Benjamin Carter - Academia.edu (original) (raw)
Papers by Benjamin Carter
Chapter 12 reviews late prehistoric maritime communities of coastal Ecuador to investigate change... more Chapter 12 reviews late prehistoric maritime communities of coastal Ecuador to investigate changes in adaptation at two sites in the Santa Elena area of southern Ecuador: Loma de los Cangrejitos and Mar Bravo. The authors find changes in the distribution of population, social organization, and the role of marine resources at around 700 cal A.D. They conclude that late communities of coastal Ecuador were successful, sophisticated exploiters of coastal resources who intensified both marine and terrestrial production over time and lived in well-organized, dense, kin-based settlements. Organization varied across space and there is no clear evidence for centralization. The paper also discusses the mollusk Spondylus, which is native to this region, and its possible roles in trade and the complexity.
This protocol details the reagents and steps required to perform antibody-guided chromatin tagmen... more This protocol details the reagents and steps required to perform antibody-guided chromatin tagmentation for two or more factors (ACT2-seq, ACT2). Like its predecessor ACT-seq, ACT2 uses a fusion of protein A and Tn5 transposase to bind and profile epigenetic marks across the genome. ACT2 builds on the capabilities of ACT-seq by directly and concurrently profiling co-occupancy of epigenetic marks, which previously required laborious, expensive, and technically challenging approaches involving fluorescence, magnetic beads, or single-cell methods. ACT2 requires only standard pipetting and centrifugation techniques and can be completed in less than a single day of bench work.
Modern next-generation sequencing-based methods have empowered researchers to assay the epigeneti... more Modern next-generation sequencing-based methods have empowered researchers to assay the epigenetic states of individual cells. Existing techniques for profiling epigenetic marks in single cells often require the use and optimization of time-intensive procedures such as drop fluidics, chromatin fragmentation, and end repair. Here we describe ACT-seq, a novel and streamlined method for mapping genome-wide distributions of histone tail modifications, histone variants, and chromatin-binding proteins in a small number of or single cells. ACT-seq utilizes a fusion of Tn5 transposase to Protein A that is targeted to chromatin by a specific antibody, allowing chromatin fragmentation and sequence tag insertion specifically at genomic sites presenting the relevant antigen. The Tn5 transposase enables the use of an index multiplexing strategy (iACT-seq), which enables construction of thousands of single-cell libraries in one day by a single researcher without the need for drop-based fluidics o...
Journal of Experimental Psychology: Human Perception and Performance, 2017
Eye movements are used to study a variety of cognitive phenomena, including attention, perception... more Eye movements are used to study a variety of cognitive phenomena, including attention, perception, memory, language, reading, decision making, and many others, as well as cognitive impairments and individual differences in cognition. These studies assume, with little evidence, that eye movements are stable across time and trials. Eye movement stability must be better characterized to understand the full theoretical and clinical implications of individual differences in eye movement behavior. The present study examined eye movement reliability in normal individuals during reading. Thirty-nine participants completed 2 sessions of a reading task separated by 1 month. Means and standard deviations of fixation duration, saccade amplitude, first fixation duration, gaze duration, total time, go-past time, skipping, refixation and regression probabilities were compared both between sessions and across trials within sessions. All correlations were highly significant, indicating that eye movement behaviors are stable within individuals across several weeks and highly stable across trials within each individual. The different components of the ex-Gaussian distribution of fixation durations were also highly stable over time. Differences in sensitivity to lexical variables (frequency, predictability, length) were also compared, and were also observed to be highly stable across time. Eye movements in reading are therefore suitable for studying cognition and its neural underpinnings, as well as cognitive development and longitudinal change. Theoretical and clinical implications of these findings are discussed. (PsycINFO Database Record
Macromolecular bioscience, Jan 24, 2017
The rapid pace of development in biotechnology has placed great importance on controlling cell-ma... more The rapid pace of development in biotechnology has placed great importance on controlling cell-material interactions. In practice, this involves attempting to decouple the contributions from adhesion molecules, cell membrane receptors, and scaffold surface chemistry and morphology, which is extremely challenging. Accordingly, a strategy is presented in which different chemical, biochemical, and morphological properties of 3D biomaterials are systematically varied to produce novel scaffolds with tuneable cell affinities. Specifically, cationized and surfactant-conjugated proteins, recently shown to have non-native membrane affinity, are covalently attached to 3D scaffolds of collagen or carboxymethyl-dextran, yielding surface-functionalized 3D architectures with predictable cell immobilization profiles. The artificial membrane-binding proteins enhance cellular adhesion of human mesenchymal stem cells (hMSCs) via electrostatic and hydrophobic binding mechanisms. Furthermore, functiona...
Molecular plant-microbe interactions : MPMI, 2017
Agrobacterium-mediated transformation is a core technology for basic plant science and agricultur... more Agrobacterium-mediated transformation is a core technology for basic plant science and agricultural biotechnology. Improving transformation frequency is a major goal for plant transgenesis. We previously showed that T-DNA insertions in some histone genes decreased transformation susceptibility, whereas overexpression of several Arabidopsis H2A and H4 isoforms increased transformation. Overexpression of several histone H2B and H3 isoforms had little effect on transformation frequency. However, overexpression of histone H3-11 (HTR11) enhanced transformation. HTR11 is a unique H3 variant that lacks lysine at positions 9 and 27. The modification status of these lysine residues in canonical H3 proteins plays a critical role in epigenetic determination of gene expression. We mutated histone H3-4 (HTR4), a canonical H3.3 protein that does not increase transformation when overexpressed, by replacing either or both K9 and K27 with the amino acids in HTR11 (either K9I, K27Q, or both). Overexp...
Advanced healthcare materials, Jan 29, 2016
3D tissue printing with adult stem cells is reported. A novel cell-containing multicomponent bioi... more 3D tissue printing with adult stem cells is reported. A novel cell-containing multicomponent bioink is used in a two-step 3D printing process to engineer bone and cartilage architectures.
Genetics, Jun 13, 2016
Angiosperm reproduction requires the integrated development of multiple tissues with different ge... more Angiosperm reproduction requires the integrated development of multiple tissues with different genotypes. To achieve successful fertilization, the haploid female gametophytes and diploid ovary must coordinate their development, after which the male gametes must navigate through the maternal sporophytic tissues to reach the female gametes. After fertilization, seed development requires coordinated development of the maternal diploid integuments, the triploid endosperm, and the diploid zygote. Transcription and signaling factors contribute to communication between these tissues, and roles for epigenetic regulation have been described for some of these processes. Here we identify a broad role for CHD3 chromatin remodelers inArabidopsis thalianareproductive development. Plants lacking the CHD3 remodelerPICKLEexhibit various reproductive defects including abnormal development of the integuments, female gametophyte, and pollen tube as well as delayed progression of ovule and embryo develo...
The American Biology Teacher, 2015
Students who enter college with a solid grounding in, and positive attitudes toward, evolutionary... more Students who enter college with a solid grounding in, and positive attitudes toward, evolutionary science are better prepared for and achieve at higher levels in university-level biology courses. We found highly significant, positive relationships between student knowledge of evolution and attitudes toward evolution, as well as between introductory biology course achievement and both precourse acceptance of evolution and precourse knowledge of evolution, among students at a medium-sized private northeastern university. Teachers who scant the teaching of evolution or who do not foster good attitudes toward evolution are compromising their students’ potential for success in science at the college level.
Evolution: Education and Outreach, 2014
Background: It is overwhelmingly acknowledged by the scientific community that evolution and glob... more Background: It is overwhelmingly acknowledged by the scientific community that evolution and global climate change (GCC) are undeniably supported by physical evidence. And yet, both topics remain politically contentious in the United States. It is thought that students' conceptions of the nature of science (NOS) may be key factors in their attitudes towards evolution and GCC. Our study explored this hypothesis guided by the following questions: Do changes in NOS conceptions correlate with changes in attitudes towards evolution or GCC? If there are correlations, are they similar for evolution and GCC? What demographic factors affect these correlations? Methods: Previously-developed tools were used to measure students' conceptions of the nature of science and attitudes towards evolution, while national public opinion poll questions were used to measure attitudes towards GCC. Demographic questions were produced to target factors thought to influence attitudes towards evolution or global climate change. Overall sample size was N = 620. Principle components analysis was used to determine which variables accounted for the most variation, and those variables were analyzed using correlation tests, ANOVA, and ANCOVA to test for significant correlations and interaction effects. Results: Changes in students' attitudes towards evolution and global climate change were both positively correlated with shifts in conceptions about the nature of science. Attitudes towards evolution were negatively correlated with religiosity. Knowledge of evolutionary science was positively correlated with attitudes towards evolution, but knowledge about GCC was not significantly correlated with attitudes towards GCC. The strongest correlates of GCC attitudes were political leanings. Conclusions: Findings support the hypothesis that a better understanding of NOS may lead to changes in attitudes towards politically contentious ideas that are not scientifically contentious. Though attitudes towards evolution correlated strongly and significantly with a number of other factors including knowledge of evolutionary science and religiosity, expected non-political correlates with attitudes towards GCC were absent. Giving students a good conception of the modern nature of science may lead to views that are closer to those of the scientific community. This study provides novel evidence of a linkage between student acceptance of evolution and attitudes towards GCC, that is, NOS conceptions.
Chapter 12 reviews late prehistoric maritime communities of coastal Ecuador to investigate change... more Chapter 12 reviews late prehistoric maritime communities of coastal Ecuador to investigate changes in adaptation at two sites in the Santa Elena area of southern Ecuador: Loma de los Cangrejitos and Mar Bravo. The authors find changes in the distribution of population, social organization, and the role of marine resources at around 700 cal A.D. They conclude that late communities of coastal Ecuador were successful, sophisticated exploiters of coastal resources who intensified both marine and terrestrial production over time and lived in well-organized, dense, kin-based settlements. Organization varied across space and there is no clear evidence for centralization. The paper also discusses the mollusk Spondylus, which is native to this region, and its possible roles in trade and the complexity.
This protocol details the reagents and steps required to perform antibody-guided chromatin tagmen... more This protocol details the reagents and steps required to perform antibody-guided chromatin tagmentation for two or more factors (ACT2-seq, ACT2). Like its predecessor ACT-seq, ACT2 uses a fusion of protein A and Tn5 transposase to bind and profile epigenetic marks across the genome. ACT2 builds on the capabilities of ACT-seq by directly and concurrently profiling co-occupancy of epigenetic marks, which previously required laborious, expensive, and technically challenging approaches involving fluorescence, magnetic beads, or single-cell methods. ACT2 requires only standard pipetting and centrifugation techniques and can be completed in less than a single day of bench work.
Modern next-generation sequencing-based methods have empowered researchers to assay the epigeneti... more Modern next-generation sequencing-based methods have empowered researchers to assay the epigenetic states of individual cells. Existing techniques for profiling epigenetic marks in single cells often require the use and optimization of time-intensive procedures such as drop fluidics, chromatin fragmentation, and end repair. Here we describe ACT-seq, a novel and streamlined method for mapping genome-wide distributions of histone tail modifications, histone variants, and chromatin-binding proteins in a small number of or single cells. ACT-seq utilizes a fusion of Tn5 transposase to Protein A that is targeted to chromatin by a specific antibody, allowing chromatin fragmentation and sequence tag insertion specifically at genomic sites presenting the relevant antigen. The Tn5 transposase enables the use of an index multiplexing strategy (iACT-seq), which enables construction of thousands of single-cell libraries in one day by a single researcher without the need for drop-based fluidics o...
Journal of Experimental Psychology: Human Perception and Performance, 2017
Eye movements are used to study a variety of cognitive phenomena, including attention, perception... more Eye movements are used to study a variety of cognitive phenomena, including attention, perception, memory, language, reading, decision making, and many others, as well as cognitive impairments and individual differences in cognition. These studies assume, with little evidence, that eye movements are stable across time and trials. Eye movement stability must be better characterized to understand the full theoretical and clinical implications of individual differences in eye movement behavior. The present study examined eye movement reliability in normal individuals during reading. Thirty-nine participants completed 2 sessions of a reading task separated by 1 month. Means and standard deviations of fixation duration, saccade amplitude, first fixation duration, gaze duration, total time, go-past time, skipping, refixation and regression probabilities were compared both between sessions and across trials within sessions. All correlations were highly significant, indicating that eye movement behaviors are stable within individuals across several weeks and highly stable across trials within each individual. The different components of the ex-Gaussian distribution of fixation durations were also highly stable over time. Differences in sensitivity to lexical variables (frequency, predictability, length) were also compared, and were also observed to be highly stable across time. Eye movements in reading are therefore suitable for studying cognition and its neural underpinnings, as well as cognitive development and longitudinal change. Theoretical and clinical implications of these findings are discussed. (PsycINFO Database Record
Macromolecular bioscience, Jan 24, 2017
The rapid pace of development in biotechnology has placed great importance on controlling cell-ma... more The rapid pace of development in biotechnology has placed great importance on controlling cell-material interactions. In practice, this involves attempting to decouple the contributions from adhesion molecules, cell membrane receptors, and scaffold surface chemistry and morphology, which is extremely challenging. Accordingly, a strategy is presented in which different chemical, biochemical, and morphological properties of 3D biomaterials are systematically varied to produce novel scaffolds with tuneable cell affinities. Specifically, cationized and surfactant-conjugated proteins, recently shown to have non-native membrane affinity, are covalently attached to 3D scaffolds of collagen or carboxymethyl-dextran, yielding surface-functionalized 3D architectures with predictable cell immobilization profiles. The artificial membrane-binding proteins enhance cellular adhesion of human mesenchymal stem cells (hMSCs) via electrostatic and hydrophobic binding mechanisms. Furthermore, functiona...
Molecular plant-microbe interactions : MPMI, 2017
Agrobacterium-mediated transformation is a core technology for basic plant science and agricultur... more Agrobacterium-mediated transformation is a core technology for basic plant science and agricultural biotechnology. Improving transformation frequency is a major goal for plant transgenesis. We previously showed that T-DNA insertions in some histone genes decreased transformation susceptibility, whereas overexpression of several Arabidopsis H2A and H4 isoforms increased transformation. Overexpression of several histone H2B and H3 isoforms had little effect on transformation frequency. However, overexpression of histone H3-11 (HTR11) enhanced transformation. HTR11 is a unique H3 variant that lacks lysine at positions 9 and 27. The modification status of these lysine residues in canonical H3 proteins plays a critical role in epigenetic determination of gene expression. We mutated histone H3-4 (HTR4), a canonical H3.3 protein that does not increase transformation when overexpressed, by replacing either or both K9 and K27 with the amino acids in HTR11 (either K9I, K27Q, or both). Overexp...
Advanced healthcare materials, Jan 29, 2016
3D tissue printing with adult stem cells is reported. A novel cell-containing multicomponent bioi... more 3D tissue printing with adult stem cells is reported. A novel cell-containing multicomponent bioink is used in a two-step 3D printing process to engineer bone and cartilage architectures.
Genetics, Jun 13, 2016
Angiosperm reproduction requires the integrated development of multiple tissues with different ge... more Angiosperm reproduction requires the integrated development of multiple tissues with different genotypes. To achieve successful fertilization, the haploid female gametophytes and diploid ovary must coordinate their development, after which the male gametes must navigate through the maternal sporophytic tissues to reach the female gametes. After fertilization, seed development requires coordinated development of the maternal diploid integuments, the triploid endosperm, and the diploid zygote. Transcription and signaling factors contribute to communication between these tissues, and roles for epigenetic regulation have been described for some of these processes. Here we identify a broad role for CHD3 chromatin remodelers inArabidopsis thalianareproductive development. Plants lacking the CHD3 remodelerPICKLEexhibit various reproductive defects including abnormal development of the integuments, female gametophyte, and pollen tube as well as delayed progression of ovule and embryo develo...
The American Biology Teacher, 2015
Students who enter college with a solid grounding in, and positive attitudes toward, evolutionary... more Students who enter college with a solid grounding in, and positive attitudes toward, evolutionary science are better prepared for and achieve at higher levels in university-level biology courses. We found highly significant, positive relationships between student knowledge of evolution and attitudes toward evolution, as well as between introductory biology course achievement and both precourse acceptance of evolution and precourse knowledge of evolution, among students at a medium-sized private northeastern university. Teachers who scant the teaching of evolution or who do not foster good attitudes toward evolution are compromising their students’ potential for success in science at the college level.
Evolution: Education and Outreach, 2014
Background: It is overwhelmingly acknowledged by the scientific community that evolution and glob... more Background: It is overwhelmingly acknowledged by the scientific community that evolution and global climate change (GCC) are undeniably supported by physical evidence. And yet, both topics remain politically contentious in the United States. It is thought that students' conceptions of the nature of science (NOS) may be key factors in their attitudes towards evolution and GCC. Our study explored this hypothesis guided by the following questions: Do changes in NOS conceptions correlate with changes in attitudes towards evolution or GCC? If there are correlations, are they similar for evolution and GCC? What demographic factors affect these correlations? Methods: Previously-developed tools were used to measure students' conceptions of the nature of science and attitudes towards evolution, while national public opinion poll questions were used to measure attitudes towards GCC. Demographic questions were produced to target factors thought to influence attitudes towards evolution or global climate change. Overall sample size was N = 620. Principle components analysis was used to determine which variables accounted for the most variation, and those variables were analyzed using correlation tests, ANOVA, and ANCOVA to test for significant correlations and interaction effects. Results: Changes in students' attitudes towards evolution and global climate change were both positively correlated with shifts in conceptions about the nature of science. Attitudes towards evolution were negatively correlated with religiosity. Knowledge of evolutionary science was positively correlated with attitudes towards evolution, but knowledge about GCC was not significantly correlated with attitudes towards GCC. The strongest correlates of GCC attitudes were political leanings. Conclusions: Findings support the hypothesis that a better understanding of NOS may lead to changes in attitudes towards politically contentious ideas that are not scientifically contentious. Though attitudes towards evolution correlated strongly and significantly with a number of other factors including knowledge of evolutionary science and religiosity, expected non-political correlates with attitudes towards GCC were absent. Giving students a good conception of the modern nature of science may lead to views that are closer to those of the scientific community. This study provides novel evidence of a linkage between student acceptance of evolution and attitudes towards GCC, that is, NOS conceptions.