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Article ; Online: Multivalent binding proteins can drive collapse and reswelling of chromatin in confinement.

Guha, Sougata / Mitra, Mithun K

2022

Abstract: Collapsed conformations of chromatin have been long suspected of being mediated by interactions with multivalent binding proteins, which can bring together distant sections of the chromatin fiber. In this study, we use Langevin dynamics simulation of a ... ...

Abstract	Collapsed conformations of chromatin have been long suspected of being mediated by interactions with multivalent binding proteins, which can bring together distant sections of the chromatin fiber. In this study, we use Langevin dynamics simulation of a coarse grained chromatin polymer to show that the role of binding proteins can be more nuanced than previously suspected. In particular, for chromatin polymer in confinement, entropic forces can drive reswelling of collapsed chromatin with increasing binder concentrations, and this reswelling transition happens at physiologically relevant binder concentrations. Both the extent of collapse, and also of reswelling depends on the strength of confinement. We also study the kinetics of collapse and reswelling and show that both processes occur in similar timescales. We characterise this reswelling of chromatin in biologically relevant regimes and discuss the non-trivial role of multivalent binding proteins in mediating the spatial organisation of the genome.
Language	English
Publishing date	2022-12-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2191476-X
ISSN	1744-6848 ; 1744-683X
ISSN (online)	1744-6848
ISSN	1744-683X
DOI	10.1039/d2sm00612j
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Article: The "3D Versascrew": An Innovative Approach for Management of Bilateral Cleft Lip and Palate Case.

Ashith, M V / Suma, N S / Mithun, K / Ahuja, Dhruv

Case reports in dentistry

2022 Volume 2022, Page(s) 2635167

Abstract: The purpose behind the innovation of modified nasoalveolar moulding appliance was to achieve simultaneous anteroposterior and transverse correction in bilateral cleft cases with minimal vomeroid bending. This paper presents a 3D Versascrew appliance that ...

Abstract	The purpose behind the innovation of modified nasoalveolar moulding appliance was to achieve simultaneous anteroposterior and transverse correction in bilateral cleft cases with minimal vomeroid bending. This paper presents a 3D Versascrew appliance that has been used for presurgical nasoalveolar moulding in a 15-day-old neonate with bilateral cleft. Treatment was initiated at 30 days and continued for 90 days following which mild expansion of posterior maxilla with establishment of arch continuity and concomitant improvement in nasal morphology was achieved towards the end.
Language	English
Publishing date	2022-10-27
Publishing country	Egypt
Document type	Case Reports
ZDB-ID	2627632-X
ISSN	2090-6455 ; 2090-6447
ISSN (online)	2090-6455
ISSN	2090-6447
DOI	10.1155/2022/2635167
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Article ; Online: Theoretical analysis of cargo transport by catch bonded motors in optical trapping assays.

Sundararajan, Naren / Guha, Sougata / Muhuri, Sudipto / Mitra, Mithun K

Soft matter

2024 Volume 20, Issue 3, Page(s) 566–577

Abstract: Dynein motors exhibit catch bonding, where the unbinding rate of the motors from microtubule filaments decreases with increasing opposing load. The implications of this catch bond on the transport properties of dynein-driven cargo are yet to be fully ... ...

Abstract	Dynein motors exhibit catch bonding, where the unbinding rate of the motors from microtubule filaments decreases with increasing opposing load. The implications of this catch bond on the transport properties of dynein-driven cargo are yet to be fully understood. In this context, optical trapping assays constitute an important means of accurately measuring the forces generated by molecular motor proteins. We investigate, using theory and stochastic simulations, the transport properties of cargo transported by catch bonded dynein molecular motors - both singly and in teams - in a harmonic potential, which mimics the variable force experienced by cargo in an optical trap. We estimate the biologically relevant measures of first passage time - the time during which the cargo remains bound to the microtubule and detachment force - the force at which the cargo unbinds from the microtubule, using both two-dimensional and one-dimensional force balance frameworks. Our results suggest that even for cargo transported by a single motor, catch bonding may play a role depending on the force scale which marks the onset of the catch bond. By comparing with experimental measurements on single dynein-driven transport, we estimate realistic bounds of this catch bond force scale. Generically, catch bonding results in increased persistent motion, and can also generate non-monotonic behaviour of first passage times. For cargo transported by multiple motors, emergent collective effects due to catch bonding can result in non-trivial re-entrant phenomena wherein average first passage times and detachment forces exhibit non-monotonic behaviour as a function of the stall force and the motor velocity.
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2191476-X
ISSN	1744-6848 ; 1744-683X
ISSN (online)	1744-6848
ISSN	1744-683X
DOI	10.1039/d3sm01122d
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Article ; Online: Predicting scale-dependent chromatin polymer properties from systematic coarse-graining

Sangram Kadam / Kiran Kumari / Vinoth Manivannan / Shuvadip Dutta / Mithun K. Mitra / Ranjith Padinhateeri

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 14

Abstract: Abstract Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of ... ...

Abstract	Abstract Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.
Keywords	Science ; Q
Subject code	612
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Twinkle R 3D Appliance - An Innovative Functional Skeletal Class ll Corrector.

Rai, Rohan / Joseph, Jacob / Mithun, K / Harshitha, V / Shetty, Suhani

Contemporary clinical dentistry

2020 Volume 11, Issue 4, Page(s) 382–386

Abstract: Functional appliances are widely used for regulating and directing growth in which commonly used are Frankel regulator and twinblock. Frankel regulator expands the orofacial arena for allowing growth by passive expansion, whereas twin block aids sagittal ...

Abstract	Functional appliances are widely used for regulating and directing growth in which commonly used are Frankel regulator and twinblock. Frankel regulator expands the orofacial arena for allowing growth by passive expansion, whereas twin block aids sagittal correction in retrusive mandible. Heres, an attempt to bring about both the changes in a single appliance where sagittal correction as well as keeping away constricted musculature is desired. In this appliance, passive and active expansion has been used simultaneously for better results. In the hindsight of the results, we could get in this case using Twinkle R 3D appliance, we hope that this appliance will be helpful in many more similar cases and act as adundum in clinician's armamentarium.
Language	English
Publishing date	2020-12-20
Publishing country	India
Document type	Case Reports
ZDB-ID	2582352-8
ISSN	0976-2361 ; 0976-237X
ISSN (online)	0976-2361
ISSN	0976-237X
DOI	10.4103/ccd.ccd_18_20
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Article ; Online: Dynamic modelling predicts lactate and IL-1β as interventional targets in metabolic-inflammation-clock regulatory loop in glioma.

Sharma, Shalini / Gowda, Pruthvi / Lathoria, Kirti / Mitra, Mithun K / Sen, Ellora

Integrative biology : quantitative biosciences from nano to macro

2023 Volume 15

Abstract: In an attempt to understand the role of dysregulated circadian rhythm in glioma, our recent findings highlighted the existence of a feed-forward loop between tumour metabolite lactate, pro-inflammatory cytokine IL-1β and circadian CLOCK. To further ... ...

Abstract	In an attempt to understand the role of dysregulated circadian rhythm in glioma, our recent findings highlighted the existence of a feed-forward loop between tumour metabolite lactate, pro-inflammatory cytokine IL-1β and circadian CLOCK. To further elucidate the implication of this complex interplay, we developed a mathematical model that quantitatively describes this lactate dehydrogenase A (LDHA)-IL-1β-CLOCK/BMAL1 circuit and predicts potential therapeutic targets. The model was calibrated on quantitative western blotting data in two glioma cell lines in response to either lactate inhibition or IL-1β stimulation. The calibrated model described the experimental data well and most of the parameters were identifiable, thus the model was predictive. Sensitivity analysis identified IL-1β and LDHA as potential intervention points. Mathematical models described here can be useful to understand the complex interrelationship between metabolism, inflammation and circadian rhythm, and in designing effective therapeutic strategies. Our findings underscore the importance of including the circadian clock when developing pharmacological approaches that target aberrant tumour metabolism and inflammation. Insight box The complex interplay of metabolism-inflammation-circadian rhythm in tumours is not well understood. Our recent findings provided evidence of a feed-forward loop between tumour metabolite lactate, pro-inflammatory cytokine IL-1β and circadian CLOCK/BMAL1 in glioma. To elucidate the implication of this complex interplay, we developed a mathematical model that quantitatively describes this LDHA-IL-1β-CLOCK/BMAL1 circuit and integrates experimental data to predict potential therapeutic targets. The study employed a multi-start optimization strategy and profile likelihood estimations for parameter estimation and assessing identifiability. The simulations are in reasonable agreement with the experimental data. Sensitivity analysis found LDHA and IL-1β as potential therapeutic points. Mathematical models described here can provide insights to understand the complex interrelationship between metabolism, inflammation and circadian rhythm, and in identifying effective therapeutic targets.
MeSH term(s)	Humans ; ARNTL Transcription Factors/metabolism ; Lactic Acid ; Inflammation/metabolism ; Glioma ; Cytokines
Chemical Substances	ARNTL Transcription Factors ; Lactic Acid (33X04XA5AT) ; Cytokines
Language	English
Publishing date	2023-07-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2480063-6
ISSN	1757-9708 ; 1757-9694
ISSN (online)	1757-9708
ISSN	1757-9694
DOI	10.1093/intbio/zyad008
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Article ; Online: Ultrafast time-resolved carrier dynamics in tellurium nanowires using optical pump terahertz probe spectroscopy.

Mithun, K P / Tripathi, Shalini / Roy, Ahin / Ravishankar, N / Sood, A K

Nanoscale

2023 Volume 15, Issue 30, Page(s) 12670–12678

Abstract: We report carrier relaxation dynamics in semiconducting tellurium nanowires (average diameter ∼ 10 nm) using ultrafast time-resolved terahertz spectroscopy. After photoexcitation using an 800 nm pump pulse, we observed an initial increase in the THz ... ...

Abstract	We report carrier relaxation dynamics in semiconducting tellurium nanowires (average diameter ∼ 10 nm) using ultrafast time-resolved terahertz spectroscopy. After photoexcitation using an 800 nm pump pulse, we observed an initial increase in the THz conductivity due to the absorption of THz radiation by photoexcited carriers. The time evolution of the differential conductivity (Δ
Language	English
Publishing date	2023-08-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/d3nr01588b
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Article ; Online: Anomalous diffusion of

Raza, Md Ramiz / George, Jijo Easo / Kumari, Savita / Mitra, Mithun K / Paul, Debjani

Soft matter

2023 Volume 19, Issue 34, Page(s) 6446–6457

Abstract: We report a two-layer microfluidic device to study the combined effect of confinement and chemical gradient on the motility of wild- ... ...

Abstract	We report a two-layer microfluidic device to study the combined effect of confinement and chemical gradient on the motility of wild-type
MeSH term(s)	Escherichia coli/genetics ; Microfluidics ; Chemotaxis ; Diffusion ; Glucose
Chemical Substances	Glucose (IY9XDZ35W2)
Language	English
Publishing date	2023-08-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2191476-X
ISSN	1744-6848 ; 1744-683X
ISSN (online)	1744-6848
ISSN	1744-683X
DOI	10.1039/d3sm00286a
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Article ; Online: Prevalence of Ectopic Canine in Different Sagittal and Vertical Skeletal Patterns.

Dash, Bhagabati Prasad / Ramanna, Pavithra K / Sam, George / Santhakumari, Prasanth Prathapan / Naik, Mithun K / Das, Ankita

The journal of contemporary dental practice

2023 Volume 24, Issue 4, Page(s) 268–273

Abstract: Aim: The present investigation aims to find out the prevalence of ectopic canines among skeletal class I, II, and III malocclusions and to evaluate its variability among different genders and their growth patterns.: Material and methods: The study ... ...

Abstract	Aim: The present investigation aims to find out the prevalence of ectopic canines among skeletal class I, II, and III malocclusions and to evaluate its variability among different genders and their growth patterns. Material and methods: The study sample included orthopantomograms (OPGs), lateral skull views, and study models of 999 patients collected from departmental archives. Among the selected samples, 258 were males and 738 were females. They were divided into skeletal class I, II, and III malocclusions sagittally and hypodivergent, normodivergent, and hyperdivergent groups according to their angle formed between point A-Nasion - point B (ANB) and angle formed between the Sella-Nasion (SN) plane and Gonion (Go) - Gnathion (Gn) plane (SnGoGn) values respectively. Results: Of the 999 samples, 738 (73.9%) were female and 260 (25.8%) were male patients. When compared to men, females had a higher proportion of ectopic canines. An estimated 62.3% of skeletal class I, 29.1% of skeletal class II, and 8.6% of skeletal class III cases were found to have ectopic canines. An estimated 720 (72.1%) patients were found to have maxillary ectopic canines and out of the available sample, 474 patients have horizontal growth patterns, 335 have average growth patterns and 190 patients have vertical growth patterns. Labial impaction was the commonest (65.4%) followed by palatal (24.8%). Bilateral impaction was comparatively more (51.1%) than unilateral impaction (48.2%). Maxilla was more prevalent (72.1%) as compared to the mandible (16.3%) and for both the arches it was (11.6%). Ectopic canines were identified in a total of 62.3% of cases with skeletal class I, 29.1% of cases with skeletal class II, and 8.6% of cases with skeletal class III. Conclusion: The bilateral ectopic canine was mostly seen in skeletal class I and class III malocclusions, whereas, a unilateral presentation was mostly seen in skeletal class II malocclusions. Clinical significance: Knowing the likelihood of a maxillary canine erupting ectopically will aid clinicians in starting with interceptive therapy since this condition necessitates complex orthodontic mechanics.
MeSH term(s)	Male ; Female ; Humans ; Prevalence ; Cephalometry ; Malocclusion ; Malocclusion, Angle Class III/epidemiology ; Mandible/diagnostic imaging ; Maxilla/diagnostic imaging ; Malocclusion, Angle Class II ; Tooth, Impacted/diagnostic imaging ; Tooth, Impacted/epidemiology
Language	English
Publishing date	2023-04-01
Publishing country	India
Document type	Journal Article
ISSN	1526-3711
ISSN (online)	1526-3711
DOI	10.5005/jp-journals-10024-3470
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Article ; Online: Predicting scale-dependent chromatin polymer properties from systematic coarse-graining.

Kadam, Sangram / Kumari, Kiran / Manivannan, Vinoth / Dutta, Shuvadip / Mitra, Mithun K / Padinhateeri, Ranjith

Nature communications

2023 Volume 14, Issue 1, Page(s) 4108

Abstract: Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead ... ...

Abstract	Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.
MeSH term(s)	Animals ; Mice ; Mouse Embryonic Stem Cells ; Chromatin/chemistry ; Nucleosomes/chemistry ; alpha-Globins/chemistry ; Models, Molecular ; Protein Structure, Tertiary ; Genome
Chemical Substances	Chromatin ; Nucleosomes ; alpha-Globins
Language	English
Publishing date	2023-07-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-39907-2
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