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Article ; Online: Detecting DNA Loops Using Tethered Particle Motion.

Qian, Jin / Collette, Dylan / Finzi, Laura / Dunlap, David

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2694, Page(s) 451–466

Abstract: The range of motion of a micron-sized bead tethered by a single polymer provides a dynamic readout of the effective length of the polymer. The excursions of the bead may reflect the intrinsic flexibility and/or topology of the polymer as well as changes ... ...

Abstract	The range of motion of a micron-sized bead tethered by a single polymer provides a dynamic readout of the effective length of the polymer. The excursions of the bead may reflect the intrinsic flexibility and/or topology of the polymer as well as changes due to the action activity of ligands that bind the polymer. This is a simple yet powerful experimental approach to investigate such interactions between DNA and proteins as demonstrated by experiments with the lac repressor. This protein forms a stable, tetrameric oligomer with two binding sites and can produce a loop of DNA between recognition sites separated along the length of a DNA molecule.
MeSH term(s)	Nucleic Acid Conformation ; Motion ; DNA/chemistry ; Lac Repressors ; Proteins ; Polymers
Chemical Substances	DNA (9007-49-2) ; Lac Repressors ; Proteins ; Polymers
Language	English
Publishing date	2023-10-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3377-9_21
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Book ; Online: Distances and shortest paths on graphs of bounded highway dimension

Collette, Sébastien / Iacono, John

simple, fast, dynamic

2023

Abstract: Dijkstra's algorithm is the standard method for computing shortest paths on arbitrary graphs. However, it is slow for large graphs, taking at least linear time. It has been long known that for real world road networks, creating a hierarchy of well-chosen ...

Abstract	Dijkstra's algorithm is the standard method for computing shortest paths on arbitrary graphs. However, it is slow for large graphs, taking at least linear time. It has been long known that for real world road networks, creating a hierarchy of well-chosen shortcuts allows fast distance and path computation, with exact distance queries seemingly being answered in logarithmic time. However, these methods were but heuristics until the work of Abraham et al.~[JACM 2016], where they defined a graph parameter called highway dimension which is constant for real-world road networks, and showed that in graphs of constant highway dimension, a shortcut hierarchy exists that guarantees shortest distance computation takes $O(\log (U+V))$ time and $O(V \log (U+V))$ space, where $U$ is the ratio of the smallest to largest edge, and $V$ is the number of vertices. The problem is that they were unable to efficiently compute the hierarchy of shortcuts. Here we present a simple and efficient algorithm to compute the needed hierarchy of shortcuts in time and space $O(V \log (U+V))$, as well as supporting updates in time $O( \log (U+V))$.
Keywords	Computer Science - Data Structures and Algorithms
Subject code	005
Publishing date	2023-12-07
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An unusual dual sugar-binding lectin domain controls the substrate specificity of a mucin-type O-glycosyltransferase.

Collette, Abbie M / Hassan, Sergio A / Schmidt, Susan I / Lara, Alexander J / Yang, Weiming / Samara, Nadine L

Science advances

2024 Volume 10, Issue 9, Page(s) eadj8829

Abstract: N-acetylgalactosaminyl-transferases (GalNAc-Ts) initiate mucin-type O-glycosylation, an abundant and complex posttranslational modification that regulates host-microbe interactions, tissue development, and metabolism. GalNAc-Ts contain a lectin domain ... ...

Abstract	N-acetylgalactosaminyl-transferases (GalNAc-Ts) initiate mucin-type O-glycosylation, an abundant and complex posttranslational modification that regulates host-microbe interactions, tissue development, and metabolism. GalNAc-Ts contain a lectin domain consisting of three homologous repeats (α, β, and γ), where α and β can potentially interact with O-GalNAc on substrates to enhance activity toward a nearby acceptor Thr/Ser. The ubiquitous isoenzyme GalNAc-T1 modulates heart development, immunity, and SARS-CoV-2 infectivity, but its substrates are largely unknown. Here, we show that both α and β in GalNAc-T1 uniquely orchestrate the O-glycosylation of various glycopeptide substrates. The α repeat directs O-glycosylation to acceptor sites carboxyl-terminal to an existing GalNAc, while the β repeat directs O-glycosylation to amino-terminal sites. In addition, GalNAc-T1 incorporates α and β into various substrate binding modes to cooperatively increase the specificity toward an acceptor site located between two existing O-glycans. Our studies highlight a unique mechanism by which dual lectin repeats expand substrate specificity and provide crucial information for identifying the biological substrates of GalNAc-T1.
MeSH term(s)	Mucins/chemistry ; Mucins/metabolism ; N-Acetylgalactosaminyltransferases/genetics ; N-Acetylgalactosaminyltransferases/chemistry ; N-Acetylgalactosaminyltransferases/metabolism ; Lectins ; Substrate Specificity ; Protein Structure, Tertiary ; Polypeptide N-acetylgalactosaminyltransferase ; Sugars
Chemical Substances	Mucins ; N-Acetylgalactosaminyltransferases (EC 2.4.1.-) ; Lectins ; Polypeptide N-acetylgalactosaminyltransferase (EC 2.4.1.41) ; Sugars
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adj8829
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Article ; Online: Impact of relative dose intensity on pathologic complete response in human epidermal growth factor receptor 2 positive breast cancer patients receiving neoadjuvant TCHP.

Collette, Kaylyn / Perkey, Cassandra L / Adams, Val / Shelton, Brent J / Corum, Lauren S / Butts, Allison

Journal of oncology pharmacy practice : official publication of the International Society of Oncology Pharmacy Practitioners

2023 , Page(s) 10781552231212206

Abstract: Purpose: The standard of care for locally advanced, human epidermal growth factor receptor 2 positive (HER2+) breast cancer includes neoadjuvant chemotherapy with docetaxel, carboplatin, trastuzumab, and pertuzumab (TCHP). Many patients do not receive ... ...

Abstract	Purpose: The standard of care for locally advanced, human epidermal growth factor receptor 2 positive (HER2+) breast cancer includes neoadjuvant chemotherapy with docetaxel, carboplatin, trastuzumab, and pertuzumab (TCHP). Many patients do not receive the full course of therapy due to various complications, possibly affecting the potential to achieve a pathologic complete response (pCR). The amount of therapy received is typically measured by relative dose intensity (RDI). This study aimed to evaluate pCR rates in patients receiving optimal and suboptimal RDI TCHP. Methods: This study was a retrospective chart review of patients treated between 2014 and 2021 at UK HealthCare. Patients included were 18 years of age or older with HER2+ breast cancer and received at least one cycle of neoadjuvant TCHP. The primary objective compared pCR rates in patients receiving ≥ 85% RDI or <85% RDI. Secondary objectives included pCR rates based on clinical stage, age, body mass index, or hormone receptor status; factors leading to discontinuation or delay in treatment; and impact of dose reductions and delays on pCR. Results: A total of 101 patients were included and divided into two cohorts: 54 patients received ≥ 85% RDI and 47 patients received <85% RDI. Patients who received ≥ 85% total RDI had an approximate increase of 17% in pCR rates (59.3% vs 42.6%, Conclusions: Patients who received ≥ 85% RDI had increased pCR rates compared to patients receiving <85% RDI. A larger patient population is needed to formulate definitive conclusions on the impact of RDI and pCR rates.
Language	English
Publishing date	2023-11-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1330764-2
ISSN	1477-092X ; 1078-1552
ISSN (online)	1477-092X
ISSN	1078-1552
DOI	10.1177/10781552231212206
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Article: Investigation of 18 physiologically dormant Australian native species: germination response, environmental correlations and the implications for conservation

Collette, Justin C / Ooi, Mark K.J

Seed science research. 2021 Mar., v. 31, no. 1

2021

Abstract: For physiologically dormant (PD) species in fire-prone environments, dormancy can be both complex due to the interaction between fire and seasonal cues, and extremely deep due to long intervals between recruitment events. Due to this complexity, there ... ...

Abstract	For physiologically dormant (PD) species in fire-prone environments, dormancy can be both complex due to the interaction between fire and seasonal cues, and extremely deep due to long intervals between recruitment events. Due to this complexity, there are knowledge gaps particularly surrounding the dormancy depth and cues of long-lived perennial PD species. This can be problematic for both in situ and ex situ species management. We used germination experiments that tested seasonal temperature, smoke, dark and heat for 18 PD shrub species distributed across temperate fire-prone Australia and assessed how germination was correlated with environmental factors associated with their home environments. We found extremely high levels of dormancy, with only eight species germinating above 10% and three species producing no germination at all. Seven of these eight species had quite specific seasonal temperature requirements and/or very strong responses to smoke cues. The maximum germination for each species was positively correlated with the mean temperature of the source population but negatively correlated with rainfall seasonality and driest months. The strong dependence on a smoke cue for some of the study species, along with examples from other studies, provides evidence that an obligate smoke response could be a fire-adapted germination cue. Germination response correlated with rainfall season of the source populations is a pattern which has often been assumed but little comparative data across sites with different rainfall seasonality exists. Further investigation of a broader range of species from different rainfall season environments would help to elucidate this knowledge gap.
Keywords	dormancy ; germination ; heat ; indigenous species ; rain ; research ; shrubs ; smoke ; temperature ; Australia
Language	English
Dates of publication	2021-03
Size	p. 30-38.
Publishing place	Cambridge University Press
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1102085-4
ISSN	1475-2735 ; 0960-2585
ISSN (online)	1475-2735
ISSN	0960-2585
DOI	10.1017/S0960258520000422
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids.

Allard, Nancy / Collette, Arianne / Paquette, Josianne / Rodrigue, Sébastien / Côté, Jean-Philippe

Communications biology

2023 Volume 6, Issue 1, Page(s) 1172

Abstract: Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed ...

Abstract	Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed the genetic requirement of recipient cells for conjugation of IncI2 plasmid TP114, which was recently shown to transfer at high rates in the gut microbiota. We performed transfer assays with ~4,000 single-gene deletion mutants of Escherichia coli. When conjugation occurs on a solid medium, we observed that recipient genes impairing transfer rates were not associated with a specific cellular function. Conversely, transfer assays performed in broth were largely dependent on the lipopolysaccharide biosynthesis pathway. We further identified specific structures in lipopolysaccharides used as recipient cell surface receptors by PilV adhesins associated with the type IVb accessory pilus of TP114. Our strategy is applicable to study other mobile genetic elements and understand important host cell factors for their dissemination.
MeSH term(s)	Plasmids/genetics ; Escherichia coli/metabolism ; Conjugation, Genetic ; Adhesins, Bacterial/genetics ; Gene Transfer, Horizontal
Chemical Substances	Adhesins, Bacterial
Language	English
Publishing date	2023-11-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05534-2
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Article ; Online: Evaluation of the Impact of Prior-to-Admission Sleep Aid Prescribing Practices on Sleep and Delirium in the Intensive Care Unit.

Chudow, Melissa / Paradiso, Vittorio / Silva, Nicole / Collette, Jillian

The Annals of pharmacotherapy

2021 Volume 56, Issue 6, Page(s) 679–684

Abstract: Background: Sleep disruptions in the intensive care unit (ICU) may lead to complications such as delirium. There is limited evidence addressing how sleep aid use before and during ICU admission affects outcomes.: Objective: The purpose of this study ... ...

Abstract	Background: Sleep disruptions in the intensive care unit (ICU) may lead to complications such as delirium. There is limited evidence addressing how sleep aid use before and during ICU admission affects outcomes. Objective: The purpose of this study is to evaluate the impact of prior-to-admission sleep aid prescribing practices in the ICU on delirium and sleep outcomes. Methods: A retrospective review was conducted of adult patients admitted to any ICU from January to June 2018 receiving a sleep aid prior to admission. Patients were categorized based on sleep aid continuation, discontinuation, or alteration during the ICU admission. The primary end point was the incidence of delirium. Secondary end points included the incidence of sleep-wake cycle disturbances, delirium scores, and ICU length of stay. Results: A total of 291 patients were included with 109 in the continued group, 121 in the discontinued group, and 61 in the altered group. There was a similar incidence of delirium at 24 hours ( Conclusion and relevance: The incidence of delirium and sleep-wake cycle disturbances was not affected by differences in prior-to-admission sleep aid prescribing patterns during ICU admission.
MeSH term(s)	Adult ; Delirium/epidemiology ; Delirium/prevention & control ; Humans ; Intensive Care Units ; Sleep
Language	English
Publishing date	2021-09-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	1101370-9
ISSN	1542-6270 ; 1060-0280
ISSN (online)	1542-6270
ISSN	1060-0280
DOI	10.1177/10600280211042632
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Article ; Online: Examining student well-being: Development and initial validation of the perceived vulnerability and hardiness scale.

Judkins, Jason L / Collette, Tyler / Gomes Student, Kimberly / Moore, Brian A

Journal of American college health : J of ACH

2022 Volume 71, Issue 9, Page(s) 2840–2847

Abstract: Objectives: The primary aim was to assess the factor structure and establish measurement invariance across sex for the Perceived Vulnerability and Hardiness Scale.: Participants: Sample 1 (: Methods: Iterative and collaborative survey-based focus ... ...

Abstract	Objectives: The primary aim was to assess the factor structure and establish measurement invariance across sex for the Perceived Vulnerability and Hardiness Scale. Participants: Sample 1 ( Methods: Iterative and collaborative survey-based focus groups were used to create the final version of the PVHS. Results: A two-factor model was identified through exploratory and confirmatory factor analyses. The psychological hardiness subscale was found to positively correlate with hardiness and resilience, and negatively correlate with psychosocial functioning, depression, and anxiety. The vulnerability subscale was found to positively, strongly correlate with the anxiety, psychological vulnerability, and psychosocial functioning, and negatively correlate with the hardiness and resilience. Men and women interpreted the PVHS in an equivalent manner. Conclusions: This brief measure provides researchers, counselors, and administrations a method for general assessment, intervention effectiveness, and evaluation of campus climates.
MeSH term(s)	Male ; Humans ; Female ; Students ; Universities ; Resilience, Psychological ; Anxiety Disorders ; Anxiety
Language	English
Publishing date	2022-01-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	604907-2
ISSN	1940-3208 ; 0744-8481
ISSN (online)	1940-3208
ISSN	0744-8481
DOI	10.1080/07448481.2021.1998072
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Article ; Online: Evidence for physiological seed dormancy cycling in the woody shrub Asterolasia buxifolia and its ecological significance in fire-prone systems.

Collette, J C / Ooi, M K J

Plant biology (Stuttgart, Germany)

2020 Volume 22, Issue 4, Page(s) 745–749

Abstract: Dormancy cycling is a key mechanism that contributes to the maintenance of long-term persistent soil seed banks, but has not been recorded in long-lived woody shrub species from fire-prone environments. Such species rely on seed banks and dormancy break ... ...

Abstract	Dormancy cycling is a key mechanism that contributes to the maintenance of long-term persistent soil seed banks, but has not been recorded in long-lived woody shrub species from fire-prone environments. Such species rely on seed banks and dormancy break as important processes for post-fire recruitment and recovery. We used germination experiments with smoke treatments on fresh seeds and those buried for 1 year (retrieved in spring) and 1.5 years (retrieved the following late autumn) to investigate whether Asterolasia buxifolia, a shrub from fire-prone south-eastern Australia with physiologically dormant seeds, exhibited dormancy cycling. All seeds had an obligation for winter seasonal temperatures and smoke to promote germination, even after ageing in the soil. A high proportion of germination was recorded from fresh seeds. but germination after the first retrieval was significantly lower, despite high seed viability. After the second retrieval, germination returned to the initial level. This indicates a pattern of annual dormancy cycling; one of the few observations, to our knowledge, for a perennial species. Additionally, A. buxifolia's winter temperature and smoke requirements did not change over time, highlighting the potential for seeds to remain conditionally dormant (i.e. restricted to a narrow range of germination conditions) for long periods. For physiologically dormant species, such as A. buxifolia, we conclude that dormancy cycling is an important driver of successful regeneration, allowing seed bank persistence, sometimes for decades, during fire-free periods unsuitable for successful recruitment, while ensuring that a large proportion of seeds are available for recruitment when a fire occurs.
MeSH term(s)	Fires ; Germination ; Plant Dormancy/physiology ; Rutaceae/physiology ; Seeds/physiology ; Soil ; Temperature
Chemical Substances	Soil
Language	English
Publishing date	2020-04-01
Publishing country	England
Document type	Journal Article
ZDB-ID	1464075-2
ISSN	1438-8677 ; 1435-8603
ISSN (online)	1438-8677
ISSN	1435-8603
DOI	10.1111/plb.13105
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Article ; Online: Distribution of seed dormancy classes across a fire-prone continent: effects of rainfall seasonality and temperature.

Collette, Justin C / Ooi, Mark K J

Annals of botany

2020 Volume 127, Issue 5, Page(s) 613–620

Abstract: Background and aims: Different seed dormancy classes control the timing of germination via different cues. The ecological dissimilarities between classes therefore suggest that they are likely to be subject to different selective pressures, and that ... ...

Abstract	Background and aims: Different seed dormancy classes control the timing of germination via different cues. The ecological dissimilarities between classes therefore suggest that they are likely to be subject to different selective pressures, and that species within each class will have diverse functional responses. We aimed to investigate this by assessing how variation in the distribution of dormancy classes is correlated with regional environmental factors, in particular rainfall seasonality and temperature. Additionally, we compare the relative proportions of species with physiological (PD) or physical (PY) dormancy to assess whether dormancy class influences their ability to persist under different rainfall seasonality regimes. Methods: Dormancy class was assigned for 3990 species from 281 genera occurring across two climate regions, with either winter or aseasonal rainfall, across temperate fire-prone Australia. All regions have similar vegetation and fire regimes. Using a Bayesian framework, we compared the distribution of dormancy classes across temperature and rainfall climate gradients, for threatened and common species. Key results: A high dormant:non-dormant species ratio highlighted the critical role of dormancy across our study regions. Critically, species showing PD were more likely to be threatened in aseasonal rainfall climate regions. Conclusions: Our results support the assumption that dormancy is favoured in environments with stochastic disturbance.
MeSH term(s)	Australia ; Bayes Theorem ; Germination ; Plant Dormancy ; Seasons ; Seeds ; Temperature
Language	English
Publishing date	2020-12-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1461328-1
ISSN	1095-8290 ; 0305-7364
ISSN (online)	1095-8290
ISSN	0305-7364
DOI	10.1093/aob/mcaa203
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