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Article ; Online: Tracking Fibrinolysis of Chandler Loop-Formed Whole Blood Clots Under Shear Flow in An In-Vitro Thrombolysis Model.

Christodoulides, Alexei / Hall, Abigail R / Umesh, Anushri / Alves, Nathan J

Journal of visualized experiments : JoVE

2024 , Issue 206

Abstract: Thromboembolism and related complications are a leading cause of morbidity and mortality worldwide and various assays have been developed to test thrombolytic drug efficiency both in vitro and in vivo. There is increasing demand for more physiologically ... ...

Abstract	Thromboembolism and related complications are a leading cause of morbidity and mortality worldwide and various assays have been developed to test thrombolytic drug efficiency both in vitro and in vivo. There is increasing demand for more physiologically relevant in-vitro clot models for drug development due to the complexity and cost associated with animal models in addition to their often lack of translatability to human physiology. Flow, pressure, and shear rate are important characteristics of the circulatory system, with clots that are formed under flow displaying different morphology and digestion characteristics than statically formed clots. These factors are often unrepresented in conventional in-vitro clot digestion assays, which can have pharmacological implications that impact drug translational success rates. The Real-Time Fluorometric Flowing Fibrinolysis (RT-FluFF) assay was developed as a high-fidelity thrombolysis testing platform that uses fluorescently tagged clots formed under shear flow, which are then digested using circulating plasma in the presence or absence of fibrinolytic pharmaceutical agents. Modifying the flow rates of both clot formation and clot digestion steps allows the system to imitate arterial, pulmonary, and venous conditions across highly diverse experimental setups. Measurements can be taken continuously using an in-line fluorometer or by taking discrete time points, as well as a conventional end point clot mass measurement. The RT-FluFF assay is a flexible system that allows for the real-time tracking of clot digestion under flow conditions that more accurately represent in-vivo physiological conditions while retaining the control and reproducibility of an in-vitro testing system.
MeSH term(s)	Humans ; Fibrinolysis/drug effects ; Fibrinolysis/physiology ; Thrombosis ; Fluorometry/methods ; Thrombolytic Therapy/methods
Language	English
Publishing date	2024-04-19
Publishing country	United States
Document type	Journal Article ; Video-Audio Media ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/66524
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Article ; Online: Prediction of potential molecular markers of bovine mastitis by meta-analysis of differentially expressed genes using combined p value and robust rank aggregation.

Umesh, Anushri / Guttula, Praveen Kumar / Gupta, Mukesh Kumar

Tropical animal health and production

2022 Volume 54, Issue 5, Page(s) 269

Abstract: Bovine mastitis causes significant economic loss to the dairy industry by affecting milk quality and quantity. Escherichia coli and Staphylococcus aureus are the two common mastitis-causing bacteria among the consortia of mastitis pathogens, wherein E. ... ...

Abstract	Bovine mastitis causes significant economic loss to the dairy industry by affecting milk quality and quantity. Escherichia coli and Staphylococcus aureus are the two common mastitis-causing bacteria among the consortia of mastitis pathogens, wherein E. coli is an opportunistic environmental pathogen, and S. aureus is a contagious pathogen. This study was designed to predict molecular markers of bovine mastitis by meta-analysis of differentially expressed genes (DEG) in E. coli- or S. aureus-infected mammary epithelial cells (MECs) using p value combination and robust rank aggregation (RRA) methods. High-throughput transcriptome of bovine MECs, infected with E. coli or S. aureus, were analyzed, and correlation of z-scores were computed for the expression datasets to identify the lineage profile and functional ontology of DEGs. Key pathways enriched in infected MECs were deciphered by Gene Set Enrichment Analysis (GSEA), following which combined p value and RRA were used to perform DEG meta-analysis to limit type I error in the analysis. The miRNA-gene networks were then built to uncover potential molecular markers of mastitis. Lineage profiling of MECs showed that the gene expression levels were associated with mammary tissue lineage. The up-regulated genes were enriched in immune-related pathways, whereas down-regulated genes influenced the cellular processes. GSEA analysis of DEGs deciphered the involvement of Toll-like receptor (TLR), and NF-kappa B signaling pathway during infection. Comparison after meta-analysis yielded with genes ZC3H12A, RND1, and MAP3K8 having significant expression levels in both E. coli and S. aureus dataset, and on evaluating miRNA-gene network, 7 pairs were common to both sets identifying them as potential molecular markers.
MeSH term(s)	Animals ; Cattle ; Cattle Diseases/metabolism ; Escherichia coli/genetics ; Female ; Mammary Glands, Animal/microbiology ; Mastitis, Bovine/genetics ; Mastitis, Bovine/microbiology ; MicroRNAs/genetics ; Staphylococcal Infections/genetics ; Staphylococcal Infections/veterinary ; Staphylococcus aureus/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2022-08-19
Publishing country	United States
Document type	Journal Article ; Meta-Analysis
ZDB-ID	603363-5
ISSN	1573-7438 ; 0049-4747
ISSN (online)	1573-7438
ISSN	0049-4747
DOI	10.1007/s11250-022-03258-9
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Article ; Online: Prediction of potential molecular markers of bovine mastitis by meta-analysis of differentially expressed genes using combined p value and robust rank aggregation

Umesh, Anushri / Guttula, Praveen Kumar / Gupta, Mukesh Kumar

Trop Anim Health Prod. 2022 Oct., v. 54, no. 5 p.269-269

2022

Abstract	Bovine mastitis causes significant economic loss to the dairy industry by affecting milk quality and quantity. Escherichia coli and Staphylococcus aureus are the two common mastitis-causing bacteria among the consortia of mastitis pathogens, wherein E. coli is an opportunistic environmental pathogen, and S. aureus is a contagious pathogen. This study was designed to predict molecular markers of bovine mastitis by meta-analysis of differentially expressed genes (DEG) in E. coli– or S. aureus–infected mammary epithelial cells (MECs) using p value combination and robust rank aggregation (RRA) methods. High-throughput transcriptome of bovine MECs, infected with E. coli or S. aureus, were analyzed, and correlation of z-scores were computed for the expression datasets to identify the lineage profile and functional ontology of DEGs. Key pathways enriched in infected MECs were deciphered by Gene Set Enrichment Analysis (GSEA), following which combined p value and RRA were used to perform DEG meta-analysis to limit type I error in the analysis. The miRNA-gene networks were then built to uncover potential molecular markers of mastitis. Lineage profiling of MECs showed that the gene expression levels were associated with mammary tissue lineage. The up-regulated genes were enriched in immune-related pathways, whereas down-regulated genes influenced the cellular processes. GSEA analysis of DEGs deciphered the involvement of Toll-like receptor (TLR), and NF-kappa B signaling pathway during infection. Comparison after meta-analysis yielded with genes ZC3H12A, RND1, and MAP3K8 having significant expression levels in both E. coli and S. aureus dataset, and on evaluating miRNA-gene network, 7 pairs were common to both sets identifying them as potential molecular markers.
Keywords	Escherichia coli ; Staphylococcus aureus ; Toll-like receptors ; bovine mastitis ; cattle ; dairy industry ; data collection ; epithelium ; financial economics ; gene expression ; gene expression regulation ; genes ; meta-analysis ; milk quality ; pathogens ; prediction ; transcriptome
Language	English
Dates of publication	2022-10
Size	p. 269.
Publishing place	Springer Netherlands
Document type	Article ; Online
ZDB-ID	603363-5
ISSN	1573-7438 ; 0049-4747
ISSN (online)	1573-7438
ISSN	0049-4747
DOI	10.1007/s11250-022-03258-9
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Article ; Online: Evidence mapping and review of long-COVID and its underlying pathophysiological mechanism.

Umesh, Anushri / Pranay, Kumar / Pandey, Ramesh Chandra / Gupta, Mukesh Kumar

Infection

2022 Volume 50, Issue 5, Page(s) 1053–1066

Abstract: Purpose: Apart from the global disease burden of acute COVID-19 disease, the health complications arising after recovery have been recognized as a long-COVID or post-COVID-19 syndrome. Evidences of long-COVID symptoms involving various organ systems are ...

Abstract	Purpose: Apart from the global disease burden of acute COVID-19 disease, the health complications arising after recovery have been recognized as a long-COVID or post-COVID-19 syndrome. Evidences of long-COVID symptoms involving various organ systems are rapidly growing in literature. The objective was to perform a rapid review and evidence mapping of systemic complications and symptoms of long-COVID and underlying pathophysiological mechanisms. Methods: Publications reporting clinical trials, observational cohort studies, case-control studies, case-series, meta-analysis, and systematic reviews, focusing on the squeal of the disease, consequences of COVID-19 treatment/hospitalization, long-COVID, chronic COVID syndrome, and post acute COVID-19 were reviewed in detail for the narrative synthesis of frequency, duration, risk factors, and pathophysiology. Results: The review highlights that pulmonary, neuro-psychological, and cardiovascular complications are major findings in most epidemiological studies. However, dysfunctional gastrointestinal, endocrine, and metabolic health are recent findings for which underlying pathophysiological mechanisms are poorly understood. Analysis of the clinical trial landscape suggests that more than 50% of the industry-sponsored trials are focused on pulmonary symptoms. In contrast to the epidemiological trends and academic trials, cardiovascular complications are not a focus of industry-sponsored trials, suggestive of the gaps in the research efforts. Conclusion: The gap in epidemiological trends and academic trials, particularly concerning cardiovascular complications not being a focus of industry-sponsored trials is suggestive of the gaps in research efforts and longer follow-up durations would help identify other long-COVID-related health issues such as reproductive health and fertility.
MeSH term(s)	COVID-19/complications ; COVID-19/epidemiology ; Hospitalization ; Humans ; Risk Factors ; COVID-19 Drug Treatment ; Post-Acute COVID-19 Syndrome
Language	English
Publishing date	2022-04-30
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	185104-4
ISSN	1439-0973 ; 0300-8126 ; 0173-2129
ISSN (online)	1439-0973
ISSN	0300-8126 ; 0173-2129
DOI	10.1007/s15010-022-01835-6
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Article ; Online: Analyzing the effect of heparin on in vitro capacitation and spermatozoal RNA population in goats.

Sahoo, Bijayalaxmi / Mishra, Balaram / Bhaskar, Rakesh / Vikas, Y N V / Umesh, Anushri / Guttula, Praveen Kumar / Gupta, Mukesh Kumar

International journal of biological macromolecules

2023 Volume 241, Page(s) 124502

Abstract: Heparin is a glycosaminoglycan polymer that is commonly used as an anticoagulant. Heparin also induces in vitro capacitation in spermatozoa, although its molecular mechanism is elusive. This study investigated the effect of heparin on in vitro ... ...

Abstract	Heparin is a glycosaminoglycan polymer that is commonly used as an anticoagulant. Heparin also induces in vitro capacitation in spermatozoa, although its molecular mechanism is elusive. This study investigated the effect of heparin on in vitro capacitation and spermatozoal RNA (spRNA) population in goats. Goat spermatozoa were treated with 20 μM heparin for 0-6 h and evaluated for motility, capacitation, acrosome reaction, and spRNA population by RNA sequencing (RNA-seq). It was observed that heparin enhanced sperm motility up to 6 h of incubation (p < 0.05). Heparin also induced capacitation and acrosome reaction within 4 h. RNA-seq identified 1254 differentially expressed genes (DEGs) between heparin-treated and control spermatozoa. Most DEGs (1251 nos.) were upregulated and included 1090 protein-coding genes. A few genes (PRND, ITPR1, LLCFC1, and CHRM2) showed >5-fold increased expression in heparin-treated spermatozoa compared to the control. The upregulated genes were found to be involved in cAMP-PKA, PI3-Akt, calcium, MAPK signaling, and oxidative stress pathways. DCFDA staining confirmed the increased oxidative stress in heparin-treated spermatozoa compared to the control (p < 0.05). In conclusion, the results of the present study suggest that heparin enhances sperm motility and induces capacitation by upregulation of the spRNA population and oxidative stress pathway.
MeSH term(s)	Animals ; Male ; Heparin/pharmacology ; Heparin/metabolism ; RNA/metabolism ; Goats ; Sperm Motility ; Spermatozoa/metabolism ; Sperm Capacitation/physiology
Chemical Substances	Heparin (9005-49-6) ; RNA (63231-63-0)
Language	English
Publishing date	2023-04-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.124502
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Article ; Online: Analyzing the effect of heparin on in vitro capacitation and spermatozoal RNA population in goats

Sahoo, Bijayalaxmi / Mishra, Balaram / Bhaskar, Rakesh / Vikas, Y.N.V. / Umesh, Anushri / Guttula, Praveen Kumar / Gupta, Mukesh Kumar

International Journal of Biological Macromolecules. 2023 Apr. 18, p.124502-

2023 , Page(s) 124502–

Abstract	Heparin is a glycosaminoglycan polymer that is commonly used as an anticoagulant. Heparin also induces in vitro capacitation in spermatozoa, although its molecular mechanism is elusive. This study investigated the effect of heparin on in vitro capacitation and spermatozoal RNA (spRNA) population in goats. Goat spermatozoa were treated with 20 μM heparin for 0–6 h and evaluated for motility, capacitation, acrosome reaction, and spRNA population by RNA sequencing (RNA-seq). It was observed that heparin enhanced sperm motility up to 6 h of incubation (p < 0.05). Heparin also induced capacitation and acrosome reaction within 4 h. RNA-seq identified 1254 differentially expressed genes (DEGs) between heparin-treated and control spermatozoa. Most DEGs (1251 nos.) were upregulated and included 1090 protein-coding genes. A few genes (PRND, ITPR1, LLCFC1, and CHRM2) showed >5-fold increased expression in heparin-treated spermatozoa compared to the control. The upregulated genes were found to be involved in cAMP-PKA, PI3-Akt, calcium, MAPK signaling, and oxidative stress pathways. DCFDA staining confirmed the increased oxidative stress in heparin-treated spermatozoa compared to the control (p < 0.05). In conclusion, the results of the present study suggest that heparin enhances sperm motility and induces capacitation by upregulation of the spRNA population and oxidative stress pathway.
Keywords	RNA ; acrosome reaction ; anticoagulants ; calcium ; gene expression regulation ; heparin ; oxidative stress ; polymers ; sequence analysis ; sperm motility ; Capacitation ; Goat ; RNA-seq ; Spermatozoal RNA ; Transcriptome
Language	English
Dates of publication	2023-0418
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.124502
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Article ; Online: Predicting biodiesel properties and its optimal fatty acid profile via explainable machine learning

Suvarna, Manu / Jahirul, Mohammad Islam / Aaron-Yeap, Wai Hung / Augustine, Cheryl Valencia / Umesh, Anushri / Rasul, Mohammad Golam / Günay, Mehmet Erdem / Yıldırım, Ramazan / Janaun, Jidon

Renewable energy. 2022 Apr., v. 189 p.245-258

2022

Abstract: The accurate prediction of biodiesel fuel properties and determination of its optimal fatty acid (FA) profiles is a non-trivial process. To this aim, machine learning (ML) based predictive models were developed for cetane number (CN) and cold filter ... ...

Abstract	The accurate prediction of biodiesel fuel properties and determination of its optimal fatty acid (FA) profiles is a non-trivial process. To this aim, machine learning (ML) based predictive models were developed for cetane number (CN) and cold filter plugging point (CFPP), where the extreme gradient boost (XGB) and random forest (RF) algorithms had the best performance with R² of 0.89 and 0.91 on the test data, respectively. A classifier model for oxidative stability (OS) was devised to predict if it would pass or fail the ASTM and EU limits, where the support vector classifier (SVC) had the highest accuracy of 0.93 and 0.77 for ASTM and EU limits. Causal analysis via Shapley and Accumulated Local Effects revealed the significance and correlation of FAs with the fuel properties. This eventually aided the determination of the optimal FA composition via evolutionary optimization, such that the properties would meet the ASTM and EU standards. This study presents an end-to-end ML framework including descriptive, predictive, causal and prescriptive analytics to predict biodiesel fuel properties as a function of its FA composition; and eventually prescribes the optimal FA composition necessary to ensure that the fuel properties meet the regulatory standards.
Keywords	biodiesel ; cold ; fatty acid composition ; fatty acids ; models ; oxidative stability ; prediction ; Cetane number ; Cold filter plugging point ; Oxidative stability ; Support vector machines ; Extreme gradient boost ; Particle-swarm optimization
Language	English
Dates of publication	2022-04
Size	p. 245-258.
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	2001449-1
ISSN	1879-0682 ; 0960-1481
ISSN (online)	1879-0682
ISSN	0960-1481
DOI	10.1016/j.renene.2022.02.124
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Article: Immunomodulatory and radioprotective property of glucans isolated from lactobacillus species

Pradeepa / Umesh, Anushri / Manasadeepika / Manjunath, Anushree / Salian, Chithralekha / Darshini, S.M. / Prabhakar, B.T. / Mutalik, Srinivas / Manjunatha, B.K. / Vidya, S.M.

Bioactive carbohydrates and dietary fibre. 2022 May, v. 27

2022

Abstract: Bacterial exopolysaccharides (EPS) have been reported to protect the radiation induced damage during radiotherapy. Recent studies suggested that, lactic acid bacteria (LAB) and their secreted products have unique radioprotective properties. In the ... ...

Abstract	Bacterial exopolysaccharides (EPS) have been reported to protect the radiation induced damage during radiotherapy. Recent studies suggested that, lactic acid bacteria (LAB) and their secreted products have unique radioprotective properties. In the present study, we evaluated the ability of EPS isolated from two LAB species i.e., Lactobacillus acidophilus and Lactobacillus plantarum as a radioprotective agent against radiation induced mice small intestinal damage. EPS was isolated, identified as glucan and named as glucan A (GA) derived from Lactobacillus acidophilus and glucan P (GP) derived from Lactobacillus plantarum. GA and GP were subjected to in vitro immunomodulatory and in vivo radioprotective activity. Both GA and GP exhibited significant mitogenic activity and increased interleukin-2 (IL-2) and interleukin-10 (IL-10) secretion in a dose dependent manner. Similarly, after 9Gy whole body irradiation, glucan pre-treated mice showed improved spleen weight, reduced radiation induced hematopoietic disorder and radiation enteritis when compared to the irradiation control mice. Both glucans were also protected mice from early death and increased survival rate when compared to irradiation control. As a result, it is possible that glucan from Lactobacillus acidophilus and Lactobacillus plantarum could be served as a novel radioprotective agent to inhibit radiation-induced intestinal damage.
Keywords	Lactobacillus acidophilus ; Lactobacillus plantarum ; death ; dietary fiber ; dose response ; enteritis ; exopolysaccharides ; glucans ; interleukin-10 ; interleukin-2 ; intestines ; irradiation ; lactic acid ; radioprotective agents ; radioprotective effect ; radiotherapy ; secretion ; spleen ; survival rate
Language	English
Dates of publication	2022-05
Publishing place	Elsevier Ltd
Document type	Article
ISSN	2212-6198
DOI	10.1016/j.bcdf.2021.100304
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Article ; Online: Optimization, kinetics and radioprotective potential of a heteropolysaccharide from L. rhamnosus RVPI.

Umesh, Anushri / Pradeepa / Manjunath, Anushree / Salian, Chithralekha / Manasadeepika / Suvarna, Manu / Muddappa, Vidya Shimoga

Biotechnology and applied biochemistry

2019

Abstract: The probiotic potential of Lactobacillus rhamnosus RVP1 isolated from Sardinella longiceps was investigated in vitro. The bacterium exhibited highest tolerance at low pH, high bile salt concentration and demonstrated good antioxidant activity, ... ...

Abstract	The probiotic potential of Lactobacillus rhamnosus RVP1 isolated from Sardinella longiceps was investigated in vitro. The bacterium exhibited highest tolerance at low pH, high bile salt concentration and demonstrated good antioxidant activity, hydrophobicity and inhibited both gram-negative and gram-positive indicator bacteria. To aid in process design and to unravel the fermentation kinetics, response surface methodology was devised to optimize the EPS production from L. rhamnosus and mechanistic models were developed to describe the fermentation kinetics. The optimum pH, dextrose and peptone concentrations for EPS production were 7.07, 19.995 g/L and 23.4 g/L, respectively, with a predicted yield of 724 mg/L. The actual yield under these conditions was 708±29 mg/L which was within the 95% confidence interval. The simulated mechanistic model fit the experimental values with a high degree of correlation with R2 = 0.99, 0.96 and 0.97 for the logistic growth, substrate consumption and EPS production and degradation curves respectively. The kinetic constants μ_max = 0.29 hr
Language	English
Publishing date	2019-11-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	883433-7
ISSN	1470-8744 ; 0885-4513
ISSN (online)	1470-8744
ISSN	0885-4513
DOI	10.1002/bab.1855
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