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Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres.

Anirban Chakraborty, S Emil Ruff, Xiyang Dong, Emily D Ellefson, Carmen Li, James M Brooks, Jayme McBee, Bernie B Bernard, Casey R J Hubert,

Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine ... Read more >>

Proc. Natl. Acad. Sci. U.S.A. (Proceedings of the National Academy of Sciences of the United States of America)
[2020, 117(20):11029-11037]

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Strongly coupled transmembrane mechanisms control MCU-mediated mitochondrial Ca2+ uptake

Horia Vais, Riley Payne, Carmen Li, Kevin Foskett,

Ca 2+ uptake by mitochondria regulates bioenergetics, apoptosis, and Ca 2+ signaling. The primary pathway for mitochondrial Ca 2+ uptake is the mitochondrial calcium uniporter (MCU), a Ca 2+ -selective ion channel in the inner mitochondrial membrane. MCU-mediated Ca 2+ uptake is driven by the sizable inner-membrane potential generated by ... Read more >>

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Variable Assembly of EMRE and MCU Creates Functional Channels with Distinct Gatekeeping Profiles.

Riley Payne, Carmen Li, J Kevin Foskett,

MCU is a Ca2+-selective channel that mediates mitochondrial Ca2+ influx. The human channel contains tetrameric pore-forming MCU, regulatory subunits MICU1/2, and EMRE that is required both for channel function and MICU1/2-mediated Ca2+ regulation. A structure of MCU with EMRE revealed a 4:4 stoichiometry, but the stoichiometry in vivo is unknown. Expression ... Read more >>

iScience (iScience)
[2020, 23(4):101037]

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Prevalence and Characteristics of Extended-Spectrum-β-Lactamase-Producing and Carbapenemase-Producing Enterobacteriaceae from Freshwater Fish and Pork in Wet Markets of Hong Kong.

Dulmini Nanayakkara Sapugahawatte, Carmen Li, Chendi Zhu, Priyanga Dharmaratne, Kam Tak Wong, Norman Lo, Margaret Ip,

This study identified and characterized extended-spectrum-β-lactamase-producing Enterobacteriaceae (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) from farmed freshwater fish and pig offal procured from the wet markets across Hong Kong. During March 2018 to January 2019, 730 food animal samples, namely, 213 snakehead fish, 198 black carp, and 339 pig organs, were examined. ... Read more >>

mSphere (mSphere)
[2020, 5(2):]

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HSF1 phase transition mediates stress adaptation and cell fate decisions.

Giorgio Gaglia, Rumana Rashid, Clarence Yapp, Gaurav N Joshi, Carmen G Li, Susan L Lindquist, Kristopher A Sarosiek, Luke Whitesell, Peter K Sorger, Sandro Santagata,

Under proteotoxic stress, some cells survive whereas others die. The mechanisms governing this heterogeneity in cell fate remain unknown. Here we report that condensation and phase transition of heat-shock factor 1 (HSF1), a transcriptional regulator of chaperones1,2, is integral to cell-fate decisions underlying survival or death. During stress, HSF1 drives ... Read more >>

Nat. Cell Biol. (Nature cell biology)
[2020, 22(2):151-158]

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Natural attenuation of spilled crude oil by cold-adapted soil bacterial communities at a decommissioned High Arctic oil well site.

Deidra K Ferguson, Carmen Li, Chunqing Jiang, Anirban Chakraborty, Stephen E Grasby, Casey R J Hubert,

Romulus C-42 is a decommissioned oil well on Ellesmere Island in the Canadian High Arctic, and is the northernmost well to have produced oil and gas anywhere in the world. The remote site has been untouched since a crude oil spill in 1972, offering a rare opportunity to examine natural ... Read more >>

Sci. Total Environ. (The Science of the total environment)
[2020, 722:137258]

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Biologicals in atopic disease in pregnancy: an EAACI position paper.

Birgit Pfaller, Juan José Yepes-Nuñez, Ioana Agache, Cezmi A Akdis, Mohammad Alsalamah, Sevim Bavbek, Apostolos Bossios, Onur Boyman, Adam Chaker, Susan Chan, Alexia Chatzipetrou, George du Toit, Marek Jutel, Paula Kauppi, Antonios Kolios, Carmen Li, Andrea Matucci, Alanna Marson, Sarah Bendien, Oscar Palomares, Barbara Rogala, Zsolt Szepfalusi, Eva Untersmayr, Alessandra Vultaggio, Thomas Eiwegger,

Biologicals have transformed the management of severe disease phenotypes in asthma, atopic dermatitis, and chronic spontaneous urticaria. As a result, the number of approved biologicals for the treatment of atopic diseases is continuously increasing. Although atopic diseases are among the most common diseases in the reproductive age, investigations, and information ... Read more >>

Allergy (Allergy)
[2020, :]

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Thermogenic hydrocarbons fuel a redox stratified subseafloor microbiome in deep sea cold seep sediments

Xiyang Dong, Jayne Rattray, Calvin Campbell, Jamie Webb, Anirban Chakraborty, Oyeboade Adebayo, Stuart Matthews, Carmen Li, Martin Fowler, Adam Macdonald, Ryan Groves, Ian Lewis, Scott Wang, Daisuke Mayumi, Chris Greening, Casey R.J. Hubert,

Abstract At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. In this work, ... Read more >>

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Methanogenic biodegradation of iso-alkanes and cycloalkanes during long-term incubation with oil sands tailings.

Tariq Siddique, Kathleen Semple, Carmen Li, Julia M Foght,

Microbes indigenous to oil sands tailings ponds methanogenically biodegrade certain hydrocarbons, including n-alkanes and monoaromatics, whereas other hydrocarbons such as iso- and cycloalkanes are more recalcitrant. We tested the susceptibility of iso- and cycloalkanes to methanogenic biodegradation by incubating them with mature fine tailings (MFT) collected from two depths (6 ... Read more >>

Environ. Pollut. (Environmental pollution (Barking, Essex : 1987))
[2020, 258:113768]

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Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments.

Xiyang Dong, Chris Greening, Jayne E Rattray, Anirban Chakraborty, Maria Chuvochina, Daisuke Mayumi, Jan Dolfing, Carmen Li, James M Brooks, Bernie B Bernard, Ryan A Groves, Ian A Lewis, Casey R J Hubert,

The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. ... Read more >>

Nat Commun (Nature communications)
[2019, 10(1):1816]

Cited: 1 time

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Role of Two-Component System Response Regulator bceR in the Antimicrobial Resistance, Virulence, Biofilm Formation, and Stress Response of Group B Streptococcus.

Ying Yang, Mingjing Luo, Haokui Zhou, Carmen Li, Alison Luk, GuoPing Zhao, Kitty Fung, Margaret Ip,

Group B Streptococcus (GBS; Streptococcus agalactiae) is a leading cause of sepsis in neonates and pregnant mothers worldwide. Whereas the hyper-virulent serogroup III clonal cluster 17 has been associated with neonatal disease and meningitis, serogroup III ST283 was recently implicated in invasive disease among non-pregnant adults in Asia. Here, through ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2019, 10:10]

Cited: 2 times

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Subspecies Typing of Streptococcus agalactiae Based on Ribosomal Subunit Protein Mass Variation by MALDI-TOF MS.

Julian Rothen, Joël F Pothier, Frédéric Foucault, Jochen Blom, Dulmini Nanayakkara, Carmen Li, Margaret Ip, Marcel Tanner, Guido Vogel, Valentin Pflüger, Claudia A Daubenberger,

Background: A ribosomal subunit protein (rsp)-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method was developed for fast subspecies-level typing of Streptococcus agalactiae (Group B Streptococcus, GBS), a major cause of neonatal sepsis and meningitis. Methods: A total of 796 GBS whole genome sequences, covering the genetic diversity of ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2019, 10:471]

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Characterizing Mobilized Virulence Factors and Multidrug Resistance Genes in Carbapenemase-Producing Klebsiella pneumoniae in a Sri Lankan Hospital.

Chendi Zhu, Veranja Liyanapathirana, Carmen Li, Vasanthi Pinto, Mamie Hui, Norman Lo, Kam T Wong, Nilanthi Dissanayake, Margaret Ip,

Limited data is available on the epidemiology and characteristics of carbapenem-resistant Enterobacteriaceae (CRE) and their associated plasmids or virulence determinants from Sri Lanka. Through whole genome sequencing of CREs from the intensive care units of a Sri Lankan teaching hospital, we identified a carbapenemase gene, blaOXA-181 in 10 carbapenemase-producing Klebsiella ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2018, 9:2044]

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Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

Xiyang Dong, Chris Greening, Jayne Rattray, Anirban Chakraborty, Maria Chuvochina, Daisuke Mayumi, Jan Dolfing, Carmen Li, James Brooks, Bernie Bernard, Ryan Groves, Ian Lewis, Casey R.J. Hubert,

Abstract The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigated energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf ... Read more >>

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The role of two-component system response regulator BceR in antimicrobial resistance, virulence, biofilm formation, and stress response of group B Streptococcus

Ying Yang, Mingjing Luo, Haokui, Carmen Li, Alison Luk, GP Zhao, Kitty Fung, Margaret Ip,

Abstract The hypervirulent Group B Streptococcus ( Streptococcus agalactiae , GBS) serogroup III clonal cluster 17 has been associated with neonatal GBS invasive disease and meningits. Serogroup III, ST283 has recently been implicated in invasive disease among non-pregnant adults in Asia. These strains cluster with strains from freshwater fishes from ... Read more >>

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Genetic determinants of resistance and virulence among carbapenemase-producing Klebsiella pneumoniae from Sri Lanka

Chendi Zhu, Veranja Liyanapathirana, Carmen Li, Pinto, Mamie Hui, Norman Lo, Kam-Tak Wong, Dissanayake, Margaret Ip,

ABSTRACT Whole genome sequencing of carbapenem-resistant Enterobacteriaceae from the intensive care units of a Sri Lankan teaching hospital revealed the presence of carbapenemase gene, bla OXA-181 among isolates of carbapenase-producing Klebsiella pneumoniae belonging to ST437 (2 strains) and ST147 (8 strains) in 2015. bla OXA-181 genes were carried in three ... Read more >>

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Thermophilic endospores associated with migrated thermogenic hydrocarbons in deep Gulf of Mexico marine sediments.

Anirban Chakraborty, Emily Ellefson, Carmen Li, Daniel Gittins, James M Brooks, Bernie B Bernard, Casey R J Hubert,

Dormant endospores of thermophilic bacteria (thermospores) can be detected in cold marine sediments following high-temperature incubation. Thermospores in the cold seabed may be explained by a dispersal history originating in deep biosphere oil reservoir habitats where upward migration of petroleum fluids at hydrocarbon seeps transports viable cells into the overlying ... Read more >>

ISME J (The ISME journal)
[2018, 12(8):1895-1906]

Cited: 3 times

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Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp.

Xiaoli Dong, Manuel Kleiner, Christine E Sharp, Erin Thorson, Carmen Li, Dan Liu, Marc Strous,

Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2017, 8:1461]

Cited: 11 times

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Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp

Xiaoli Dong, Manuel Kleiner, Christine Sharp, Erin Thorson, Carmen Li, Dan Liu, Marc Strous,

Abstract Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we ... Read more >>

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Assessing species biomass contributions in microbial communities via metaproteomics

Manuel Kleiner, Erin Thorson, Christine Sharp, Xiaoli Dong, Dan Liu, Carmen Li, Marc Strous,

Abstract Assessment of microbial community composition is the cornerstone of microbial ecology. Microbial community composition can be analyzed by quantifying cell numbers or by quantifying biomass for individual populations. However, as cell volumes can differ by orders of magnitude, these two approaches yield vastly different results. Methods for quantifying cell ... Read more >>

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Long-Term Incubation Reveals Methanogenic Biodegradation of C5 and C6 iso-Alkanes in Oil Sands Tailings.

Tariq Siddique, Mohd Faidz Mohamad Shahimin, Saima Zamir, Kathleen Semple, Carmen Li, Julia M Foght,

iso-Alkanes are major components of petroleum and have been considered recalcitrant to biodegradation under methanogenic conditions. However, indigenous microbes in oil sands tailings ponds exposed to solvents rich in 2-methylbutane, 2-methylpentane, 3-methylpentane, n-pentane, and n-hexane produce methane in situ. We incubated defined mixtures of iso- or n-alkanes with mature fine ... Read more >>

Environ. Sci. Technol. (Environmental science & technology)
[2015, 49(24):14732-14739]

Cited: 6 times

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Draft Genome Sequences of Two Streptococcus pneumoniae Serotype 19F Sequence Type 271 Clinical Isolates with Low- and High-Level Cefotaxime Resistance.

Margaret Ip, Helen Ma, Carmen Li, Stephen Tsui, Haokui Zhou,

We report here the draft genomes of two pneumococcal isolates in Hong Kong, CU_SPNE1_05 and CU_SPNE32_06. Strain CU_SPNE1_05 had a cefotaxime MIC of 1 µg/ml, and CU_SPNE32_06 had an MIC of 32 µg/ml. Both strains belong to the multidrug-resistant serogroup 19, sequence type 271 (clonal complex 3200/271). ... Read more >>

Genome Announc (Genome announcements)
[2015, 3(3):]

Cited: 1 time

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Draft Genome Sequence of Uncultivated Firmicutes (Peptococcaceae SCADC) Single Cells Sorted from Methanogenic Alkane-Degrading Cultures.

BoonFei Tan, Rhianna Charchuk, Carmen Li, Camilla Nesbø, Nidal Abu Laban, Julia Foght,

The draft genome of an uncultivated bacterium affiliated with the Peptococcaceae was reconstructed by co-assembling Illumina MiSeq sequences from three single cells sorted by microfluidics from two methanogenic alkane-degrading cultures. Peptococcaceae SCADC (short-chain alkane-degrading culture) may be genetically capable of anaerobic alkane activation by fumarate addition in the absence of ... Read more >>

Genome Announc (Genome announcements)
[2014, 2(5):]

Cited: 11 times

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Altered regulation of DNA ligase IV activity by aberrant promoter DNA methylation and gene amplification in colorectal cancer.

Christine Kuhmann, Carmen Li, Matthias Kloor, Mariam Salou, Christoph Weigel, Christopher R Schmidt, Linda W C Ng, Wendy W Y Tsui, Suet Y Leung, Siu T Yuen, Natalia Becker, Dieter Weichenhan, Christoph Plass, Peter Schmezer, Tsun L Chan, Odilia Popanda,

Colorectal cancer (CRC) presents as a very heterogeneous disease which cannot sufficiently be characterized with the currently known genetic and epigenetic markers. To identify new markers for CRC we scrutinized the methylation status of 231 DNA repair-related genes by methyl-CpG immunoprecipitation followed by global methylation profiling on a CpG island ... Read more >>

Hum. Mol. Genet. (Human molecular genetics)
[2014, 23(8):2043-2054]

Cited: 5 times

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Metagenomics of hydrocarbon resource environments indicates aerobic taxa and genes to be unexpectedly common.

Dongshan An, Sean M Caffrey, Jung Soh, Akhil Agrawal, Damon Brown, Karen Budwill, Xiaoli Dong, Peter F Dunfield, Julia Foght, Lisa M Gieg, Steven J Hallam, Niels W Hanson, Zhiguo He, Thomas R Jack, Jonathan Klassen, Kishori M Konwar, Eugene Kuatsjah, Carmen Li, Steve Larter, Verlyn Leopatra, Camilla L Nesbø, Thomas Oldenburg, Antoine P Pagé, Esther Ramos-Padron, Fauziah F Rochman, Alireeza Saidi-Mehrabad, Christoph W Sensen, Payal Sipahimalani, Young C Song, Sandra Wilson, Gregor Wolbring, Man-Ling Wong, Gerrit Voordouw,

Oil in subsurface reservoirs is biodegraded by resident microbial communities. Water-mediated, anaerobic conversion of hydrocarbons to methane and CO2, catalyzed by syntrophic bacteria and methanogenic archaea, is thought to be one of the dominant processes. We compared 160 microbial community compositions in ten hydrocarbon resource environments (HREs) and sequenced twelve ... Read more >>

Environ. Sci. Technol. (Environmental science & technology)
[2013, 47(18):10708-10717]

Cited: 59 times

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