11 research outputs found
âCandidatus Thermonerobacter thiotrophicus,â A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities
In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named âCandidatus Thermonerobacter thiotrophicus,â which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (âCa. Kapabacteriaâ) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism
Defining Electron Bifurcation in the Electron-Transferring Flavoprotein Family
Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low- and high-potential electrons. It is the third recognized form of energy conservation in biology and was recently described for select electron-transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via Etf-quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer, as well as a non-redox-active AMP. However, Etfs demonstrated to bifurcate electrons contain a second FAD in place of the AMP. To expand our understanding of the functional variety and metabolic significance of Etfs and to identify amino acid sequence motifs that potentially enable electron bifurcation, we compiled 1,314 Etf protein sequences from genome sequence databases and subjected them to informatic and structural analyses. Etfs were identified in diverse archaea and bacteria, and they clustered into five distinct well-supported groups, based on their amino acid sequences. Gene neighborhood analyses indicated that these Etf group designations largely correspond to putative differences in functionality. Etfs with the demonstrated ability to bifurcate were found to form one group, suggesting that distinct conserved amino acid sequence motifs enable this capability. Indeed, structural modeling and sequence alignments revealed that identifying residues occur in the NADH- and FAD-binding regions of bifurcating Etfs. Collectively, a new classification scheme for Etf proteins that delineates putative bifurcating versus nonbifurcating members is presented and suggests that Etf-mediated bifurcation is associated with surprisingly diverse enzymes
Menstrual and Reproductive Factors and Risk of Gastric and Colorectal Cancer in Spain
BACKGROUND:
Sex hormones play a role in gastric cancer and colorectal cancer etiology, however, epidemiological evidence is inconsistent. This study examines the influence of menstrual and reproductive factors over the risk of both tumors.
METHODS:
In this case-control study 128 women with gastric cancer and 1293 controls, as well as 562 female and colorectal cancer cases and 1605 controls were recruited in 9 and 11 Spanish provinces, respectively. Population controls were frequency matched to cases by age and province. Demographic and reproductive data were directly surveyed by trained staff. The association with gastric, colon and rectal cancer was assessed using logistic and multinomial mixed regression models.
RESULTS:
Our results show an inverse association of age at first birth with gastric cancer risk (five-year trend: OR = 0.69; p-value = 0.006). Ever users of hormonal contraception presented a decreased risk of gastric (OR = 0.42; 95%CI = 0.26-0.69), colon (OR = 0.64; 95%CI = 0.48-0.86) and rectal cancer (OR = 0.61; 95%CI = 0.43-0.88). Postmenopausal women who used hormone replacement therapy showed a decreased risk of colon and rectal tumors. A significant interaction of educational level with parity and months of first child lactation was also observed.
CONCLUSION:
These findings suggest a protective role of exogenous hormones in gastric and colorectal cancer risk. The role of endogenous hormones remains unclear
Models of classroom assessment for course-based research experiences
Course-based research pedagogy involves positioning students as contributors to authentic research projects as part of an engaging educational experience that promotes their learning and persistence in science. To develop a model for assessing and grading students engaged in this type of learning experience, the assessment aims and practices of a community of experienced course-based research instructors were collected and analyzed. This approach defines four aims of course-based research assessmentâ(1) Assessing Laboratory Work and Scientific Thinking; (2) Evaluating Mastery of Concepts, Quantitative Thinking and Skills; (3) Appraising Forms of Scientific Communication; and (4) Metacognition of Learningâalong with a set of practices for each aim. These aims and practices of assessment were then integrated with previously developed models of course-based research instruction to reveal an assessment program in which instructors provide extensive feedback to support productive student engagement in research while grading those aspects of research that are necessary for the student to succeed. Assessment conducted in this way delicately balances the need to facilitate studentsâ ongoing research with the requirement of a final grade without undercutting the important aims of a CRE education
Ultrastructural Analysis and Identification of Envelope Proteins of âCandidatus Chloracidobacterium thermophilumâ Chlorosomesâż
Chlorosomes are sac-like, light-harvesting organelles that characteristically contain very large numbers of bacteriochlorophyll (BChl) c, d, or e molecules. These antenna structures occur in chlorophototrophs belonging to some members of the Chlorobi and Chloroflexi phyla and are also found in a recently discovered member of the phylum Acidobacteria, âCandidatus Chloracidobacterium thermophilum.â âCa. Chloracidobacterium thermophilumâ is the first aerobic organism discovered to possess chlorosomes as light-harvesting antennae for phototrophic growth. Chlorosomes were isolated from âCa. Chloracidobacterium thermophilumâ and subjected to electron microscopic, spectroscopic, and biochemical analyses. The chlorosomes of âCa. Chloracidobacterium thermophilumâ had an average size of âŒ100 by 30 nm. Cryo-electron microscopy showed that the BChl c molecules formed folded or twisted, sheet-like structures with a lamellar spacing of âŒ2.3 nm. Unlike the BChls in the chlorosomes of the green sulfur bacterium Chlorobaculum tepidum, concentric cylindrical nanotubes were not observed. Chlorosomes of âCa. Chloracidobacterium thermophilumâ contained a homolog of CsmA, the BChl a-binding, baseplate protein; CsmV, a protein distantly related to CsmI, CsmJ, and CsmX of C. tepidum, which probably binds a single [2Fe-2S] cluster; and five unique polypeptides (CsmR, CsmS, CsmT, CsmU, and a type II NADH dehydrogenase homolog). Although âCa. Chloracidobacterium thermophilumâ is an aerobe, energy transfer among the BChls in these chlorosomes was very strongly quenched in the presence of oxygen (as measured by quenching of fluorescence emission). The combined analyses showed that the chlorosomes of âCa. Chloracidobacterium thermophilumâ possess a number of unique features but also share some properties with the chlorosomes found in anaerobic members of other phyla
The Electron Bifurcating FixABCX Protein Complex from <i>Azotobacter vinelandii</i>: Generation of Low-Potential Reducing Equivalents for Nitrogenase Catalysis
The biological reduction of dinitrogen
(N<sub>2</sub>) to ammonia
(NH<sub>3</sub>) by nitrogenase is an energetically demanding reaction
that requires low-potential electrons and ATP; however, pathways used
to deliver the electrons from central metabolism to the reductants
of nitrogenase, ferredoxin or flavodoxin, remain unknown for many
diazotrophic microbes. The FixABCX protein complex has been proposed
to reduce flavodoxin or ferredoxin using NADH as the electron donor
in a process known as electron bifurcation. Herein, the FixABCX complex
from <i>Azotobacter vinelandii</i> was purified and demonstrated
to catalyze an electron bifurcation reaction: oxidation of NADH (<i>E</i><sub>m</sub> = â320 mV) coupled to reduction of
flavodoxin semiquinone (<i>E</i><sub>m</sub> = â460
mV) and reduction of coenzyme Q (<i>E</i><sub>m</sub> =
10 mV). Knocking out <i>fix</i> genes rendered Î<i>rnf A. vinelandii</i> cells unable to fix dinitrogen, confirming
that the FixABCX system provides another route for delivery of electrons
to nitrogenase. Characterization of the purified FixABCX complex revealed
the presence of flavin and ironâsulfur cofactors confirmed
by native mass spectrometry, electron paramagnetic
resonance spectroscopy, and transient absorption spectroscopy. Transient
absorption spectroscopy further established the presence of a short-lived
flavin semiquinone radical, suggesting that a thermodynamically unstable
flavin semiquinone may participate as an intermediate in the transfer
of an electron to flavodoxin. A structural model of FixABCX, generated
using chemical cross-linking in conjunction with homology modeling,
revealed plausible electron transfer pathways to both high- and low-potential
acceptors. Overall, this study informs a mechanism for electron bifurcation,
offering insight into a unique method for delivery of low-potential
electrons required for energy-intensive biochemical conversions