scholarly journals A case for subgenera in a foraminiferal classification

1990 ◽  
Vol 9 (1) ◽  
pp. 36-36
Author(s):  
D. Graham Jenkins
Keyword(s):  
Amino Acids ◽  
Related Species ◽  
Genetic Information ◽  
Additional Data ◽  
Planktonic Foraminifera ◽  
Similar Test ◽  
Number Of Factors ◽  
Living Species

Abstract. There has been a progression in palaeobiological classifications from the more primitive empirical “stamp collecting” stage where similar shapes were grouped together, to the more sophisticated phylogenetic classifications where supposed genetically related foraminiferal taxa are categorised together. But how do we know that certain extinct taxa were genetically related? This is a major problem where a number of factors interplay together: a belief in evolution, the experience of the operator and consequent recognition of phyletic lineages. In the study of Cenozoic planktonic foraminifera we are fortunate to have recognised a number of now well established lineages; also we have some data on amino-acids found in the tests of living species (King and Hare, 1972) which range back well into the Neogene. These latter data not only provide us with essential genetic information but they also give us confidence when dealing with the classification of extinct species.So how do we build this evolutionary knowledge into a classification? Clearly, genetically related species can be grouped together into subgenera, and related subgenera into broader genera. In their classification Loeblich and Tappan (1988) held a different view and decided not to use subgenera because (1) their usage produces an unwieldy classification, and (2) lineage concepts change when additional data are collected. If we follow their classification, then when you read about Globorotalia menardii, Globorotalia fohsi and Globorotalia hirsuta you could assume that they are closely related; this is not true. The three species have similar test morphologies but these have resulted from iterative. . .

scholarly journals Determinants of adenine-mutagenesis in diversity-generating retroelements

2020 ◽  
Author(s):  
Sumit Handa ◽  
Andres Reyna ◽  
Timothy Wiryaman ◽  
Partho Ghosh
Keyword(s):  
Amino Acids ◽  
Dark Matter ◽  
Reverse Transcription ◽  
Genetic Information ◽  
Human Microbiome ◽  
Protein Sequences ◽  
Catalytic Efficiency ◽  
Natural World ◽  
In Vitro System

Abstract Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial ‘dark matter’. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.

The clinical utility of the glycemic index and its application to mixed meals

1991 ◽  
Vol 69 (1) ◽  
pp. 100-107 ◽  
Author(s):  
Clarie B. Hollenbeck ◽  
Ann M. Coulston
Keyword(s):  
Glycemic Index ◽  
Clinical Utility ◽  
Postprandial Glucose ◽  
Dependent Diabetes Mellitus ◽  
Glycemic Response ◽  
Glucose Response ◽  
Number Of Factors ◽  
Carbohydrate Intolerance ◽  
Low Glycemic Index

A classification of carbohydrate-containing foods based on their glycemic response to 50-g carbohydrate portions has recently been developed. The relative glycemic potency of many of these carbohydrate-containing foods have been compared, and these data have been published in the form of a glycemic index. It has been suggested that meals containing low glycemic index foods will result in a lower postprandial glucose response than meals with a higher glycemic index. However, whether or not these data will lead to a clinically useful reduction in postprandial hyperglycemia in individuals with carbohydrate intolerance remains controversial. In this review, we will try to delineate why we believe that the glycemic index, as currently developed, may be a specious issue. In addition, we will briefly discuss a number of factors that may explain the apparent discrepancy in viewpoints on this issue.Key words: glycemic index, noninsulin-dependent diabetes mellitus, glycemic response, dietary carbohydrate.

scholarly journals PredicTF: a tool to predict bacterial transcription factors in complex microbial communities

2021 ◽  
Author(s):  
Lummy Maria Oliveira Monteiro ◽  
Joao Saraiva ◽  
Rodolfo Brizola Toscan ◽  
Peter F Stadler ◽  
Rafael Silva-Rocha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Microbial Communities ◽  
Open Source ◽  
Genetic Information ◽  
Environmental Isolate ◽  
Ammonium Oxidation ◽  
Cellular Gene ◽  
Bacterial Transcription

AbstractTranscription Factors (TFs) are proteins that control the flow of genetic information by regulating cellular gene expression. Here we describe PredicTF, a first platform supporting the prediction and classification of novel bacterial TF in complex microbial communities. We evaluated PredicTF using a two-step approach. First, we tested PredictTF’s ability to predict TFs for the genome of an environmental isolate. In the second evaluation step, PredicTF was used to predict TFs in a metagenome and 11 metatranscriptomes recovered from a community performing anaerobic ammonium oxidation (anammox) in a bioreactor. PredicTF is open source pipeline available at https://github.com/mdsufz/PredicTF.

scholarly journals Cardiomyopathy Classification: Ongoing Debate in the Genomics Era

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Charles McCartan ◽  
Robert Mason ◽  
S. R. Jayasinghe ◽  
Lyn R. Griffiths
Keyword(s):  
Adverse Effects ◽  
Genetic Information ◽  
Molecular Basis ◽  
Genetic Basis ◽  
Muscle Size ◽  
Systemic Diseases ◽  
Ongoing Debate ◽  
Traditional Classification ◽  
And Function

Cardiomyopathies represent a group of diseases of the myocardium of the heart and include diseases both primarily of the cardiac muscle and systemic diseases leading to adverse effects on the heart muscle size, shape, and function. Traditionally cardiomyopathies were defined according to phenotypical appearance. Now, as our understanding of the pathophysiology of the different entities classified under each of the different phenotypes improves and our knowledge of the molecular and genetic basis for these entities progresses, the traditional classifications seem oversimplistic and do not reflect current understanding of this myriad of diseases and disease processes. Although our knowledge of the exact basis of many of the disease processes of cardiomyopathies is still in its infancy, it is important to have a classification system that has the ability to incorporate the coming tide of molecular and genetic information. This paper discusses how the traditional classification of cardiomyopathies based on morphology has evolved due to rapid advances in our understanding of the genetic and molecular basis for many of these clinical entities.

Applications to Silicate, Carbonate, and Borate Minerals and Related Species

1992 ◽  
Author(s):  
John A. Tossell ◽  
David J. Vaughan
Keyword(s):  
Related Species ◽  
The Other ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Solid Solution Series ◽  
Silicate Minerals ◽  
Borate Minerals ◽  
Cluster Unit ◽  
Silicate Carbonate

The most abundant materials making up the crust of the earth (i.e., the “rock-forming minerals”) can be regarded as dominated by oxyanion units; notably, the units that can be formally represented by SiO44- and AlO45- clusters of the silicate minerals, and the CO32- unit of the carbonates. less common, but geochemically interesting, oxyanion units include, for example, BO33-, BeO46- , and PO43-. in this chapter, applications of quantum-mechanical calculations and experimental techniques to such materials are considered. first, the silicates are discussed, commencing with the large amount of work undertaken on the olivines, before considering such work as has so far been done on the other silicate minerals and related materials. second, the most important of the nonsilicate rock-forming mineral groups, the carbonates, are discussed. finally, although of less petrological importance but interesting geochemically and in terms of contrast with the othergroups, the borates and related species are considered. in each case, geometric aspects of structure and the problems of calculating structural properties are considered before going on to consider electronic structures and the factors controlling stabilities and a wider range of physical properties. in all of these materials, there is considerable interest in the, bonding in the oxyanion unit and how this is affected by, and controls, the interaction with counterions or the polymeric units. the building up of the minerals by such interactions exerts the dominant control over their crystal chemistries and properties and thus forms a central theme of this chapter. the silicate minerals are, of course, characterized by the presence of the tetrahedral siO4 cluster unit and the crystal chemistry and classification of silicates dominated by the structures built up by the linking together (polymerization) of these units. in the “simplest” of the silicates, the island silicates such as the olivine minerals (dominated by the forsterite (Mg2 SiO4)-fayalite (Fe2SiO4) solid solution series), the sio4 units are isolated by counterions such as Mg2+, Fe2+, Ca2+.

scholarly journals SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species

2020 ◽  
Vol 21 (24) ◽  
pp. 9421
Author(s):  
Lidia Skuza ◽  
Ewa Filip ◽  
Izabela Szućko ◽  
Jan Bocianowski
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Markers ◽  
Related Species ◽  
Economic Importance ◽  
Closely Related Species ◽  
Coding Sequences ◽  
Coding Regions ◽  
Genomic Regions ◽  
Tribe Triticeae

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.

Nematobothrium labeonis n.sp., a Member of the Family Didymozooidae (Trematoda) from a Freshwater Fish

1955 ◽  
Vol 29 (1-2) ◽  
pp. 55-64 ◽  
Author(s):  
W. F. J. McClelland
Keyword(s):  
Freshwater Fish ◽  
Related Species ◽  
Recent Literature ◽  
The Family

1. Nematobothrium labeonis n. sp. from the orbit of three species of Labeo is described.2. The more recent literature relating to the classification of the genus is considered.3. N. labeonis is contrasted with related species.

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