Alicia Santiago - Academia.edu (original) (raw)

Papers by Alicia Santiago

Women and girls, particularly women and girls of color, remain underrepresented in STEM disciplin... more Women and girls, particularly women and girls of color, remain underrepresented in STEM disciplines. This underrepresentation begins as early as late elementary school age. Educators, particularly those in informal STEM education, can help address gender inequity in STEM by understanding how research can be translated into actionable strategies. This article summarizes research on gender equitable practices for middle school girls in the last decade and addresses the disconnect between research and practice by presenting the findings in a way that educators can immediately act on. The research falls into six strategies that have demonstrated positive influences on gender inequity in STEM education: (1) connecting STEM experiences to girls’ lives; (2) supporting girls as they investigate questions and solve problems using STEM practices; (3) empowering girls to embrace struggle, overcome challenges, and increase self-confidence in STEM; (4) encouraging girls to identify and challenge...

The American journal of bioethics : AJOB, 2021

Little is known about the mechanisms that direct neural crest cells to the appropriate migratory ... more Little is known about the mechanisms that direct neural crest cells to the appropriate migratory pathways. Our aim was to determine how neural crest cells that are specified as neurons and glial cells only migrate ventrally and are prevented from migrating dorsolaterally into the skin, whereas neural crest cells specified as melanoblasts are directed into the dorsolateral pathway. Eph receptors and their ephrin ligands have been shown to be essential for migration of many cell types during embryonic development. Consequently, we asked if ephrin-B proteins participate in the guidance of melanoblasts along the dorsolateral pathway, and prevent early migratory neural crest cells from invading the dorsolateral pathway. Using Fc fusion proteins, we detected the expression of ephrin-B ligands in the dorsolateral pathway at the stage when neural crest cells are migrating ventrally. Furthermore, we show that ephrins block dorsolateral migration of early-migrating neural crest cells because ...

Reverse signaling by ephrin-As upon binding EphAs controls axon guidance and mapping. Ephrin-As a... more Reverse signaling by ephrin-As upon binding EphAs controls axon guidance and mapping. Ephrin-As are GPI-anchored to the membrane, requiring that they complex with transmembrane proteins that trans-duce their signals. We show that the p75 neurotro-phin receptor (NTR) serves this role in retinal axons. p75NTR and ephrin-A colocalize within caveolae along retinal axons and form a complex required for Fyn phosphorylation upon binding EphAs, activating a signaling pathway leading to cytoskeletal changes. In vitro, retinal axon repulsion to EphAs by ephrin-A reverse signaling requires p75NTR, but repulsion to ephrin-As by EphA forward signaling does not. Constitutive and retina-specific p75NTR knockout mice have aberrant anterior shifts in retinal axon terminations in superior colliculus, consistent with diminished repellent activity mediated by graded ephrin-A reverse signaling induced by graded collic-ular EphAs. We conclude that p75NTR is a signaling partner for ephrin-As and the ephri...

The American Journal of Bioethics

The COVID-19 pandemic has taken a substantial human, social and economic toll globally, but its i... more The COVID-19 pandemic has taken a substantial human, social and economic toll globally, but its impact on Black/African Americans, Latinx, and American Indian/Alaska Native communities in the U.S. is unconscionable. As the U.S. continues to combat the current COVID-19 cycle and prepares for future pandemics, it will be critical to learn from and rectify past and contemporary wrongs. Drawing on experiences in genomic research and intersecting areas in medical ethics, health disparities, and human rights, this article considers three key COVID-19-related issues: research to identify remedies; testing, contact tracing and surveillance; and lingering health needs and disability. It provides a pathway for the future: community engagement to develop culturally-sensitive responses to the myriad genomic/ bioethical dilemmas that arise, and the establishment of a Truth and Reconciliation Commission to transition the country from its contemporary state of segregation in healthcare and health outcomes into an equitable and prosperous society for all.

A mutation directing an amino acid substitution in the conserved b-hinge region of one of the hum... more A mutation directing an amino acid substitution in the conserved b-hinge region of one of the human Cks isoforms, CksHs2, was constructed by Biology, MB-7, The Scripps site-directed mutagenesis. Replacement of glutamine for glutamate 63 Research Institute, 10550 North Torrey Pines Road (E63Q) was predicted to stabilize the b-interchanged dimeric and hexameric assembly of CksHs2. However, such an effect was seen only at high, La Jolla, CA 92037, USA non-physiological pH. Three-dimensional structures of the E63Q hexameric mutant protein were determined to 2.6 Å resolution in a P4 3 2 1 2 space group and 2.1 Å in the C 2 space group isostructural with wild-type, and both were shown to be virtually identical to the refined 1.7 Å wild-type structure. Thus, the E63Q mutation did not alter the wild-type structure and assembly of CksHs2 but, surprisingly, disrupted the essential biological function of the protein and significantly reduced its ability to bind to cyclin-dependent kinases. The K d of wild-type CksHs2 for CDK2 was 5.05 × 10 −8 M, whereas the affinity of the mutant protein for CDK2 was too low to allow a determination. These data, coupled with the observation that monomeric but not hexameric CksHs2 interacts with cyclin-dependent kinases, suggest that glutamine 63 is likely to be directly involved in cyclin-dependent kinase binding in vitro and in vivo.

Development, Aug 1, 2002

Fertile Japanese quail eggs (Coturnix japonica) from the Animal Sciences Department (University o... more Fertile Japanese quail eggs (Coturnix japonica) from the Animal Sciences Department (University of California, Davis) were incubated in a humidified 37°C incubator until they reached stage 13. Neural tubes at somite level I to VIII (between the last-formed somite to the eight from the last-formed somite) were dissected from embryos and separated from surrounding tissues, including ectoderm, somite and notochord, after a brief digestion in Pancreatin (Gibco). Cleaned

Development (Cambridge, England), 2002

Little is known about the mechanisms that direct neural crest cells to the appropriate migratory ... more Little is known about the mechanisms that direct neural crest cells to the appropriate migratory pathways. Our aim was to determine how neural crest cells that are specified as neurons and glial cells only migrate ventrally and are prevented from migrating dorsolaterally into the skin, whereas neural crest cells specified as melanoblasts are directed into the dorsolateral pathway. Eph receptors and their ephrin ligands have been shown to be essential for migration of many cell types during embryonic development. Consequently, we asked if ephrin-B proteins participate in the guidance of melanoblasts along the dorsolateral pathway, and prevent early migratory neural crest cells from invading the dorsolateral pathway. Using Fc fusion proteins, we detected the expression of ephrin-B ligands in the dorsolateral pathway at the stage when neural crest cells are migrating ventrally. Furthermore, we show that ephrins block dorsolateral migration of early-migrating neural crest cells because ...

Chemical Communications, 2013

The synthesis and mechanistic study of the unprecedented reactivity of a series of zwitterionic g... more The synthesis and mechanistic study of the unprecedented reactivity of a series of zwitterionic g 1 -metal allenyls are reported.

Molecular and Cellular Neuroscience, 2014

The projection from the retina to the superior colliculus in mice is organized in a retinotopic m... more The projection from the retina to the superior colliculus in mice is organized in a retinotopic map that develops through the formation and guidance of interstitial branches extended by retinal ganglion cell axons. Bidirectional branch guidance along the lateral-medial collicular axis is critical to mapping the dorsal-ventral retinal axis. EphB receptor tyrosine kinases expressed in an overall low to high dorsal-ventral retinal gradient have been implicated in this mapping in response to the graded low to high lateral-medial expression of a ligand, ephrin-B1, in the superior colliculus. However, the relative contributions of EphBs and ephrin-B1 are not well understood. We examined EphB1, EphB2, and EphB3 mutant mice and find that each has ectopic arborizations of retinal axon branches lateral to their appropriate termination zone, with no qualitative differences in aberrant mapping, suggesting a similar role for each EphB. However, the frequency of cases with map defects progressively rises in compound EphB mutants coincident with the number of EphB null alleles from one to five of the six total alleles indicating that EphB level is critical. We analyzed branch extension in vitro and find that dorsal branches, with low EphB levels, exhibit a negative response to ephrin-B1, whereas ventral branches, with high EphB levels, exhibit a positive response to ephrin-B1. Using EphB mutant retina, we show that both of these differential branch extension responses are dependent on EphB level. Our findings show a bifunctional action of ephrin-B1 regulated by EphB levels that can account for the bidirectional extension of interstitial branches required to establish a retinotopic map.

Neuron, 2008

Reverse signaling by ephrin-As upon binding EphAs controls axon guidance and mapping. Ephrin-As a... more Reverse signaling by ephrin-As upon binding EphAs controls axon guidance and mapping. Ephrin-As are GPI-anchored to the membrane, requiring that they complex with transmembrane proteins that transduce their signals. We show that the p75 neurotrophin receptor (NTR) serves this role in retinal axons. p75 NTR and ephrin-A colocalize within caveolae along retinal axons and form a complex required for Fyn phosphorylation upon binding EphAs, activating a signaling pathway leading to cytoskeletal changes. In vitro, retinal axon repulsion to EphAs by ephrin-A reverse signaling requires p75 NTR , but repulsion to ephrin-As by EphA forward signaling does not. Constitutive and retina-specific p75 NTR knockout mice have aberrant anterior shifts in retinal axon terminations in superior colliculus, consistent with diminished repellent activity mediated by graded ephrin-A reverse signaling induced by graded collicular EphAs. We conclude that p75 NTR is a signaling partner for ephrin-As and the ephrin-A-p75 NTR complex reverse signals to mediate axon repulsion required for guidance and mapping.

Journal of Neuroscience Research, 2001

Several molecules have been identified as potential sources of the barriers to glial cell mixing ... more Several molecules have been identified as potential sources of the barriers to glial cell mixing and sensory regeneration that exist at the boundary between the peripheral and central nervous systems, including tenascin-C, tenascin-R, chondroitin sulfate proteoglycans, and NG2. Here we show that tenascin-Y, the avian homologue of tenascin-X, is concentrated in the proximal portions of peripheral nerves in the chicken. In vitro analyses of cultures enriched for Schwann cells demonstrate that recombinant tenascin-Y has dose-dependent effects on glial cell attachment, spreading, and migration. In addition, nanomolar concentrations of tenascin-Y cause the rapid collapse of sensory growth cones cultured on fibronectin, and regenerating sensory neurites preferentially migrate on fibronectin and avoid tenascin-Y in microstripe assays. We conclude that the expression pattern of tenascin-Y and its properties in vitro are consistent with a role as an inhibitor of glial cell migration and sensory regeneration in nerve roots. J. Neurosci. Res. 66:439–447, 2001. © 2001 Wiley-Liss, Inc.

Journal of Molecular Biology, 1996

A mutation directing an amino acid substitution in the conserved b-hinge region of one of the hum... more A mutation directing an amino acid substitution in the conserved b-hinge region of one of the human Cks isoforms, CksHs2, was constructed by Biology, MB-7, The Scripps site-directed mutagenesis. Replacement of glutamine for glutamate 63 Research Institute, 10550 North Torrey Pines Road (E63Q) was predicted to stabilize the b-interchanged dimeric and hexameric assembly of CksHs2. However, such an effect was seen only at high, La Jolla, CA 92037, USA non-physiological pH. Three-dimensional structures of the E63Q hexameric mutant protein were determined to 2.6 Å resolution in a P4 3 2 1 2 space group and 2.1 Å in the C 2 space group isostructural with wild-type, and both were shown to be virtually identical to the refined 1.7 Å wild-type structure. Thus, the E63Q mutation did not alter the wild-type structure and assembly of CksHs2 but, surprisingly, disrupted the essential biological function of the protein and significantly reduced its ability to bind to cyclin-dependent kinases. The K d of wild-type CksHs2 for CDK2 was 5.05 × 10 −8 M, whereas the affinity of the mutant protein for CDK2 was too low to allow a determination. These data, coupled with the observation that monomeric but not hexameric CksHs2 interacts with cyclin-dependent kinases, suggest that glutamine 63 is likely to be directly involved in cyclin-dependent kinase binding in vitro and in vivo.

Human Mutation, 2005

The identification of common genetic variants such as single nucleotide polymorphisms (SNPs) in t... more The identification of common genetic variants such as single nucleotide polymorphisms (SNPs) in the human genome has become central in human population genetics and evolution studies, as well as in the study of the genetic basis of complex traits and diseases. Crucial for the accurate identification of genetic variants is the availability of high quality genomic DNA (gDNA). Since popular sources of gDNA (buccal cells, lymphocytes, hair bulb) often do not yield sufficient quantities of DNA for molecular genetic applications, whole genome amplification methods have recently been introduced to generate a renewable source of double-stranded linear DNA. Here, we assess the fidelity of one method, multiple displacement amplification (MDA), which utilizes bacteriophage Φ29 DNA polymerase to generate amplified DNA from an original source of gDNA, in a representative SNP discovery and genetic association study at the melanocortin 1 receptor (MC1R) locus, a highly polymorphic gene in humans involved in skin and hair pigmentation. We observed that MDA has high fidelity for novel SNP discovery and can be a valuable tool in generating a potentially indefinite source of DNA. However, we observed an allele amplification bias that causes genotype miscalls at heterozygous sites. At loci with multiple polymorphic sites in linkage disequilibrium, such as at MC1R, this bias can create a significant number of heterozygote genotype errors that subsequently misrepresents haplotypes. Hum Mutat 26(2), 1–8, 2005. © 2005 Wiley-Liss, Inc.

Women and girls, particularly women and girls of color, remain underrepresented in STEM disciplin... more Women and girls, particularly women and girls of color, remain underrepresented in STEM disciplines. This underrepresentation begins as early as late elementary school age. Educators, particularly those in informal STEM education, can help address gender inequity in STEM by understanding how research can be translated into actionable strategies. This article summarizes research on gender equitable practices for middle school girls in the last decade and addresses the disconnect between research and practice by presenting the findings in a way that educators can immediately act on. The research falls into six strategies that have demonstrated positive influences on gender inequity in STEM education: (1) connecting STEM experiences to girls’ lives; (2) supporting girls as they investigate questions and solve problems using STEM practices; (3) empowering girls to embrace struggle, overcome challenges, and increase self-confidence in STEM; (4) encouraging girls to identify and challenge...

The American journal of bioethics : AJOB, 2021

Little is known about the mechanisms that direct neural crest cells to the appropriate migratory ... more Little is known about the mechanisms that direct neural crest cells to the appropriate migratory pathways. Our aim was to determine how neural crest cells that are specified as neurons and glial cells only migrate ventrally and are prevented from migrating dorsolaterally into the skin, whereas neural crest cells specified as melanoblasts are directed into the dorsolateral pathway. Eph receptors and their ephrin ligands have been shown to be essential for migration of many cell types during embryonic development. Consequently, we asked if ephrin-B proteins participate in the guidance of melanoblasts along the dorsolateral pathway, and prevent early migratory neural crest cells from invading the dorsolateral pathway. Using Fc fusion proteins, we detected the expression of ephrin-B ligands in the dorsolateral pathway at the stage when neural crest cells are migrating ventrally. Furthermore, we show that ephrins block dorsolateral migration of early-migrating neural crest cells because ...

Reverse signaling by ephrin-As upon binding EphAs controls axon guidance and mapping. Ephrin-As a... more Reverse signaling by ephrin-As upon binding EphAs controls axon guidance and mapping. Ephrin-As are GPI-anchored to the membrane, requiring that they complex with transmembrane proteins that trans-duce their signals. We show that the p75 neurotro-phin receptor (NTR) serves this role in retinal axons. p75NTR and ephrin-A colocalize within caveolae along retinal axons and form a complex required for Fyn phosphorylation upon binding EphAs, activating a signaling pathway leading to cytoskeletal changes. In vitro, retinal axon repulsion to EphAs by ephrin-A reverse signaling requires p75NTR, but repulsion to ephrin-As by EphA forward signaling does not. Constitutive and retina-specific p75NTR knockout mice have aberrant anterior shifts in retinal axon terminations in superior colliculus, consistent with diminished repellent activity mediated by graded ephrin-A reverse signaling induced by graded collic-ular EphAs. We conclude that p75NTR is a signaling partner for ephrin-As and the ephri...

The American Journal of Bioethics

The COVID-19 pandemic has taken a substantial human, social and economic toll globally, but its i... more The COVID-19 pandemic has taken a substantial human, social and economic toll globally, but its impact on Black/African Americans, Latinx, and American Indian/Alaska Native communities in the U.S. is unconscionable. As the U.S. continues to combat the current COVID-19 cycle and prepares for future pandemics, it will be critical to learn from and rectify past and contemporary wrongs. Drawing on experiences in genomic research and intersecting areas in medical ethics, health disparities, and human rights, this article considers three key COVID-19-related issues: research to identify remedies; testing, contact tracing and surveillance; and lingering health needs and disability. It provides a pathway for the future: community engagement to develop culturally-sensitive responses to the myriad genomic/ bioethical dilemmas that arise, and the establishment of a Truth and Reconciliation Commission to transition the country from its contemporary state of segregation in healthcare and health outcomes into an equitable and prosperous society for all.

A mutation directing an amino acid substitution in the conserved b-hinge region of one of the hum... more A mutation directing an amino acid substitution in the conserved b-hinge region of one of the human Cks isoforms, CksHs2, was constructed by Biology, MB-7, The Scripps site-directed mutagenesis. Replacement of glutamine for glutamate 63 Research Institute, 10550 North Torrey Pines Road (E63Q) was predicted to stabilize the b-interchanged dimeric and hexameric assembly of CksHs2. However, such an effect was seen only at high, La Jolla, CA 92037, USA non-physiological pH. Three-dimensional structures of the E63Q hexameric mutant protein were determined to 2.6 Å resolution in a P4 3 2 1 2 space group and 2.1 Å in the C 2 space group isostructural with wild-type, and both were shown to be virtually identical to the refined 1.7 Å wild-type structure. Thus, the E63Q mutation did not alter the wild-type structure and assembly of CksHs2 but, surprisingly, disrupted the essential biological function of the protein and significantly reduced its ability to bind to cyclin-dependent kinases. The K d of wild-type CksHs2 for CDK2 was 5.05 × 10 −8 M, whereas the affinity of the mutant protein for CDK2 was too low to allow a determination. These data, coupled with the observation that monomeric but not hexameric CksHs2 interacts with cyclin-dependent kinases, suggest that glutamine 63 is likely to be directly involved in cyclin-dependent kinase binding in vitro and in vivo.

Development, Aug 1, 2002

Fertile Japanese quail eggs (Coturnix japonica) from the Animal Sciences Department (University o... more Fertile Japanese quail eggs (Coturnix japonica) from the Animal Sciences Department (University of California, Davis) were incubated in a humidified 37°C incubator until they reached stage 13. Neural tubes at somite level I to VIII (between the last-formed somite to the eight from the last-formed somite) were dissected from embryos and separated from surrounding tissues, including ectoderm, somite and notochord, after a brief digestion in Pancreatin (Gibco). Cleaned

Development (Cambridge, England), 2002

Little is known about the mechanisms that direct neural crest cells to the appropriate migratory ... more Little is known about the mechanisms that direct neural crest cells to the appropriate migratory pathways. Our aim was to determine how neural crest cells that are specified as neurons and glial cells only migrate ventrally and are prevented from migrating dorsolaterally into the skin, whereas neural crest cells specified as melanoblasts are directed into the dorsolateral pathway. Eph receptors and their ephrin ligands have been shown to be essential for migration of many cell types during embryonic development. Consequently, we asked if ephrin-B proteins participate in the guidance of melanoblasts along the dorsolateral pathway, and prevent early migratory neural crest cells from invading the dorsolateral pathway. Using Fc fusion proteins, we detected the expression of ephrin-B ligands in the dorsolateral pathway at the stage when neural crest cells are migrating ventrally. Furthermore, we show that ephrins block dorsolateral migration of early-migrating neural crest cells because ...

Chemical Communications, 2013

The synthesis and mechanistic study of the unprecedented reactivity of a series of zwitterionic g... more The synthesis and mechanistic study of the unprecedented reactivity of a series of zwitterionic g 1 -metal allenyls are reported.

Molecular and Cellular Neuroscience, 2014

The projection from the retina to the superior colliculus in mice is organized in a retinotopic m... more The projection from the retina to the superior colliculus in mice is organized in a retinotopic map that develops through the formation and guidance of interstitial branches extended by retinal ganglion cell axons. Bidirectional branch guidance along the lateral-medial collicular axis is critical to mapping the dorsal-ventral retinal axis. EphB receptor tyrosine kinases expressed in an overall low to high dorsal-ventral retinal gradient have been implicated in this mapping in response to the graded low to high lateral-medial expression of a ligand, ephrin-B1, in the superior colliculus. However, the relative contributions of EphBs and ephrin-B1 are not well understood. We examined EphB1, EphB2, and EphB3 mutant mice and find that each has ectopic arborizations of retinal axon branches lateral to their appropriate termination zone, with no qualitative differences in aberrant mapping, suggesting a similar role for each EphB. However, the frequency of cases with map defects progressively rises in compound EphB mutants coincident with the number of EphB null alleles from one to five of the six total alleles indicating that EphB level is critical. We analyzed branch extension in vitro and find that dorsal branches, with low EphB levels, exhibit a negative response to ephrin-B1, whereas ventral branches, with high EphB levels, exhibit a positive response to ephrin-B1. Using EphB mutant retina, we show that both of these differential branch extension responses are dependent on EphB level. Our findings show a bifunctional action of ephrin-B1 regulated by EphB levels that can account for the bidirectional extension of interstitial branches required to establish a retinotopic map.

Neuron, 2008

Reverse signaling by ephrin-As upon binding EphAs controls axon guidance and mapping. Ephrin-As a... more Reverse signaling by ephrin-As upon binding EphAs controls axon guidance and mapping. Ephrin-As are GPI-anchored to the membrane, requiring that they complex with transmembrane proteins that transduce their signals. We show that the p75 neurotrophin receptor (NTR) serves this role in retinal axons. p75 NTR and ephrin-A colocalize within caveolae along retinal axons and form a complex required for Fyn phosphorylation upon binding EphAs, activating a signaling pathway leading to cytoskeletal changes. In vitro, retinal axon repulsion to EphAs by ephrin-A reverse signaling requires p75 NTR , but repulsion to ephrin-As by EphA forward signaling does not. Constitutive and retina-specific p75 NTR knockout mice have aberrant anterior shifts in retinal axon terminations in superior colliculus, consistent with diminished repellent activity mediated by graded ephrin-A reverse signaling induced by graded collicular EphAs. We conclude that p75 NTR is a signaling partner for ephrin-As and the ephrin-A-p75 NTR complex reverse signals to mediate axon repulsion required for guidance and mapping.

Journal of Neuroscience Research, 2001

Several molecules have been identified as potential sources of the barriers to glial cell mixing ... more Several molecules have been identified as potential sources of the barriers to glial cell mixing and sensory regeneration that exist at the boundary between the peripheral and central nervous systems, including tenascin-C, tenascin-R, chondroitin sulfate proteoglycans, and NG2. Here we show that tenascin-Y, the avian homologue of tenascin-X, is concentrated in the proximal portions of peripheral nerves in the chicken. In vitro analyses of cultures enriched for Schwann cells demonstrate that recombinant tenascin-Y has dose-dependent effects on glial cell attachment, spreading, and migration. In addition, nanomolar concentrations of tenascin-Y cause the rapid collapse of sensory growth cones cultured on fibronectin, and regenerating sensory neurites preferentially migrate on fibronectin and avoid tenascin-Y in microstripe assays. We conclude that the expression pattern of tenascin-Y and its properties in vitro are consistent with a role as an inhibitor of glial cell migration and sensory regeneration in nerve roots. J. Neurosci. Res. 66:439–447, 2001. © 2001 Wiley-Liss, Inc.

Journal of Molecular Biology, 1996

A mutation directing an amino acid substitution in the conserved b-hinge region of one of the hum... more A mutation directing an amino acid substitution in the conserved b-hinge region of one of the human Cks isoforms, CksHs2, was constructed by Biology, MB-7, The Scripps site-directed mutagenesis. Replacement of glutamine for glutamate 63 Research Institute, 10550 North Torrey Pines Road (E63Q) was predicted to stabilize the b-interchanged dimeric and hexameric assembly of CksHs2. However, such an effect was seen only at high, La Jolla, CA 92037, USA non-physiological pH. Three-dimensional structures of the E63Q hexameric mutant protein were determined to 2.6 Å resolution in a P4 3 2 1 2 space group and 2.1 Å in the C 2 space group isostructural with wild-type, and both were shown to be virtually identical to the refined 1.7 Å wild-type structure. Thus, the E63Q mutation did not alter the wild-type structure and assembly of CksHs2 but, surprisingly, disrupted the essential biological function of the protein and significantly reduced its ability to bind to cyclin-dependent kinases. The K d of wild-type CksHs2 for CDK2 was 5.05 × 10 −8 M, whereas the affinity of the mutant protein for CDK2 was too low to allow a determination. These data, coupled with the observation that monomeric but not hexameric CksHs2 interacts with cyclin-dependent kinases, suggest that glutamine 63 is likely to be directly involved in cyclin-dependent kinase binding in vitro and in vivo.

Human Mutation, 2005

The identification of common genetic variants such as single nucleotide polymorphisms (SNPs) in t... more The identification of common genetic variants such as single nucleotide polymorphisms (SNPs) in the human genome has become central in human population genetics and evolution studies, as well as in the study of the genetic basis of complex traits and diseases. Crucial for the accurate identification of genetic variants is the availability of high quality genomic DNA (gDNA). Since popular sources of gDNA (buccal cells, lymphocytes, hair bulb) often do not yield sufficient quantities of DNA for molecular genetic applications, whole genome amplification methods have recently been introduced to generate a renewable source of double-stranded linear DNA. Here, we assess the fidelity of one method, multiple displacement amplification (MDA), which utilizes bacteriophage Φ29 DNA polymerase to generate amplified DNA from an original source of gDNA, in a representative SNP discovery and genetic association study at the melanocortin 1 receptor (MC1R) locus, a highly polymorphic gene in humans involved in skin and hair pigmentation. We observed that MDA has high fidelity for novel SNP discovery and can be a valuable tool in generating a potentially indefinite source of DNA. However, we observed an allele amplification bias that causes genotype miscalls at heterozygous sites. At loci with multiple polymorphic sites in linkage disequilibrium, such as at MC1R, this bias can create a significant number of heterozygote genotype errors that subsequently misrepresents haplotypes. Hum Mutat 26(2), 1–8, 2005. © 2005 Wiley-Liss, Inc.