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Article ; Online: Design and Additive Manufacturing of Acetabular Implant with Continuously Graded Porosity

Sumanta Mukherjee / Santanu Dhara / Partha Saha

Bioengineering, Vol 10, Iss 675, p

2023 Volume 675

Abstract: Porous structured metallic implants are preferable as bone graft substitutes due to their faster tissue integration mediated by bone in-growth and vascularization. The porous scaffolds/implants should also mimic the graded structure of natural bone to ... ...

Abstract	Porous structured metallic implants are preferable as bone graft substitutes due to their faster tissue integration mediated by bone in-growth and vascularization. The porous scaffolds/implants should also mimic the graded structure of natural bone to ensure a match of mechanical properties. This article presents a method for designing a graded porous structured acetabular implant and identifies suitable parameters for manufacturing the model through additive manufacturing. The design method is based on slice-wise modification to ensure continuity of gradation. Modification of the slices was achieved through the binary image processing route. A geodesic dome-type design was adopted for developing the acetabular cup model from the graded porous structure. The model had a solid shell with the target porosity and pore size gradually changing from 65% and 950 µm, respectively, in the inner side to 75% and 650 µm, respectively, towards the periphery. The required dimensions of the unit structures and the combinations of pore structure and strut diameter necessary to obtain the target porosity and pore size were determined analytically. Suitable process parameters were identified to manufacture the model by Direct Metal Laser Sintering (DMLS) using Ti6Al4V powder after carrying out a detailed experimental study to minimize the variation of surface roughness and warping over different build angles of the strut structures. Dual-contour scanning was implemented to simplify the scan strategy. The minimum diameter of struts that could be manufactured using the selected scanning strategy and scanning parameters was found to be 375 µm. Finally, the model was built and from the micro-CT data, the porosities and pore sizes were found to be closely conforming to the designed values. The stiffness of the structures, as found from compression testing, was also found to match with that of human trabecular bone well. Further, the structure exhibited compliant bending-dominated behaviour under compressive loading.
Keywords	additive manufacturing ; graded porosity ; acetabular cup ; Ti6Al4V ; DMLS ; Technology ; T ; Biology (General) ; QH301-705.5
Subject code	670
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: ABS–Scan

Praveen Anand / Deepesh Nagarajan / Sumanta Mukherjee / Nagasuma Chandra

F1000Research, Vol

In silico alanine scanning mutagenesis for binding site residues in protein–ligand complex [v2; ref status: indexed, http://f1000r.es/4sf]

2014 Volume 3

Abstract: Most physiological processes in living systems are fundamentally regulated by protein–ligand interactions. Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. It is well known that the ... ...

Abstract	Most physiological processes in living systems are fundamentally regulated by protein–ligand interactions. Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. In many cases, the boundaries of these sites are not well defined. Here, we provide a web-server to systematically evaluate important residues in the binding site of the protein that contribute towards the ligand recognition through in silico alanine-scanning mutagenesis experiments. Each of the residues present at the binding site is computationally mutated to alanine. The ligand interaction energy is computed for each mutant and the corresponding ΔΔG values are calculated by comparing it to the wild type protein, thus evaluating individual residue contributions towards ligand interaction. The server will thus provide a ranked list of residues to the user in order to obtain loss-of-function mutations. This web-tool can be freely accessed through the following address: http://proline.biochem.iisc.ernet.in/abscan/.
Keywords	Bioinformatics ; Biomacromolecule-Ligand Interactions ; Experimental Biophysical Methods ; Structural Genomics ; Theory & Simulation ; Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2014-12-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Investigations of thermophysico-chemical properties of Ba2TiSi2O8(s) and Sr2TiSi2O8(s)

Sahu, Manjulata / B.S. Tomar / K. Krishnan / Meera Keskar / Smruti Dash / Sumanta Mukherjee

Thermochimica acta. 2018 May 10, v. 663

2018

Abstract: The titanosilicates: Ba2TiSi2O8(s)(BTS) and Sr2TiSi2O8(s)(STS) were synthesized by citrate nitrate gel combustion and complex polymerisation method, respectively and characterized using X-ray diffraction (XRD) technique. The heat capacity, thermal ... ...

Abstract	The titanosilicates: Ba2TiSi2O8(s)(BTS) and Sr2TiSi2O8(s)(STS) were synthesized by citrate nitrate gel combustion and complex polymerisation method, respectively and characterized using X-ray diffraction (XRD) technique. The heat capacity, thermal diffusivity, average thermal expansion coefficient, the standard molar Gibbs energy of formation of BTS and STS were measured with a heat flux-type differential scanning calorimeter, laser flash technique, high temperature XRD and solid oxide Gavanic cell, respectively. The heat capacities of BTS and STS were found to be comparable upto 600 K and afterwards, the increase is higher in BTS. Thermal conductivity of BTS was found to be higher than that of STS. The average volume thermal expansion coefficient of BTS was found to be lower than that of STS. The enthalpy of formation of BTS and STS were derived from their respective Gibbs energy data and their thermodynamic functions were calculated.
Keywords	citrates ; combustion ; differential scanning calorimetry ; energy ; enthalpy ; gels ; heat ; nitrates ; polymerization ; temperature ; thermal conductivity ; thermal diffusivity ; thermal expansion ; X-ray diffraction
Language	English
Dates of publication	2018-0510
Size	p. 215-226.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1500974-9
ISSN	0040-6031
ISSN	0040-6031
DOI	10.1016/j.tca.2018.02.003
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza.

Narmada Sambaturu / Sumanta Mukherjee / Martín López-García / Carmen Molina-París / Gautam I Menon / Nagasuma Chandra

PLoS Computational Biology, Vol 14, Iss 3, p e

2018 Volume 1006069

Abstract: Genetic differences contribute to variations in the immune response mounted by different individuals to a pathogen. Such differential response can influence the spread of infectious disease, indicating why such diseases impact some populations more than ... ...

Abstract	Genetic differences contribute to variations in the immune response mounted by different individuals to a pathogen. Such differential response can influence the spread of infectious disease, indicating why such diseases impact some populations more than others. Here, we study the impact of population-level genetic heterogeneity on the epidemic spread of different strains of H1N1 influenza. For a population with known HLA class-I allele frequency and for a given H1N1 viral strain, we classify individuals into sub-populations according to their level of susceptibility to infection. Our core hypothesis is that the susceptibility of a given individual to a disease such as H1N1 influenza is inversely proportional to the number of high affinity viral epitopes the individual can present. This number can be extracted from the HLA genetic profile of the individual. We use ethnicity-specific HLA class-I allele frequency data, together with genome sequences of various H1N1 viral strains, to obtain susceptibility sub-populations for 61 ethnicities and 81 viral strains isolated in 2009, as well as 85 strains isolated in other years. We incorporate these data into a multi-compartment SIR model to analyse the epidemic dynamics for these (ethnicity, viral strain) epidemic pairs. Our results show that HLA allele profiles which lead to a large spread in individual susceptibility values can act as a protective barrier against the spread of influenza. We predict that populations skewed such that a small number of highly susceptible individuals coexist with a large number of less susceptible ones, should exhibit smaller outbreaks than populations with the same average susceptibility but distributed more uniformly across individuals. Our model tracks some well-known qualitative trends of influenza spread worldwide, suggesting that HLA genetic diversity plays a crucial role in determining the spreading potential of different influenza viral strains across populations.
Keywords	Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2018-03-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: A novel encystation specific protein kinase regulates chitin synthesis in Entamoeba invadens

Samanta, Sintu Kumar / Deepak Krishnan / Digant Nayak / Mithu Baidya / Sneha Susan Varghese / Sudip K. Ghosh / Sumanta Mukherjee

Molecular and biochemical parasitology. 2018 Mar., v. 220

2018

Abstract: Phosphorylation is an important post-translational modification of proteins and is involved in the regulation of a variety of cellular events. The proteome of Entamoeba invadens, the reptilian counterpart of Entamoeba histolytica consists of an ... ...

Abstract	Phosphorylation is an important post-translational modification of proteins and is involved in the regulation of a variety of cellular events. The proteome of Entamoeba invadens, the reptilian counterpart of Entamoeba histolytica consists of an overwhelming number of putative protein kinases, and some may have a role to play in Entamoeba encystation. In this study, we have identified a novel protein kinase named as EiCSpk (Entamoeba invadenscyst specific protein kinase) which expressed almost exclusively during encystation. It is an active Protein kinase C with a characteristic substrate phosphorylation and auto-phosphorylation property. Gene silencing study has unveiled its role as a regulator of chitin synthesis through transcriptional activation of the chitin synthesis pathway genes along with glycogen phosphorylases that are involved in the influx of glucose from glycogen breakdown for chitin synthesis.
Keywords	chitin ; encystment ; Entamoeba histolytica ; Entamoeba invadens ; gene silencing ; genes ; glucose ; glycogen ; phosphorylation ; post-translational modification ; protein kinase C ; proteins ; proteome ; reptiles ; transcriptional activation
Language	English
Dates of publication	2018-03
Size	p. 19-27.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	756166-0
ISSN	1872-9428 ; 0166-6851
ISSN (online)	1872-9428
ISSN	0166-6851
DOI	10.1016/j.molbiopara.2018.01.003
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Towards stratified treatment of JIA

Stephanie J.W. Shoop-Worrall / Saskia Lawson-Tovey / Lucy R. Wedderburn / Kimme L. Hyrich / Nophar Geifman / Aline Kimonyo / Alyssia McNeece / Andrew Dick / Andrew Morris / Annie Yarwood / Athimalaipet Ramanan / Bethany R. Jebson / Chris Wallace / Daniela Dastros-Pitei / Damian Tarasek / Elizabeth Ralph / Emil Carlsson / Emily Robinson / Emma Sumner /

Fatema Merali / Fatjon Dekaj / Helen Neale / Hussein Al-Mossawi / Jacqui Roberts / Jenna F. Gritzfeld / Joanna Fairlie / John Bowes / John Ioannou / Melissa Kartawinata / Melissa Tordoff / Michael Barnes / Michael W. Beresford / Michael Stadler / Paul Martin / Rami Kallala / Sandra Ng / Samantha Smith / Sarah Clarke / Soumya Raychaudhuri / Stephen Eyre / Sumanta Mukherjee / Teresa Duerr / Thierry Sornasse / Vasiliki Alexiou / Victoria J. Burton / Wei-Yu Lin / Wendy Thomson / Zoe Wanstall

EBioMedicine, Vol 100, Iss , Pp 104946- (2024)

machine learning identifies subtypes in response to methotrexate from four UK cohortsResearch in context

2024

Abstract: Summary: Background: Methotrexate (MTX) is the gold-standard first-line disease-modifying anti-rheumatic drug for juvenile idiopathic arthritis (JIA), despite only being either effective or tolerated in half of children and young people (CYP). To ... ...

Abstract	Summary: Background: Methotrexate (MTX) is the gold-standard first-line disease-modifying anti-rheumatic drug for juvenile idiopathic arthritis (JIA), despite only being either effective or tolerated in half of children and young people (CYP). To facilitate stratified treatment of early JIA, novel methods in machine learning were used to i) identify clusters with distinct disease patterns following MTX initiation; ii) predict cluster membership; and iii) compare clusters to existing treatment response measures. Methods: Discovery and verification cohorts included CYP who first initiated MTX before January 2018 in one of four UK multicentre prospective cohorts of JIA within the CLUSTER consortium. JADAS components (active joint count, physician (PGA) and parental (PGE) global assessments, ESR) were recorded at MTX start and over the following year.Clusters of MTX ‘response’ were uncovered using multivariate group-based trajectory modelling separately in discovery and verification cohorts. Clusters were compared descriptively to ACR Pedi 30/90 scores, and multivariate logistic regression models predicted cluster-group assignment. Findings: The discovery cohorts included 657 CYP and verification cohorts 1241 CYP. Six clusters were identified: Fast improvers (11%), Slow Improvers (16%), Improve-Relapse (7%), Persistent Disease (44%), Persistent PGA (8%) and Persistent PGE (13%), the latter two characterised by improvement in all features except one. Factors associated with clusters included ethnicity, ILAR category, age, PGE, and ESR scores at MTX start, with predictive model area under the curve values of 0.65–0.71. Singular ACR Pedi 30/90 scores at 6 and 12 months could not capture speeds of improvement, relapsing courses or diverging disease patterns. Interpretation: Six distinct patterns following initiation of MTX have been identified using methods in artificial intelligence. These clusters demonstrate the limitations in traditional yes/no treatment response assessment (e.g., ACRPedi30) and can form the basis ...
Keywords	Juvenile idiopathic arthritis ; Machine learning ; Treatment outcome ; Epidemiology ; Methotrexate ; Medicine ; R ; Medicine (General) ; R5-920
Subject code	310
Language	English
Publishing date	2024-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: RSV-Induced H3K4 Demethylase KDM5B Leads to Regulation of Dendritic Cell-Derived Innate Cytokines and Exacerbates Pathogenesis In Vivo.

Catherine Ptaschinski / Sumanta Mukherjee / Martin L Moore / Mareike Albert / Kristian Helin / Steven L Kunkel / Nicholas W Lukacs

PLoS Pathogens, Vol 11, Iss 6, p e

2015 Volume 1004978

Abstract: Respiratory syncytial virus (RSV) infection can result in severe disease partially due to its ability to interfere with the initiation of Th1 responses targeting the production of type I interferons (IFN) and promoting a Th2 immune environment. ... ...

Abstract	Respiratory syncytial virus (RSV) infection can result in severe disease partially due to its ability to interfere with the initiation of Th1 responses targeting the production of type I interferons (IFN) and promoting a Th2 immune environment. Epigenetic modulation of gene transcription has been shown to be important in regulating inflammatory pathways. RSV-infected bone marrow-derived DCs (BMDCs) upregulated expression of Kdm5b/Jarid1b H3K4 demethylase. Kdm5b-specific siRNA inhibition in BMDC led to a 10-fold increase in IFN-β as well as increases in IL-6 and TNF-α compared to control-transfected cells. The generation of Kdm5bfl/fl-CD11c-Cre+ mice recapitulated the latter results during in vitro DC activation showing innate cytokine modulation. In vivo, infection of Kdm5bfl/fl-CD11c-Cre+ mice with RSV resulted in higher production of IFN-γ and reduced IL-4 and IL-5 compared to littermate controls, with significantly decreased inflammation, IL-13, and mucus production in the lungs. Sensitization with RSV-infected DCs into the airways of naïve mice led to an exacerbated response when mice were challenged with live RSV infection. When Kdm5b was blocked in DCs with siRNA or DCs from Kdm5bfl/fl-CD11c-CRE mice were used, the exacerbated response was abrogated. Importantly, human monocyte-derived DCs treated with a chemical inhibitor for KDM5B resulted in increased innate cytokine levels as well as elicited decreased Th2 cytokines when co-cultured with RSV reactivated CD4+ T cells. These results suggest that KDM5B acts to repress type I IFN and other innate cytokines to promote an altered immune response following RSV infection that contributes to development of chronic disease.
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2015-06-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Structural annotation of Mycobacterium tuberculosis proteome.

Praveen Anand / Sandhya Sankaran / Sumanta Mukherjee / Kalidas Yeturu / Roman Laskowski / Anshu Bhardwaj / Raghu Bhagavat / OSDD Consortium / Samir K Brahmachari / Nagasuma Chandra

PLoS ONE, Vol 6, Iss 10, p e

2011 Volume 27044

Abstract: Of the ∼4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of ...

Abstract	Of the ∼4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of the underlying biology, we seek to obtain a structural annotation for the genome, using computational methods. Structural models were obtained and validated for ∼2877 ORFs, covering ∼70% of the genome. Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. New algorithms for binding site detection and genome scale binding site comparison at the structural level, recently reported from the laboratory, were utilized. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides an opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses. The resource (http://proline.physics.iisc.ernet.in/Tbstructuralannotation), being one of the first to be based on structure-derived functional annotations at a genome scale, is expected to be useful for better understanding of TB and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2011-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cytokine induced phenotypic and epigenetic signatures are key to establishing specific macrophage phenotypes.

Nicolai A Kittan / Ronald M Allen / Abhay Dhaliwal / Karen A Cavassani / Matthew Schaller / Katherine A Gallagher / William F Carson / Sumanta Mukherjee / Jolanta Grembecka / Tomasz Cierpicki / Gabor Jarai / John Westwick / Steven L Kunkel / Cory M Hogaboam

PLoS ONE, Vol 8, Iss 10, p e

2013 Volume 78045

Abstract: Macrophages (MΦ) play an essential role in innate immune responses and can either display a pro-inflammatory, classically activated phenotype (M1) or undergo an alternative activation program (M2) promoting immune regulation. M-CSF is used to ... ...

Abstract	Macrophages (MΦ) play an essential role in innate immune responses and can either display a pro-inflammatory, classically activated phenotype (M1) or undergo an alternative activation program (M2) promoting immune regulation. M-CSF is used to differentiate monocytes into MΦ and IFN-γ or IL-4+IL-13 to further polarize these cells towards M1 or M2, respectively. Recently, differentiation using only GM-CSF or M-CSF has been described to induce a M1- or M2-like phenotype, respectively. In this study, we combined both approaches by differentiating human MΦ in GM-CSF or M-CSF followed by polarization with either IFN-γ or IL-4+IL-13. We describe the phenotypic differences between CD14(hi) CD163(hi) CD206(int) FOLR2-expressing M-CSF MΦ and CD14(lo) CD163(lo) CD206(hi) GM-CSF MΦ but show that both macrophage populations reacted similarly to further polarization with IFN-γ or IL-4+IL-13 with up- and down-regulation of common M1 and M2 marker genes. We also show that high expression of the mannose receptor (CD206), a marker of alternative activation, is a distinct feature of GM-CSF MΦ. Changes of the chromatin structure carried out by chromatin modification enzymes (CME) have been shown to regulate myeloid differentiation. We analyzed the expression patterns of CME during MΦ polarization and show that M1 up-regulate the histone methyltransferase MLL and demethylase KDM6B, while resting and M2 MΦ were characterized by DNA methyltransferases and histone deacetylases. We demonstrate that MLL regulates CXCL10 expression and that this effect could be abrogated using a MLL-Menin inhibitor. Taken together we describe the distinct phenotypic differences of GM-CSF or M-CSF MΦ and demonstrate that MΦ polarization is regulated by specific epigenetic mechanisms. In addition, we describe a novel role for MLL as marker for classical activation. Our findings provide new insights into MΦ polarization that could be helpful to distinguish MΦ activation states.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Delta-like 4 differentially regulates murine CD4 T cell expansion via BMI1.

Matthew A Schaller / Hannah Logue / Sumanta Mukherjee / Dennis M Lindell / Ana Lucia Coelho / Pamela Lincoln / William F Carson / Toshihiro Ito / Karen A Cavassani / Stephen W Chensue / Cory M Hogaboam / Nicholas W Lukacs / Steven L Kunkel

PLoS ONE, Vol 5, Iss 8, p e

2010 Volume 12172

Abstract: Studies have shown that Notch is essential for the maintenance of a T cell Th2 phenotype in vivo. It has also been shown that Notch ligands have diverse functions during T cell activation. We chose to investigate the role of Notch ligands during the Th2 ... ...

Abstract	Studies have shown that Notch is essential for the maintenance of a T cell Th2 phenotype in vivo. It has also been shown that Notch ligands have diverse functions during T cell activation. We chose to investigate the role of Notch ligands during the Th2 response.We studied the relationship of two Notch ligands, delta-like 4 and jagged-1, to T cell proliferation in C57 Bl/6 mice. Our findings indicate that jagged-1 does not affect the rate of T cell proliferation in any subset examined. However, delta-like 4 causes an increase in the expansion of Th2 memory cells and a decrease in effector cell proliferation. Our in vivo studies indicate that the Notch system is dynamically regulated, and that blocking one Notch ligand increases the effective concentration of other Notch ligands, thus altering the response. Examination of genes related to the Notch pathway revealed that the Notch receptors were increased in memory T cells. Expression of BMI1, a gene involved in T cell proliferation, was also higher in memory T cells. Further experiments demonstrated that Notch directly regulates the expression of the BMI1 gene in T cells and may govern T cell proliferation through this pathway.From these experiments we can make several novel conclusions about the role of Notch ligands in T cell biology. The first is that delta-like 4 suppresses effector cell proliferation and enhances Th2 memory cell proliferation. The second is that blocking one Notch ligand in vivo effectively increases the concentration of other Notch ligands, which can then alter the response.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2010-08-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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