Size has a profound effect on the structure of brain. Many brain structures scale allometrically, that is, their relative size changes systematically as function size. Here we use independent contrasts analysis to examine scaling frontal cortex in 43 species mammals including 25 primates and 15 carnivores. We find evidence for significant differences between Primate hyperscales rest neocortex The slope is 1.18 (95% confidence interval, 1.06-1.30) primates, which significantly greater than...

A major goal in the study of human evolution is to identify key genetic changes which occurred over course primate evolution. According one school thought, many such are likely be found noncoding sequence. An approach identifying these involves comparing multiple genomes conserved regions with an accelerated substitution rate a particular lineage. Such acceleration could result positive selection.Here we develop likelihood ratio test method regions. We apply it not only terminal lineage, as...

The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli level functional differs depending on the stress. effect these differing concentrations global transcriptional remains unclear. We investigated concentration transcriptome during stationary phase rich media. found that 23% genes E. genome are regulated by RpoS, and we identified RpoS-transcribed promoters. observed three distinct classes response to regulon: whose expression changes linearly...

In honey bees (Apis mellifera), the epigenetic mark of DNA methylation is central to developmental regulation caste differentiation, but may also be involved in additional biological functions. this study, we examine whole genome profiles three stages haploid bee genome: unfertilised eggs, adult drones that develop from these eggs and sperm produced by drones. These methylomes reveal distinct patterns methylation. Eggs show 381 genes with significantly different CpG patterns, vast majority...

Abstract The epigenetic mark of DNA methylation, the addition a methyl (CH3) group to cytosine residue, has been extensively studied in many mammalian genomes and, although it is commonly found at promoter regions genes, also involved number different biological functions. In other complex animals, such as social insects, methylation determined be caste differentiation and occur primarily gene bodies. role nonsocial however, not yet explored thoroughly. Here, we present whole-genome profile...

1. Linezolid (ZYVOX), the first of a new class antibiotics, oxazolidinones, is approved for treatment Gram-positive bacterial infections. 2. The aim was to determine absorption, distribution, metabolism and excretion (ADME) linezolid in mouse, rat dog support preclinical safety studies clinical development. 3. Conventional replicate study designs were employed animal experiments, biofluids assayed by HPLC or HPLC-MS. 4. rapidly absorbed after p.o. dosing with an bioavailability > 95% dog,...

It is known that the white matter of neocortex increases disproportionately with brain size. However, relatively few measurements have been made matter/gray scaling in cerebellum. We present data on volumes and gray both structures, taken from 45 species mammals. find a exponent 1.13 for cerebellum 1.28 neocortex. The 95% confidence intervals our estimates these two exponents do not overlap. This difference likely reflects differences connectivity and/or micro-structure regions.

Abstract Background Models of sequence evolution typically assume that different nucleotide positions evolve independently. This assumption is widely appreciated to be an over-simplification. The best known violations involve biases due adjacent nucleotides. There have also been suggestions exist at larger scales, however this possibility has not systematically explored. Results To address we developed a method which identifies over- and under-represented substitution patterns assesses their...

We believe that undergraduate biology students must acquire a foundational background in computing including how to formulate computational problem; develop an algorithmic solution; implement their solution software and then test, document use code explore biological phenomena. Moreover, by learning these skills the first year, powerful tool set they can build on throughout studies.

Abstract Extant anthropoids have large brains, small olfactory bulbs, and high‐acuity vision compared with other primates. The relative timing of the evolution these characteristics may important implications for brain evolution. Here computed tomography is used to examine cranium a fossil anthropoid, Parapithecus grangeri . It found that P. had relatively living In addition, it an bulb in middle range Methods relating optic foramen area cranial measurements acuity are discussed. Multiple...

We present the curriculum, deployment, and initial evaluation of a course, BioCS1, designed to serve as CS1 Biology1 for majors either (or both) disciplines. Cotaught by professors in both fields, BioCS1 interweaves fundamental biology computational topics manner similar contextual approaches CS1. In contrast other approaches, however, emphasizes CS its context equally. The results suggest that cross-disciplinary collaborations can succeed at introductory level, they have later stages curriculum.

We present the curriculum, deployment, and initial evaluation of a course, BioCS1, designed to serve as an introductory course in both biology CS. Co-taught by professors fields, BioCS1 interweaves fundamental computational topics manner similar contextual approaches CS1. In contrast other approaches, however, emphasizes CS its context equally. The results suggest that such cross-disciplinary collaborations can thrive at level, just they have later curriculum.

An important challenge for human evolutionary biology is to understand the genetic basis of human-chimpanzee differences. One influential idea holds that such differences depend, a large extent, on adaptive changes in gene expression. step assessing this hypothesis involves gaining better understanding selective constraint noncoding regions hominid genomes. In sequence, functional elements are frequently small and can be separated by nonfunctional regions. For reason, genomes likely patchy....

A significant proportion of enzymes display cooperativity in binding ligand molecules, and such effects have an important impact on metabolic regulation. This is easiest to understand the case positive cooperativity. Sharp responses changes metabolite concentrations can allow organisms better respond environmental maintain homeostasis. However, despite fact that negative almost as common positive, it has been harder imagine what advantages provides. Here we use computational models explore...

Abstract In this study, three‐dimensional reconstructions of primate primary visual cortex (V1) were used to address questions about its evolution. The shape V1 in anthropoids is significantly longer and narrower than strepsirrhines. This difference an effect clade not due differences activity pattern or size. New measurements volume also provided order reassess size between strepsirrhines anthropoids. It was found that for a given lateral geniculate nucleus (LGN) volume, have larger do....

For a decade, our institution has offered both biology-based CS1 (CS1-B) and traditional, breadth-based CS1. This project follows the paths of students in courses -- tracking their subsequent interests (what do two groups choose afterwards') grades those courses. Within cohort, we also contrast futures who chose biology-themed introduction with group expressed no preference or requested approach. Even when student was not accommodated, equitable downstream performance results hold. We...

Genomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt new ecological conditions. A variety of computational methods, both genome-composition based and comparative, have been developed identify them. Some these methods are explicitly designed work single strains, while others make use multiple strains. In general, existing do not the context phylogeny which they evolved. Even strain approaches best suited identifying genomic that...

Abstract The nucleotide sequences of 16S ribosomal RNA (rRNA) genes have been used to inform the taxonomic placement prokaryotes for several decades. Whole-genome approaches can better resolve evolutionary relationships organisms, but these analyses often require computational proficiencies that are uncommon among microbiologists. PHANTASM is a new tool capable automating workflows. This was designed work wide range and first example an automated reconciliation NCBI’s Taxonomy database with...

We recently described two opposing states of transcriptional competency. One is termed 'competent' whereby a gene capable responding to trans-acting transcription factors the cell, such that it active if appropriate activators are present, though can also be silent absent or repressors present. The other 'occluded' silenced by cis-acting, chromatin-based mechanisms in manner blocks from factors, even when present cellular milieu. proposed occlusion mechanism which differentiated cells stably...

The field of molecular evolution provides many examples the principle that differences between species contain information about evolutionary history. One surprising case can be found in frequency short words DNA: more closely related have similar word compositions. Interest this has often focused on its utility deducing phylogenetic relationships. However, it is also interest because opportunity for studying genome function. Word-frequency change too slowly to purely result random...