Eukaryota
tRNA Methyltransferases
Eukaryotic Cells
Archaea
Sequence Alignment
Evolution, Molecular
Bacteria
Molecular Sequence Data
Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (1/2647)
Group II self-splicing requires the 5' exon to form base pairs with two stretches of intronic sequence (EBS1 and EBS2) which also bind the DNA target during retrotransposition of the intron. We have used dimethyl sulfate modification of bases to obtain footprints of the 5' exon on intron Pl.LSU/2 from the mitochondrion of the alga Pylaiella littoralis, as well as on truncated intron derivatives. Aside from the EBS sites, which are part of the same subdomain (ID) of ribozyme secondary structure, three distant adenines become either less or more sensitive to modification in the presence of the exon. Unexpectedly, one of these adenines in subdomain IC1 is footprinted only in the presence of the distal helix of domain V, which is involved in catalysis. While the loss of that footprint is accompanied by a 100-fold decrease in the affinity for the exon, both protection from modification and efficient binding can be restored by a separate domain V transcript, whose binding results in its own, concise footprint on domains I and III. Possible biological implications of the need for the group II active site to be complete in order to observe high-affinity binding of the 5' exon to domain I are discussed. (+info)Growth characteristics of Heterosigma akashiwo virus and its possible use as a microbiological agent for red tide control. (2/2647)
The growth characteristics of Heterosigma akashiwo virus clone 01 (HaV01) were examined by performing a one-step growth experiment. The virus had a latent period of 30 to 33 h and a burst size of 7.7 x 10(2) lysis-causing units in an infected cell. Transmission electron microscopy showed that the virus particles formed on the peripheries of viroplasms, as observed in a natural H. akashiwo cell. Inoculation of HaV01 into a mixed algal culture containing four phytoplankton species, H. akashiwo H93616, Chattonella antiqua (a member of the family Raphidophyceae), Heterocapsa triquetra (a member of the family Dinophyceae), and Ditylum brightwellii (a member of the family Bacillariophyceae), resulted in selective growth inhibition of H. akashiwo. Inoculation of HaV01 and H. akashiwo H93616 into a natural seawater sample produced similar results. However, a natural H. akashiwo red tide sample did not exhibit any conspicuous sensitivity to HaV01, presumably because of the great diversity of the host species with respect to virus infection. The growth characteristics of the lytic virus infecting the noxious harmful algal bloom-causing alga were considered, and the possibility of using this virus as a microbiological agent against H. akashiwo red tides is discussed. (+info)Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. (3/2647)
We analyzed changes in bacterioplankton morphology and composition during enhanced protozoan grazing by image analysis and fluorescent in situ hybridization with group-specific rRNA-targeted oligonucleotide probes. Enclosure experiments were conducted in a small, fishless freshwater pond which was dominated by the cladoceran Daphnia magna. The removal of metazooplankton enhanced protozoan grazing pressure and triggered a microbial succession from fast-growing small bacteria to larger grazing-resistant morphotypes. These were mainly different types of filamentous bacteria which correlated in biomass with the population development of heterotrophic nanoflagellates (HNF). Small bacterial rods and cocci, which showed increased proportion after removal of Daphnia and doubling times of 6 to 11 h, belonged nearly exclusively to the beta subdivision of the class Proteobacteria and the Cytophaga-Flavobacterium cluster. The majority of this newly produced bacterial biomass was rapidly consumed by HNF. In contrast, the proportion of bacteria belonging to the gamma and alpha subdivisions of the Proteobacteria increased throughout the experiment. The alpha subdivision consisted mainly of rods that were 3 to 6 microm in length, which probably exceeded the size range of bacteria edible by protozoa. Initially, these organisms accounted for less than 1% of total bacteria, but after 72 h they became the predominant group of the bacterial assemblage. Other types of grazing-resistant, filamentous bacteria were also found within the beta subdivision of Proteobacteria and the Cytophaga-Flavobacterium cluster. We conclude that the predation regimen is a major structuring force for the bacterial community composition in this system. Protozoan grazing resulted in shifts of the morphological as well as the taxonomic composition of the bacterial assemblage. Grazing-resistant filamentous bacteria can develop within different phylogenetic groups of bacteria, and formerly underepresented taxa might become a dominant group when protozoan predation is the major selective pressure. (+info)Fermentation substrate and dilution rate interact to affect microbial growth and efficiency. (4/2647)
The effect of dilution rate (D) on carbohydrate, fibrous and nonfibrous, and protein fermentation by ruminal microorganisms was studied using a single-effluent continuous-culture system. The diets of fibrous carbohydrate, nonfibrous carbohydrate, or protein were formulated with soybean hulls (FC), ground corn (NFC), or isolated soy protein (PR) as the primary ingredient, respectively. Six dilution rates (.025, .050, .075, .10, .15, and .20/h of fermenter volume) were used. Digestibilities of DM, OM, and CP for the three diets and of NDF and ADF for the FC diet decreased (P<.001) as D increased, although the response of the digestibility to D varied with diet. Increasing D resulted in an increase in pH (P<.001) and a decrease (P<.001) in ammonia concentration. Daily volatile fatty acid production increased (quadratic; P<.01) for the FC and NFC diets, but decreased (quadratic; P<.001) for the PR diet. Increasing D quadratically increased (P<.001) the molar percentage of acetate and propionate, but quadratically decreased (P<.001) butyrate and valerate for the FC and NFC diets. For the PR diet, the molar percentage of propionate and valerate increased (quadratic; P<.01), whereas acetate and butyrate decreased (linear; P<.001) in response to increasing D. Molar percentage of isobutyrate and isovalerate decreased (P<.01) with increasing D for all three diets. As D increased, daily microbial N production showed quadratic responses with maximum values achieved at .126, .143, and .187/h D for the FC, NFC, and PR diet, respectively. There was a positive correlation between microbial growth efficiency (MOEFF) and D. A quadratic model fit the data of MOEFF as affected by D, and maximum MOEFF of 37.3, 59.6, and 71.4 g of bacterial N/kg OM truly fermented were calculated to be achieved at .177, .314, and .207/h D for the FC, NFC, and PR diet, respectively. Dilution rate significantly influenced the ruminal microbial fermentation of fibrous and nonfibrous carbohydrates and proteins, and was positively related to microbial yield and growth efficiency. In addition, microbial nitrogen composition, and therefore efficiency, was affected by substrate fermented. (+info)Whirling disease: host specificity and interaction between the actinosporean stage of Myxobolus cerebralis and rainbow trout Oncorhynchus mykiss. (5/2647)
Scanning electron microscopic studies were conducted on rainbow trout Oncorhynchus mykiss in the first 60 min after their exposure to the triactinomyxon spores of Myxobolus cerebralis. The results demonstrated that as early as 1 min post exposure the whole process, from the attachment of the triactinomyxon spores to the complete penetration of their sporoplasm germs, had occurred. The triactinomyxon spores sought out the secretory openings of mucous cells of the epidermis, the respiratory epithelium and the buccal cavity of trout and used them as portals of entry. Exposure experiments of the triactinomyxon spores of M. cerebralis to non-salmonid fish, such as goldfish Carassius auratus, carp Cyprinus carpio, nose Chondrostoma nasus, medaka Oryzias latipes, guppy Poecilia reticulata and also the amphibian tadpole Rana pipiens as well as to rainbow trout fry indicated a specificity for salmonids. Attempts to activate the triactinomyxon spores by exposure to mucus prepared from cyprinid and salmonid fish showed no significant differences from those conducted in tap water. The results suggest that the simultaneous presence of both mechano- and chemotactic stimuli was required for finding the salmonid fish host. (+info)Pathogenicity of Ichthyophonus hoferi for laboratory-reared Pacific herring Clupea pallasi and its early appearance in wild Puget Sound herring. (6/2647)
Laboratory-reared pathogen-free Pacific herring were exposed to pure cultures of Ichthyophonus hoferi, and reproduced the disease seen in naturally infected fish--thus fulfilling Koch's Postulates. Pathogen-free herring used in this study were reared from artificially spawned eggs incubated in filtered, UV-sterilized seawater, eliminating the variables associated with multiple infections, which are common in wild herring. Wild free-ranging herring were captured monthly from June through October by dip net from 'herring balls' located in the northern Puget Sound. I. hoferi infections were identified in these fish soon after metamorphoses, about 4 mo post-hatch. The prevalence increased from 5 to 6% in 0-yr fish to 24% in 1-yr-old fish to 50 to 70% in fish over 2 yr old, with no associated increase in mortality. The route of natural transmission to wild herring was not determined, but carnivorous fish became infected and died when they were experimentally fed tissues infected with the organism. In vitro culture of tissues was the most sensitive method for identifying both clinical and subclinical infections. (+info)Nosema notabilis (Microsporidia), its ultrastructure and effect on the myxosporean host Ortholinea polymorpha. (7/2647)
Nosema notabilis Kudo, 1939 produces chain-forming meronts with a dense cell coat in direct contact with the host cell cytoplasm. Cytoplasmic microtubules and membranaceous whorls could be observed in meront cytoplasm. Sporonts differ in that they have a thicker cell wall and more conspicuous endoplasmic reticulum (ER) cisternae. Sporoblasts have an externally ridged cell wall. Spores have an apically located anchoring disc, an isofilar polar tube with 6 to 9 turns and polyribosomal strands in the sporoplasm. Diplokarya occur in all stages. Heavily infected plasmodia of Ortholinea polymorpha (Davis, 1917) reveal marked pathological signs. The most prominent are reduction of surface projections and/or pinocytosis, inflated mitochondria with altered inner structures, affected vegetative nuclei, damage to generative cells and occurrence of various anomalous formations in the plasmodium cytoplasm. The damage may result in complete disintegration of the plasmodium. However, the development of the microsporidian is affected by a remarkably high percentage of teratological stages revealing membranaceous and tubular structures. (+info)Nitrate removal in closed-system aquaculture by columnar denitrification. (8/2647)
The columnar denitrification method of nitrate-nitrogen removal from high-density, closed system, salmonid aquaculture was investigated and found to be feasible. However, adequate chemical monitoring was found to be necessary for the optimization and quality control of this method. When methanol-carbon was not balanced with inlet nitrate-nitrogen, the column effluent became unsatisfactory for closed-system fish culture due to the presence of excess amounts of nitrite, ammonia, sulfide, and dissolved organic carbon. Sulfide production was also influenced by column maturity and residence time. Methane-carbon was found to be unsatisfactory as an exogenous carbon source. Endogenous carbon could not support high removal efficiencies. Freshwater columns adpated readily to an artificial seawater with a salinity of 18% without observable inhibition. Scanning electron microscopy revealed that the bacterial flora was mainly rod forms with the Peritricha (protozoa) dominating as the primary consumers. Denitrifying bacteria isolated from freshwater columns were tentatively identified as species of Pseudomonas and Alcaligenes. A pilot plant column was found to behave in a manner similar to the laboratory columns except that nitrite production was never observed. (+info)Eukaryota is a domain that consists of organisms whose cells have a true nucleus and complex organelles. This domain includes animals, plants, fungi, and protists. The term "eukaryote" comes from the Greek words "eu," meaning true or good, and "karyon," meaning nut or kernel. In eukaryotic cells, the genetic material is housed within a membrane-bound nucleus, and the DNA is organized into chromosomes. This is in contrast to prokaryotic cells, which do not have a true nucleus and have their genetic material dispersed throughout the cytoplasm.
Eukaryotic cells are generally larger and more complex than prokaryotic cells. They have many different organelles, including mitochondria, chloroplasts, endoplasmic reticulum, and Golgi apparatus, that perform specific functions to support the cell's metabolism and survival. Eukaryotic cells also have a cytoskeleton made up of microtubules, actin filaments, and intermediate filaments, which provide structure and shape to the cell and allow for movement of organelles and other cellular components.
Eukaryotes are diverse and can be found in many different environments, ranging from single-celled organisms that live in water or soil to multicellular organisms that live on land or in aquatic habitats. Some eukaryotes are unicellular, meaning they consist of a single cell, while others are multicellular, meaning they consist of many cells that work together to form tissues and organs.
In summary, Eukaryota is a domain of organisms whose cells have a true nucleus and complex organelles. This domain includes animals, plants, fungi, and protists, and the eukaryotic cells are generally larger and more complex than prokaryotic cells.
tRNA (transfer RNA) methyltransferases are a group of enzymes that catalyze the transfer of a methyl group (-CH3) to specific positions on the tRNA molecule. These enzymes play a crucial role in modifying and regulating tRNA function, stability, and interaction with other components of the translation machinery during protein synthesis.
The addition of methyl groups to tRNAs can occur at various sites, including the base moieties of nucleotides within the anticodon loop, the TψC loop, and the variable region. These modifications help maintain the structural integrity of tRNA molecules, enhance their ability to recognize specific codons during translation, and protect them from degradation by cellular nucleases.
tRNA methyltransferases are classified based on the type of methylation they catalyze:
1. N1-methyladenosine (m1A) methyltransferases: These enzymes add a methyl group to the N1 position of adenosine residues in tRNAs. An example is TRMT6/TRMT61A, which methylates adenosines at position 58 in human tRNAs.
2. N3-methylcytosine (m3C) methyltransferases: These enzymes add a methyl group to the N3 position of cytosine residues in tRNAs. An example is Dnmt2, which methylates cytosines at position 38 in various organisms.
3. N7-methylguanosine (m7G) methyltransferases: These enzymes add a methyl group to the N7 position of guanosine residues in tRNAs, primarily at position 46 within the TψC loop. An example is Trm8/Trm82, which catalyzes this modification in yeast and humans.
4. 2'-O-methylated nucleotides (Nm) methyltransferases: These enzymes add a methyl group to the 2'-hydroxyl group of ribose sugars in tRNAs, which can occur at various positions throughout the molecule. An example is FTSJ1, which methylates uridines at position 8 in human tRNAs.
5. Pseudouridine (Ψ) synthases: Although not technically methyltransferases, pseudouridine synthases catalyze the isomerization of uridine to pseudouridine, which can enhance tRNA stability and function. An example is Dyskerin (DKC1), which introduces Ψ at various positions in human tRNAs.
These enzymes play crucial roles in modifying tRNAs, ensuring proper folding, stability, and function during translation. Defects in these enzymes can lead to various diseases, including neurological disorders, cancer, and premature aging.
Eukaryotic cells are complex cells that characterize the cells of all living organisms except bacteria and archaea. They are typically larger than prokaryotic cells and contain a true nucleus and other membrane-bound organelles. The nucleus houses the genetic material, DNA, which is organized into chromosomes. Other organelles include mitochondria, responsible for energy production; chloroplasts, present in plant cells and responsible for photosynthesis; endoplasmic reticulum, involved in protein synthesis; Golgi apparatus, involved in the processing and transport of proteins and lipids; lysosomes, involved in digestion and waste disposal; and vacuoles, involved in storage and waste management. Eukaryotic cells also have a cytoskeleton made up of microtubules, intermediate filaments, and actin filaments that provide structure, support, and mobility to the cell.
Archaea are a domain of single-celled microorganisms that lack membrane-bound nuclei and other organelles. They are characterized by the unique structure of their cell walls, membranes, and ribosomes. Archaea were originally classified as bacteria, but they differ from bacteria in several key ways, including their genetic material and metabolic processes.
Archaea can be found in a wide range of environments, including some of the most extreme habitats on Earth, such as hot springs, deep-sea vents, and highly saline lakes. Some species of Archaea are able to survive in the absence of oxygen, while others require oxygen to live.
Archaea play important roles in global nutrient cycles, including the nitrogen cycle and the carbon cycle. They are also being studied for their potential role in industrial processes, such as the production of biofuels and the treatment of wastewater.
Phylogeny is the evolutionary history and relationship among biological entities, such as species or genes, based on their shared characteristics. In other words, it refers to the branching pattern of evolution that shows how various organisms have descended from a common ancestor over time. Phylogenetic analysis involves constructing a tree-like diagram called a phylogenetic tree, which depicts the inferred evolutionary relationships among organisms or genes based on molecular sequence data or other types of characters. This information is crucial for understanding the diversity and distribution of life on Earth, as well as for studying the emergence and spread of diseases.
In genetics, sequence alignment is the process of arranging two or more DNA, RNA, or protein sequences to identify regions of similarity or homology between them. This is often done using computational methods to compare the nucleotide or amino acid sequences and identify matching patterns, which can provide insight into evolutionary relationships, functional domains, or potential genetic disorders. The alignment process typically involves adjusting gaps and mismatches in the sequences to maximize the similarity between them, resulting in an aligned sequence that can be visually represented and analyzed.
Molecular evolution is the process of change in the DNA sequence or protein structure over time, driven by mechanisms such as mutation, genetic drift, gene flow, and natural selection. It refers to the evolutionary study of changes in DNA, RNA, and proteins, and how these changes accumulate and lead to new species and diversity of life. Molecular evolution can be used to understand the history and relationships among different organisms, as well as the functional consequences of genetic changes.
Bacteria are single-celled microorganisms that are among the earliest known life forms on Earth. They are typically characterized as having a cell wall and no membrane-bound organelles. The majority of bacteria have a prokaryotic organization, meaning they lack a nucleus and other membrane-bound organelles.
Bacteria exist in diverse environments and can be found in every habitat on Earth, including soil, water, and the bodies of plants and animals. Some bacteria are beneficial to their hosts, while others can cause disease. Beneficial bacteria play important roles in processes such as digestion, nitrogen fixation, and biogeochemical cycling.
Bacteria reproduce asexually through binary fission or budding, and some species can also exchange genetic material through conjugation. They have a wide range of metabolic capabilities, with many using organic compounds as their source of energy, while others are capable of photosynthesis or chemosynthesis.
Bacteria are highly adaptable and can evolve rapidly in response to environmental changes. This has led to the development of antibiotic resistance in some species, which poses a significant public health challenge. Understanding the biology and behavior of bacteria is essential for developing strategies to prevent and treat bacterial infections and diseases.
Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.
An amino acid sequence is the specific order of amino acids in a protein or peptide molecule, formed by the linking of the amino group (-NH2) of one amino acid to the carboxyl group (-COOH) of another amino acid through a peptide bond. The sequence is determined by the genetic code and is unique to each type of protein or peptide. It plays a crucial role in determining the three-dimensional structure and function of proteins.
Paulinella