Cell Biology

• CELL BIOLOGY • active transport • apoptosis • cell membranes • centrioles • cilia• communication • concentration gradients • cytoplasm • cytoskeleton • death of cells• energy transducers • endoplasmic reticulum • endosomes • eukaryotic • exosome• Golgi apparatus • ion channels • lysosome • meiosis • microtubules • mitosis• mitochondrion • nuclear membrane • nuclear pore • nucleolus • nucleus • peroxisome• phagocytosis • photosynthesis • physiological function • pinocytosis • plant cell• prokaryotic • protein degradation • pumps • receptor proteins• receptor-mediated endocytosis • reproduction • ribosomes • spindle • structure• transport • vacuole • vesicle• CELL SIGNALING • GPCRs • GPCR families • hormones • Nitric Oxide• neurotransmission • neuronal interconnections • phosphotransfer-mediated signaling pathways • Protein Kinase Signaling Networks • signaling gradients• MOLECULAR BIOLOGY • amino acids • caspases • proteins

Chemistry of Life

~ SITE MAP ~ alphabetic ~ MOLECULAR GENETICS ~ Molecular Genetics Overview~ alternative splicing ~ archival DNA~ base ~ base excision repair BER ~ capping ~ chloroplasts ~ cilia and flagella ~ cis versus trans-acting factors ~ codon ~ DNA ~ DNA damage C to T C to U ~ DNA repair ~ DNA damage by ROS ~ DNA polymerases ~ targetted genetic repair ~ double strand breaks ~ endoplasmic reticulum ~ enhancer ~ epigenetics ~ eukaryotes and prokaryotes ~ exon ~ genes ~ genome ~ gene regulation ~ genetic template ~ Group I and II introns ~ helicases ~ heterochromatin ~ insulator ~ intron ~ DNA mutation and alkylation ~ ionizing radiation ~ mismatch repair T U mismatch ~ nonsense-mediated decay ~ nonstop decay ~ nucleic acids ~ nucleobases & nucleosides & nucleotides / AMP / ATP / cAMP /adenosine / CDP / DNA RNA / GDP / GMP / GTP / UDP / UMP /~ nucleosome ~ nucleotide ~ nucleotide excision repair ~ nuclear speckles ~ open reading frame ORF ~ oxoG repair ~ oxidative stress and DNA damage ~ polyadenylation ~ post-transcriptional modulation ~ RNA processing~ pre-mRNA ~ pre-mRNA splicing ~ proteome ~ regulatory proteins ~ regulatory sequence ~ reverse transcriptase ~ replication~ ribosomes ~ ribosomal structure ~ RNA ~ RNA polymerase ~ mRNA ~ miRNAs ~ tRNA~ rRNAs ~ ribozymes in repair of RNA and DNA ~ ribozymes ~ self-splicing ~ silencers ~ snoRNAs~ splice-site splice-sites ~ spliceosome ~ SSOs ~ template ~trans-splicing ribozymes and therapeutics ~ transcription ~ termination of transcription ~ translation ~ Research techniques ~ SITE MAP ~BIOCHEMISTRY ~ Biochemistry overview ~ amines ~ amino acids : acidic amino acids : acidic and basic amino acids : basic amino acids : polar amino acids : non-polar amino acids ~ adenine cytosine guanine thymine uracil ~ amphipathic ~ cofactor cofactors ~ enzyme ~ heterocyclic ~ hormones ~ hydrogen bond ~ hydrophilic ~ hydrophobic ~ neurotransmitters ~ peptide ~ polypeptide ~ phospolipid ~ proteins ~ thermochemistry ~ Horizontal Genomics: Mobile genetic elements: the agents of open source evolution. ~ Item links

Molecular Genetics

~ SITE MAP ~ Molecular Genetics ~ Molecular Genetics Overview~ alternative splicing ~ transcription ~ base excision repair ~ cis versus trans-acting factors~ capping ~ codon ~ DNA polymerases ~ DNA ~ DNA repair ~ DNA damage by ROS~ targetted genetic repair ~ double strand breaks ~ enhancer ~ epigenetics ~ exon~ genes ~ genome ~ gene regulation ~ helicases ~ heterochromatin ~ insulator ~ intron~ mismatch repair ~ nonsense-mediated decay ~ nonstop decay ~ nucleic acids ~ nucleosome~ nucleotide ~ nucleotide excision repair ~ nuclear speckles ~ open reading frame~ oxidative stress and DNA damage ~ oxoG repair ~ polyadenylation ~ RNA processing~ pre-mRNA ~ pre-mRNA splicing ~ proteome ~ regulatory proteins ~ replication~ ribosomes ~ ribosomal structure ~ ribozymes ~ ribozymes in repair of RNA and DNA~ RNA ~ RNA polymerase ~ messenger RNA ~ miRNAs ~ tRNA ~ silencers ~ snoRNAs~ spliceosome ~ SSOs ~ trans-splicing ribozymes and therapeutics~ termination of transcription ~ translation ~ Research techniques~ SITE MAP

Eubacteria & Archaea

~ Prokaryote structure ~ The Who's Who of Bugs ~ Eubacteria ~ The Archaea~ Interactions in Bacteria ~ Phosphorylation switches ~ Horizontal Gene Transfer~ Conjugation ~ Transduction ~ Transformation ~ Domains ~ Kingdoms ~ Symbiosis~ Phylum ~ Aquifex ~ Thermotoga ~ Green nonsulfur ~ Deinococcus ~ Bacteroides-Flavobacteria ~ Planctomyces ~ Gram-positive ~ Chlamydia ~ Cyanobacteria~ Spirochetes ~ Green sulfur ~ Proteobacteria ~ Further reading

Serial Endosymbiosis

~ Serial EndosymbiosisTheory (SET) ~ Experimental evidence for Endosymbiosis~ History of ideas concerning endosymbiosis ~ Endosymbiotic Gene Transfer~ Endosymbiotic transfers ~ Diagrams of proposed mechanism of SET

Endosymbiosis

• Serial Endosymbiosis Theory (SET) • Diagrams of endosymbiotic cells• Endosymbiotic transfers • Evidence for Endosymbiosis • History of ideas concerning endosymbiosis

Photosynthesis

• Photosynthesis • Cyanobacterial cell • Plant cell • Chloroplast• Pigments and absorption spectra • Chlorophylls and accessory pigments• Oxygenic photosynthesis • Nonoxygenic photosynthesis • Light-reactions• Antenna and Reaction Center • Bacteriochlorophylls • Carotenoids • Phycobilins

Cyanobacteria

Items~ The Cyanobacteria ~ Photochemistry ~ Phylogenetic relationships ~ Fossilized cyanobacteria

Stromatolites

~ Cyanobacteria and stromatolites ~ Modern stromatolites – living fossils~ Stromatolite structure ~ Ancient stromatolite reefs ~ Imaging fossil cyanobacteria~ Stromatolite fossils~ Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia.~ Microbial diversity of extant stromatolites in the hypersaline marine environment of Shark Bay, Australia.~ Lipophilic pigments from cyanobacterial (blue-green algal) and diatom mats in Hamelin Pool, Shark Bay, Western Australia.~ Genetic potential for secondary metabolite production in stromatolite communities.~ Cyanobacteria: Fossilized cyanobacteria

Origin of Life

~ In the Beginning was Abiogenesis ~ What Is Life? ~ Origin of Life and Early Life on Earth~ Before the Beginning ~ The RNA world on ice: a new scenario for the emergence of RNA information.~ Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world -- Vlassov et al. 32 (9): 2966 -- Nucleic Acids Research~ Primordial Atmosphere.~ Efficient near ultraviolet light induced formation of hydrogen by ferrous hydroxide.~ Early Earth Atmosphere Hydrogen-rich, Favorable To Life~ The sugar model: catalysis by amines and amino acid products.~ Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions.~ On the emergence of biological complexity: life as a kinetic state of matter.~ Kinetics of organic transformations under mild aqueous conditions: implications for the origin of life and its metabolism.~ Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate.~ Entropy and charge in molecular evolution--the case of phosphate.~ Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions.~ Ammonia formation by the reduction of nitrite/nitrate by fes: ammonia formation under acidic conditions.~ What Is Life and How Do We Search for It in Other Worlds?~ Top Down & Bottom Up ~ Primordial Soup : Theories~ The Miller-Urey experiments and beyond ~ RNA world hypothesis~ Concentration of simple aldehydes by sulfite-containing double-layer hydroxide minerals: implications for biopoesis.~ Primordial Peptides and Proteins ~ Hydrothermal vents~ Sulphate metabolism among thermophiles and hyperthermophiles in natural aquatic systems.~ The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front.~ On the origin of genomes and cells within inorganic compartments.~ Thermal force approach to molecular evolution.~ Astrobiology ~ The universe: a cryogenic habitat for microbial life.~ Possible steps to the emergence of life: the [GADV]-protein world hypothesis.~ Metabolic Life Theory ~ Minimal Genome ~ Cairns-Smith model~ Intercalation of amino acids and peptides into Mg-Al layered double hydroxide by reconstruction method.~ In Search of the Simplest Cell ~ Cyanophyta ~ Cyanobacteria abstracts~ Modern stromatolites -- living fossils ~ Structure of stromatolites ~ Fossilized stromatolites~ Stromatolite fossils~ Three subsets of sequence complexity and their relevance to biopolymeric information.~ Photosynthesis and the origin of life. ~ Chance and necessity do not explain the origin of life.~ Of Ice and Then~ Acetogenic bacteria: what are the in situ consequences of their diverse metabolic versatilities?~ Liquid Water At Earth's Surface 4.3 Billion Years Ago, Scientists Discover~ Early Earth Likely Had Continents, Was Habitable, According To New Study~ A new pathway of autotrophic growth utilizing carbon monoxide or carbon dioxide and hydrogen.~ Identifying Noncoding RNAs in Genome Sequences~ Clays May Have Aided Formation of Primordial Cells~ Some consequences of the RNA world hypothesis.~ Obcells as Proto-Organisms: Membrane Heredity, Lithophosphorylation, and the Origins of the Genetic Code, the First Cells, and Photosynthesis~ The habitat and nature of early life : Nature~ Self-organizing biochemical cycles -- Orgel 97 (23): 12503 -- Proceedings of the National Academy of Sciences~ High solubility of random-sequence proteins consisting of five kinds of primitive amino acids.~ Catalytic effects of glycine on prebiotic divaline and diproline formation.~ How was membrane permeability produced in an RNA world?~ The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells.~ Gas hydrates and bacteria ~ Debate over origins of modern central Europeans~ Expression of acetylcholine (ACh) and ACh-synthesizing activity in Archaea.~ Darwinism and the origin of life: the role of H.C. Bastian in the British spontaneous generation debates, 1868-1873.

Abiogenesis & Evo

~ In the Beginning was Abiogenesis ~ Before the Beginning ~ Miller-Urey & Beyond~ CHONSP and RNA world ~ The evolution of the prebiotic atmosphere ~ Primordial Soup : Theories ~ Top Down & Bottom Up ~ Minimal Molecules ~ Minimal Genome ~ Archaea~ Illogical Deceit theory ~ RNA world ~ protein catalysts and ribozymes ~ A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. ~ genome and proteome~ Evidence Found for Origin of Genes ~ mtDNA ~ Ancient DNA ~ DNA evolutionary connections ~ evolution and organogenesis ~ Darwin ~ Darwin in the Galapagos~ MicroRNAs Have Shaped The Evolution Of The Majority Of Mammalian Genes ~ Diversity~ Selection ~ Analyses of physiological evolutionary response. ~ Multi-Level Selection~ optimization ~ Logic & Science ~ Neo-Darwinism ~ Stephen Jay Gould ~ Computer Modeling~ PLoS Genetics: The Evolutionary Value of Recombination Is Constrained by Genome Modularity ~ Evolutionary Distance Analysis & Maximum Parsimony Analysis ~ Tree of Life~ Tree of Life or Fuzzy Bush of Life ~ Comparing Gene Trees and Genome Trees: A Cobweb of Life? ~ Genomes and the Tree of Life ~ Protozoa ~ Horizontal Gene Transfer in Prokayotes~ Protists in Evolution, and Symbiogenesis ~ Proterozoic and Archaean ~ Prokaryote Systematics: The Evolution of a Science