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Article ; Online: Ocean acidification interacts with growth light to suppress CO

Qu, Liming / Campbell, Douglas A / Gao, Kunshan

2021 Volume 163, Page(s) 112008

Abstract: Diatom responses to ocean acidification have been documented with variable and controversial results. We grew the coastal diatom Thalassiosira weissflogii under 410 (LC, pH 8.13) vs 1000 μatm (HC, pH 7.83) ... ...

Abstract	Diatom responses to ocean acidification have been documented with variable and controversial results. We grew the coastal diatom Thalassiosira weissflogii under 410 (LC, pH 8.13) vs 1000 μatm (HC, pH 7.83) pCO
MeSH term(s)	Carbon Dioxide ; Diatoms ; Hydrogen-Ion Concentration ; Oceans and Seas ; Photosynthesis ; Respiration ; Seawater
Chemical Substances	Carbon Dioxide (142M471B3J)
Language	English
Publishing date	2021-01-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2001296-2
ISSN	1879-3363 ; 0025-326X
ISSN (online)	1879-3363
ISSN	0025-326X
DOI	10.1016/j.marpolbul.2021.112008
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Article: Ocean acidification interacts with growth light to suppress CO2 acquisition efficiency and enhance mitochondrial respiration in a coastal diatom

Qu, Liming / Campbell, Douglas A / Gao, Kunshan

Marine pollution bulletin. 2021 Feb., v. 163

2021

Abstract	Diatom responses to ocean acidification have been documented with variable and controversial results. We grew the coastal diatom Thalassiosira weissflogii under 410 (LC, pH 8.13) vs 1000 μatm (HC, pH 7.83) pCO₂ and at different levels of light (80, 140, 220 μmol photons m⁻² s⁻¹), and found that light level alters physiological responses to OA. CO₂ concentrating mechanisms (CCMs) were down-regulated in the HC-grown cells across all the light levels, as reflected by lowered activity of the periplasmic carbonic anhydrase and decreased photosynthetic affinity for CO₂ or dissolved inorganic carbon. The specific growth rate was, however, enhanced significantly by 9.2% only at the limiting low light level. These results indicate that rather than CO₂ “fertilization”, the energy saved from down-regulation of CCMs promoted the growth rate of the diatom when light availability is low, in parallel with enhanced respiration under OA to cope with the acidic stress by providing extra energy.
Keywords	Bacillariophyceae ; Thalassiosira ; carbon dioxide ; carbonate dehydratase ; energy ; inorganic carbon ; marine pollution ; mitochondria ; ocean acidification ; pH ; photosynthesis ; specific growth rate
Language	English
Dates of publication	2021-02
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2001296-2
ISSN	1879-3363 ; 0025-326X
ISSN (online)	1879-3363
ISSN	0025-326X
DOI	10.1016/j.marpolbul.2021.112008
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Article ; Online: FILER: a framework for harmonizing and querying large-scale functional genomics knowledge.

Kuksa, Pavel P / Leung, Yuk Yee / Gangadharan, Prabhakaran / Katanic, Zivadin / Kleidermacher, Lauren / Amlie-Wolf, Alexandre / Lee, Chien-Yueh / Qu, Liming / Greenfest-Allen, Emily / Valladares, Otto / Wang, Li-San

NAR genomics and bioinformatics

2022 Volume 4, Issue 1, Page(s) lqab123

Abstract: Querying massive functional genomic and annotation data collections, linking and summarizing the query results across data sources/data types are important steps in high-throughput genomic and genetic analytical workflows. However, these steps are made ... ...

Abstract	Querying massive functional genomic and annotation data collections, linking and summarizing the query results across data sources/data types are important steps in high-throughput genomic and genetic analytical workflows. However, these steps are made difficult by the heterogeneity and breadth of data sources, experimental assays, biological conditions/tissues/cell types and file formats. FILER (FunctIonaL gEnomics Repository) is a framework for querying large-scale genomics knowledge with a large, curated integrated catalog of harmonized functional genomic and annotation data coupled with a scalable genomic search and querying interface. FILER uniquely provides: (i) streamlined access to >50 000 harmonized, annotated genomic datasets across >20 integrated data sources, >1100 tissues/cell types and >20 experimental assays; (ii) a scalable genomic querying interface; and (iii) ability to analyze and annotate user's experimental data. This rich resource spans >17 billion GRCh37/hg19 and GRCh38/hg38 genomic records. Our benchmark querying 7 × 10
Language	English
Publishing date	2022-01-14
Publishing country	England
Document type	Journal Article
ISSN	2631-9268
ISSN (online)	2631-9268
DOI	10.1093/nargab/lqab123
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Article: Diurnal pH fluctuations of seawater influence the responses of an economic red macroalga Gracilaria lemaneiformis to future CO2-induced seawater acidification

Qu, Liming / Jiazhen Sun / Juntian Xu / Kunshan Gao / Xinshu Li

Aquaculture. 2017 Apr. 20, v. 473

2017

Abstract: The diurnal fluctuation of pH in costal seawater in sea-farming areas is larger than that the pH reduction induced by progressive seawater acidification by the end of this century. To best understand how seawater acidification influences the primary ... ...

Abstract	The diurnal fluctuation of pH in costal seawater in sea-farming areas is larger than that the pH reduction induced by progressive seawater acidification by the end of this century. To best understand how seawater acidification influences the primary productivity of macroalgae in coastal waters under the pH fluctuation conditions, Gracilaria lemaneiformis, an important economical red macroalgae, was selected in our study. pH fluctuation (pH-F, high density cultivation) and pH stabilization (pH-S, low density cultivation) conditions were set to study the effects of seawater acidification on the production of G. lemaneiformis experiencing different pH fluctuation conditions. The results showed that seawater acidification significantly decreased the relative growth rate (RGR) of G. lemaneiformis grown at pH-S condition, but the enhancement of RGR was found in the pH-F-grown thalli. The similar trends were showed in the net photosynthetic rates of G. lemaneiformis. The different responses of RGR and net photosynthetic rates to seawater acidification between pH-S and pH-F conditions might be attributed to different daily pH variations. Under pH-S treatment, pH values varied <0.2units with all values <8.3, indicating a relative sufficient CO2 supply. Therefore, the effect of seawater acidification was more determined by the negative effect of elevated acidity rather than positive effect of the increased CO2 supply. While under pH-F level, pH values varied >0.6units and it could reach 9.09 in the LC-grown thalli, suggesting limited CO2 supply as CO2 level decreases about 14.1μmolkg−1 (from 15.8 to 0.7μmolkg−1) with the increase of pH (from 8.11 to 9.09). Increased CO2 at the seawater acidification condition could significantly relieve this carbon resource limitation, resulting in the enhancement of RGR of HC-grown plants.It can be predicted that the carbon resource limitation for high-density cultivation of G. lemaneiformis will be significantly relieved by coastal ocean acidification, resulting in the production increases in the future ocean, which can provide some reference values for the aquaculture of macroalgae.
Keywords	acidification ; acidity ; aquaculture ; carbon ; carbon dioxide ; coastal water ; diurnal variation ; Gracilaria ; macroalgae ; normal values ; ocean acidification ; pH ; photosynthesis ; primary productivity ; seawater ; thallus
Language	English
Dates of publication	2017-0420
Size	p. 383-388.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	185380-6
ISSN	0044-8486 ; 0044-8516
ISSN	0044-8486 ; 0044-8516
DOI	10.1016/j.aquaculture.2017.03.001
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Article ; Online: Alzheimer's Disease Variant Portal: A Catalog of Genetic Findings for Alzheimer's Disease.

Kuksa, Pavel P / Liu, Chia-Lun / Fu, Wei / Qu, Liming / Zhao, Yi / Katanic, Zivadin / Clark, Kaylyn / Kuzma, Amanda B / Ho, Pei-Chuan / Tzeng, Kai-Teh / Valladares, Otto / Chou, Shin-Yi / Naj, Adam C / Schellenberg, Gerard D / Wang, Li-San / Leung, Yuk Yee

Journal of Alzheimer's disease : JAD

2022 Volume 86, Issue 1, Page(s) 461–477

Abstract: Background: Recent Alzheimer's disease (AD) genetics findings from genome-wide association studies (GWAS) span progressively larger and more diverse populations and outcomes. Currently, there is no up-to-date resource providing harmonized and searchable ...

Abstract	Background: Recent Alzheimer's disease (AD) genetics findings from genome-wide association studies (GWAS) span progressively larger and more diverse populations and outcomes. Currently, there is no up-to-date resource providing harmonized and searchable information on all AD genetic associations found by GWAS, nor linking the reported genetic variants and genes with functional and genomic annotations. Objective: Create an integrated/harmonized, and literature-derived collection of population-specific AD genetic associations. Methods: We developed the Alzheimer's Disease Variant Portal (ADVP), an extensive collection of associations curated from >200 GWAS publications from Alzheimer's Disease Genetics Consortium and other consortia. Genetic associations were systematically extracted, harmonized, and annotated from both the genome-wide significant and suggestive loci reported in these publications. To ensure consistent representation of AD genetic findings, all the extracted genetic association information was harmonized across specifically designed publication, variant, and association categories. Results: ADVP V1.0 (February 2021) catalogs 6,990 associations related to disease-risk, expression quantitative traits, endophenotypes, or neuropathology. This extensive harmonization effort led to a catalog containing >900 loci, >1,800 variants, >80 cohorts, and 8 populations. Besides, ADVP provides investigators with a seamless integration of genomic and publicly available functional annotations across multiple databases per harmonized variant and gene records, thus facilitating further understanding and analyses of these genetics findings. Conclusion: ADVP is a valuable resource for investigators to quickly and systematically explore high-confidence AD genetic findings and provides insights into population-specific AD genetic architecture. ADVP is continually maintained and enhanced by NIAGADS and is freely accessible at https://advp.niagads.org.
MeSH term(s)	Alzheimer Disease/genetics ; Endophenotypes ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study ; Humans ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2022-01-07
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1440127-7
ISSN	1875-8908 ; 1387-2877
ISSN (online)	1875-8908
ISSN	1387-2877
DOI	10.3233/JAD-215055
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Article ; Online: Differential Photosynthetic Response of a Green Tide Alga Ulva linza to Ultraviolet Radiation, Under Short- and Long-term Ocean Acidification Regimes.

Ma, Jing / Wang, Wen / Qu, Liming / Liu, Xiaoyan / Wang, Zhiqin / Qiao, Sen / Wu, Hailong / Gao, Guang / Xu, Juntian

Photochemistry and photobiology

2019 Volume 95, Issue 4, Page(s) 990–998

Abstract: Both ocean acidification (OA) and solar ultraviolet (UV) radiation can bring about changes in macroalgal physiological performance. However, macroalgal responses to UV radiation when acclimatized to OA under different time scales are rare. Here, we ... ...

Abstract	Both ocean acidification (OA) and solar ultraviolet (UV) radiation can bring about changes in macroalgal physiological performance. However, macroalgal responses to UV radiation when acclimatized to OA under different time scales are rare. Here, we investigate the response of Ulva linza, a green tide alga, to UV radiation in the form of photosynthetically active radiation (PAR) or PAB (PAR+UVA+UVB) radiation. Radiation exposures were assessed following long-term (from spore to adult stage, 1 month) and short-term (adult stage, 1 week) OA treatments. Results showed that increased CO
MeSH term(s)	Hydrogen-Ion Concentration ; Photosystem II Protein Complex ; Seawater/chemistry ; Ultraviolet Rays ; Ulva/physiology ; Ulva/radiation effects
Chemical Substances	Photosystem II Protein Complex
Language	English
Publishing date	2019-03-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	123540-0
ISSN	1751-1097 ; 0031-8655
ISSN (online)	1751-1097
ISSN	0031-8655
DOI	10.1111/php.13083
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Article ; Online: Human whole-exome genotype data for Alzheimer's disease.

Leung, Yuk Yee / Naj, Adam C / Chou, Yi-Fan / Valladares, Otto / Schmidt, Michael / Hamilton-Nelson, Kara / Wheeler, Nicholas / Lin, Honghuang / Gangadharan, Prabhakaran / Qu, Liming / Clark, Kaylyn / Kuzma, Amanda B / Lee, Wan-Ping / Cantwell, Laura / Nicaretta, Heather / Haines, Jonathan / Farrer, Lindsay / Seshadri, Sudha / Brkanac, Zoran /

Cruchaga, Carlos / Pericak-Vance, Margaret / Mayeux, Richard P / Bush, William S / Destefano, Anita / Martin, Eden / Schellenberg, Gerard D / Wang, Li-San

Nature communications

2024 Volume 15, Issue 1, Page(s) 684

Abstract: The heterogeneity of the whole-exome sequencing (WES) data generation methods present a challenge to a joint analysis. Here we present a bioinformatics strategy for joint-calling 20,504 WES samples collected across nine studies and sequenced using ten ... ...

Abstract	The heterogeneity of the whole-exome sequencing (WES) data generation methods present a challenge to a joint analysis. Here we present a bioinformatics strategy for joint-calling 20,504 WES samples collected across nine studies and sequenced using ten capture kits in fourteen sequencing centers in the Alzheimer's Disease Sequencing Project. The joint-genotype called variant-called format (VCF) file contains only positions within the union of capture kits. The VCF was then processed specifically to account for the batch effects arising from the use of different capture kits from different studies. We identified 8.2 million autosomal variants. 96.82% of the variants are high-quality, and are located in 28,579 Ensembl transcripts. 41% of the variants are intronic and 1.8% of the variants are with CADD > 30, indicating they are of high predicted pathogenicity. Here we show our new strategy can generate high-quality data from processing these diversely generated WES samples. The improved ability to combine data sequenced in different batches benefits the whole genomics research community.
MeSH term(s)	Humans ; Alzheimer Disease ; Exome ; Computational Biology ; Data Accuracy ; Genotype
Language	English
Publishing date	2024-01-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-44781-7
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Article ; Online: Genetic Variants Associated With Plasma Lipids Are Associated With the Lipid Response to Niacin.

Tuteja, Sony / Qu, Liming / Vujkovic, Marijana / Dunbar, Richard L / Chen, Jinbo / DerOhannessian, Stephanie / Rader, Daniel J

Journal of the American Heart Association

2018 Volume 7, Issue 19, Page(s) e03488

Abstract: Background Niacin is a broad-spectrum lipid-modulating drug, but its mechanism of action is unclear. Genome-wide association studies have identified multiple loci associated with blood lipid levels and lipoprotein (a). It is unknown whether these loci ... ...

Abstract	Background Niacin is a broad-spectrum lipid-modulating drug, but its mechanism of action is unclear. Genome-wide association studies have identified multiple loci associated with blood lipid levels and lipoprotein (a). It is unknown whether these loci modulate response to niacin. Methods and Results Using data from the AIM - HIGH (Atherothrombosis Intervention in Metabolic Syndrome with Low HDL /High Triglycerides and Impact on Global Health Outcomes) trial (n=2054 genotyped participants), we determined whether genetic variations at validated loci were associated with a differential change in plasma lipids and lipoprotein (a) 1 year after randomization to either statin+placebo or statin+niacin in a variant-treatment interaction model. Nominally significant interactions ( P<0.05) were found for genetic variants in MVK , LIPC , PABPC 4, AMPD 3 with change in high-density lipoprotein cholesterol; SPTLC 3 with change in low-density lipoprotein cholesterol; TOM 1 with change in total cholesterol; PDXDC 1 and CYP 26A1 with change in triglycerides; and none for lipoprotein (a). We also investigated whether these loci were associated with cardiovascular events. The risk of coronary disease related death was higher in the minor allele carriers at the LIPC locus in the placebo group (odds ratio 2.08, 95% confidence interval 1.11-3.90, P=0.02) but not observed in the niacin group (odds ratio 0.89, 95% confidence interval 0.48-1.65, P=0.7); P-interaction =0.02. There was a greater risk for acute coronary syndrome (odds ratio 1.85, 95% confidence interval 1.16-2.77, P=0.02) and revascularization events (odds ratio 1.64, 95% confidence interval 1.2-2.22, P=0.002) in major allele carriers at the CYP 26A1 locus in the placebo group not seen in the niacin group. Conclusions Genetic variation at loci previously associated with steady-state lipid levels displays evidence for lipid response to niacin treatment. Clinical Trials Registration URL: https://www.clinicaltrials.gov . Unique identifier: NCT00120289.
MeSH term(s)	Biomarkers/blood ; Drug Therapy, Combination ; Dyslipidemias/blood ; Dyslipidemias/drug therapy ; Dyslipidemias/genetics ; Female ; Genetic Variation ; Genome-Wide Association Study ; Genotype ; Humans ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/therapeutic use ; Hypolipidemic Agents/therapeutic use ; Lipids/blood ; Male ; Middle Aged ; Niacin/therapeutic use
Chemical Substances	Biomarkers ; Hydroxymethylglutaryl-CoA Reductase Inhibitors ; Hypolipidemic Agents ; Lipids ; Niacin (2679MF687A)
Language	English
Publishing date	2018-11-18
Publishing country	England
Document type	Journal Article ; Multicenter Study ; Randomized Controlled Trial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2653953-6
ISSN	2047-9980 ; 2047-9980
ISSN (online)	2047-9980
ISSN	2047-9980
DOI	10.1161/JAHA.117.008461
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Article ; Online: Global inventory of atmospheric fibrous microplastics input into the ocean: An implication from the indoor origin.

Liu, Kai / Wang, Xiaohui / Song, Zhangyu / Wei, Nian / Ye, Haoda / Cong, Xin / Zhao, Longwei / Li, You / Qu, Liming / Zhu, Lixin / Zhang, Feng / Zong, Changxing / Jiang, Chunhua / Li, Daoji

Journal of hazardous materials

2020 Volume 400, Page(s) 123223

Abstract: Atmospheric transport could be a significant pathway for inland microplastics (MPs, with size＜5 mm) to the ocean in addition to catchment runoff and coastal discharge. However, atmospheric input of MPs to the ocean is rarely quantified. To address this ... ...

Abstract	Atmospheric transport could be a significant pathway for inland microplastics (MPs, with size＜5 mm) to the ocean in addition to catchment runoff and coastal discharge. However, atmospheric input of MPs to the ocean is rarely quantified. To address this issue, transport of atmospheric MPs from source to sink was studied in the Asia-Pacific region during nine cruises from October 2018 to September 2019. Both deposited atmospheric MPs (DAMPs) and suspended atmospheric MPs (SAMPs) were collected, ranging from 23.04 n/(m
Language	English
Publishing date	2020-06-17
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2020.123223
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Article: Global inventory of atmospheric fibrous microplastics input into the ocean: An implication from the indoor origin

Liu, Kai / Wang, Xiaohui / Song, Zhangyu / Wei, Nian / Ye, Haoda / Cong, Xin / Zhao, Longwei / Li, You / Qu, Liming / Zhu, Lixin / Zhang, Feng / Zong, Changxing / Jiang, Chunhua / Li, Daoji

Journal of hazardous materials. 2020 Dec. 05, v. 400

2020

Abstract	Atmospheric transport could be a significant pathway for inland microplastics (MPs, with size＜5 mm) to the ocean in addition to catchment runoff and coastal discharge. However, atmospheric input of MPs to the ocean is rarely quantified. To address this issue, transport of atmospheric MPs from source to sink was studied in the Asia-Pacific region during nine cruises from October 2018 to September 2019. Both deposited atmospheric MPs (DAMPs) and suspended atmospheric MPs (SAMPs) were collected, ranging from 23.04 n/(m²·d) to 67.54 n/(m²·d), and 0 to 1.37 n/m³, respectively. Size composition revealed that atmospheric deposition of MPs originating in terrestrial regions seems inadequate and insufficient to quantify the atmospheric input to the ocean. In addition, combined with aerodynamic modelling, for the first time, we estimated that 7.64–33.76 t of fibrous atmospheric MPs was globally generated in 2018, which is 3 % and 31 % of riverine input MPs of The Yangtze River and The Pearl River in terms of mid-point mass, respectively. The increasing load of ingestible plastics from sea air could have a far-reaching impact on marine ecosystem.
Keywords	aerodynamics ; air ; atmospheric deposition ; inventories ; marine ecosystems ; microplastics ; riparian areas ; rivers ; runoff ; watersheds ; Yangtze River
Language	English
Dates of publication	2020-1205
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2020.123223
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