND MAVACAMTEN-TREATED MODELS

A hallmark feature of myosin-II is that it can spontaneously self-assemble into bipolar synthetic thick filaments (STFs) in low ionic strength buffers, thereby serving as a reconstituted in vitro model for muscle thick filament. While these STFs have been extensively used for structural characterization, their use for functional studies has been very limited. In this report, we show that the ultra-low ATP-consuming super-relaxed (SRX) state of myosin is electrostatically more stable in STFs as compared with shorter myosin sub-fragments that lack the distal tail required for thick filament assembly. However, this electrostatic stability of the SRX state is weakened by phosphorylation of myosin light chains or the hypertrophic cardiomyopathy-causing myosin R403Q mutation. We also show that ADP binding to myosin depopulates the SRX population in STFs made of wild-type (WT) myosin, but not in S1, HMM, or STFs made of mutant R403Q myosin. Collectively, these findings emphasize that a critical network of inter- and intra-molecular interactions that underlie the SRX state of myosin are mostly preserved in STFs, establishing it as a native-like tool to interrogate myosin regulation. Next, using STFs, we show that a clinical-stage small molecule inhibitor, mavacamten, is more effective in promoting the myosin SRX state in STFs than in S1 or HMM and that it is equally potent in STFs made of atrial-WT, ventricular-WT, and mutant-R403Q myosin. Also, we found that mavacamten-bound heads are not permanently protected in the SRX state but can be recruited in response to physiological perturbations, thus providing new insights into its inhibitory mechanism.

biochemistry↗

bioRxiv2019

Neuromodulation of pelvic nerve during early phase of spinal cord injury in rats using implantable prototype devices - a preliminary study.

ObjectivesThe bladder becomes retentive during the early phase of spinal cord injury, and requires proper bladder management to prevent damage to the lower urinary tract and kidney. We investigated the effects of on-demand pelvic nerve stimulation on the areflexive bladder during the earliest phase of complete spinal cord injury in rats and the use of pelvic nerve signals as a proxy to estimate intravesical pressure for closed-loop applications.\n\nMaterials and MethodsIn order to stimulate the pelvic nerves in female Sprague-Dawley rats with complete spinal cord transection (T7 level), a flexible electrode was implanted unilaterally on pelvic nerve, and electrical stimulation was provided by a custom-built nerve stimulator. Stimulation-evoked voiding was monitored in the awake state while size, capacity and spontaneous contractions of the bladder were analysed under anaesthesia. Separately, recordings of the pelvic nerve signals, external urethral sphincter activity and intravesical pressure were performed in animals with intact and transected spinal cord under anaesthesia.\n\nResultsSuccessful pelvic nerve stimulation enabled more frequent voiding, reduced overdistension of bladder, and preserved non-voiding spontaneous bladder contractions. Typical bladder management protocol for SCI rats (manual expression every 8 - 12 hours) resulted in more severe bladder overdistention. Signal processing of the recorded extraneural pelvic nerve signals successfully reconstructed changes in intravesical pressure, demonstrating their use in estimating the fullness and contractions of the bladder.\n\nConclusionsThe preliminary results suggest that pelvic nerve stimulators can serve as an alternative method for frequent emptying of the areflexive bladder. Simultaneous recording of the same pelvic nerve will be useful for development of a closed-loop neuroprosthesis.

neuroscience↗

bioRxiv2018

Proof of concept: Malaria rapid diagnostic tests and massively parallel sequencing for surveillance of molecular markers of antimalarial resistance in Bissau, Guinea-Bissau during 2014-2017

Real-time and large-scale surveillance of molecular markers of antimalarial drug resistance is a potential method of resistance monitoring, to complement therapeutic efficacy studies in settings where the latter are logistically challenging. This study investigates whether routinely used malaria rapid diagnostic tests (RDTs) can be used for massive parallel amplicon sequencing. RDTs used for malaria diagnosis were routinely collected together with patient age and sex between 2014 and 2017, from two health centres in Bissau, Guinea-Bissau. A subset of positive RDTs (n=2,184) were tested for Plasmodium DNA content. Those containing sufficient Plasmodium DNA (n=1,390) were used for library preparation, consisting of amplification of gene fragments from pfcrt, pfmdr1, pfdhfr, pfdhps and pfK13. A total of 5532 gene fragments were successfully analysed on a single Illumina Miseq flow cell. Pre-screening of samples for Plasmodium DNA content proved necessary and the nested PCR protocol applied for library preparation varied notably in PCR-positivity from 13-87%. We found a high frequency of the pfmdr1 codon 86N at 88%-97%, a significant decrease of the pfcrt wildtype CVMNK haplotype and elevated levels of the pfdhfr/pfdhps quadruple mutant ranging from 33%-51% between 2014-2017. No polymorphisms indicating artemisinin tolerance were discovered. Lastly, the demographic data indicate a large proportion of young adults (66%, interquartile range 11-28 years) presenting with P. falciparum infections. With some caution, our findings suggest that routine collection of RDTs could facilitate large-scale molecular surveillance of antimalarial resistance.\n\nImportance (word count: 147)Continuous spread and repeated emergence of Plasmodium falciparum parasites resistant towards one or more antimalarials represents an enormous threat to current treatment efficacy levels, especially in sub-Saharan Africa, where 90% of malaria infections occur. In order to prevent substantial treatment failure, it is therefore recommended to monitor treatment efficacy every 2-3 years. Therapeutic efficacy studies, however, can present insurmountable logistical and financial challenges in some settings in sub-Saharan Africa. Molecular surveillance of antimalarial resistance is therefore an important proxy for treatment efficacy. However, the scale by which such studies can be performed depends on the development of high-throughput protocols and the accessibility of samples. If RDTs can be used in the high-throughput protocols available with Next Generation Sequencing (NGS)-technology, surveillance can be performed efficiently for any setting in which RDTs are already used for malaria diagnosis. The majority of settings in sub-Saharan Africa have access to RDTs.

molecular biology↗

bioRxiv2017

Comparative Analysis of Non-linear Behaviour with Power Spectral Intensity Response Between Normal and Epileptic EEG Signals

Epilepsy is a neurological condition which affects the nervous system. It is a general term used for a group of disorders in which nerve cells of the brain discharge anomalous electrical impulses from time to time, causing a temporary malfunction of the other nerve cells of the brain. EEG signal provides an important cue for diagnosis and interpretation related to prognosis of epilepsy. In this work we envisage to provide novel tool which can be used to detect the prognosis of epileptic disorder by comparing linear and nonlinear modalities of EEG analysis conventionally used Power spectral analysis and a robust non linear method, Detrended Fluctuation Analysis (DFA). Publicly available dataset is used for this work consisting of 100 normal patients EEG data as control group and 100 epileptic patients EEG data for comparison. Response for different frequency bands (alpha, theta, beta) of the EEG spectrum have been analyzed using Detrended Fluctuation Analysis (DFA) and Power Spectral Intensity (PSI). The comparison of the DFA scaling exponent with the spectral power data is calculated for all the 3 different frequency bands of EEG signal provide new and interesting results which have been discussed in detail.

neuroscience↗