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Article ; Online: COVID19 therapeutics

Tom Gallagher

EBioMedicine, Vol 66, Iss , Pp 103289- (2021)

Expanding the antiviral arsenal

2021

Keywords	Medicine ; R ; Medicine (General) ; R5-920
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The first few days of a SARS-CoV-2 infection viewed at single-cell resolution.

Tom Gallagher / Paul B McCray

PLoS Biology, Vol 19, Iss 4, p e

2021 Volume 3001217

Abstract: What transpires soon after inhaling Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the respiratory virus causing Coronavirus Disease 2019 (COVID-19)? Where does infection begin? What are the features of subsequent virus spread? How might ... ...

Abstract	What transpires soon after inhaling Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the respiratory virus causing Coronavirus Disease 2019 (COVID-19)? Where does infection begin? What are the features of subsequent virus spread? How might host responses quickly contain infection? Two recently published manuscripts have evaluated infection in primary cultures of well-differentiated cells to address these questions and bring more light on the proviral and antiviral components operating during the initial days after SARS-CoV-2 exposure.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-04-01T00:00:00Z
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: Assembly and Entry of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2)

Binod Kumar / Grant M. Hawkins / Tom Kicmal / Enya Qing / Emily Timm / Tom Gallagher

Cells, Vol 10, Iss 853, p

Evaluation Using Virus-Like Particles

2021 Volume 853

Abstract: Research on infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is currently restricted to BSL-3 laboratories. SARS-CoV2 virus-like particles (VLPs) offer a BSL-1, replication-incompetent system that can be used to evaluate virus ... ...

Abstract	Research on infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is currently restricted to BSL-3 laboratories. SARS-CoV2 virus-like particles (VLPs) offer a BSL-1, replication-incompetent system that can be used to evaluate virus assembly and virus-cell entry processes in tractable cell culture conditions. Here, we describe a SARS-CoV2 VLP system that utilizes nanoluciferase (Nluc) fragment complementation to track assembly and entry. We utilized the system in two ways. Firstly, we investigated the requirements for VLP assembly. VLPs were produced by concomitant synthesis of three viral membrane proteins, spike (S), envelope (E), and matrix (M), along with the cytoplasmic nucleocapsid (N). We discovered that VLP production and secretion were highly dependent on N proteins. N proteins from related betacoronaviruses variably substituted for the homologous SARS-CoV2 N, and chimeric betacoronavirus N proteins effectively supported VLP production if they contained SARS-CoV2 N carboxy-terminal domains (CTD). This established the CTDs as critical features of virus particle assembly. Secondly, we utilized the system by investigating virus-cell entry. VLPs were produced with Nluc peptide fragments appended to E, M, or N proteins, with each subsequently inoculated into target cells expressing complementary Nluc fragments. Complementation into functional Nluc was used to assess virus-cell entry. We discovered that each of the VLPs were effective at monitoring virus-cell entry, to various extents, in ways that depended on host cell susceptibility factors. Overall, we have developed and utilized a VLP system that has proven useful in identifying SARS-CoV2 assembly and entry features.
Keywords	coronavirus ; SARS-CoV2 ; D614G ; MERS-CoV ; MHV ; virus-like particles ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Inter-domain communication in SARS-CoV-2 spike proteins controls protease-triggered cell entry

Enya Qing / Pengfei Li / Laura Cooper / Sebastian Schulz / Hans-Martin Jäck / Lijun Rong / Stanley Perlman / Tom Gallagher

Cell Reports, Vol 39, Iss 5, Pp 110786- (2022)

2022

Abstract: Summary: SARS-CoV-2 continues to evolve into variants of concern (VOC), with greatest variability in the multidomain, entry-facilitating spike proteins. To recognize the significance of adaptive spike protein changes, we compare variant SARS-CoV-2 virus ... ...

Abstract	Summary: SARS-CoV-2 continues to evolve into variants of concern (VOC), with greatest variability in the multidomain, entry-facilitating spike proteins. To recognize the significance of adaptive spike protein changes, we compare variant SARS-CoV-2 virus particles in several assays reflecting authentic virus-cell entry. Virus particles with adaptive changes in spike amino-terminal domains (NTDs) are hypersensitive to proteolytic activation of membrane fusion, an essential step in virus-cell entry. Proteolysis is within fusion domains (FDs), at sites over 10 nm from the VOC-specific NTD changes, indicating allosteric inter-domain control of fusion activation. In addition, NTD-specific antibodies block FD cleavage, membrane fusion, and virus-cell entry, suggesting restriction of inter-domain communication as a neutralization mechanism. Finally, using structure-guided mutagenesis, we identify an inter-monomer β sheet structure that facilitates NTD-to-FD transmissions and subsequent fusion activation. This NTD-to-FD axis that sensitizes viruses to infection and to NTD-specific antibody neutralization provides new context for understanding selective forces driving SARS-CoV-2 evolution.
Keywords	CP: Microbiology ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Field Assessment of Downed Timber Strength Deterioration Rate and Wood Quality Using Acoustic Technologies

Munkaila Musah / Javier Hernandez Diaz / Abiodun Oluseun Alawode / Tom Gallagher / Maria Soledad Peresin / Dana Mitchell / Mathew Smidt / Brian Via

Forests, Vol 13, Iss 752, p

2022 Volume 752

Abstract: Hurricane and tornado events cause significant damage to high-value timber in the United States each year. Forest managers and landowners are keenly interested in finding solutions to salvage and repurpose these downed timbers before they cause pest ... ...

Abstract	Hurricane and tornado events cause significant damage to high-value timber in the United States each year. Forest managers and landowners are keenly interested in finding solutions to salvage and repurpose these downed timbers before they cause pest infestations and fire outbreaks, completely losing their value or increasing processing costs. To better understand the wood quality of the downed timber, we used acoustic waves techniques as a nondestructive testing approach to assess the wood degradation rate of downed trees and determine the extent of fracture and voids in the damaged regions. We periodically monitored the acoustic velocity of the downed trees for 12 consecutive months using a time of flight (TOF) acoustic method. Acoustic measurements were conducted using three different techniques—longitudinal, transverse, and off-set methods. Wood density, age, and the diameter at breast height (dbh) class measurement for southern timber (chip-n-saw for dbh 8″–11″ and sawtimber with dbh 12″ and up) were used as the predictive parameters of the downed trees. The results indicated positive relationships between dbh class, stand age, and acoustic velocity measurement ( R 2 > 65%). The TOF acoustic velocity was indicated to potentially separate higher-stiffness timber from lower-stiffness timber in a hurricane event for structural or non-structural applications. The regression coefficient from the repeated measurements indicated that both age and diameter class strongly impacted the acoustic properties of the downed trees ( p -value ≤ 0.001). The sawtimber dbh class recorded a higher acoustic velocity compared to the chip-n-saw type. Fracture, voids, and massive decay in downed trees were detected beyond the visible inspection, features that often are identified by loggers in lower quality wood; however, TOF showed a weak response in picking up incremental deterioration due to changes in specific environmental factors that affected acoustic readings. This study showed that acoustic wave methods could potentially ...
Keywords	acoustic velocity ; dbh class ; downed timber ; non-destructive evaluation ; wood stiffness ; Plant ecology ; QK900-989
Subject code	690
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ready, Set, Fuse! The Coronavirus Spike Protein and Acquisition of Fusion Competence

Tom Gallagher / Taylor Heald-Sargent

Viruses, Vol 4, Iss 4, Pp 557-

2012 Volume 580

Abstract: Coronavirus-cell entry programs involve virus-cell membrane fusions mediated by viral spike (S) proteins. Coronavirus S proteins acquire membrane fusion competence by receptor interactions, proteolysis, and acidification in endosomes. This review ... ...

Abstract	Coronavirus-cell entry programs involve virus-cell membrane fusions mediated by viral spike (S) proteins. Coronavirus S proteins acquire membrane fusion competence by receptor interactions, proteolysis, and acidification in endosomes. This review describes our current understanding of the S proteins, their interactions with and their responses to these entry triggers. We focus on receptors and proteases in prompting entry and highlight the type II transmembrane serine proteases (TTSPs) known to activate several virus fusion proteins. These and other proteases are essential cofactors permitting coronavirus infection, conceivably being in proximity to cell-surface receptors and thus poised to split entering spike proteins into the fragments that refold to mediate membrane fusion. The review concludes by noting how understanding of coronavirus entry informs antiviral therapies.
Keywords	coronavirus ; virus entry ; viral pathogenesis ; spike protein ; carcinoembryonic antigen ; angiotensin converting enzyme 2 ; endocytosis ; cathepsin ; transmembrane protease ; membrane fusion ; Microbiology ; QR1-502 ; Science ; Q ; DOAJ:Microbiology ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Language	English
Publishing date	2012-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs

Debajit Dey / Enya Qing / Yanan He / Yihong Chen / Benjamin Jennings / Whitaker Cohn / Suruchi Singh / Lokesh Gakhar / Nicholas J. Schnicker / Brian G. Pierce / Julian P. Whitelegge / Balraj Doray / John Orban / Tom Gallagher / S. Saif Hasan

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

2023 Volume 17

Abstract: Abstract The spike (S) protein of SARS-CoV-2 is delivered to the virion assembly site in the ER-Golgi Intermediate Compartment (ERGIC) from both the ER and cis-Golgi in infected cells. However, the relevance and modulatory mechanism of this bidirectional ...

Abstract	Abstract The spike (S) protein of SARS-CoV-2 is delivered to the virion assembly site in the ER-Golgi Intermediate Compartment (ERGIC) from both the ER and cis-Golgi in infected cells. However, the relevance and modulatory mechanism of this bidirectional trafficking are unclear. Here, using structure-function analyses, we show that S incorporation into virus-like particles (VLP) and VLP fusogenicity are determined by coatomer-dependent S delivery from the cis-Golgi and restricted by S-coatomer dissociation. Although S mimicry of the host coatomer-binding dibasic motif ensures retrograde trafficking to the ERGIC, avoidance of the host-like C-terminal acidic residue is critical for S-coatomer dissociation and therefore incorporation into virions or export for cell-cell fusion. Because this C-terminal residue is the key determinant of SARS-CoV-2 assembly and fusogenicity, our work provides a framework for the export of S protein encoded in genetic vaccines for surface display and immune activation.
Keywords	Science ; Q
Subject code	572
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Application of a Small-Scale Equipment System for Biomass Harvesting

Yu, Aihua / Brandon OâNeal / Dana Mitchell / Tom Gallagher

Small-scale forestry. 2017 Mar., v. 16, no. 1

2017

Abstract: The small-scale harvesting equipment system has been and continues to grow in use in forestry operations in some regions in the world. This harvest system can include a range of equipment types, such as feller-bunchers or chainsaws, skidders or farm ... ...

Abstract	The small-scale harvesting equipment system has been and continues to grow in use in forestry operations in some regions in the world. This harvest system can include a range of equipment types, such as feller-bunchers or chainsaws, skidders or farm tractors, and chippers. These machines are generally smaller, lower cost and less productive than larger, more advanced forestry machines. The objective of this project was to investigate the feasibility of a small scale harvesting system that would produce feedstock for a biomass power plant. The system had to be cost competitive. A boom-type feller-buncher, a small grapple skidder and a chipper were tested as a small-scale system. In this study, feller-buncher and skidder productivity was determined to be 10.5Â mÂ³ per productive machine hour, and production for the chipper was determined to be 18Â mÂ³ per productive machine hour. Production from the system did not reach the desired levels of 4 loads/day (25Â mÂ³/load); however, the system was able to produce about 3 loads/day. The results showed that the system currently could fill a roadside van for $16.90/mÂ³, but suggested machine modifications could potentially reduce the system cost to $12.73/mÂ³. Residual stand damage was minimal, especially on flatter ground and not operating on a slash layer. Soil disturbance from the harvesting system was predominantly undisturbed or classified as a shallow disturbance.
Keywords	biomass ; chainsaws ; disturbed soils ; farms ; feedstocks ; feller bunchers ; forestry ; harvesting ; harvesting equipment ; power plants ; skidders ; slash ; tractors
Language	English
Dates of publication	2017-03
Size	p. 133-146.
Publishing place	Springer Netherlands
Document type	Article
ZDB-ID	2365256-1
ISSN	1873-7854 ; 1873-7617
ISSN (online)	1873-7854
ISSN	1873-7617
DOI	10.1007/s11842-016-9347-9
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: High Throughput Screening of Elite Loblolly Pine Families for Chemical and Bioenergy Traits with Near Infrared Spectroscopy

Gifty E. Acquah / Brian K. Via / Tom Gallagher / Nedret Billor / Oladiran O. Fasina / Lori G. Eckhardt

Forests, Vol 9, Iss 7, p

2018 Volume 418

Abstract: Pinus taeda L. (loblolly pine) dominates 13.4 million ha of US southeastern forests and contributes over $30 billion to the economy of the region. The species will also form an important component of the renewable energy portfolio as the United States ... ...

Abstract	Pinus taeda L. (loblolly pine) dominates 13.4 million ha of US southeastern forests and contributes over $30 billion to the economy of the region. The species will also form an important component of the renewable energy portfolio as the United States seeks national and energy security as well as environmental sustainability. This study employed NIR-based chemometric models as a high throughput screening tool to estimate the chemical traits and bioenergy potential of 351 standing loblolly pine trees representing 14 elite genetic families planted on two forest sites. The genotype of loblolly pine families affected the chemical, proximate and energy traits studied. With a range of 36.7% to 42.0%, the largest genetic variation (p-value < 0.0001) was detected in the cellulose content. Furthermore, although family by site interactions were significant for all traits, cellulose was the most stable across the two sites. Considering that cellulose content has strong correlations with other properties, selecting and breeding for cellulose could generate some gains.
Keywords	Pinus taeda ; wood traits ; bioenergy potential ; genotype × environment interaction ; non-destructive testing ; bioeconomy ; Plant ecology ; QK900-989
Subject code	580
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: High Tonnage Harvesting and Skidding for Loblolly Pine Energy Plantations

Jernigan, Patrick / Dana Mitchell / Larry Teeter / Mathew Smidt / Tom Gallagher

Forest products journal. 2016, v. 66, no. 3-4

2016

Abstract: The southeastern United States has a promising source for renewable energy in the form of woody biomass. To meet the energy needs, energy plantations will likely be utilized. These plantations will contain a high density of small-stem pine trees. Since ... ...

Abstract	The southeastern United States has a promising source for renewable energy in the form of woody biomass. To meet the energy needs, energy plantations will likely be utilized. These plantations will contain a high density of small-stem pine trees. Since the stems are relatively small when compared with traditional product removal, the harvesting costs will increase. The purpose of this research was to evaluate specialized harvesting and skidding equipment that would harvest these small stems cost efficiently. The feller-buncher utilized was a Tigercat 845D with a specialized biomass shear head. The skidder was a Tigercat 630D equipped with an oversized grapple. This equipment was evaluated in a 4-hectare stand with characteristics of a southern pine energy plantation. During the study, the feller-buncher achieved an average production rate of 47 green tonnes/productive machine hour (gt/PMH) and the skidder had an average production rate of 112 gt/PMH. A before-tax cash-flow model was used to determine a cost per ton for each machine. The feller-buncher costs were $3.85/gt over a 10-year life span, whereas the skidder costs were $1.95/gt over the same 10-year life. The results suggested that the current system working in a southern pine energy plantation could harvest and skid small stems for approximately $5.80/gt.
Keywords	biomass ; energy ; harvesting ; longevity ; models ; Pinus taeda ; plantations ; renewable energy sources ; skidding equipment ; stand characteristics ; stems ; Southeastern United States
Language	English
Size	p. 185-191.
Publishing place	[Forest Products Society, etc.]
Document type	Article
ZDB-ID	240509-x
ISSN	0015-7473
ISSN	0015-7473
DOI	10.13073/FPJ-D-14-00055
Database	NAL-Catalogue (AGRICOLA)

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