Biology subjects

Balasubramanian, S.

Publications and source records attributed to Balasubramanian, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Older individuals do not show task specific variations in EEG band power and finger force coordination

BackgroundControlling and coordinating finger force is crucial for performing everyday tasks and maintaining functional independence. Aging naturally weakens neural, muscular, and musculoskeletal systems, leading to compromised hand motor function. This decline reduces cortical activity, finger force control and coordination in older adults. ObjectiveTo examine the relationship between EEG band power and finger force coordination in older individuals and compare the results with young adults. MethodsTwenty healthy young adults aged 20-30 (26.96{+/-}2.68) and fourteen older adults aged 58-72 (62.57{+/-}3.58) participated in this study. Participants held the instrumented handle gently for five seconds then lifted and held it for an additional five seconds in the two conditions: fixed (thumb platform secured) and free condition (thumb platform may slide on slider). ResultsIn the older individuals there was no difference observed in the finger force synergy indices, and EEG beta band power between the two task conditions. However, in the young group synergy indices and EEG beta band power were less in free condition compared to fixed condition. Additionally, in the fixed condition, older adults showed a reduced synergy indices and reduced EEG beta band power than the young adults. ConclusionOlder participants showed consistent synergy indices and beta band power across conditions, unlike young adults who adjusted strategies based on tasks. Young adults exhibited task-dependent finger force synergy indices contrasting with older individuals. These results suggest that the EEG beta band power may serve as a marker for finger force coordination rather than indicating the magnitude of force.

neuroscience↗

bioRxiv2023

Atomic-scale structural insights into the functional roles of the full low complexity domain of the hnRNPA1 protein

hnRNPA1, a protein from the heterogeneous-nuclear ribonucleoprotein fam-ily, mediates cellular processes such as RNA metabolism and DNA telomere maintenance. Besides the folded RNA recognition motifs, hnRNPA1 has a [~] 135 amino-acids long low-complexity domain (LCD) consisting of an RGG-rich region and a prion-like domain (PrLD). Biochemical data suggest that RGG-rich region modulates recognition of G-quadruplexes (GQs) in the telomeric repeats. Here, we utilize an in-house developed replica exchange technique (REHT) to generate the heterogeneous conformation ensemble of hnRNPA1-RGG and explore its functional significance in telomere maintenance. Single chain statistics and abundance of structural motifs, as well as consistency with experimentally reported struc-tural data, suggest faithful recapitulation of local interactions. We also introduce a protocol to generate functionally significant IDP-nucleic acid complex structures that corroborate well with the experimental knowledge of their binding. We find that RGG-box preferentially binds to the grooves and loops of GQs providing specificity towards certain GQ structures with its Phe, Tyr, and Asn residues forming essential hydrogen bonds and electrostatic interactions. Several of these residues were also identified as important by the reported HSQC chemical shift data. Our binding and simulations studies also revealed that a minor population of the RGG-box can destabilize telomeric GQs, thereby expediting the unfolding activities of hnRNPA1-UP1 at the telomeric end.

biophysics↗

bioRxiv2023

Bloodmeal metabarcoding of the argasid tick (Ornithodoros turicata Duges) reveals extensive vector-host associations

Molecular methods to understand host feeding patterns of arthropod vectors are critical to assess exposure risk to vector-borne disease and unveil complex ecological interactions. We build on our prior work discovering the utility of PCR-Sanger sequencing bloodmeal analysis that work remarkably well for soft ticks (Acari: Argasidae), unlike for hard ticks (Acari: Ixodidae), thanks to their unique physiology that retains vertebrate DNA from prior bloodmeals viable for years. Here, we capitalize on this feature and apply bloodmeal metabarcoding using amplicon deep sequencing to identify multiple host species in individual Ornithodoros turicata soft ticks collected from two natural areas in Texas, United States. Of 788 collected O. turicata, 394 were evaluated for bloodmeal source via metabarcoding, revealing 27 different vertebrate host species (17 mammals, 5 birds, 1 reptile, and 4 amphibians) fed upon by 274 soft ticks. Information on multiple hosts for individual O. turicata was derived from 168 of these (61%). Metabarcoding revealed more mixed vertebrate bloodmeals in O. turicata previously processed using Sanger sequencing. These data reveal wide host range of O. turicata and demonstrate the value of bloodmeal metabarcoding for understanding the ecology for known and potential tick-borne pathogens circulating among humans, domestic animals and wildlife such as relapsing fever caused by Borrelia turicatae. Our results also document, for the first time an off-host soft tick collected to have evidence of prior feeding on wild pig which is a critical observation in the context of the threat of enzootic transmission of African swine fever virus if it were introduced to the US. This research enhances our understanding of vector-host associations and offers a promising perspective for biodiversity monitoring and disease control strategies.

ecology↗

bioRxiv2023

SUMO protease FUG1, histone reader AL3 and the PRC1 Complex are integral to repeat-expansion induced epigenetic silencing in Arabidopsis thaliana

Epigenetic gene silencing induced by expanded repeats can cause diverse phenotypes ranging from severe growth defects in plants to genetic diseases such as Friedreichs ataxia in humans1. The molecular mechanisms underlying repeat expansion-induced epigenetic silencing remain largely unknown2,3. Using a plant model, we have previously shown that expanded repeats can induce smallRNAs which in turn can lead to epigenetic silencing through the RNA-dependent DNA methylation pathway4,5. Here, using a genetic suppressor screen, we confirm a key role for the RdDM pathway and identify novel components required for epigenetic silencing caused by expanded repeats. We show that FOURTH ULP LIKE GENE CLASS 1 (FUG1) - a SUMO protease, ALFIN-LIKE 3 - a histone reader and LIKE HETEROCHROMATIN 1 (LHP1) - a component of the PRC1 complex are required for repeat expansion-induced epigenetic silencing. Loss of any of these components suppress repeat expansion-associated phenotypes. SUMO protease FUG1 physically interacts with AL3 and perturbing its potential SUMOylation site disrupts its nuclear localisation. AL3 physically interacts with LHP1 of the PRC1 complex and the FUG1-AL3-LHP1 module is essential to confer repeat expansion-associated epigenetic silencing. Our findings highlight the importance post-translational modifiers and histone readers in epigenetic silencing caused by repeat expansions.

genetics↗

bioRxiv2022

Interplay of the folded domain and disordered low-complexity domains along with RNA sequence mediate efficient binding of FUS with RNA

RNA binding ability of Fused in Sarcoma (FUS) protein is crucial to its cellular function. Our molecular simulation study on FUS-RNA complex provides atomic resolution insights into the observations from biochemical studies and also illuminate our understanding of molecular driving forces that mediate the structure, stability, and interaction of RRM and RGG domains of FUS with a stem-loop junction RNA. We observe a clear cooperativity and division of labour among the ordered (RRM) and disordered domains (RGG1 and RGG2 domain) of FUS that leads to an organized and tighter RNA binding. Irrespective of the length of RGG2, the RGG2-RNA interaction is confined to the stem-loop junction and the proximal stem regions. On the other hand, the RGG1-RNA interactions are primarily with the longer RNA stem. We find that the C-terminus of RRM, which make up the "boundary residues" that connect the folded RRM with the long disordered RGG2 stretch of the protein, plays a critical role in RNA binding with the RRM domain. Our study provides high-resolution molecular insights into the FUS-RNA interactions and forms the basis for understanding the molecular origins of full-length FUS interaction with RNA.

biophysics↗

bioRxiv2022

Revisiting the burden borne by fumarase: enzymatic hydration of an olefin

Fumarate hydratase (FH) is a remarkable catalyst that decreases the free energy of the catalyzed reaction by 30 kcal mol-1, much larger than most exceptional enzymes with extraordinary catalytic rates. Two classes of FH are observed in nature: class-I and class-II, that have different folds, yet catalyze the same reversible hydration/dehydration reaction of the dicarboxylic acids fumarate/malate, with equal efficiencies. Using class-I FH from the hyperthermophilic archaeon Methanocaldococcus jannaschii (Mj) as a model along with comparative analysis with the only other available class-I FH structure from Leishmania major (Lm), we provide insights into the molecular mechanism of catalysis in this class of enzymes. The structure of MjFH apo-protein has been determined, revealing that large inter-subunit rearrangements occur across apo- and the holo-protein forms, with a largely preorganized active site for substrate binding. Site-directed mutagenesis of active site residues, kinetic analysis and computational studies including DFT and natural population analysis, together show that residues interacting with the carboxylate group of the substrate play a pivotal role in catalysis. Our study establishes that an electrostatic network at the active site of class-I FH, polarizes the substrate fumarate through interactions with its carboxylate groups, thereby permitting an easier addition of a water molecule across the olefinic bond. We propose a mechanism of catalysis in FH that occurs through transition state stabilization involving the distortion of the electronic structure of the substrate olefinic bond mediated by the charge polarization of the bound substrate at the enzyme active site. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/506457v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@f2f7feorg.highwire.dtl.DTLVardef@1774e6aorg.highwire.dtl.DTLVardef@1bd180eorg.highwire.dtl.DTLVardef@1764941_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

Accurate simultaneous sequencing of genetic and epigenetic bases in DNA

DNA comprises molecular information stored via genetic bases (G, C, T, A) and also epigenetic bases, principally 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Both genetic and epigenetic information are vital to our understanding of biology and disease states. Most DNA sequencing approaches address either genetics or epigenetics and thus capture incomplete information. Methods widely used to detect epigenetic DNA bases typically fail to capture common C-to-T mutations or distinguish 5mC from 5hmC. Here, we present a single-base-resolution sequencing methodology that will simultaneously sequence complete genetics and complete epigenetics in a single workflow. The approach is non-destructive to DNA and provides a digital readout of bases, which we exemplify by simultaneous sequencing of G, C, T, A, 5mC and 5hmC; 6-Letter sequencing. We demonstrate sequencing of human genomic DNA and also cell-free DNA taken from a blood sample of a cancer patient. The approach is accurate, requires low DNA input and has a simple workflow and analysis pipeline. We envisage it will be versatile across many applications in life sciences.

genomics↗

bioRxiv2022

Comparing algorithms for assessing upper limb use with inertial measurement units

The various existing measures to quantify upper limb use from wrist-worn inertial measurement units (IMU) can be grouped into three categories: (a) Thresholded activity counting, (b) Gross movement score and (c) machine learning. While machine learning algorithms are a promising approach to detect upper limb use, there is currently no knowledge of the information used by these methods, and the data-related factors that influence their performance. A comparison of existing methods was carried out using data from a previous study which was collected from 10 unimpaired and 5 hemiparetic subjects, with annotation to identify periods of functional and non-functional upper limb use. Intra-subject random forest machine learning measures were found to classify upper limb use more accurately than other measures. The random forest measure uses information about the orientation and the amount of movement of the forearm to detect upper limb use. The types of movements and the proportion of functional data included in training/testing set influences the performance of machine learning measures. This study presents the first step towards understanding and optimizing machine learning methods for upper limb use assessment using wearable sensors.

bioengineering↗

bioRxiv2022

Sequence-directed RNA remodeling within a topologically complex RNP substrate

DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes is at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-directed remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize a post-catalytic, high-energy intermediate that drives the organization of the root helix structure within rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly.

biophysics↗

bioRxiv2022

Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA

Methylation of carbon-5 of cytosines (m5C) is a post-transcriptional nucleotide modification of RNA with widespread distribution across organisms. m5C has been shown to participate in mRNA transport and maintain mRNA stability through its recognition by the reader proteins ALYREF and YBX1, respectively. We recently showed that m5C is required for Caenorhabditis elegans development and fertility under heat stress. To contribute to the understanding of how m5C and its oxidative derivatives mediate their functions, we developed RNA baits bearing modified cytosines in diverse structural contexts to pulldown potential readers in C. elegans. Our mass spectrometry analyses reveal unique binding proteins for each of the modifications. We validate our dataset by demonstrating that the nematode ALYREF homologues ALY-1 and ALY-2 preferentially bind m5C in vitro. The dataset presented here serves as an important scientific resource that will support the discovery of new functions of m5C and its derivatives.

biochemistry↗

bioRxiv2021

Protection of nascent DNA at stalled replication forks is mediated by phosphorylation of RIF1 intrinsically disordered region

RIF1 is a multifunctional protein that plays key roles in the regulation of DNA processing. During repair of DNA double-strand breaks (DSBs), RIF1 functions in the 53BP1-Shieldin pathway that inhibits resection of DNA ends to modulate the cellular decision on which repair pathway to engage. Under conditions of replication stress, RIF1 protects nascent DNA at stalled replication forks from degradation by the DNA2 nuclease. How these RIF1 activities are regulated at the post-translational level has not yet been elucidated. Here, we identified a cluster of conserved ATM/ATR consensus SQ motifs within the intrinsically disordered region (IDR) of mouse RIF1 that are phosphorylated in proliferating B lymphocytes. We found that phosphorylation of the conserved IDR SQ cluster is dispensable for the inhibition of DSB resection by RIF1, but is essential to counteract DNA2-dependent degradation of nascent DNA at stalled replication forks. Therefore, our study identifies a key molecular switch that enables the genome-protective function of RIF1 during DNA replication stress.

molecular biology↗

bioRxiv2021

MOV10 facilitates messenger RNA decay in an N6-methyladenosine (m6A) dependent manner to maintain the mouse embryonic stem cells state

N6-methyladenosine (m6A) is the most predominant internal mRNA modification in eukaryotes, recognised by its reader proteins (so-called m6A-readers) for regulating subsequent mRNA fates -- splicing, export, localisation, decay, stability, and translation -- to control several biological processes. Although a few m6A-readers have been identified, yet the list is incomplete. Here, we identify a new m6A-reader protein, Moloney leukaemia virus 10 homologue (MOV10), in the m6A pathway. MOV10 recognises m6A-containing mRNAs with a conserved GGm6ACU motif. Mechanistic studies uncover that MOV10 facilitates mRNA decay of its bound m6A-containing mRNAs in an m6A-dependent manner within the cytoplasmic processing bodies (P-bodies). Furthermore, MOV10 decays the Gsk-3{beta} mRNA through m6A that stabilises the {beta}-CATENIN expression of a WNT/{beta}-CATENIN signalling pathway to regulate downstream NANOG expression for maintaining the mouse embryonic stem cells (mESCs) state. Thus, our findings reveal how a newly identified m6A-reader, MOV10 mediates mRNA decay via m6A that impact embryonic stem cell biology.

biochemistry↗

bioRxiv2021

Structural basis for the hyperthermostability of an archaeal glutaminase induced by post-translational succinimide formation

Stability of proteins from hyperthermophiles enabled by reduction of conformational flexibility is realized through various mechanisms. Presence of a stable, hydrolysis-resistant succinimide arising from cyclization of the side chains of aspartyl/asparaginyl residues with backbone amide -NH of the succeeding residue would restrain the torsion angle {Psi}. Here, we describe the crystal structure of Methanocaldococcus jannaschii glutamine amidotransferase (MjGATase) and address the mechanism of a succinimide-induced increased thermostability using molecular dynamics simulations. This study reveals the interplay of negatively charged electrostatic shield and n[->]{pi}* interactions in preventing succinimide hydrolysis. The stable succinimidyl residue induces formation of a conformational-lock, reducing protein flexibility. Protein destabilization upon replacement with the {Phi}-restricted prolyl residue highlights the specificity of the conformationally restrained succinimidyl residue in imparting hyperthermostability. The conservation of succinimide-forming tripeptide sequence (E(N/D)(E/D)) in a group of archaeal GATases suggests an adaptation of this otherwise detrimental post-translational modification as an inducer of thermostability.

biochemistry↗

bioRxiv2021

A Framework for Sensor-based Assessment of Upper-limb Functioning

AO_SCPLOWBSTRACTC_SCPLOWThe ultimate goal of any upper-limb neurorehabilitation procedure is to improve upper-limb functioning in daily life. While clinic-based assessments provide an assessment of what a patient can do, they do not completely reflect what a patient does in his/her daily life. The compensatory use of the less affected upper-limb (e.g. "learned non-use") in daily life is a common behavioral pattern seen in patients with hemiparesis. To this end, there has been an increasing interest in the use of wearable sensors to objectively assess upper-limb functioning. This paper presents a framework for assessing upper-limb functioning using sensors by providing: (a) a set of definitions of important construct associated with upper-limb functioning; (b) presenting different visualization methods for evaluating upper-limb functioning, along ways to qualitatively analyze different visualization methods; and (c) two new measures for quantifying how much an upper-limb is used and the relative bias in the use of the two upper-limbs. The demonstration of some of these components is presented using data collected from inertial measurement units from a previous study. The proposed framework can help guide the future technical and clinical work in this area to realize a valid, objective, and robust tool for assessing upper-limb functioning. This will in turn drive the refinement and standardization of the assessment of upper-limb functioning.

bioengineering↗

bioRxiv2020

Validating gene-phenotype associations using relationships in the UMLS

ObjectiveLarge scale next-generation sequencing of population cohorts paired with patients electronic health records (EHR) provides an excellent resource for the study of gene-disease associations. To validate those associations, researchers often consult databases that identify relationships between genes of interest and relevant disease phenotypes, which we refer to as simply "phenotypes". However, most of these databases contain phenotypes that are not suited for automated analysis of EHR data, which often captured these phenotypes in the form of International Classification of Diseases (ICD) codes. There is a need for a resource that comprehensively provides gene-phenotype mappings in a format that can be used to evaluate phenotypes from EHR. MethodsWe built a directed graph database of genes, medical concepts and ICD codes based on a subset of the National Library of Medicines Unified Medical Language System (UMLS) and other resources. To obtain associations between genes and ICD codes, we traversed the defined relationships from gene, variant and disease concepts to ICD codes, resulting in a set of mappings that link specific genes and variants to these ICD codes. ResultsOur method created 249,764 mappings between genes and ICD codes, including 27,226 "disease" phenotypes and 222,538 "symptom" phenotypes, and provided mappings for 4,456 unique genes. Paths were validated by manual review of a diverse sample of paths. In a cohort of 92,455 samples, we used these mappings to validate gene-phenotype associations in 32,786 samples where a person had a potentially disease-causing genetic mutation and at least one corresponding diagnosis in their EHR. ConclusionThe concepts and relationships in the UMLS can be used to generate gene-ICD phenotype mappings that are not explicit in the source vocabularies. We were able use these mappings to validate gene-disease associations in a large cohort of sequenced exomes paired with EHR.

bioinformatics↗

bioRxiv2020

Estimating Movement Smoothness from Inertial Measurement Units

AO_SCPLOWBSTRACTC_SCPLOWThere is an increasing trend in using inertial measurement units (IMUs) to estimate movement quality and quantity, and infer the nature of motor behavior. The current literature contains several attempts to estimate movement smoothness using data from IMUs, most of which assume that the translational and rotational kinematics measured by IMUs can be directly used with existing smoothness measures - spectral arc length (SPARC) and log dimensionless jerk (LDLJ-V). However, there has been no investigation of the validity of these approaches. In this paper, we systematically evaluate the appropriateness of the using these measures on the kinematics measured by an IMU. We show that: (a) current measures (SPARC and LDLJ-V) are inappropriate for translational movements; and (b) SPARC and LDLJ-V can be used rotational kinematics measured by an IMU. For discrete translational movements, we propose a modified version of the LDLJ-V measure, which can be applied to acceleration data (LDLJ-A), while roughly maintaining the properties of the original measure. However, accuracy of LDLJ-A depends on the IMU orientation estimation error. We evaluate the performance of these measures using simulated and experimental data. We then provide recommendations for how to appropriately apply these measures in practice, and the various factors to be aware of when performing smoothness analysis using IMU data.

bioengineering↗

bioRxiv2020

Specialisation and plasticity in a primitively social insect

Biological systems not only have the remarkable capacity to build and maintain complex spatio-temporal structures in noisy environments, they can also rapidly break up and rebuild such structures. How such systems can simultaneously achieve both robust specialisation and plasticity is poorly understood. Here we use primitive societies of Polistes wasps as a model system where we experimentally perturb the social structure by removing the queen and follow the re-establishment of the social steady state over time. We combine a unique experimental strategy correlating time-resolved measurements across vastly different scales with a theoretical approach. We show that Polistes integrates antagonistic processes on multiple scales to distinguish between extrinsic and intrinsic perturbations and thereby achieve both robust specialisation and rapid plasticity. The long-term stability of the social structure relies on dynamic DNA methylation which controls transcriptional noise. Such dynamics provide a general principle of how both specialization and plasticity can be achieved in biological systems. One Sentence SummaryA primitive social insect simultaneously achieves specialisation and plasticity by integrating antagonistic dynamics on different scales. HighlightsO_LIWe employ a unique experimental approach correlating dynamics of societies, individuals, and epigenetic gene regulation C_LIO_LIA social insect simultaneously achieves specialisation and plasticity by integrating antagonistic processes on different spatial scales C_LIO_LIRegulation of population-level noise by DNA methylation ensures long-term stability of phenotypic specialisation C_LI

biophysics↗

bioRxiv2020

Splice-site Strength Estimation: A simple yet powerful approach to analyse RNA splicing

RNA splicing, and variations in this process referred to as alternative splicing, are critical aspects of gene regulation in eukaryotes. From environmental responses in plants to being a primary link between genetic variation and disease in humans, splicing differences confer extensive phenotypic changes across diverse organisms1-3. Current approaches for analysing splicing rely on quantifying variant transcripts (i.e., isoforms) or splicing events (i.e., intron retention, exon skipping etc)4, 5. However, regulation of splicing occurs at the level of selection of individual splice sites, which results in variation in the abundance of isoforms and/or splicing events. Here, we present a simple approach to quantify the strength of individual splice sites, which determines their selection in a splicing reaction. Splice-site strength, as a quantitative phenotype, allows us to analyse splicing precisely in unprecedented ways. We demonstrate the power of this approach in defining the genomic determinants of the strength of individual splice-sites through GWAS. Our pilot-GWAS with more than thousand splice sites hints that cis-sequence divergence and competition between splice-sites and are among the primary determinants of variation in splicing among natural accessions of Arabidopsis thaliana. This approach allows deciphering the principles of splicing, which in turn has implications that range from agriculture to medicine.

genetics↗