James Linzel's List: AP Biology

• an enzyme that breaks down sucrose into smaller sugars (glucose and fructose) that cells can import
• multicellular clumps of cells can grow when sucrose is scarce, whereas single cells cannot.
• clumps of cells have an advantage when competing against “cheating” cells that import sugars but do not make invertase
• we argue that the social benefits conferred by secreted enzymes were the driving force for the evolution of cell clumps that were the first, primitive form of multicellular life.

2 more annotations...

• there is a generally predictable pattern of coiling in the developing gut, and it's species-specific.
• the reproducible pattern of coiling is an emergent property of some general parameters of the tissues
• The gut begins embryonically as a simple, straight tube, fixed at both ends at the mouth and anus. Initially, the gut is the same length as the body, and is suspended from the back of the body cavity by a continuous sheet of tissue, the mesentery, that is also the same length as the gut. But then what happens is that the gut elongates, while the mesentery grows much more slowly. This difference in growth rates means that the gut is under compression along its length, restrained by the mesenteries, which causes it to periodically buckle.
• start disemboweling other species, and ask if their formulas work to describe their gut coiling
• The form is not laid out in tightly-coded, case-by-case specification in the genome, but by the genetic definition of only a few parameters, in this case the relative rates of growth of two adherent tissues and the compression they impose on an elongating tube, from which a lovely arrangement flowers elegantly.

3 more annotations...

• The genes for hormone receptors in humans and other vertebrates show clear signs of having evolved from common ancestor.
• MR and GR are the product of an ancient gene duplication. An ancestral gene for a hormone receptor was accidentally copied, and two version of the receptor began to be produced on ancient fish. Over time, each gene acquired mutations that altered how its receptor responded to hormones, and eventually the two versions evolved into MR and GR.
• Here’s where the lock and key metaphor can cause mischief. Receptors are not built out of metal. They’re loops and spirals of atoms that can flex. So a receptor that is adapted to respond to one hormone may have the capacity to respond to another one. Scientists call such molecules promiscuous. The promiscuity of proteins is a big area of research these days. It explains, for example, why bacteria can feed on pollutants that were nearly nonexistent a century ago. Some of their proteins evolved for other functions, but had the potential to be used to eat a new kind of food.
• Depending on which mutations are already there, a mutation may be harmful, neutral, or even beneficial.

2 more annotations...

• adaptive combinations of mutations can and do evolve by pathways involving neutral intermediates.
• If the initial mutations have no negative effect on the ancestral function, they can arise and hang around in populations for substantial periods of time due to genetic drift, creating the background in which an additional mutation can then yield the new function and be subject to selection.   This is precisely what we  observed in our studies of the evolution of the glucocorticoid receptor (GR).
• some of the mutations that trigger the change in function are deleterious if introduced in isolation, but others are “permissive”: they have no apparent effect on the function of the protein, but once they are in place the protein can tolerate the other mutations that shift and then optimize the new function.
• there were indeed pathways from the ancestral protein to the new function that passed only through permissive and beneficial intermediate states.
• A path to a new function that involves neutral intermediates is entirely accessible to the evolutionary processes of mutation, drift, and selection.
• The chance effects of genetic drift could allow the protein to “float” along such paths, producing the appropriate background in which the function-shifting mutations could be reversed.

4 more annotations...

• Hagfish are unusual creatures. For starters, they aren’t really vertebrates, let alone fish – they aren’t endowed with a vertebral column. They lack jaws. They have multiple hearts. They can absorb organic matter through their skins, not unlike several lower invertebrates. They bear two simple eye spots which can detect differences in light levels but cannot, as far as we know, construct detailed images.
• clade Craniata,
• We need a bundle of nerve cells (and their attendant supporting cells) to run along the back to carry electrochemical signals to and from each of these muscle blocks – this is the nerve cord
• Cartilage performs this task adequately. We have just constructed the Notochord – a rod of cartilaginous tissue that runs below the nerve cord.
• nerve cord, notochord, pharynx, gill slits- at some point in its life cycle (humans display these during embryonic development, many tunicates in the larval stage and lanclets in the adult stage) may be identified as a chordate
• Although a “front end” can certainly be identified in lancelets and tunicate larvae, there is no “head”, so to speak. The notochord extends right up to where we’d expect the head to be
• The anterior (or front) end of the nerve cord must be expanded into a complex brain which can wield centralized command over the nervous system. New sensory apparatus and cranial nerves must be built to detect oncoming sources of food or possible predators
• Furthermore, a cartilaginous brain case became neccessary to house and protect this new equipment. We have now constructed a “craniate” – a chordate with a highly specialized head. This group contains both true vertebrates and hagfishes.
• This transition was made possible by the duplication of clusters of “Hox genes” over evolutionary time by mutations (gene duplications are a widely observed and studied phenomenon). The end result of this was the creation of a special zone of tissue above the nerve cord in the embryo, the neural crest, from which cells migrate away during development to create various features important to the form and function of the brain
• To provide for further muscle attachment and protection of the nerve cord, a series of cartilagnous arches called neural arches running along the length of the back became neccessary at some point. A complementary series of inverted arches called centra was added to this design. A neural arch plus a centrum constitutes a vertebra – and the series of vertebra may be referred to as the vertebral column. In vertebrates, this segmented backbone replaces the notochord during embryonic development. Congratulations, we have now constructed a primitive vertebrate!
• The formation of bone involves the secretion of a matrix of long chain sugars and fibrous protein by certain cells (called Osteoblasts) and the consequent deposition and crystallization of calcium phosphate in this matrix, hardening it.
• Bone might have initially served as a storehouse for phosphate and calcium. Calcium plays a massive role in cell signalling and in maintaining osmotic pressure in the body. Phosphate plays a similarly major role in cell metabolism and the generation of energy. By maintaining a ready supply of these, marine jawless fish might have been able to venture into brackish or fresh waters with lower calcium or phosphate levels without experiencing any distress
• Bones can serve as a protective casing for delicate sensory apparatus or viscera. A rather picturesque suggestion from some workers in the field has it that bone evolved in early fishes in response to predation from giant sea-scorpions called Eurypterids in the Ordovician seas. Indeed, early fish are often described as “armored” – and with good reason.

11 more annotations...

• The reappraisal of animal evolution  rests on several congruent approaches ranging from primary gene  sequence analysis to qualitative molecular signatures within  appropriate genes.
• phenetics  vs. cladistics
• mutational  saturation and unequal rates of evolution between homologous sequences  are the most pervasive
• they  have accumulated multiple substitutions at certain nucleotide  positions
• Indeed, this is a major characteristic of the new results: Discovering  new and unexpected kinship relationships, between nematodes and  arthropods, for example, is a stronger argument than merely claiming  that nematodes should be placed at the base of protostomes and  deuterostomes because they are different from them and less complex.
• These consist in genomic rearrangements, such as  those in the mitochondrial genome (4) and transposition events of SINEs  and LINEs in nuclear genomes (5). They are almost totally immune from  homoplasy and therefore constitute very powerful “signatures” for  kinship when they are found in the same arrangement in two taxa
• homoplasy
• congruence between results obtained from  independent data sets remains the most decisive argument
• First, any gene may be  unsuitable for very ancient events, if too variable, or for very recent  events, if too conservative. A tradeoff must be found between the level  of variability of the sequences used and the time interval one wishes  to analyze
• Second, even a gene that appears to be suitable for a given  time interval may fail to resolve closely spaced speciation events  within this interval
• Of these, the most serious is “adaptive  radiation.” Such a rapid splitting of lineages appears to have  occurred repeatedly during evolution, and it renders reconstruction of  the order of splits very difficult even with large amounts of sequence  data

  • What is adaptive radiation?
• lophophorates, a group  that comprised brachiopods, bryozoans, and phoronids, which all share a  horseshoe-shaped feeding device made of ciliated tentacles
• Small subunit ribosomal RNA remains the molecule for which the largest  database is available for phylogenetic reconstruction.

• These animals, lacking a  coelome, segmentation, elaborate organs, and an anus (in flatworms)  were considered, in a gradist perspective, to be the most primitive  bilaterians. However, they were brought, through rRNA, inside the  lophotrochozoans (25–28), with whom they share a spiral mode of  cleavage and ciliated larval forms that may be considered as  modified trochophores. 

   

       

     
• It is a good illustration of the long prevailing notion that  animal evolution went from simple to complex through gradual steps,  with extant animals actually representing grades of intermediate  complexity supposed to have been those of their ancestors.
• These phyla all share the  presence of a molting cuticle (albeit of very different composition,  chitin in arthropods, collagen in nematodes), hence the name  “Ecdysozoa” given to them

• All molecular phylogenies show the bilaterians as a monophyletic group  clearly separated from sponges, cnidarians, and ctenophores.
• the phyla have emerged in a relatively rapid historical succession,  thus leading to a case in which rRNA reaches its limits of resolution
• Recent detailed studies based on rRNA  involving sponges, cnidarians, and ctenophores (12–15) failed to fully  resolve the phylogeny of the outgroups of Bilateria
• the explosion would have occurred simultaneously in three  already well separated and poorly diversified lineages (the  lophotrochozoan stem line, the ecdysozoan one, and the deuterostome  one), implying that such an explosion would have been caused not by a  single “internal” genetic innovation but, more likely, by an  “external” (i.e., ecological) set of events
• The concept of Articulés, i.e., the clade uniting  annelids and arthropods on the basis of shared segmentation of the body  trunk, is as old as comparative anatomy (18) and has been maintained  for nearly two centuries in all major textbooks and even in some recent  cladistic treatments (19, 20) of metazoan phylogeny
• It has been known for about the same length of  time, however, that annelids share with molluscs and several other  unsegmented phyla a very typical mode of spiral cleavage of the egg,  usually followed by the formation of a so-called trochophore larva
• it  resurrects the question of the ancestry of segmentation in a new frame.
• These were  considered as basal deuterostomes
• because of the radial mode of cleavage  of their egg and their trimeric coelom.
• Foremost among them is the disappearance of “intermediate” taxa  between sponges, cnidarians, ctenophores, and the last common ancestor  of bilaterians or “Urbilateria.“
• the name  “Lophotrochozoa” for the whole clade uniting lophophore-bearing  animals with those displaying a trochophore larva.
• nematodes had been misplaced outside of the bilaterians by a  long-branch attraction artifact and that their true position was as a  sister group of arthropods
• both molecular and morphological, showing that  pseudocoelomates (or aschelminths) did not make up a monophyletic  group
• They are all  essentially small animals having some form of internal cavity but  devoid of a true coelom.
• Displacement of the nematodes to a much higher position in  the metazoan tree, if true, is a major result because it forces a  complete reinterpretation of the data originating from their now fully  sequenced genome as well as of all of their biological features: hence,  the importance of confirming this placement with independent data, as  described below.
• In short, the subdivision of protostomes into two large group was  confirmed and extended

• In the face of the deep restructuring of protostome phylogeny,  deuterostomes have remained stable as a monophyletic group but have  undergone significant internal reorganization
• The 60-amino acid homeodomain of the Hox genes and its  flanking sequences contain specific phylogenetic information in the  form of signature amino acids or short characteristic peptides (35)
• Ruiz-Trillo et al.
• there are reasons to be doubtful
• Several lineages  previously thought to branch at the base of the bilaterian tree, most  notably acoelomates (such as platyhelminths) and pseudocoelomates (such  as nematodes) are now embedded within or next to groups that display  elaborate morphologies and complex genomic arrays
• secondarily simplified
• We have lost the  hope, so common in older evolutionary reasoning, of reconstructing the  morphology of the “coelomate ancestor” through a scenario  involving successive grades of increasing complexity based on the  anatomy of extant “primitive” lineages. For example, the  traditional view of an acoel-like ancestor, progressively acquiring a  coelome, differentiated internal organs, segments, and so on must be  abandoned
• How then can we attempt to reconstruct the path to the  Urbilateria?
• First, through comparison of extant terminal taxa  belonging to the two big branches, protostomes and deuterostomes, and  careful evaluation of all of their possible homologous characters, we  should be able to reconstruct an image of the urbilaterian
• The second approach will consist of better characterizing the  outgroups to bilaterians, sponges, cnidarians, and ctenophores.
• comparison of diploblasts vs. bilateria gene content should  enable us to characterize the basal metazoan genome and hence the one  from which the urbilaterian was progressively  constructed.
• This emphasizes the importance  of the third approach, that of paleaontological investigations on the  pre-Cambrian and early Cambrian, which may well yield the crucial  missing information (41, 46).
• Through comparative analysis of  early development in all metazoan phyla, these authors were led to  conclude that the ancestral mode of development was one in which a  small animal of the size and design of extant larvae was first  constructed on the basis of short-range cell-to-cell interactions.
• undifferentiated set aside  cells with much greater multiplication potential, together with the  recruitment of genetically based large scale patterning mechanisms  (such as those using the Hox complex) would have enabled the  evolution of the adult body plans of the major animal phyla
• Because all of the bilaterians are now seen to descend from  the same ancestor, they have shared the stock of genes possessed by  this ancestor.
• The number of genes  is now known precisely or carefully estimated in several invertebrate  phyla belonging both to protostomes  (Caenorhabditis elegans, 20,000;  Drosophila melanogaster, over 12,000) or to deuterostomes  (Ciona intestinalis, 16,000). One may therefore wander to  suggest that the basal metazoan genome was made up of 15–20,000 genes

46 more annotations...

• At least two types  of cell cycle control mechanisms are recognized: a cascade of protein  phosphorylations that relay a cell from one stage to the next and a set  of checkpoints that monitor completion of critical events and delay  progression to the next stage if necessary
• Kinase activation  generally requires association with a second subunit that is  transiently expressed at the appropriate period of the cell cycle; the  periodic “cyclin” subunit associates with its partner  “cyclin-dependent kinase” (CDK) to create an active complex with  unique substrate specificity.

  Regulatory phosphorylation and  dephosphorylation fine-tune the activity of CDK–cyclin complexes,  ensuring well-delineated transitions between cell cycle stages. In the  future, additional molecular definition of the cell cycle may lead to a  more intricate progression than indicated in Fig. 1
• a highly regulated kinase family (2
• Cell cycle checkpoints sense flaws in critical events such  as DNA replication and chromosome segregation (4). When checkpoints are  activated, for example by underreplicated or damaged DNA, signals are  relayed to the cell cycle-progression machinery. These signals cause a  delay in cycle progression, until the danger of mutation has been  averted.
• Superficially, the connection between the cell cycle and cancer is  obvious: cell cycle machinery controls cell proliferation, and cancer  is a disease of inappropriate cell proliferation
• However, this cell  number excess is linked in a vicious cycle with a reduction in  sensitivity to signals that normally tell a cell to adhere,  differentiate, or die. This combination of altered properties increases  the difficulty of deciphering which changes are primarily responsible  for causing cancer.
• “oncogenes”
• “protooncogenes.”
• “tumor suppressor”

7 more annotations...

• More than 200 species of free-living actinomycete bacteria have been shown to produce antimicrobial compounds
• For instance, the macrolide antibiotic erythromycin originates in the actinomycete Saccharopolyspora erythraea and has been derivatized by numerous pharmaceutical companies over the past 50 y to yield thousands of compounds
• After finally entering the clinic, the lifespan of an antimicrobial drug might be  short and risks being curtailed at any time by bacterial resistance

1 more annotation...