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Article ; Online: A Positively Selected

Loh, John T / Struttmann, Emily L / Favret, Natalie / Harvey, M Lorena / Pakala, Suman B / Chopra, Abha / McClain, Mark S / Cover, Timothy L

Infection and immunity

2023 Volume 91, Issue 2, Page(s) e0042022

Abstract: Both Helicobacter pylori infection and a high-salt diet are risk factors for gastric cancer. We previously showed that a mutation ... ...

Abstract	Both Helicobacter pylori infection and a high-salt diet are risk factors for gastric cancer. We previously showed that a mutation in
MeSH term(s)	Humans ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Helicobacter Infections ; Helicobacter pylori/genetics ; Helicobacter pylori/physiology ; Mutation ; Sodium Chloride/metabolism ; Repressor Proteins/genetics ; Repressor Proteins/metabolism
Chemical Substances	Bacterial Proteins ; Sodium Chloride (451W47IQ8X) ; Repressor Proteins
Language	English
Publishing date	2023-01-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	218698-6
ISSN	1098-5522 ; 0019-9567
ISSN (online)	1098-5522
ISSN	0019-9567
DOI	10.1128/iai.00420-22
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Article: Transcriptomic profiling of Paulownia elongata in response to heat stress

Katiyar, Neerja / Ramadoss, Niveditha / Gupta, Dinesh / Pakala, Suman B. / Cooper, Kerry / Basu, Chhandak

Plant gene. 2021 Dec., v. 28

2021

Abstract: Rising global temperatures have caused a substantial loss in crop productivity throughout the world. Understanding the fundamental mechanisms underlying tolerance to heat stress in plants has become increasingly relevant, particularly as global warming ... ...

Abstract	Rising global temperatures have caused a substantial loss in crop productivity throughout the world. Understanding the fundamental mechanisms underlying tolerance to heat stress in plants has become increasingly relevant, particularly as global warming continues to rise. The goal of our study was to identify and analyze heat stress-induced transcriptomic changes in Paulownia elongata plants. Paulownia elongata are fast growing trees known for their ability to grow in a wide range of temperatures. However, the genes responsible for its thermotolerance have not yet been identified and studied in detail. In our study, we used RNA-sequencing (RNA-seq) to analyze changes in gene expression at the transcriptomic level after inducing heat stress and identified 4,435 genes as differentially expressed. Most of the genes found to be upregulated play a critical role in protein binding, unfolding, retention, and transport, suggesting that heat tolerance in plants can be achieved by protecting native proteins. The genes and pathways identified in this study can serve as valuable targets in heat tolerance studies and development of heat tolerant plants. To the best of our knowledge, this is the first in-depth report of heat-induced transcriptome analysis in P. elongata.
Keywords	Paulownia elongata ; genes ; heat ; heat stress ; heat tolerance ; sequence analysis ; transcriptomics
Language	English
Dates of publication	2021-12
Publishing place	Elsevier B.V.
Document type	Article
ISSN	2352-4073
DOI	10.1016/j.plgene.2021.100330
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Article ; Online: Ligation-based assay for variant typing without sequencing: Application to SARS-CoV-2 variants of concern.

Nelson, Dalton J / Shilts, Meghan H / Pakala, Suman B / Das, Suman R / Schmitz, Jonathan E / Haselton, Frederick R

Influenza and other respiratory viruses

2022 Volume 17, Issue 1, Page(s) e13083

Abstract: Background: COVID-19 prevalence has remained high throughout the pandemic with intermittent surges, due largely to the emergence of genetic variants, demonstrating the need for more accessible sequencing technologies for strain typing.: Methods: A ... ...

Abstract	Background: COVID-19 prevalence has remained high throughout the pandemic with intermittent surges, due largely to the emergence of genetic variants, demonstrating the need for more accessible sequencing technologies for strain typing. Methods: A ligation-based typing assay was developed to detect known variants of severe acute respiratory syndrome virus 2 (SARS-CoV-2) by identifying the presence of characteristic single-nucleotide polymorphisms (SNPs). General principles for extending the strategy to new variants and alternate diseases with SNPs of interest are described. Of note, this strategy leverages commercially available reagents for assay preparation, as well as standard real-time polymerase chain reaction (PCR) instrumentation for assay performance. Results: The assay demonstrated a combined sensitivity and specificity of 96.6% and 99.5%, respectively, for the classification of 88 clinical samples of the Alpha, Delta, and Omicron variants relative to the gold standard of viral genome sequencing. It achieved an average limit of detection of 7.4 × 10 Conclusions: The assay demonstrates the potential for robust variant typing with performance comparable with next-generation sequencing without the need for the time delays and resources required for sequencing. The reduced resource dependency and generalizability could expand access to variant classification information for pandemic surveillance.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; COVID-19/epidemiology ; High-Throughput Nucleotide Sequencing ; Genome, Viral
Language	English
Publishing date	2022-12-12
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2274538-5
ISSN	1750-2659 ; 1750-2640
ISSN (online)	1750-2659
ISSN	1750-2640
DOI	10.1111/irv.13083
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Article ; Online: Mucosal Gene Expression in Response to SARS-CoV-2 Is Associated with Viral Load.

Rajagopala, Seesandra V / Strickland, Britton A / Pakala, Suman B / Kimura, Kyle S / Shilts, Meghan H / Rosas-Salazar, Christian / Brown, Hunter M / Freeman, Michael H / Wessinger, Bronson C / Gupta, Veerain / Phillips, Elizabeth / Mallal, Simon A / Turner, Justin H / Das, Suman R

Journal of virology

2023 Volume 97, Issue 2, Page(s) e0147822

Abstract: Little is known about the relationships between symptomatic early severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and upper airway mucosal gene expression and immune response. To examine the association of symptomatic SARS-CoV-2 ... ...

Abstract	Little is known about the relationships between symptomatic early severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and upper airway mucosal gene expression and immune response. To examine the association of symptomatic SARS-CoV-2 early viral load with upper airway mucosal gene expression, we profiled the host mucosal transcriptome from nasopharyngeal swab samples from 68 adults with symptomatic, mild-to-moderate coronavirus disease 19 (COVID-19). We measured SARS-CoV-2 viral load using reverse transcription-quantitative PCR (RT-qPCR). We then examined the association of SARS-CoV-2 viral load with upper airway mucosal immune response. We detected SARS-CoV-2 in all samples and recovered >80% of the genome from 95% of the samples from symptomatic COVID-19 adults. The respiratory virome was dominated by SARS-CoV-2, with limited codetection of other respiratory viruses, with the human Rhinovirus C being identified in 4 (6%) samples. This limited codetection of other respiratory viral pathogens may be due to the implementation of public health measures, like social distancing and masking practices. We observed a significant positive correlation between SARS-CoV-2 viral load and interferon signaling (OAS2, OAS3, IFIT1, UPS18, ISG15, ISG20, IFITM1, and OASL), chemokine signaling (CXCL10 and CXCL11), and adaptive immune system (IFITM1, CD300E, and SIGLEC1) genes in symptomatic, mild-to-moderate COVID-19 adults, when adjusting for age, sex, and race. Interestingly, the expression levels of most of these genes plateaued at a cycle threshold (
MeSH term(s)	Adult ; Humans ; Chemokines/physiology ; COVID-19/immunology ; COVID-19/virology ; Gene Expression/immunology ; Immunity, Mucosal/immunology ; Interferons/physiology ; SARS-CoV-2/genetics ; Viral Load ; Respiratory Mucosa/immunology ; Respiratory Mucosa/virology
Chemical Substances	Chemokines ; Interferons (9008-11-1)
Language	English
Publishing date	2023-01-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.01478-22
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Article ; Online: Malaria disrupts the rhesus macaque gut microbiome.

Farinella, Danielle N / Kaur, Sukhpreet / Tran, ViLinh / Cabrera-Mora, Monica / Joyner, Chester J / Lapp, Stacey A / Pakala, Suman B / Nural, Mustafa V / DeBarry, Jeremy D / Kissinger, Jessica C / Jones, Dean P / Moreno, Alberto / Galinski, Mary R / Cordy, Regina Joice

Frontiers in cellular and infection microbiology

2023 Volume 12, Page(s) 1058926

Abstract: Previous studies have suggested that a relationship exists between severity and transmissibility of malaria and variations in the gut microbiome, yet only limited information exists on the temporal dynamics of the gut microbial community during a ... ...

Abstract	Previous studies have suggested that a relationship exists between severity and transmissibility of malaria and variations in the gut microbiome, yet only limited information exists on the temporal dynamics of the gut microbial community during a malarial infection. Here, using a rhesus macaque model of relapsing malaria, we investigate how malaria affects the gut microbiome. In this study, we performed 16S sequencing on DNA isolated from rectal swabs of rhesus macaques over the course of an experimental malarial infection with
MeSH term(s)	Animals ; Humans ; Macaca mulatta/genetics ; Macaca mulatta/metabolism ; Gastrointestinal Microbiome ; Malaria/parasitology ; Malaria, Vivax/parasitology ; Plasmodium cynomolgi/genetics ; Plasmodium cynomolgi/metabolism ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2023-01-13
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2022.1058926
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Article ; Online: Species-specific transcriptomic changes upon respiratory syncytial virus infection in cotton rats.

Strickland, Britton A / Rajagopala, Seesandra V / Kamali, Arash / Shilts, Meghan H / Pakala, Suman B / Boukhvalova, Marina S / Yooseph, Shibu / Blanco, Jorge C G / Das, Suman R

Scientific reports

2022 Volume 12, Issue 1, Page(s) 16579

Abstract: The cotton rat (Sigmodon) is the gold standard pre-clinical small animal model for respiratory viral pathogens, especially for respiratory syncytial virus (RSV). However, without a reference genome or a published transcriptome, studies requiring gene ... ...

Abstract	The cotton rat (Sigmodon) is the gold standard pre-clinical small animal model for respiratory viral pathogens, especially for respiratory syncytial virus (RSV). However, without a reference genome or a published transcriptome, studies requiring gene expression analysis in cotton rats are severely limited. The aims of this study were to generate a comprehensive transcriptome from multiple tissues of two species of cotton rats that are commonly used as animal models (Sigmodon fulviventer and Sigmodon hispidus), and to compare and contrast gene expression changes and immune responses to RSV infection between the two species. Transcriptomes were assembled from lung, spleen, kidney, heart, and intestines for each species with a contig N50 > 1600. Annotation of contigs generated nearly 120,000 gene annotations for each species. The transcriptomes of S. fulviventer and S. hispidus were then used to assess immune response to RSV infection. We identified 238 unique genes that are significantly differentially expressed, including several genes implicated in RSV infection (e.g., Mx2, I27L2, LY6E, Viperin, Keratin 6A, ISG15, CXCL10, CXCL11, IRF9) as well as novel genes that have not previously described in RSV research (LG3BP, SYWC, ABEC1, IIGP1, CREB1). This study presents two comprehensive transcriptome references as resources for future gene expression analysis studies in the cotton rat model, as well as provides gene sequences for mechanistic characterization of molecular pathways. Overall, our results provide generalizable insights into the effect of host genetics on host-virus interactions, as well as identify new host therapeutic targets for RSV treatment and prevention.
MeSH term(s)	Animals ; Antibodies, Viral ; Disease Models, Animal ; Keratin-6/genetics ; Lung ; Respiratory Syncytial Virus Infections ; Respiratory Syncytial Virus, Human/genetics ; Sigmodontinae ; Transcriptome
Chemical Substances	Antibodies, Viral ; Keratin-6
Language	English
Publishing date	2022-10-04
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-19810-4
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Article ; Online: COVID-19 severity from Omicron and Delta SARS-CoV-2 variants.

Wrenn, Jesse O / Pakala, Suman B / Vestal, Grant / Shilts, Meghan H / Brown, Hunter M / Bowen, Sara M / Strickland, Britton A / Williams, Timothy / Mallal, Simon A / Jones, Ian D / Schmitz, Jonathan E / Self, Wesley H / Das, Suman R

Influenza and other respiratory viruses

2022 Volume 16, Issue 5, Page(s) 832–836

Abstract: The Omicron variant of SARS-CoV-2 achieved worldwide dominance in late 2021. Early work suggests that infections caused by the Omicron variant may be less severe than those caused by the Delta variant. We sought to compare clinical outcomes of infections ...

Abstract	The Omicron variant of SARS-CoV-2 achieved worldwide dominance in late 2021. Early work suggests that infections caused by the Omicron variant may be less severe than those caused by the Delta variant. We sought to compare clinical outcomes of infections caused by these two strains, confirmed by whole genome sequencing, over a short period of time, from respiratory samples collected from SARS-CoV-2 positive patients at a large medical center. We found that infections caused by the Omicron variant caused significantly less morbidity, including admission to the hospital and requirement for oxygen supplementation, and significantly less mortality than those caused by the Delta variant.
MeSH term(s)	COVID-19 ; Humans ; SARS-CoV-2/genetics
Language	English
Publishing date	2022-04-13
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2274538-5
ISSN	1750-2659 ; 1750-2640
ISSN (online)	1750-2659
ISSN	1750-2640
DOI	10.1111/irv.12982
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Article: Mucosal gene expression in response to SARS-CoV-2 is associated with early viral load.

bioRxiv : the preprint server for biology

2022

Abstract: Little is known about the relationships between symptomatic early-time SARS-CoV-2 viral load and upper airway mucosal gene expression and immune response. To examine the association of symptomatic SARS-CoV-2 early viral load with upper airway mucosal ... ...

Abstract	Little is known about the relationships between symptomatic early-time SARS-CoV-2 viral load and upper airway mucosal gene expression and immune response. To examine the association of symptomatic SARS-CoV-2 early viral load with upper airway mucosal gene expression, we profiled the host mucosal transcriptome from nasopharyngeal swab samples from 68 adults with symptomatic, mild-to-moderate COVID-19. We measured SARS-CoV-2 viral load using qRT-PCR. We then examined the association of SARS-CoV-2 viral load with upper airway mucosal immune response. We detected SARS-CoV-2 in all samples and recovered >80% of the genome from 85% of the samples from symptomatic COVID-19 adults. The respiratory virome was dominated by SARS-CoV-2, with limited co-detection of common respiratory viruses i.e., only the human Rhinovirus (HRV) being identified in 6% of the samples. We observed a significant positive correlation between SARS-CoV-2 viral load and interferon signaling (OAS2, OAS3, IFIT1, UPS18, ISG15, ISG20, IFITM1, and OASL), chemokine signaling (CXCL10 and CXCL11), and adaptive immune system (IFITM1, CD300E, and SIGLEC1) genes in symptomatic, mild-to-moderate COVID-19 adults, when adjusted for age, sex and race. Interestingly, the expression levels of most of these genes plateaued at a CT value of ~25. Overall, our data shows that early nasal mucosal immune response to SARS-CoV-2 infection is viral load dependent, which potentially could modify COVID-19 outcomes. Author summary: Several prior studies have shown that SARS-CoV-2 viral load can predict the likelihood of disease spread and severity. A higher detectable SARS-CoV-2 plasma viral load was associated with worse respiratory disease severity. However, the relationship between SARS-CoV-2 viral load and airway mucosal gene expression and immune response remains elusive. We profiled the nasal mucosal transcriptome from nasal samples collected from adults infected with SARS-CoV-2 during Spring 2020 with mild-to-moderate symptoms using a comprehensive metatranscriptomics method. We observed a positive correlation between SARS-CoV-2 viral load with interferon signaling, chemokine signaling, and adaptive immune system in adults with COVID-19. Our data suggest that early nasal mucosal immune response to SARS-CoV-2 infection was viral load-dependent and may modify COVID-19 outcomes.
Language	English
Publishing date	2022-08-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.08.23.504908
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Article ; Online: Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples.

Rajagopala, Seesandra V / Bakhoum, Nicole G / Pakala, Suman B / Shilts, Meghan H / Rosas-Salazar, Christian / Mai, Annie / Boone, Helen H / McHenry, Rendie / Yooseph, Shibu / Halasa, Natasha / Das, Suman R

Cell reports methods

2021 Volume 1, Issue 6

Abstract: We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low biomass samples. Using nasal swab samples, we capture RNA virome with sufficient sequencing depth required ... ...

Abstract	We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low biomass samples. Using nasal swab samples, we capture RNA virome with sufficient sequencing depth required to assemble complete genomes. We find a surprisingly high frequency of respiratory syncytial virus (RSV) and coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-detections in children with symptomatic RSV. In addition, we have identified commensal and pathogenic bacteria and fungi at the species level. Functional analysis revealed that
MeSH term(s)	Child ; Humans ; Respiratory Syncytial Virus Infections/genetics ; Virome/genetics ; Respiratory Syncytial Virus, Human/genetics ; Microbiota/genetics ; Transcriptome/genetics
Language	English
Publishing date	2021-12-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ISSN	2667-2375
ISSN (online)	2667-2375
DOI	10.1016/j.crmeth.2021.100091
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Article: Suppression subtractive hybridization and comparative expression of a pore-forming toxin and glycosyl hydrolase genes in Rhizoctonia solani during potato sprout infection

Chamoun, Rony / Samsatly, Jamil / Pakala, Suman B / Cubeta, Marc A / Jabaji, Suha

Molecular genetics and genomics. 2015 June, v. 290, no. 3

2015

Abstract: Rhizoctonia solani is a plant pathogenic fungus that causes black scurf on tubers and stem and stolon canker on underground parts of potato plant. Early in the season, the fungus attacks germinating sprouts underground before they emerge from the soil. ... ...

Abstract	Rhizoctonia solani is a plant pathogenic fungus that causes black scurf on tubers and stem and stolon canker on underground parts of potato plant. Early in the season, the fungus attacks germinating sprouts underground before they emerge from the soil. Damage at this stage results in delayed emergence of weakened plants with poor and uneven stands. The mechanism underlying this phenomenon has been investigated in this study by coupling a cDNA-suppression subtractive hybridization (SSH) library to differential screening to identify transcripts of R. solani that are down-regulated during infection of potato sprouts. We report on the identification of 33 unique genes with functions related to carbohydrate binding, vitamin synthesis, pathogenicity, translation, ATP and nucleic acid binding and other categories. RACE-PCR was used to clone and characterize the first full-length cDNA clones, RSENDO1 and RSGLYC1 that encode for an eukaryotic delta-endotoxin CytB protein and an intracellular glycosyl hydrolase, respectively. Quantitative real-time PCR revealed the down-regulation of RSENDO1 during infection of potato sprouts and the up-regulation of RSGLYC1 when the fungus was grown on a cellulose-based nutrient medium. In contrast, additional experiments have highlighted the down-regulation of RSENDO1 when R. solani was co-cultured with the mycoparasite Stachybotrys elegans and the bacterial antagonist Bacillus subtilis B26. These results advance our understanding of R. solani–potato interaction in subterranean parts of the plant. Such approaches could be considered in building an efficient integrated potato disease management program.
Keywords	Bacillus subtilis ; Solanum tuberosum ; Stachybotrys ; Thanatephorus cucumeris ; adenosine triphosphate ; antagonists ; carbohydrate binding ; clones ; coculture ; complementary DNA ; delta-endotoxins ; disease control ; fungal antagonists ; fungal diseases of plants ; gene expression regulation ; genes ; pathogenicity ; plant pathogenic fungi ; potatoes ; quantitative polymerase chain reaction ; screening ; soil ; suppression subtractive hybridization ; translation (genetics) ; tubers ; underground parts
Language	English
Dates of publication	2015-06
Size	p. 877-900.
Publishing place	Springer-Verlag
Document type	Article
ISSN	1617-4615
DOI	10.1007/s00438-014-0962-x
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