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Ecological variation in adult social play reveals a hidden cost of motherhood for wild chimpanzees. Curr Biol 2024; 34:1364-1369.e2. [PMID: 38490201 PMCID: PMC11002997 DOI: 10.1016/j.cub.2024.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 03/17/2024]
Abstract
Though common among humans, social play by adults is an uncommon occurrence in most animals, even between parents and offspring.1,2,3 The most common explanation for why adult play is so rare is that its function and benefits are largely limited to development, so that social play has little value later in life.3,4,5,6 Here, we draw from 10 years of behavioral data collected by the Kibale Chimpanzee Project to consider an alternative hypothesis: that despite its benefits, adult play in non-humans is ecologically constrained by energy shortage or time limitations. We further hypothesized that, since they may be the only available partners for their young offspring, mother chimpanzees pay greater costs of play than other adults. Our analysis of nearly 4,000 adult play bouts revealed that adult chimpanzees played both among themselves and with immature partners. Social play was infrequent when diet quality was low but increased with the proportion of high-quality fruits in the diet. This suggests that adults engage in play facultatively when they have more energy and/or time to do so. However, when diet quality was low and most adult play fell to near zero, play persisted between mothers and offspring. Increased use of play by adult chimpanzees during periods of resource abundance suggests that play retains value as a social currency beyond development but that its costs constrain its use. At the same time, when ecological conditions constrain opportunities for young to play, play by mothers fills a critical role to promote healthy offspring development.
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2
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A card-sorting tool to measure expert versus novice thinking in scientific research. CBE LIFE SCIENCES EDUCATION 2023; 22:ar38. [PMID: 37751508 PMCID: PMC10756038 DOI: 10.1187/cbe.22-11-0230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/20/2023] [Accepted: 07/27/2023] [Indexed: 09/28/2023]
Abstract
Undergraduate research and laboratory experiences provide a wide range of benefits to student learning in science and are integral to imbed authentic research experiences in biology labs. While the benefit of courses with research experience is widely accepted, it can be challenging to measure conceptual research skills in a quick and easily scalable manner. We developed a card-sorting task to differentiate between novice and expert conceptualization of research principles. There were significant differences in the way faculty/postdocs, graduate students, and undergraduate students organized their information, with faculty/postdocs more likely to use deep feature sorting patterns related to research approach. When provided scaffolding of group names reflecting expert-like organization, participant groups were better able to sort by that organization, but undergraduate students did not reach expert levels. Undergraduates with Advanced Placement experience were more likely to display expert-like thinking than undergraduates without Advanced Placement Biology experience and non-PEER (persons excluded because of their Ethnicity or Race) students displayed more expert-like thinking than PEER students. We found evidence of undergraduates in various stages of development toward expert-like thinking in written responses. This card-sorting task can provide a framework for analyzing student's conceptualizations of research and identify areas to provide added scaffolding to help shift from novice-like to expert-like thinking.
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3
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Viruses in saliva from sanctuary chimpanzees (Pan troglodytes) in Republic of Congo and Uganda. PLoS One 2023; 18:e0288007. [PMID: 37384730 PMCID: PMC10310015 DOI: 10.1371/journal.pone.0288007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
Pathogen surveillance for great ape health monitoring has typically been performed on non-invasive samples, primarily feces, in wild apes and blood in sanctuary-housed apes. However, many important primate pathogens, including known zoonoses, are shed in saliva and transmitted via oral fluids. Using metagenomic methods, we identified viruses in saliva samples from 46 wild-born, sanctuary-housed chimpanzees at two African sanctuaries in Republic of Congo and Uganda. In total, we identified 20 viruses. All but one, an unclassified CRESS DNA virus, are classified in five families: Circoviridae, Herpesviridae, Papillomaviridae, Picobirnaviridae, and Retroviridae. Overall, viral prevalence ranged from 4.2% to 87.5%. Many of these viruses are ubiquitous in primates and known to replicate in the oral cavity (simian foamy viruses, Retroviridae; a cytomegalovirus and lymphocryptovirus; Herpesviridae; and alpha and gamma papillomaviruses, Papillomaviridae). None of the viruses identified have been shown to cause disease in chimpanzees or, to our knowledge, in humans. These data suggest that the risk of zoonotic viral disease from chimpanzee oral fluids in sanctuaries may be lower than commonly assumed.
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Can We Quantify If It's a CURE? JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2023; 24:00210-22. [PMID: 37089237 PMCID: PMC10117072 DOI: 10.1128/jmbe.00210-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/04/2023] [Indexed: 05/03/2023]
Abstract
Course-based undergraduate research experiences (CUREs) rapidly have become more common in biology laboratory courses. The effort to implement CUREs has stimulated attempts to differentiate CUREs from other types of laboratory teaching. The Laboratory Course Assessment Survey (LCAS) was developed to measure students' perceptions of how frequently they participate in activities related to iteration, discovery, broader relevance, and collaboration in their laboratory courses. The LCAS has been proposed as an instrument that can be used to define whether a laboratory course fits the criteria for a CURE or not. However, the threshold LCAS scores needed to define a course as a CURE are unclear. As a result, we examined variation in published LCAS scores among different laboratory course types. In addition, we examined the distribution of LCAS scores for students enrolled in our research-for-credit course. Overall, we found substantial variation in scores among CUREs and broad overlap among course types in scores related to all three scales measured by the LCAS. Furthermore, the mean LCAS scores for all course types fell within the main part of the distribution of scores for our mentored research students. These results suggest that the LCAS cannot be used to easily quantify whether a course is a CURE or not. We propose that the biology education community needs to move beyond trying to quantitatively identify whether a course is a CURE. Instead, we should use tools like the LCAS to investigate what students are actually doing in their laboratory courses and how those activities impact student outcomes.
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5
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Viruses in sanctuary chimpanzees across Africa. Am J Primatol 2023; 85:e23452. [PMID: 36329642 PMCID: PMC9812903 DOI: 10.1002/ajp.23452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Infectious disease is a major concern for both wild and captive primate populations. Primate sanctuaries in Africa provide critical protection to thousands of wild-born, orphan primates confiscated from the bushmeat and pet trades. However, uncertainty about the infectious agents these individuals potentially harbor has important implications for their individual care and long-term conservation strategies. We used metagenomic next-generation sequencing to identify viruses in blood samples from chimpanzees (Pan troglodytes) in three sanctuaries in West, Central, and East Africa. Our goal was to evaluate whether viruses of human origin or other "atypical" or unknown viruses might infect these chimpanzees. We identified viruses from eight families: Anelloviridae, Flaviviridae, Genomoviridae, Hepadnaviridae, Parvoviridae, Picobirnaviridae, Picornaviridae, and Rhabdoviridae. The majority (15/26) of viruses identified were members of the family Anelloviridae and represent the genera Alphatorquevirus (torque teno viruses) and Betatorquevirus (torque teno mini viruses), which are common in chimpanzees and apathogenic. Of the remaining 11 viruses, 9 were typical constituents of the chimpanzee virome that have been identified in previous studies and are also thought to be apathogenic. One virus, a novel tibrovirus (Rhabdoviridae: Tibrovirus) is related to Bas-Congo virus, which was originally thought to be a human pathogen but is currently thought to be apathogenic, incidental, and vector-borne. The only virus associated with disease was rhinovirus C (Picornaviridae: Enterovirus) infecting one chimpanzee subsequent to an outbreak of respiratory illness at that sanctuary. Our results suggest that the blood-borne virome of African sanctuary chimpanzees does not differ appreciably from that of their wild counterparts, and that persistent infection with exogenous viruses may be less common than often assumed.
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Developmental Trajectories of Student Self-Perception over a Yearlong Introductory Biology Sequence. CBE LIFE SCIENCES EDUCATION 2022; 21:ar59. [PMID: 35998158 PMCID: PMC9582810 DOI: 10.1187/cbe.21-12-0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Student self-perception is related to persistence in science. Yet how self-perception develops over time is less clear. We examined student self-perception trajectories and their relationship with gender, persons excluded due to ethnicity or race (PEER) status, and first-generation college student (FGCS) status across a yearlong introductory biology sequence. While we found similar rates of change in self-efficacy and science identity for all groups, females and PEER students had lower initial scores that failed to "catch up" to male and non-PEER scores by the end of the year. Students grouped into either high and stable or lower and decreasing trajectories for scientific community values, with first-generation college students overrepresented in the latter group. Additionally, we found no evidence for intersectionality of subgroups. We did find evidence that the relationship between gender and PEER status and science identity is likely mediated via self-efficacy. Taken together, our results suggest that introductory biology students develop self-efficacy and science identity at similar rates regardless of gender, PEER status, or FGCS status and that interventions targeting scientific community values for all students and self-efficacy of female and PEER students may be fruitful areas to pursue to increase persistence of students in the sciences and to reduce score differences between groups.
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Assessment of Course-Based Research Modules Based on Faculty Research in Introductory Biology. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021; 22:jmbe00148-21. [PMID: 34594452 PMCID: PMC8442019 DOI: 10.1128/jmbe.00148-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/04/2021] [Indexed: 06/13/2023]
Abstract
Calls for early exposure of all undergraduates to research have led to the increased use and study of course-based research experiences (CREs). CREs have been shown to increase measures of persistence in the sciences, such as science identity, scientific self-efficacy, project ownership, scientific community values, and networking. However, implementing CREs can be challenging and resource-intensive. These barriers may be partly mitigated by the use of short-term CRE modules rather than semester- or year-long projects. One study has shown that a CRE module captures some of the known benefits of CREs as measured by the Persistence in the Sciences (PITS) survey. Here, we used this same survey to assess outcomes for introductory biology students who completed a semester of modular CREs based on faculty research at an R1 university. The results indicated levels of self-efficacy, science community values, and science identity similar to those previously reported for students in the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) full-semester CRE. Scores for project ownership (content) were between previously reported traditional lab and CRE scores, while project ownership (emotion) and networking were similar to those of traditional labs. Our results suggest that modular CREs can lead to significant gains in student affect measures that have been linked to persistence in the sciences in other studies. Although gains were not as great in all measures as with a semester-long CRE, implementation of modular CREs may be more feasible and offers the added benefits of exposing students to diverse research fields and lab techniques.
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Healthy cardiovascular biomarkers across the lifespan in wild-born chimpanzees ( Pan troglodytes). Philos Trans R Soc Lond B Biol Sci 2020; 375:20190609. [PMID: 32951545 PMCID: PMC7540951 DOI: 10.1098/rstb.2019.0609] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2020] [Indexed: 12/13/2022] Open
Abstract
Chimpanzees (Pan troglodytes) are a crucial model for understanding the evolution of human health and longevity. Cardiovascular disease is a major source of mortality during ageing in humans and therefore a key issue for comparative research. Current data indicate that compared to humans, chimpanzees have proatherogenic blood lipid profiles, an important risk factor for cardiovascular disease in humans. However, most work to date on chimpanzee lipids come from laboratory-living populations where lifestyles diverge from a wild context. Here, we examined cardiovascular profiles in chimpanzees living in African sanctuaries, who range semi-free in large forested enclosures, consume a naturalistic diet, and generally experience conditions more similar to a wild chimpanzee lifestyle. We measured blood lipids, body weight and body fat in 75 sanctuary chimpanzees and compared them to publicly available data from laboratory-living chimpanzees from the Primate Aging Database. We found that semi-free-ranging chimpanzees exhibited lower body weight and lower levels of lipids that are risk factors for human cardiovascular disease, and that some of these disparities increased with age. Our findings support the hypothesis that lifestyle can shape health indices in chimpanzees, similar to effects observed across human populations, and contribute to an emerging understanding of human cardiovascular health in an evolutionary context. This article is part of the theme issue 'Evolution of the primate ageing process'.
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9
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Incorporation of Modified Amino Acids by Engineered Elongation Factors with Expanded Substrate Capabilities. ACS Synth Biol 2019; 8:287-296. [PMID: 30609889 PMCID: PMC6379855 DOI: 10.1021/acssynbio.8b00305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Noncanonical
amino acid (ncAA) incorporation has led to significant
advances in protein science and engineering. Traditionally, in vivo incorporation of ncAAs is achieved via amber codon suppression using an engineered orthogonal aminoacyl-tRNA
synthetase:tRNA pair. However, as more complex protein products are
targeted, researchers are identifying additional barriers limiting
the scope of currently available ncAA systems. One barrier is elongation
factor Tu (EF-Tu), a protein responsible for proofreading aa-tRNAs,
which substantially restricts ncAA scope by limiting ncaa-tRNA delivery
to the ribosome. Researchers have responded by engineering ncAA-compatible
EF-Tus for key ncAAs. However, this approach fails to address the
extent to which EF-Tu inhibits efficient ncAA incorporation. Here,
we demonstrate an alternative strategy leveraging computational analysis
to broaden EF-Tu’s substrate specificity. Evolutionary analysis
of EF-Tu and a naturally evolved specialized elongation factor, SelB,
provide the opportunity to engineer EF-Tu by targeting amino acid
residues that are associated with functional divergence between the
two ancient paralogues. Employing amber codon suppression, in combination
with mass spectrometry, we identified two EF-Tu variants with non-native
substrate compatibility. Additionally, we present data showing these
EF-Tu variants contribute to host organismal fitness, working cooperatively
with components of native and engineered translation machinery. These
results demonstrate the viability of our computational method and
lend support to corresponding assumptions about molecular evolution.
This work promotes enhanced polyspecific EF-Tu behavior as a viable
strategy to expand ncAA scope and complements ongoing research emphasizing
the importance of a comprehensive approach to further expand the genetic
code.
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10
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Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus. Structure 2018; 26:118-129.e3. [PMID: 29276038 PMCID: PMC5785943 DOI: 10.1016/j.str.2017.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/18/2017] [Accepted: 11/27/2017] [Indexed: 01/07/2023]
Abstract
Rationally engineering thermostability in proteins would create enzymes and receptors that function under harsh industrial applications. Several sequence-based approaches can generate thermostable variants of mesophilic proteins. To gain insight into the mechanisms by which proteins become more stable, we use structural and dynamic analyses to compare two popular approaches, ancestral sequence reconstruction (ASR) and the consensus method, used to generate thermostable variants of Elongation Factor Thermo-unstable (EF-Tu). We present crystal structures of ancestral and consensus EF-Tus, accompanied by molecular dynamics simulations aimed at probing the strategies employed to enhance thermostability. All proteins adopt crystal structures similar to extant EF-Tus, revealing no difference in average structure between the methods. Molecular dynamics reveals that ASR-generated sequences retain dynamic properties similar to extant, thermostable EF-Tu from Thermus aquaticus, while consensus EF-Tu dynamics differ from evolution-based sequences. This work highlights the advantage of ASR for engineering thermostability while preserving natural motions in multidomain proteins.
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11
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Interchanging functionality among homologous elongation factors using signatures of heterotachy. J Mol Evol 2013; 76:4-12. [PMID: 23370546 PMCID: PMC3585904 DOI: 10.1007/s00239-013-9540-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 01/06/2013] [Indexed: 01/05/2023]
Abstract
Numerous models of molecular evolution have been formulated to describe the forces that shape sequence divergence among homologous proteins. These models have greatly enhanced our understanding of evolutionary processes. Rarely are such models empirically tested in the laboratory, and even more rare, are such models exploited to generate novel molecules useful for synthetic biology. Here, we experimentally demonstrate that the heterotachy model of evolution captures signatures of functional divergence among homologous elongation factors (EFs) between bacterial EF-Tu and eukaryotic eEF1A. These EFs are GTPases that participate in protein translation by presenting aminoacylated-tRNAs to the ribosome. Upon release from the ribosome, the EFs are recharged by nucleotide exchange factors EF-Ts in bacteria or eEF1B in eukaryotes. The two nucleotide exchange factors perform analogous functions despite not being homologous proteins. The heterotachy model was used to identify a set of sites in eEF1A/EF-Tu associated with eEF1B binding in eukaryotes and another reciprocal set associated with EF-Ts binding in bacteria. Introduction of bacterial EF-Tu residues at these sites into eEF1A protein efficiently disrupted binding of cognate eEF1B as well as endowed eEF1A with the novel ability to bind bacterial EF-Ts. We further demonstrate that eEF1A variants, unlike yeast wild-type, can function in a reconstituted in vitro bacterial translation system.
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12
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Utilizing natural diversity to evolve protein function: applications towards thermostability. Curr Opin Chem Biol 2011; 15:399-406. [PMID: 21470898 DOI: 10.1016/j.cbpa.2011.03.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/11/2011] [Accepted: 03/15/2011] [Indexed: 10/18/2022]
Abstract
Protein evolution relies on designing a library of sequences that capture meaningful functional diversity in a limited number of protein variants. Several approaches take advantage of the sequence space already explored through natural selection by incorporating sequence diversity available from modern genomes (and their ancestors) when designing these libraries. The success of these approaches is, partly, owing to the fact that modern sequence diversity has already been subjected to evolutionary selective forces and thus the diversity has already been deemed 'fit to survive'. Five of these approaches will be discussed in this review to highlight how protein engineers can use evolutionary sequence history/diversity of homologous proteins in unique ways to design protein libraries.
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13
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Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature 2010; 463:374-8. [PMID: 20090754 DOI: 10.1038/nature08684] [Citation(s) in RCA: 221] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 11/18/2009] [Indexed: 12/23/2022]
Abstract
Cyclin D1 belongs to the core cell cycle machinery, and it is frequently overexpressed in human cancers. The full repertoire of cyclin D1 functions in normal development and oncogenesis is unclear at present. Here we developed Flag- and haemagglutinin-tagged cyclin D1 knock-in mouse strains that allowed a high-throughput mass spectrometry approach to search for cyclin D1-binding proteins in different mouse organs. In addition to cell cycle partners, we observed several proteins involved in transcription. Genome-wide location analyses (chromatin immunoprecipitation coupled to DNA microarray; ChIP-chip) showed that during mouse development cyclin D1 occupies promoters of abundantly expressed genes. In particular, we found that in developing mouse retinas-an organ that critically requires cyclin D1 function-cyclin D1 binds the upstream regulatory region of the Notch1 gene, where it serves to recruit CREB binding protein (CBP) histone acetyltransferase. Genetic ablation of cyclin D1 resulted in decreased CBP recruitment, decreased histone acetylation of the Notch1 promoter region, and led to decreased levels of the Notch1 transcript and protein in cyclin D1-null (Ccnd1(-/-)) retinas. Transduction of an activated allele of Notch1 into Ccnd1(-/-) retinas increased proliferation of retinal progenitor cells, indicating that upregulation of Notch1 signalling alleviates the phenotype of cyclin D1-deficiency. These studies show that in addition to its well-established cell cycle roles, cyclin D1 has an in vivo transcriptional function in mouse development. Our approach, which we term 'genetic-proteomic', can be used to study the in vivo function of essentially any protein.
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Mapping key features of transcriptional regulatory circuitry in embryonic stem cells. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2008; 73:183-93. [PMID: 19022761 DOI: 10.1101/sqb.2008.73.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The process by which a single fertilized egg develops into a human being with more than 200 cell types--each with a distinct gene expression pattern controlling its cellular state--is poorly understood. Knowledge of the transcriptional regulatory circuitry that establishes and maintains gene expression programs in mammalian cells is fundamental to understanding development and should provide the foundation for improved diagnosis and treatment of disease. Although it is not yet feasible to map the entirety of this circuitry in vertebrate cells, recent work in embryonic stem (ES) cells has demonstrated that core features of the circuitry can be discovered through studies involving selected regulators. Here, we highlight the fundamental insights that have emerged from studies that examined the role of transcription factors, chromatin regulators, signaling pathways, and noncoding RNAs in the regulatory circuitry of ES cells. Maps of regulatory circuitry and the insights that have emerged from these studies have improved our understanding of global gene expression and are facilitating efforts to reprogram cells for disease therapeutics and regenerative medicine.
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15
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Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008; 134:521-33. [PMID: 18692474 DOI: 10.1016/j.cell.2008.07.020] [Citation(s) in RCA: 1018] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 06/12/2008] [Accepted: 07/14/2008] [Indexed: 01/04/2023]
Abstract
MicroRNAs (miRNAs) are crucial for normal embryonic stem (ES) cell self-renewal and cellular differentiation, but how miRNA gene expression is controlled by the key transcriptional regulators of ES cells has not been established. We describe here the transcriptional regulatory circuitry of ES cells that incorporates protein-coding and miRNA genes based on high-resolution ChIP-seq data, systematic identification of miRNA promoters, and quantitative sequencing of short transcripts in multiple cell types. We find that the key ES cell transcription factors are associated with promoters for miRNAs that are preferentially expressed in ES cells and with promoters for a set of silent miRNA genes. This silent set of miRNA genes is co-occupied by Polycomb group proteins in ES cells and shows tissue-specific expression in differentiated cells. These data reveal how key ES cell transcription factors promote the ES cell miRNA expression program and integrate miRNAs into the regulatory circuitry controlling ES cell identity.
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16
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Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev 2008; 22:746-55. [PMID: 18347094 PMCID: PMC2275428 DOI: 10.1101/gad.1642408] [Citation(s) in RCA: 402] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 01/18/2008] [Indexed: 12/13/2022]
Abstract
Embryonic stem (ES) cells have a unique regulatory circuitry, largely controlled by the transcription factors Oct4, Sox2, and Nanog, which generates a gene expression program necessary for pluripotency and self-renewal. How external signals connect to this regulatory circuitry to influence ES cell fate is not known. We report here that a terminal component of the canonical Wnt pathway in ES cells, the transcription factor T-cell factor-3 (Tcf3), co-occupies promoters throughout the genome in association with the pluripotency regulators Oct4 and Nanog. Thus, Tcf3 is an integral component of the core regulatory circuitry of ES cells, which includes an autoregulatory loop involving the pluripotency regulators. Both Tcf3 depletion and Wnt pathway activation cause increased expression of Oct4, Nanog, and other pluripotency factors and produce ES cells that are refractory to differentiation. Our results suggest that the Wnt pathway, through Tcf3, brings developmental signals directly to the core regulatory circuitry of ES cells to influence the balance between pluripotency and differentiation.
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17
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Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006; 125:301-13. [PMID: 16630818 PMCID: PMC3773330 DOI: 10.1016/j.cell.2006.02.043] [Citation(s) in RCA: 1737] [Impact Index Per Article: 96.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 01/20/2006] [Accepted: 02/23/2006] [Indexed: 12/31/2022]
Abstract
Polycomb group proteins are essential for early development in metazoans, but their contributions to human development are not well understood. We have mapped the Polycomb Repressive Complex 2 (PRC2) subunit SUZ12 across the entire nonrepeat portion of the genome in human embryonic stem (ES) cells. We found that SUZ12 is distributed across large portions of over two hundred genes encoding key developmental regulators. These genes are occupied by nucleosomes trimethylated at histone H3K27, are transcriptionally repressed, and contain some of the most highly conserved noncoding elements in the genome. We found that PRC2 target genes are preferentially activated during ES cell differentiation and that the ES cell regulators OCT4, SOX2, and NANOG cooccupy a significant subset of these genes. These results indicate that PRC2 occupies a special set of developmental genes in ES cells that must be repressed to maintain pluripotency and that are poised for activation during ES cell differentiation.
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18
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Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005; 122:947-56. [PMID: 16153702 PMCID: PMC3006442 DOI: 10.1016/j.cell.2005.08.020] [Citation(s) in RCA: 3271] [Impact Index Per Article: 172.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Revised: 07/08/2005] [Accepted: 08/17/2005] [Indexed: 02/06/2023]
Abstract
The transcription factors OCT4, SOX2, and NANOG have essential roles in early development and are required for the propagation of undifferentiated embryonic stem (ES) cells in culture. To gain insights into transcriptional regulation of human ES cells, we have identified OCT4, SOX2, and NANOG target genes using genome-scale location analysis. We found, surprisingly, that OCT4, SOX2, and NANOG co-occupy a substantial portion of their target genes. These target genes frequently encode transcription factors, many of which are developmentally important homeodomain proteins. Our data also indicate that OCT4, SOX2, and NANOG collaborate to form regulatory circuitry consisting of autoregulatory and feedforward loops. These results provide new insights into the transcriptional regulation of stem cells and reveal how OCT4, SOX2, and NANOG contribute to pluripotency and self-renewal.
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Enterobacterial repetitive intergenic consensus polymerase chain reaction typing of isolates of Enterobacter cloacae from an outbreak of infection in a neonatal intensive care unit. Am J Infect Control 2000; 28:123-9. [PMID: 10760220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
BACKGROUND Enterobacter cloacae has become a common cause of nosocomial infections. This study was designed to investigate the pattern of spread of E cloacae during an outbreak in a neonatal intensive care unit. METHODS Enterobacterial repetitive intergenic consensus polymerase chain reaction was used to examine 111 E cloacae isolates from 17 patients, including 81 from surveillance cultures, 23 from endotracheal tubes, 3 from eyes, and 1 each from blood, urine, skin, and throat. Antibiotic susceptibility profiles were also obtained. RESULTS Infection with E cloacae resulted from endogenous bacteria and from horizontal transmission. One group of 61 isolates, a third of which were obtained from clinical specimens, was uniformly susceptible to imipenem and ciprofloxacin only. A second group of 50 isolates, only 18% of which were obtained from clinical specimens, was susceptible to all antibiotics tested except for aminopenicillins and first-generation cephalosporins. CONCLUSION These data indicate that (1) patient-to-patient spread is an important cause of E cloacae infection in the neonatal intensive care unit and (2) highly antibiotic-resistant E cloacae may emerge during an outbreak.
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Characterization of the mucosal immune response in breast milk after peroral immunization of chimpanzees (Pan troglodytes) with Streptococcus mutans. Arch Oral Biol 1999; 44:871-83. [PMID: 10530920 DOI: 10.1016/s0003-9969(99)00075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The characteristics of the mucosal immune response to Streptococcus mutans cells, antigen A, antigen B, glucosyltransferases and glucan-binding proteins were examined in four pregnant chimpanzees that had been immunized perorally with Strep. mutans. Six pregnant chimpanzees served as non-immunized controls. None of the chimpanzees harbored S. mutans. Samples of milk were collected from all animals throughout the experiment. Peroral immunization resulted in an overall 17-fold median increase in SIgA in milk. Although SIgA1 comprised almost two-thirds of milk SIgA, Strep. mutans whole-cell antibody activity was contained predominantly in the SIgA2 subclass. The difference between the specific activities of anti-Strep. mutans SIgA1 and SIgA2 antibodies compared over time reached the borderline of statistical significance (p = 0.08). The avidity of anti-Strep. mutans antibodies was low in three of four chimpanzees and there was no evidence of affinity maturation. SIgA antibodies from the milk of all four immunized chimpanzees recognized antigen A. In three animals these antibodies were restricted to the SIgA1 subclass and, in one animal, anti-A antibodies were confined to SIgA2. Antibodies from all of the immunized chimpanzees recognized degradation products of antigen B in both the SIgA1 and the SIgA2 subclasses. Only two of four immunized chimpanzees responded to glucosyltransferases and these antibodies were restricted to the SIgA1 subclass. None of the chimpanzees responded to the 74-kDa glucan-binding protein. However, three animals produced SIgA1 antibodies against the 59-kDa glucan-binding protein and two of these also produced SIgA2 antibodies against this protein.
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Complement resistance in Borrelia burgdorferi strain 297: outer membrane proteins prevent MAC formation at lysis susceptible sites. Microb Pathog 1999; 27:25-41. [PMID: 10371707 DOI: 10.1006/mpat.1999.0280] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two variants of Borrelia burgdorferi strain 297, complement-resistant wild-type (WT297) and complement-sensitive mutant (MUT297), were used as a model to study the mechanism of resistance to the alternative complement pathway in this organism. No difference in the quantity of membrane attack complex (MAC) deposition on WT297 and MUT297 was observed after 2 h incubation with normal human serum (NHS), at which time 4% of WT297 and 95% of MUT297 were killed. The polymerization of C9 bound to WT297 and MUT297 was demonstrated by immunoblotting using an anti-C9 polyclonal antibody. Immunofluorescence and thin-section immunoelectron microscopy showed MAC to be diffusely distributed on the outer membrane of both variants. Furthermore, MAC appeared to be tightly bound to the surface of both variants as demonstrated by elution studies. Protease treatment rendered WT297 susceptible to killing by NHS, suggesting that outer membrane proteins may be associated with complement resistance of WT297. One- and two-dimensional gel electrophoreses showed that proteins of 20 and 30 kDa, and 66 kDa were present in WT297 but were absent or sparse in trypsin-treated WT297 and MUT297. Interestingly, immunoblotting using a polyclonal antibody against C3 showed that C3 fragments appeared to bind different acceptors on WT297 than on trypsin-treated WT297, or MUT297. Therefore, the binding of C3 fragments to acceptors on WT297, in contrast to MUT297, may not direct the formation of the MAC to lysis-susceptible sites on the surface of the bacterium, resulting in the complement resistance of WT297.
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Humoral immunity to commensal oral bacteria in human infants: salivary secretory immunoglobulin A antibodies reactive with Streptococcus mitis biovar 1, Streptococcus oralis, Streptococcus mutans, and Enterococcus faecalis during the first two years of life. Infect Immun 1999; 67:1878-86. [PMID: 10085031 PMCID: PMC96541 DOI: 10.1128/iai.67.4.1878-1886.1999] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Secretory immunoglobulin A (SIgA) antibodies reactive with the pioneer oral streptococci Streptococcus mitis biovar 1 and Streptococcus oralis, the late oral colonizer Streptococcus mutans, and the pioneer enteric bacterium Enterococcus faecalis in saliva samples from 10 human infants from birth to age 2 years were analyzed. Low levels of salivary SIgA1 and SIgA2 antibodies reactive with whole cells of all four species were detected within the first month after birth, even though S. mutans and E. faecalis were not recovered from the mouths of the infants during the study period. Although there was a fivefold increase in the concentration of SIgA between birth and age 2 years, there were no differences between the concentrations of SIgA1 and SIgA2 antibodies reactive with the four species over this time period. When the concentrations of SIgA1 and SIgA2 antibodies reactive with all four species were normalized to the concentrations of SIgA1 and SIgA2 in saliva, SIgA1 and SIgA2 antibodies reactive with these bacteria showed a significant decrease from birth to 2 years of age. Adsorption of each infant's saliva with cells of one species produced a dramatic reduction of antibodies recognizing the other three species. Sequential adsorption of saliva samples removed all SIgA antibody to the bacteria, indicating that the SIgA antibodies were directed to antigens shared by all four species. The induction by the host of a limited immune response to common antigens that are likely not involved in adherence may be among the mechanisms that commensal streptococci employ to persist in the oral cavity.
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Correlations among Epworth Sleepiness Scale scores, multiple sleep latency tests and psychological symptoms. J Sleep Res 1998; 7:248-53. [PMID: 9844851 DOI: 10.1046/j.1365-2869.1998.00123.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The aim of this study was to identify factors other than objective sleep tendency associated with scores on the Epworth Sleepiness Scale (ESS). There were 225 subjects, of whom 40% had obstructive sleep apnoea (OSA), 16% had simple snoring, and 4.9% had snoring with sleep disruption (upper airway resistance syndrome); 9.3% had narcolepsy and 7.5% had hypersomnolence without REM sleep abnormalities; 12% had chronic fatigue syndrome; 7.5% had periodic limb movement disorder and 3% had diurnal rhythm disorders. ESS, the results of overnight polysomnography and multiple sleep latency test (MSLT) and SCL-90 as a measure of psychological symptoms were recorded. The ESS score and the mean sleep latency (MSL) were correlated (Spearman rho = -0.30, P < 0.0001). The MSL was correlated with total sleep time (TST) and with sleep efficiency but not with apnoea/hypopnoea index. There was no association between the MSL and any aspect of SCL-90 scores, except a borderline significant association with the somatisation subscale. The ESS was correlated with TST but not with sleep efficiency or apnoea/hypopnoea index. The ESS was correlated with all subscales of the SCL-90 except psychoticism. An ESS > or = 10 had poor sensitivity and specificity as a predictor of MSL < 10 min or MSL < 5 min. We conclude that the MSLT and the ESS are not interchangeable. The ESS was influenced by psychological factors by which the MSL was not affected. The ESS cannot be used to demonstrate or exclude sleepiness as it is measured by MSLT.
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Clonal diversity of vancomycin-resistant enterococci from an outbreak in a tertiary care university hospital. Am J Infect Control 1998; 26:563-8. [PMID: 9836839 DOI: 10.1053/ic.1998.v26.a91614] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Enterococci have become important nosocomial pathogens and now account for approximately 12% of nosocomial infections. Enterococci can be transferred from patient to patient and from health care personnel to patient. We investigated the clonal diversity of vancomycinresistant enterococci (VRE) causing an outbreak of infections and attempted to determine the patterns of spread of these bacteria in a university hospital. METHODS Ribotyping was used to examine the clonal diversity of 50 VRE isolates, including 23 from wounds, 14 from urine, 8 from blood, 3 from the rectum, 1 from drainage, and 1 from the cornea. RESULTS Nine patients were infected with Enterococcus faecalis, 10 with Enterococcus faecium, 3 with both E faecalis and E faecium, and 1 with Enterococcus avium. The results suggest that the sources of the VRE infections included endogenous strains and strains acquired by transmission from attending staff or from the environment. Three patients were infected by both nosocomial and endogenous strains. CONCLUSIONS These data suggest that the collection and analysis of several isolates from repeated specimens is necessary to obtain a fuller understanding of the epidemiology and population structure of antibiotic-resistant enterococci.
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Humoral immunity to commensal oral bacteria in human infants: salivary antibodies reactive with Actinomyces naeslundii genospecies 1 and 2 during colonization. Infect Immun 1998; 66:4283-9. [PMID: 9712779 PMCID: PMC108517 DOI: 10.1128/iai.66.9.4283-4289.1998] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The secretory immune response in saliva to colonization by Actinomyces naeslundii genospecies 1 and 2 was studied in 10 human infants from birth to 2 years of age. Actinomyces species were not recovered from the mouths of the infants until approximately 4 months after the eruption of teeth. However, low levels of secretory immunoglobulin A1 (SIgA1) and SIgA2 antibodies reactive with whole cells of A. naeslundii genospecies 1 and 2 were detected within the first month after birth. Although there was a fivefold increase in the concentration of SIgA between birth and age 2 years, there were no differences between the concentrations of SIgA1 and SIgA2 antibodies reactive with A. naeslundii genospecies 1 and 2 over this period. When the concentrations of SIgA1 and SIgA2 antibodies reactive with whole cells of A. naeslundii genospecies 1 and 2 were normalized to the concentrations of SIgA1 and SIgA2 in saliva, the A. naeslundii genospecies 1- and 2-reactive SIgA1 and SIgA2 antibodies showed a significant decrease from birth to 2 years of age. The fine specificities of A. naeslundii genospecies 1- and 2-reactive SIgA1 and SIgA2 antibodies were examined by Western blotting of envelope proteins. Similarities in the molecular masses of proteins recognized by SIgA1 and SIgA2 antibodies, both within and between subjects over time, were examined by cluster analysis and showed considerable variability. Taken overall, our data suggest that among the mechanisms Actinomyces species employ to persist in the oral cavity are the induction of a limited immune response and clonal replacement with strains differing in their antigen profiles.
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Effect of IgA1 protease on the ability of secretory IgA1 antibodies to inhibit the adherence of Streptococcus mutans. Microbiol Immunol 1998; 42:503-8. [PMID: 9719103 DOI: 10.1111/j.1348-0421.1998.tb02316.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Secretory IgA (SIgA) is the principal immunoglobulin isotype present in the mucosal secretions of humans. SIgA is thought to play a major role in host defense at these surfaces by inhibiting the colonization of potentially pathogenic microorganisms. A number of bacteria that are mucosal pathogens of humans produce a protease that specifically cleaves the IgA1 subclass of humans and great apes at the hinge region to produce Fab and Fc fragments. In order to study the effect of IgA1 protease on the ability of SIgA1 antibodies to inhibit bacterial adherence, an in vitro assay that quantifies the adsorption of radiolabeled Streptococcus mutans to hydroxyapatite (HA) beads was employed. High titer S. mutans-specific SIgA1 and SIgA2 antibodies were induced in chimpanzee milk for use in the assay. Fab alpha1 fragments had significantly reduced ability to inhibit adherence of S. mutans to saliva-coated HA compared to intact SIgA1 or SIgA2 anti-S. mutans antibodies. These data support the potential importance of IgA1 proteases as an ecological determinant in the oral cavity and their role as a determinant of pathogenesis of pathogenic bacteria whose portal of entry is the mucosal surface.
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Increased titre and avidity of IgG antibodies to Porphyromonas gingivalis whole cells and a cell surface protein in subjects with adult periodontitis. J Periodontal Res 1997; 32:31-9. [PMID: 9085240 DOI: 10.1111/j.1600-0765.1997.tb01379.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The titre and avidity of IgG antibodies to Porphyromonas gingivalis whole cells and a 47 kDa cell surface protein were determined in serum samples taken from 20 subjects with adult periodontitis and 20 controls, matched for age, gender, ethnic origin and oral hygiene status. Antibody titres were measured by ELISA and antibody avidity was determined by a chaotrope-dissociation ELISA. Avidity was defined as the molarity of chaotrope required to reduce absorbance by 50% (ID50). The mean IgG antibody log titre to whole cells (8.29 vs. 6.92; p < 0.01) and to the 47 kDa antigen (7.61 vs. 6.77; p < 0.05) were higher in cases than in controls. Mean IgG antibody avidity to whole cells (4.59 vs. 2.47; p < 0.001) and to the surface protein (2.54 vs. 1.67; p < 0.001) were also higher in cases than in controls. In cases, IgG antibody titre was highly correlated with avidity for both whole cells (r = 0.878; p = < 0.001) and the 47 kDa protein (r = 0.683; p < 0.001). There was a weaker positive correlation between the titre and the avidity of antibody to whole cells (r = 0.591; p < 0.01) in the control population but antibody titre and avidity for the 47 kDa sonicate antigen were not correlated in the controls (r = 0.104). We conclude that many patients with adult periodontitis have effective humoral immunity to P. gingivalis. However, in up to half the patients with adult periodontitis, antibody titres and avidities were low and similar to control values, indicating either susceptibility due to poor host response or that disease is not associated with this particular pathogen.
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Abstract
Actinomyces naeslundii and Streptococcus gordonii, oral bacteria that possess Gal/GalNAc- and sialic acid-reactive lectins, respectively, were adherent to immobilized secretory immunoglobulin A (IgA) and two IgA1 myeloma proteins but not to two IgA2 myeloma proteins. Apparently, O-linked oligosaccharides at the hinge region of the IgA1 heavy chain are receptors for lectin-mediated adhesion of these bacteria.
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Requirement for the Candida albicans FAS2 gene for infection in a rat model of oropharyngeal candidiasis. MICROBIOLOGY (READING, ENGLAND) 1996; 142 ( Pt 9):2509-14. [PMID: 8828218 DOI: 10.1099/00221287-142-9-2509] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The virulence of Candida albicans strains deficient in fatty acid synthase activity by virtue of disruption/deletion of the FAS2 gene was examined in a rat model of oropharyngeal candidiasis. The FAS2 alleles of C. albicans CAI4 (delta ura3::imm434/delta ura3::imm434) were sequentially disrupted with a cassette that included a portion of FAS2 from which a 984 bp fragment containing the FAS condensing reaction domain was deleted and replaced with hisG-URA3-hisG sequences. Verification of fatty acid synthase inactivation was obtained from assays of enzyme activity. Strains in which a single allele was disrupted (CFD1 and CFD3) exhibited an approximately 20% reduction in activity, when compared to wild-type. In addition, fatty acid synthase activity was abolished in a FAS2 null mutant strain (CFD2), and growth of CFD2 occurred only when the growth medium was supplemented with Tween 40 and certain fatty acids. Strain CFD2 was avirulent in the rat model, indicating that fatty acid synthase activity is required for C. albicans oropharyngeal infection. Strains with a single FAS2 allele disruption colonized the oral cavity, but the number of cells recovered from infected animals was approximately fivefold less than for the parental strain. The results suggest that FAS may be exploited as a possible target for the development of new antifungal agents.
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Clonal diversity of Streptococcus mitis biovar 1 isolates from the oral cavity of human neonates. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 1996; 3:517-22. [PMID: 8877128 PMCID: PMC170399 DOI: 10.1128/cdli.3.5.517-522.1996] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The clonal diversity of 101 isolates of the pioneer bacterium Streptococcus mitis biovar 1 obtained from the oral cavities of 40 human neonates 1 to 3 days, 2 weeks, and 1 month postpartum was examined by using rRNA gene restriction patterns. There was a high degree of genetic diversity, with the 101 isolates comprising 93 unique PvuII ribotypes. There were eight identical pairs of ribotype patterns, and seven of the eight pairs were obtained from individual neonates. Only one identical pair comprised isolates obtained from different neonates. In all but two cases, isolates with matching ribotypes were obtained at one visit. Two pairs of isolates with matching ribotype patterns were obtained from neonates on successive visits. The ribotype patterns of the isolates were examined by cluster analysis. The isolates forming each cluster were very similar, yet each cluster was well separated from its neighbors. When several isolates were obtained from individual neonates at a particular visit, in some instances they were contained in a single cluster, whereas in other cases each isolate was contained in a separate cluster. Isolates obtained from individual neonates on successive visits tended to be contained in different clusters. This high degree of diversity, which has been observed in other mucosal commensal bacteria, may serve as a mechanism for avoiding immune elimination of these bacteria.
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Humoral immunity to commensal oral bacteria: quantitation, specificity and avidity of serum IgG and IgM antibodies reactive with Actinobacillus actinomycetemcomitans in children. Microbiol Immunol 1995; 39:591-8. [PMID: 7494498 DOI: 10.1111/j.1348-0421.1995.tb02247.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The levels, specificity and avidities of serum IgM and IgG antibodies reactive with Actinobacillus actinomycetemcomitans (Aa) serotypes a, b and c were determined in periodontally healthy (PH) children and compared with subjects with localized juvenile periodontitis (LJP). All PH children exhibited IgM and IgG Aa-reactive antibodies whether or not Aa was detected subgingivally but the antibodies were not specific for Aa. In contrast, LJP sera contained high concentrations of IgM and IgG antibodies reactive with Aa that were largely specific for this bacterium. IgM and IgG antibodies in both PH and LJP subjects were of low avidity. With one exception, the avidities of IgG anti-Aa antibodies were significantly greater than those of IgM antibodies in both PH and LJP subjects. However, although the LJP subjects had as much as 115-fold more Aa-reactive IgG antibody than did the PH subjects the avidities of their IgG antibodies were no greater than those of the PH group. The induction by the host of low-avidity antibodies, that are ineffective in immune elimination, may be a reason why commensal bacteria persist at mucosal surfaces and why persons with LJP fail to eliminate Aa from their periodontal pockets.
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Abstract
The virulence of Candida albicans strain SC5413 and two isogenic derivatives have been investigated in a rat model of oropharyngeal candidiasis. The results demonstrate that both mutant strains are avirulent in this animal model while the parental strain readily initiates infection. Avirulence is not related to altered growth characteristics or the inability of the strains to undergo yeast-to-hyphal morphogenesis. The potential importance of nutritional sufficiency as a virulence factor as well as the possibility of utilizing such strains in the development of an in vitro expression technology system for Candida albicans is discussed.
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Abstract
Three hundred and sixty-seven strains of pioneer streptococci isolated from the mouths of 40 healthy, full-term infants during the first month of life were examined by two taxonomic schemes that incorporated biochemical and physiological characteristics, IgA1 protease production and glycosidase activities. Streptococcus mitis biovar 1 and S. oralis comprised 55.0% of the pioneer streptococci isolated from neonates. S. salivarius constituted 25.3% of the isolates, while S. anginosus, S. mitis biovar 2, S. sanguis and S. gordonii accounted collectively for 11.4%. Difficulties in identifying streptococci were encountered and 8.4% of the 367 isolates could not be assigned to a recognised species.
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Abstract
As part of a longitudinal study of the relationship between bacterial colonization and the secretory immune response, 367 isolates of pioneer viridans streptococci collected from 40 breast- and bottle-fed neonates within the first month postpartum were tested for the production of immunoglobulin A1 (IgA1) protease and glycosidases. Fifty percent of the streptococci isolated produced IgA1 protease, including all isolates of Streptococcus oralis and S. sanguis, 60.7% of S. mitis biovar 1 isolates, and some isolates that could not be identified. Three cleavage patterns of alpha 1 heavy chains were observed. Six isolates of S. mitis biovar 1 that did not produce IgA1 protease attacked the alpha 1 chain. Incubation of IgA1 protease-negative S. mitis biovar 1 isolates with IgA1, either prior to or together with S. sanguis, rendered the IgA1 paraprotein resistant to cleavage by the IgA1 protease of S. sanguis. The ability of some pioneer streptococci in the human oral cavity to produce IgA1 protease and of others to modify the susceptibility of IgA1 to cleavage by IgA1 protease perhaps enhances their ability to survive in this habitat.
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Abstract
We sought to determine (1) the ontogeny of secretory IgA subclasses in saliva of breast- and formula-fed infants and (2) the influence of breast-feeding on the maturation of secretory salivary IgA subclasses. Secretory IgA and subclasses 1 and 2 concentrations were determined in saliva from 40 healthy, term infants from birth to age 18 months, and in parallel milk samples from the infants' mothers who were breast-feeding during the first 6 months after birth. Secretory IgA was detected in the neonates' saliva as early as 3 days after birth, increased rapidly during the next 6 months, but then stabilized at a level approximately one-sixth that of the mothers' salivary secretory IgA. Secretory IgA2 represented less than 15% of secretory IgA in saliva collected 2 weeks after birth but by 6 months represented 24.4% of secretory IgA, a value approaching that of the mothers' salivary secretory IgA2 (30.4%). This increase in the proportion of secretory IgA2 was temporally related to a reduction in the proportion of secretory IgA2 in milk throughout lactation. The secretory IgA concentration increased more rapidly during the first 6 months after birth in infants exclusively breast fed than in those exclusively bottle fed. We conclude that although secretory immunity is immature in infants, breast-feeding may aid in protection against pathogenic microorganisms by increasing the rate of mucosal IgA maturation.
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Identification of two subclasses of IgA in the chimpanzee (Pan troglodytes). J Med Primatol 1992; 21:275-8. [PMID: 1404336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chimpanzee secretory immunoglobulin A (SIgA) was separated into two fractions by chromatography using the terminal galactose-binding lectin Jacalin. The SIgA fraction bound by Jacalin was cleaved by Haemophilus influenzae IgA1 protease, whereas the SIgA nonbinding fraction was not cleaved. It is proposed that these fractions represent IgA1 and IgA2 subclasses because the presence or absence of galactose-terminal oligosaccharides (Jacalin binding) and susceptibility or resistance to IgA1 protease are properties that define human IgA1 and IgA2 subclasses.
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Natural transmission of Streptococcus sobrinus in rats: saliva and serum antibody responses to colonization. Infect Immun 1992; 60:778-83. [PMID: 1531814 PMCID: PMC257554 DOI: 10.1128/iai.60.3.778-783.1992] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
One hundred and twenty weanling rats fed diet NIH 2000 that were free of Streptococcus sobrinus and other mutans streptococci were employed in this study. Sixty rats were inoculated orally with S. sobrinus 6715. Each infected rat (donor) was paired and housed with an uninfected recipient. Saliva and serum samples were collected from 24 (12 donor and 12 recipient) rats at the baseline (day 0) and from groups of 12 recipients sacrificed on days 10, 24, 38, and 52, and the level of infection with S. sobrinus was monitored. Salivary immunoglobulin A (IgA) and IgG and serum IgM and IgG antibodies reactive with whole cells (WC), glucosyltransferase (GTF), and the serotype carbohydrate (g) of S. sobrinus were measured by an indirect enzyme-linked immunosorbent assay. Although the rats were free of S. sobrinus and other mutans streptococci at baseline, they exhibited salivary IgA and serum IgM antibodies reactive with S. sobrinus WC, GTF, and g and serum IgG antibodies reactive with WC and GTF. Infection of recipients with S. sobrinus did not induce salivary antibodies reactive with WC, GTF, or g. In contrast, increases in serum IgM and IgG antibodies reactive with WC and serum IgM antibodies reactive with g were observed.
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Abstract
Immunoglobulin (Ig)A proteases synthesized by human mucosal pathogens have a unique specificity for human IgA and will not cleave IgA from other species. In contrast, animal pathogens have not reliably been shown to cleave IgA of the animals they infect. This lack of an animal model has prevented an understanding of the importance of IgA1 proteases as virulence factors. One strategy to develop an animal model would be to identify a species capable of infection by a human IgA-producing pathogen whose IgA was susceptible to cleavage by IgA1 protease of that bacterium. The chimpanzee can be infected with Haemophilus influenzae and is closely related immunologically to man. For these reasons it was sought to determine whether chimpanzee secretory IgA (SIgA) is susceptible to cleavage by IgA1 protease of H. influenzae. This report shows that chimpanzee SIgA can indeed be cleaved at the hinge region by H. influenzae IgA1 protease into Fab alpha and (Fc alpha)2.SC fragments. The susceptibility of chimpanzee SIgA to IgA1 protease of a human pathogen could serve as the basis of an animal model to determine the importance of IgA1 protease in pathogenesis.
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Abstract
The structural integrity of immunoglobulin A (IgA), IgG, and IgM and lactoferrin in dental plaque fluid samples from two populations of Colombian children with contrasting levels of dental caries was examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by electrophoretic transfer to nitrocellulose. The immune factors or their fragments or both were detected with monospecific antibody conjugated with horseradish peroxidase. All the immune factors examined were extensively degraded, although there appeared to be small amounts of intact IgA and IgG in some samples. Analysis of the samples with antibody to secretory component showed that secretory IgA as well as serum IgA was degraded. IgG appeared to be cleaved into two major fragments, one fragment having a relative mobility similar to the F(ab')2 fragment of IgG and the other a relative mobility slightly greater than Fc. IgM and lactoferrin were virtually completely degraded. There was no apparent relationship between the fragmentation patterns of IgA and IgG in the plaque fluid samples from the two communities and their susceptibility to dental caries.
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Abstract
Groups of rats immunized in the vicinity of the major salivary glands or immunized intraperitoneally with Actinomyces viscosus T6 and their sham-immunized controls were infected with the homologous bacterium. Significantly higher levels of salivary and serum antibody were induced by intraperitoneal than by salivary gland immunization. There were also significant inverse correlations between the levels of salivary and serum antibody and the levels of implantation of A. viscosus T6. The level of implantation of A. viscosus T6 was significantly lower in the immunized animals than in the controls. However, antibody had limited capacity to inhibit the establishment of this bacterium.
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Effect of peroral immunization of humans with Streptococcus mutans on induction of salivary and serum antibodies and inhibition of experimental infection. Infect Immun 1984; 46:703-9. [PMID: 6389359 PMCID: PMC261601 DOI: 10.1128/iai.46.3.703-709.1984] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Naturally occurring antibodies reactive with Streptococcus mutans whole cells were assayed in whole saliva, parotid saliva, and blood samples collected from eight human volunteers. The levels and serotypes of indigenous S. mutans in plaque and whole saliva samples were also determined. After baseline sampling the teeth were cleaned and the subjects were inoculated with streptomycin-resistant S. mutans strains Ingbritt (serotype c) and OMZ65 (serotype g). The level of implantation and duration of colonization were determined in plaque and saliva, and antibodies reactive with these strains were monitored in saliva and serum. After the implanted bacteria were shed, the subjects wee immunized by the daily ingestion of an enteric-coated capsule containing 25 mg of Formalin-killed, freeze-dried OMZ65 cells for 3 days and inoculation was repeated. The levels of antibodies and of implantation and the duration of colonization were monitored as before. One month after the bacteria could no longer be detected, the immunization and inoculation cycle was repeated except that the subjects were immunized for 7 days. Five of the eight subjects were successfully colonized by strains Ingbritt and OMZ65. The remaining three did not become colonized with either strain. Strain OMZ65 implanted at a higher level than did strain Ingbritt. Oral immunization did not result in a detectable antibody response in saliva or serum to whole bacterial cells. However, after both the first and second immunizations there were marked reductions in the peak levels of infection and the duration of colonization of both OMZ65 and Ingbritt.
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Abstract
Mucosal defense is provided by a number of host factors countering the specific virulence factors of the many microorganisms infecting the mucous membranes. Secretory IgA antibodies presumably play an important role. Increase of the sIgA antibodies may most advantageously be attained by parenteral immunization, following mucosal priming. This was demonstrated in a rat model, where it was also noted that antigen injection into PP induced high milk IgA antibody levels. In man, parenteral vaccination against polio increased the sIgA antibody levels in the milk of mothers previously exposed naturally to the poliovirus. The response was relatively short-lived. In the previously unexposed, there was little or no response. By contrast peroral immunization with live poliovirus vaccine did not increase, or even decrease, the milk sIgA poliovirus antibody levels. Although salivary sIgA antibodies against antigens of colonizing E. coli appear during the first days of life, they are slow to increase. This deficiency is richly compensated for by all the sIgA antibodies that are provided the baby through the milk. No transfer of dimeric IgA into the milk could be shown in lactating rats, in contrast to what has been reported in mice. There is no evidence for a contribution to milk sIgA from serum in man. Close to parturition, human milk often contains some 7S IgA and various sizes of free SC, in addition to the dominating 11S sIgA. A few days later there is almost exclusively monomeric SC and 11S sIgA. IgG antibodies also play a role at the mucosal level. IgG2 antibodies against the bacterial polysaccharide capsule are as slow to appear as sIgA in ontogeny, possibly explaining the prevalence of infections with encapsulated bacteria and the poor response to polysaccharide vaccines in early childhood. Other defense factors preventing infections by way of mucous membranes may be important. Thus, oligosaccharides present in human milk seem to specifically prevent pneumococcal attachment to retropharyngeal cells. This anti-attachment capacity, in addition to that provided by milk and salivary IgA antibodies, may explain why breast-fed babies have less otitis media than formula-fed ones.
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A fluorescein-linked immunoabsorbent assay for the detection of antibacterial antibodies in secretions and serum. J Immunol Methods 1982; 53:335-43. [PMID: 6754816 DOI: 10.1016/0022-1759(82)90180-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A rapid, quantitative solid-phase immunofluorescence assay has been developed to measure antibodies reactive with Streptococcus mutans in saliva and serum. Formalin killed bacteria were adsorbed to cellulose acetate discs and antibodies bound to the antigen-coated immunoabsorbent were detected by use of fluorescein-labeled antibody to human immunoglobulin isotypes. Quantitation was performed by placing the immunoabsorbent discs in a fluorometer. Low levels of naturally occurring antibodies reactive with S. mutans were easily detected in saliva and serum from normal human subjects.
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Abstract
Irradiation of the major salivary glands of monkeys (Macaca mulatta) fed cariogenic diets leads to caries clinically indistinguishable from radiation caries in man. This study compares the organic composition of individual samples of plaque fluid and saliva from irradiated and control monkeys receiving the same cariogenic diet. Plaque and saliva were collected from fasting, tranquillised animals. Four irradiated animals were sampled repeatedly as were non-irradiated controls. Total protein, albumin, immunoglobulins A, G, and M, and the third component of complement (C'3) were quantitated in plaque fluid and whole saliva. Salivary amylase and peroxidase activities were also determined. Plaque fluid and saliva samples were also subjected to polyacrylamide gel electrophoresis. The total viable anaerobic count and numbers of Streptococcus mutans were determined in samples of plaque. The results suggest that the major effect of irradiation leading to increased numbers of S. mutans and caries susceptibility is in the amount, and not the composition, of the saliva produced by the residual gland tissue. The scanty flow of saliva may reduce the effectiveness of cleansing, buffering and lubrication mechanisms as well as resulting in a marked reduction in the total amount of specific and non-specific immune factors entering the mouth.
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Development of rampant dental caries, and composition of plaque fluid and saliva in irradiated primates. JOURNAL OF ORAL PATHOLOGY 1981; 10:284-95. [PMID: 6798188 DOI: 10.1111/j.1600-0714.1981.tb01275.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Co-60 gamma irradiation of the salivary glands of Macaca mulata monkeys fed a cariogenic diet led to the rapid onset of dental caries resembling that in irradiated human patients. Plaque fluid and saliva were sampled from irradiated monkeys, nonirradiated controls and a group of animals fed a noncariogenic diet in order to look for changes which might occur in inorganic composition related to the caries development and to dietary differences. Salivary calcium and phosphate levels were not markedly changed after irradiation: iodide levels were raised, while thiocyanate levels fell. In plaque fluid, calcium concentrations were not affected by irradiation, but were higher in animals fed a noncariogenic diet. Phosphate levels were higher with a cariogenic diet and further increased in irradiated animals. Magnesium levels were occasionally higher than those of calcium. Other differences in plaque fluid composition may be related to secondary effects of the concomitant gingival disease. The results do not point clearly at a specific change in the quality of the saliva produced by the residual gland tissue after irradiation which precipitates the rampant caries. It is more likely that the great reduction in the quantity of saliva with its protective constituents is responsible.
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Specific and nonspecific immune factors in dental plaque fluid and saliva from young and old populations. Infect Immun 1981; 31:998-1002. [PMID: 7228411 PMCID: PMC351417 DOI: 10.1128/iai.31.3.998-1002.1981] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Separate samples of supragingival dental plaque overtly free of blood were centrifuged to obtain the free fluid phase (plaque fluid). Bound protein was eluted from the plaque bacteria and matrix by washing the plaque with a low-pH buffer. The plaque fluid, low pH eluate, and whole saliva were assayed for immunoglobulins A, G, and M, the third component of complement, lysozyme, lactoferrin, and lactoperoxidase. Concentrations of total protein and albumin were also determined. Antibody reactive with specific plaque bacteria was detected by indirect immunofluorescent microscopy. Specific and nonspecific immune proteins were present in plaque fluid from adult subjects at significantly greater concentrations than in their saliva, which suggests that these proteins are concentrated in dental plaque. The results indicate that both saliva and gingival exudate contribute to the immunological proteins found in the free fluid phase of dental plaque. The observation that immunoglobulin A antibody reactive with plaque bacteria could be detected in plaque fluid suggests that a wide variety of immunological reactions may occur in the dental plaque. These potential interactions between host, plaque bacteria, and their products could serve to influence the plaque flora and its ability to induce disease.
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Abstract
By feeding rats their essential nutrition through gastric intubation and test foods on a programmed feeder it is possible to determine the cariogenicity of many foods in animals. Because the test food is the only substance that contacts teeth, all carious lesions that develop can be ascribed solely to the ingestion of the test food. Caries scores can be expressed as ratios of those occurring when animals are fed pure sucrose, thereby comparisons can be made from one experiment to another. The number of carious lesions that develop is directly related to the frequency of ingestion of sucrose. In addition, frequency of ingestion of sucrose has a significant effect on the establishment of S mutans in the mouths of animals. We believe that the approach used here can establish differences in the cariogenic potential of foods in a simple, unequivocal, and reproducible manner.
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Effects of pyridoxine, phytate and invert sugar on plaque composition and caries activity in the monkey (Macaca fascicularis). Caries Res 1980; 14:1-15. [PMID: 6765919 DOI: 10.1159/000260428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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Immunoglobulins and antibodies in plaque fluid and saliva in two populations with contrasting levels of caries. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1978; 107:383-92. [PMID: 742496 DOI: 10.1007/978-1-4684-3369-2_43] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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The effect of pyridoxine, phytate and invert sugar on production of plaque acids in situ in the monkey (M. fascicularis). Caries Res 1978; 12:190-201. [PMID: 99237 DOI: 10.1159/000260333] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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