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Hait, S.

Publications and source records attributed to Hait, S..

6 recordsLinked to original sources

When Does a Pathway Score Preserve a Mediated Effect? Aggregation Geometry, Minimax Adequacy, and Gap Inference for High-Dimensional Mediation

High-dimensional mediators are routinely collapsed into low-dimensional scores before mediation analysis, but aggregation can change the mediated estimand rather than merely reduce noise. We characterize when a linear score preserves the full mediated effect. Exact preservation for every outcome model occurs precisely when the score contains the covariance-adjusted exposure-predictive mediator direction, the classical sufficient reduction for exposure under a Gaussian inverse-regression model. We introduce a distribution-free minimax adequacy loss equal to the fraction of exposure-relevant mediator information discarded by the score and exactly linked to overlap recovered by aggregation. A split-sample inverse-Wishart correction yields unbiased estimators of retained and full exposure information in moderate dimensions. Under spherically symmetric outcome-effect benchmarks, relative aggregation error has a Cauchy location-scale profile, and paired influence-function inference targets the realized gap for an observed outcome. In simulations, paired interval coverage ranged from 93.3% to 97.5%. In an outcome-free TCGA lung adenocarcinoma audit of 1,314 smoking-responsive genes, the pooled gene-mean loss was 0.811 (descriptive 95% gene-bootstrap interval 0.797 to 0.823), versus a dimension-only random-subspace benchmark of 0.913; retaining promoter and non-promoter means separately reduced pooled loss to 0.625. Independent half-sample screening was unstable, but top-100 and top-250 cross-screen pooled gene-mean losses ranged from 0.827 to 0.932. The framework separates structural adequacy, benchmark fragility, and outcome-specific discrepancy.

bioinformatics↗

Translation coupled mRNA-decay is a function of both structural and codon level characteristics

The majority of mRNA degradation occurs co-translationally. Several works in the past elucidated the role of codon composition in regulating co-translational mRNA decay. Integration of mRNA sequence, structure and ribosomal density unravels common regulatory factors of translational and degradation and helps in understanding the intricate association between these two important processes. Co-translational degradation is a two-step process, involving translational stalling and mRNA release for degradation. Our findings highlight the role of Codon Adaptation Index, a sequence-level feature that serves as the primary determinant of translation rates facilitating transcript release from translational machinery upon stalling. Concurrently, cellular endonucleases targeting Internal Unstructured Segments, facilitating easy degradation of the stalled mRNA transcripts, influencing their half-lives across the genome and over evolutionary timescales.

bioinformatics↗

Revisiting structural organization of proteins at high temperature from network perspective

Interactions between distantly placed amino acids in the primary chain (long-range) play a very crucial role in the formation and stabilization of the tertiary structure of a protein, while interactions between closely placed amino acids in the primary chain (short-range) mostly stabilize the secondary structures. Every protein needs to maintain marginal stability in order to perform its physiological functions in its native environment. The requirements for this stability in mesophilic and thermophilic proteins are different. Thermophilic proteins need to form more interactions as well as more stable interactions to survive in the extreme environment, they live in. Here, we aim to find out how the interacting amino acids in three-dimensional space are positioned in the primary chains in thermophilic and mesophilic. How does this arrangement help thermophiles to maintain their structural integrity at high temperatures? Working on a dataset of 1560 orthologous pairs we perceive that thermophiles are not only enriched with long-range interactions, they feature bigger connected clusters and higher network densities compared to their mesophilic orthologs, at higher interaction strengths between the amino acids. Moreover, we have observed the enrichment of different types of interactions at different secondary structural regions.

bioinformatics↗

Factors regulating translation coupled mRNA degradation in yeast

Codon optimality is a major factor governing translation speed and efficiency, mRNA expression, and stability. Presence of optimal codons maintains a steady translation time, while non-optimal codons can lead to slow peptidyl transfer, prolonged translation time and frequent halt. Owing to this, there are co-translational surveillance protein complexes which monitor this process meticulously and can trigger the release of the mRNA transcript after prolonged halt. The surveillance protein complexes are closely associated with various degradation enzymes which can break down these released transcripts. Degradation of the released transcripts will be ensured if they contain amenable regions for enzyme binding and action. Here, we have used sequence data to estimate the relative abundance of non-optimal codons within a transcript. We found that transcripts with high relative abundance of non-optimal codon show reduced stability and half-life compared to transcripts with lower relative abundance of non-optimal codon. We have further integrated the relative abundance of non-optimal codons with internal unstructured segments for the transcripts, to show that the former is responsible for transcript release and the latter provides susceptible platform for endonuclease cleavage, which together is capable of destabilising and reducing the transcripts half-life. Since this is a translational system, sequestration of mRNA into a dense forest of ribosomes is seen to prolong the transcripts half-life even in the presence of destabilising factors.

bioinformatics↗

Can charge-reversal be considered as a strategy for attaining thermal stability in proteins?

Do charge reversal mutations (CRM) naturally occur in mesophilic-thermophilic/hyperthermophilic (M-T/HT) orthologous proteins? Do they contribute to thermal stability by altering charge-charge interactions? A careful investigation on 1550 M-T/HT orthologous protein pairs with remarkable structural and topological similarity extracts the role of buried and partially exposed CRMs in enhancing thermal stability. Our findings could assist in engineering thermo-stable variants of proteins. SIGNIFICANCEProtein engineering is one of the hot topics for decades specifically for its applications in different fields like de-novo protein design, directed evolution, making highly stable variants for food and drug industry etc. Proteins from organisms living in extreme environments are therefore a matter of common interest for scientists from different disciplines. Over three decades of study has already found several sequence and structural adaptations related to thermal stability, while charge reversal study remains ignored to a large extent. Influenced by natures strategy, our study provides a systemic understanding of how proper designing of few partially exposed and buried CRMs significantly contributes to thermal stability by altering the short distance electrostatic interactions.

bioinformatics↗

Genome-scale conserved molecular principles of mRNA half-life regulation

Precise control of protein and mRNA degradation is essential for cellular metabolism and homeostasis. Controlled and specific degradation of both molecular species necessitates their engagements with the respective degradation machineries; this engagement involves a disordered/unstructured segment of the substrate traversing the degradation tunnel of the machinery and accessing the catalytic sites. Here, we report that mRNAs comprising longer terminal and/or internal unstructured segments have significantly shorter half-lives; the lengths of the 5' terminal, 3' terminal and internal unstructured segments that affect mRNA half-life are compatible with molecular structures of the 5' exo- 3' exo- and endo-ribonuclease machineries. Sequestration into ribonucleoprotein complexes elongates mRNA half-life, presumably by burying ribonuclease engagement sites under oligomeric interfaces. After gene duplication, differences in terminal unstructured lengths, proportions of internal unstructured segments and oligomerization modes result in significantly altered half-lives of paralogous mRNAs. Side-by-side comparison of molecular principles underlying controlled protein and mRNA degradation unravels their remarkable mechanistic similarities, and suggests how the intrinsic structural features of the two molecular species regulate their half-lives on genome-scale and during evolution.

systems biology↗