Laterality in Termite-Fishing by Fongoli Chimpanzees: Preliminary Report

Many studies in both free-ranging and captive apes have shown that some forms of laterality of hand function occur in non-human primates1. However, true handedness (sensu McGrew and Marchant2), when most individuals show a skew in hand preference in the same direction across different tasks, seems to be restricted to humans. Other hominoids appear unlateralized in simpler tasks, such as reaching, picking up objects, and grooming3, but they show hand preference for more complex tasks, such as tool-using2, 4, 5 or elaborate food processing6, 7. Laterality in termite-fishing8 has been studied only at Gombe, and the two published data-sets are congruent. McGrew and Marchant2, 9 reported that most (27 of 36) chimpanzees showed an individualized hand preference for right or left, as did Lonsdorf and Hopkins10 (16 of 17) for termite-fishing in the same community. No other data have been published for chimpanzee communities elsewhere. This study asks if termite-fishing by Fongoli chimpanzees is lateralized, shows hand preference (individuals are lateralized, but with no populational preference for either hand), or task specialization (all or most individuals use the same hand)

Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression

It is tempting to believe that we now own the genome. The ability to read and rewrite it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles’ heel exposed by all of the genomic data that has accrued: We still do not know how to interpret them. Many genes are subject to sophisticated programs of transcriptional regulation, mediated by DNA sequences that harbor binding sites for transcription factors, which can up- or down-regulate gene expression depending upon environmental conditions. This gives rise to an input–output function describing how the level of expression depends upon the parameters of the regulated gene—for instance, on the number and type of binding sites in its regulatory sequence. In recent years, the ability to make precision measurements of expression, coupled with the ability to make increasingly sophisticated theoretical predictions, has enabled an explicit dialogue between theory and experiment that holds the promise of covering this genomic Achilles’ heel. The goal is to reach a predictive understanding of transcriptional regulation that makes it possible to calculate gene expression levels from DNA regulatory sequence. This review focuses on the canonical simple repression motif to ask how well the models that have been used to characterize it actually work. We consider a hierarchy of increasingly sophisticated experiments in which the minimal parameter set learned at one level is applied to make quantitative predictions at the next. We show that these careful quantitative dissections provide a template for a predictive understanding of the many more complex regulatory arrangements found across all domains of life

Controlled synthesis of SPION@SiO₂ nanoparticles using design of experiments

The synthesis of single-core superparamagnetic iron oxide nanoparticles (SPIONs) coated with a silica shell of controlled thickness remains a challenge, due to the dependence on a multitude of experimental variables. Herein, we utilise design of experiment (DoE) to study the formation of SPION@SiO2 nanoparticles (NPs) via reverse microemulsion. Using a 33 full factorial design, the influence of reactant concentration of tetraethyl orthosilicate (TEOS) and ammonium hydroxide (NH4OH), as well as the number of fractionated additions of TEOS on the silica shell was investigated with the aim of minimising polydispersity and increasing the population of SPION@SiO2 NPs formed. This investigation facilitated a reproducible and controlled approach for the high yield synthesis of SPION@SiO2 NPs with uniform silica shell thickness. Application of a multiple linear regression analysis established a relationship between the applied experimental variables and the resulting silica shell thickness. These experimental variables were similarly found to dictate the monodispersity of the SPION@SiO2 NPs formed. The overall population of single-core@shell particles was dependent on the interaction between the number of moles of TEOS and NH4OH, with no influence from the number of fractionated additions of TEOS. This work demonstrates the complexity of the preparative method and produces an accessible and flexible synthetic model to achieve monodisperse SPION@SiO2 NPs with controllable shell thickness

Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression

It is tempting to believe that we now own the genome. The ability to read and rewrite it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles’ heel exposed by all of the genomic data that has accrued: We still do not know how to interpret them. Many genes are subject to sophisticated programs of transcriptional regulation, mediated by DNA sequences that harbor binding sites for transcription factors, which can up- or down-regulate gene expression depending upon environmental conditions. This gives rise to an input–output function describing how the level of expression depends upon the parameters of the regulated gene—for instance, on the number and type of binding sites in its regulatory sequence. In recent years, the ability to make precision measurements of expression, coupled with the ability to make increasingly sophisticated theoretical predictions, has enabled an explicit dialogue between theory and experiment that holds the promise of covering this genomic Achilles’ heel. The goal is to reach a predictive understanding of transcriptional regulation that makes it possible to calculate gene expression levels from DNA regulatory sequence. This review focuses on the canonical simple repression motif to ask how well the models that have been used to characterize it actually work. We consider a hierarchy of increasingly sophisticated experiments in which the minimal parameter set learned at one level is applied to make quantitative predictions at the next. We show that these careful quantitative dissections provide a template for a predictive understanding of the many more complex regulatory arrangements found across all domains of life

Cell Behaviors during Closure of the Choroid Fissure in the Developing Eye

Coloboma is a defect in the morphogenesis of the eye that is a consequence of failure of choroid fissure fusion. It is among the most common congenital defects in humans and can significantly impact vision. However, very little is known about the cellular mechanisms that regulate choroid fissure closure. Using high-resolution confocal imaging of the zebrafish optic cup, we find that apico-basal polarity is re-modeled in cells lining the fissure in proximal to distal and inner to outer gradients during fusion. This process is accompanied by cell proliferation, displacement of vasculature, and contact between cells lining the choroid fissure and periocular mesenchyme (POM). To investigate the role of POM cells in closure of the fissure, we transplanted optic vesicles onto the yolk, allowing them to develop in a situation where they are depleted of POM. The choroid fissure forms normally in ectopic eyes but fusion fails in this condition, despite timely apposition of the nasal and temporal lips of the retina. This study resolves some of the cell behaviors underlying choroid fissure fusion and supports a role for POM in choroid fissure fusion

Laterality in Termite-Fishing by Fongoli Chimpanzees: Preliminary Report

Many studies in both free-ranging and captive apes have shown that some forms of laterality of hand function occur in non-human primates1. However, true handedness (sensu McGrew and Marchant2), when most individuals show a skew in hand preference in the same direction across different tasks, seems to be restricted to humans. Other hominoids appear unlateralized in simpler tasks, such as reaching, picking up objects, and grooming3, but they show hand preference for more complex tasks, such as tool-using2, 4, 5 or elaborate food processing6, 7. Laterality in termite-fishing8 has been studied only at Gombe, and the two published data-sets are congruent. McGrew and Marchant2, 9 reported that most (27 of 36) chimpanzees showed an individualized hand preference for right or left, as did Lonsdorf and Hopkins10 (16 of 17) for termite-fishing in the same community. No other data have been published for chimpanzee communities elsewhere. This study asks if termite-fishing by Fongoli chimpanzees is lateralized, shows hand preference (individuals are lateralized, but with no populational preference for either hand), or task specialization (all or most individuals use the same hand).This is an article from PAN Africa News 14 (2007): 1. Posted with permission.</p

Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression.

It is tempting to believe that we now own the genome. The ability to read and rewrite it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles heel exposed by all of the genomic data that has accrued: We still do not know how to interpret them. Many genes are subject to sophisticated programs of transcriptional regulation, mediated by DNA sequences that harbor binding sites for transcription factors, which can up- or down-regulate gene expression depending upon environmental conditions. This gives rise to an input-output function describing how the level of expression depends upon the parameters of the regulated gene-for instance, on the number and type of binding sites in its regulatory sequence. In recent years, the ability to make precision measurements of expression, coupled with the ability to make increasingly sophisticated theoretical predictions, has enabled an explicit dialogue between theory and experiment that holds the promise of covering this genomic Achilles heel. The goal is to reach a predictive understanding of transcriptional regulation that makes it possible to calculate gene expression levels from DNA regulatory sequence. This review focuses on the canonical simple repression motif to ask how well the models that have been used to characterize it actually work. We consider a hierarchy of increasingly sophisticated experiments in which the minimal parameter set learned at one level is applied to make quantitative predictions at the next. We show that these careful quantitative dissections provide a template for a predictive understanding of the many more complex regulatory arrangements found across all domains of life

SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences.

DNA-binding proteins control many fundamental biological processes such as transcription, recombination and replication. A major goal is to decipher the role that DNA sequence plays in orchestrating the binding and activity of such regulatory proteins. To address this goal, it is useful to rationally design DNA sequences with desired numbers, affinities and arrangements of protein binding sites. However, removing binding sites from DNA is computationally non-trivial since one risks creating new sites in the process of deleting or moving others. Here we present an online binding site removal tool, SiteOut, that enables users to design arbitrary DNA sequences that entirely lack binding sites for factors of interest. SiteOut can also be used to delete sites from a specific sequence, or to introduce site-free spacers between functional sequences without creating new sites at the junctions. In combination with commercial DNA synthesis services, SiteOut provides a powerful and flexible platform for synthetic projects that interrogate regulatory DNA. Here we describe the algorithm and illustrate the ways in which SiteOut can be used; it is publicly available at https://depace.med.harvard.edu/siteout/

SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences

DNA-binding proteins control many fundamental biological processes such as transcription, recombination and replication. A major goal is to decipher the role that DNA sequence plays in orchestrating the binding and activity of such regulatory proteins. To address this goal, it is useful to rationally design DNA sequences with desired numbers, affinities and arrangements of protein binding sites. However, removing binding sites from DNA is computationally non-trivial since one risks creating new sites in the process of deleting or moving others. Here we present an online binding site removal tool, SiteOut, that enables users to design arbitrary DNA sequences that entirely lack binding sites for factors of interest. SiteOut can also be used to delete sites from a specific sequence, or to introduce site-free spacers between functional sequences without creating new sites at the junctions. In combination with commercial DNA synthesis services, SiteOut provides a powerful and flexible platform for synthetic projects that interrogate regulatory DNA. Here we describe the algorithm and illustrate the ways in which SiteOut can be used; it is publicly available at https://depace.med.harvard.edu/siteout/