Quadruplexes of human telomere DNA analogs designed to contain G:A:G:A,G:G:A:A,and A:A:A:A tetrads

Replacement of two to four guanines by adenines in the human telomere DNA repeat dG₃(TTAG₃)₃ did not hinder the formation of quadruplexes if the substitutions took place in the terminal tetrad bridged by the diagonal loop of the intramolecular antiparallel three‐tetrad scaffold, as proved by CD and PAGE in both Na⁺ and K⁺ solutions. Thermodynamic data showed that, in Na⁺ solution, the dG₃(TTAG₃)₃ quadruplex was destabilized, the least by the two G:A:G:A tetrads, the most by the G:G:A:A tetrad in which the adenosines replaced syn‐guanosines. In physiological K⁺ solution, the highest destabilization was caused by the 4A tetrad. In K⁺, only the unmodified dG₃(TTAG₃)₃ quadruplex rearranged into a K⁺‐dependent quadruplex form, none of the multiple adenine‐modified structures did so. This may imply biological consequences for nonrepaired A‐for‐G mutations. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 880–886, 2010.     

Antimicrobials: Genomics: Web alert

A selection of World Wide Web sites relevant to the reviews published in this issue of Current Opinion in Microbiology.     

Focus: Personalized Medicine: Bygiene: The New Paradigm of Bidirectional Hygiene

The pervasive dogma surrounding the evolution of virulence — namely, that a pathogen’s virulence decreases over time to prevent threatening its host — is an archaic assertion that is more appropriately cast as an optimization of virulence cost and benefit. However, the prevailing attitudes underlying practices of medical hygiene and sanitization remain entrenched in these passé ideas. This is true despite the emergence of evidence linking those practices to mounting virulence and antimicrobial resistance in the hospital. It is, therefore, our position that just as the microbe has sought an optimized balance in virulence, so should we seek such an optimized balance in vigilance, complementing warfare with restoration. We call this approach “bygiene,” or bidirectional hygiene.     

Review: Beef-eating quality: a European journey

This paper reviews recent research into predicting the eating qualities of beef. A range of instrumental and grading approaches have been discussed, highlighting implications for the European beef industry. Studies incorporating a number of instrumental and spectroscopic techniques illustrate the potential for online systems to non-destructively measure muscle pH, colour, fat and moisture content of beef with R² (coefficient of determination) values >0.90. Direct predictions of eating quality (tenderness, flavour, juiciness) and fatty acid content using these methods are also discussed though success is greatly variable. R² values for instrumental measures of tenderness have been quoted as high as 0.85 though R² values for sensory tenderness values can be as low as 0.01. Discriminant analysis models can improve prediction of variables such as pH and shear force, correctly classifying beef samples into categorical groups with >90% accuracy. Prediction of beef flavour continues to challenge researchers and the industry alike, with R² values rarely quoted above 0.50, regardless of instrumental or statistical analysis used. Beef grading systems such as EUROP and United States Department of Agriculture systems provide carcase classification and some indication of yield. Other systems attempt to classify the whole carcase according to expected eating quality. These are being supplemented by schemes such as Meat Standards Australia (MSA), based on consumer satisfaction for individual cuts. In Australia, MSA has grown steadily since its inception generating a 10% premium for the beef industry in 2015-16 of $187 million. There is evidence that European consumers would respond to an eating quality guarantee provided it is simple and independently controlled. A European beef quality assurance system might encompass environmental and nutritional measures as well as eating quality and would need to be profitable, simple, effective and sufficiently flexible to allow companies to develop their own brands.     

Focus: Health Equity: The Sick Bias

This perspectives piece shares the experience of a trainee during the COVID-19 pandemic as it pertains to initial patient evaluations and the subsequent impact they have on patient outcomes. Specifically highlighting the value of approaching every patient as sick before deeming them as well – this approach to triaging is defined as a “sick bias” throughout the piece. Unfortunately, this initial evaluation can be influenced by explicit and implicit biases of the provider that highlight health inequities within their patient’s care.     

Focus: Addiction: How Menthol Alters Tobacco-Smoking Behavior: A Biological Perspective

Mentholated cigarettes gained popularity in the 1950s and were often marketed as “healthy” cigarettes, attributable to their pleasurable mint flavor and cooling sensation in the mouth, lungs, and throat. While it is clear that nicotine is the primary psychoactive component in tobacco cigarettes, recent work has suggested that menthol may also play a role in exacerbating smoking behavior, despite original health claims. Recent evidence highlights four distinct biological mechanisms that can alter smoking behavior: 1) menthol acts to reduce the initially aversive experiences associated with tobacco smoking; 2) menthol can serve as a highly reinforcing sensory cue when associated with nicotine and promote smoking behavior; 3) menthol''s actions on nicotinic acetylcholine receptors may change the reinforcing value of nicotine; and 4) menthol can alter nicotine metabolism, thus increasing nicotine bioavailability. The purpose of this review is to highlight and evaluate potential biological mechanisms by which menthol can alter smoking behavior.     

Evolutionary history of frogfishes (Teleostei: Lophiiformes: Antennariidae): a molecular approach

Fishes of the family Antennariidae (order Lophiiformes) are primarily shallow-water benthic forms found in nearly all tropical and subtropical oceans and seas of the world, with some taxa extending into temperate waters. Despite an earlier attempt based on morphology, no previous hypothesis of intergeneric relationships of the Antennariidae exists. To resolve phylogenetic relationships within the Antennariidae, and to test the validity of species groups within Antennarius, DNA sequences from the mitochondrial 16S and cytochrome oxidase c subunit 1 (COI) genes, and nuclear recombination activating gene 2 (RAG2), for 25 described and four undescribed antennariid species, representing 10 of 12 known genera and one undescribed genus, were unambiguously aligned and analyzed using Bayesian and maximum likelihood methods. The markers were partitioned and analyzed for substitution saturation and only the third codon position of COI (COI-3) was found to have reached saturation. However, analysis of both datasets, one with the saturated data and one without, differed only slightly. All molecular analyses recovered two major clades, one comprised of Fowlerichthys, Antennarius, Histrio, and Antennatus; and another containing Rhycherus, Antennariidae gen. et sp. nov., Kuiterichthys, Phyllophryne, Echinophryne, Tathicarpus, Lophiocharon, and Histiophryne. Evidence is presented to illustrate a correlation between phylogeny, geographic distribution, and reproductive life history. The results of these analyses provide the first hypothesis of evolutionary relationships within the Antennariidae.     

Revision of the Clytra subfasciata species group (Coleoptera: Chrysomelidae: Cryptocephalinae: Clytrini)

The Clytra subfasciata species group is proposed, to comprise Clytra subfasciata Lacordaire, 1848 Lacordaire, J. T. (1848): Monographie des coléoptères subpentamères de la famille des phytophages. Tome second. Mémoires de la Société Royale des Sciences de Liége, 5, 1–890 pp. [Google Scholar], C. hajeki Medvedev &; Kantner, 2002 Medvedev, L. N., &; Kantner, F. (2002): Some new and poorly know Clytrinae (Coleoptera, Chrysomelidae) of the Old World. Entomologica Basiliensia, 24, 259–269. [Google Scholar] and C. kadleci sp. n. (Yemen). The species of the group are characterised by the peculiar shape of the aedeagus, with a dorsal plate separated from the rest of aedeagus by a deep narrow slit. Colour photographs of habitus and drawings of genitalia are provided for all three species.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:F6706A76-CD49-4A5A-A109-A6E6C23514A5     

Revision of the section Anillochlamys Jeannel, 1909 (Coleoptera: Leiodidae: Cholevinae: Leptodirini)

The taxonomy of the Iberian Leptodirini species of the section Anillochlamys Jeannel, 1909 has been revised. The proposed classification is based on the study of the genital structures of both sexes, in particular the internal sac of the aedeagus. According to the different models of internal sacs, the following genera, species and subspecies are identified: genus Anillochlamys Jeannel, 1909: A. aurouxi Español, 1965, A. bueni Jeannel, 1909 (= A. avariae Comas, 1977 n.syn.), A. cullelli Lagar, 1978, A. moroderi Bolívar, 1923 (= A. negrei Comas, 1990 n. syn.), A. subtruncatus Jeannel, 1930 (= A. baguenai Jeannel, 1930) and A. tropicus (Abeille, 1881) (= Adelops hispanicus Ehlers, 1893; A. tropicus var. apicalis Jeannel, 1909); genus Paranillochlamys Zariquiey, 1940: P. catalonicus (Jeannel, 1913), P. urgellesi (Español, 1965) and P. velox Zariquiey, 1940 (= P. velox montadai Lagar, 1963 n. syn.); genus Pseudochlamys Comas, 1977: P. raholai (Zariquiey, 1922) (= Anillochlamys raholai luis-bofilli Zariquiey, 1940 n. syn.); genus Spelaeochlamys Dieck, 1870 (= Typhlochlamys Español, 1975 n.syn.): S.bardisai (Español, 1975) (= Typhlochlamys escolai Comas, 1978 n. syn.), S. ehlersi Dieck, 1870 and S. ehlersi verai Comas, 1977 n. stat.     

Gobies are deeply divided: phylogenetic evidence from nuclear DNA (Teleostei: Gobioidei: Gobiidae)

Gobies (Gobiidae sensu Gill & Mooi, 2012 Gill, A. and Mooi, R. 2012. Thalasseleotrididae, new family of marine gobioid fishes from New Zealand and temperate Australia, with a revised definition of its sister taxon, the Gobiidae (Teleostei: Acanthomorpha). Zootaxa, 3266: 41–52.  [Google Scholar]) are one of the most diverse families of vertebrates, and comprise over 1700 species of marine, brackish and freshwater fishes. Phylogenetic studies based on morphological characters and mtDNA have suggested that goby diversity is asymmetrically split between a speciose clade of predominantly marine species, and a less rich, but ecologically diverse, clade comprising predominantly freshwater and brackish species. This study is the first to explore this deep divide in gobies and their relationships at the family level using phylogenetic data from nuclear genes (RAG1, rhodopsin). Our results confirm the split within the Gobiidae, and agree with prior molecular studies on the inclusion of the following taxa within the two goby clades: (i) the more diverse of the two clades of gobies (the ‘Gobiidae’ sensu stricto of Thacker 2009 Thacker, C. E. 2009. Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia, 1: 93–104. doi:10.1643/CI-08-004[Crossref], [Web of Science ®] , [Google Scholar]) comprises the gobiines, microdesmines, ptereleotrines and kraemeriines; (ii) the less diverse of the two gobiid clades (‘Gobionellidae’ sensu Thacker 2009 Thacker, C. E. 2009. Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia, 1: 93–104. doi:10.1643/CI-08-004[Crossref], [Web of Science ®] , [Google Scholar]) includes the gobionellines, oxudercines, amblyopines, sicydiines, as well as the European sand gobies. Some relationships within the two major gobiid clades remain unclear. Specifically, there remains confusion regarding the monophyly and interrelationships between the northern Pacific gobionellines, the Mugilogobius group gobionellines, and the European sand gobies. Additionally, within Thacker's (2009 Thacker, C. E. 2009. Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia, 1: 93–104. doi:10.1643/CI-08-004[Crossref], [Web of Science ®] , [Google Scholar]) Gobiidae sensu stricto, there are several well-supported groups (e.g. the wormfishes and dartfishes, the Coral Gobies, the Gobiosomatini), yet relationships among these groups are still poorly resolved despite the use of data from two conserved nuclear genes. Future phylogenetic analyses of gobies will benefit greatly from taxon sampling that includes groups that have been historically under-represented in molecular studies (e.g. European sand gobies, northern Pacific gobionellines, African species), as well as deeper genetic sampling including large numbers of independent loci from throughout the genome (i.e. a phylogenomic approach).     

BIO::Phylo-phyloinformatic analysis using perl

Background  

Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces.     

Anomala trapezifera species-group: a burst of diversity (Coleoptera: Scarabaeidae: Rutelinae)

The species Anomala aereiventris n. sp., A. aspersa n. sp., A. atrivillosa n. sp., A. clarivillosa n. sp., A. contusa n. sp., A. eusticta n. sp., A. hiata n. sp., A. latifalculata n. sp., A. leopardina n. sp., A. levicollis n. sp., A. longisacculata n. sp., A. m-fuscum n. sp., A. perspicax n. sp., A. piccolina n. sp., A. globulata n. sp., A. stillaticia n. sp., A. subridens n. sp., A. subusta n. sp., A. tenoriensis n. sp., A. tuberculata n. sp. and A. vallisneria n. sp. from Costa Rica are described. These species and A. polygona Bates 1888, A. trapezifera Bates 1888 and A. vulcanicola Ohaus 1897 are placed in a new species-group, named after A. trapezifera, whose diagnosis is provided. Their distribution patterns are discussed.     

Photochemistry of heteropoly electrolytes: the 1:12 tungstates

1:12 tungstates are photosensitive in near visible and ultra-violet areas at the oxygen to metal charge transfer bands, in the presence of a great variety of organic reagents. Photosensitivity results in multi- electoral reduction of tungstates with concomitant oxidation of oganic compounds. Photosensitivity follows the order PW₁₂O_4o^3? > SiW₁₂O_4o^4? > FeW₁₂O_4o^5? > H₂W₁₂O_4o^6?, which is the same order with the increasing negative redox potentials. Maximum quantum yield ～ 15% is obtained with high concentrations of organic reagents (1–10 M). The reduced heteropoly compounds (HPC) are eacily re-oxidized by atmospheirc oxygen. They are also capable of reducing hydrogen ions and this limits the extent of photoreduction.     

O-ethylidene-D-allopyranoses: 1,2-O-,1,2:4,6-, and 2,3:4,6-di-O-ethylidene derivatives

Solutions of 1,2-O-acetoxonium chlorides derived from O-acetylated D-allopyranose derivatives were treated with sodium borohydride to give three pairs of previously unknown 1,2-O-ethylidene-α-D-allopyranose diastereoisomers: 3,4,6-tri-O-acetyl-1,2-O-ethylidene-α-D-allopyranoses; 4,6-di-O-acetyl-3-O-benzyl-1,2-O-ethylidene-α-D-allopyranoses; and 3-O-benzyl-1,2:4,6-di-O-ethylidene-α-D-allopyranoses. Examples of a second class of novel O-ethylidene-D-allopyranoses, the diastereoisomeric methyl 2,3:4,6-di-O-ethylidene-α-D-allopyranosides, were prepared by treating methyl 4,6-O-benzylidene-α-D-alloside with acetaldehyde-sulfuric acid. Assignments of dioxolane ring configurations and pyranose conformations were made by n.m.r. analyses.     

Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines

Background

To reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results.

Results

Log::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution. It can also be used to compare the environments of two executions to determine whether there were any differences that might affect (or explain) their operation.

Availability

The source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/).

Conclusion

Using Log::ProgramInfo in programs creating result data for publishable research, and including the Log::ProgramInfo output log as part of the publication of that research is a valuable method to assist others to duplicate the programming environment as a precursor to validating and/or extending that research.

     

Unexpected distribution patterns of Carduiceps feather lice (Phthiraptera: Ischnocera: Philopteridae) on sandpipers (Aves: Charadriiformes: Scolopacidae)

The louse genus Carduiceps Clay & Meinertzhagen, 1939 is widely distributed on sandpipers and stints (Calidrinae). The current taxonomy includes three species on the Calidrinae (Carduiceps meinertzhageni, Carduiceps scalaris, Carduiceps zonarius) and four species on noncalidrine hosts. We estimated a phylogeny of four of the seven species of Carduiceps (the three mentioned above and Carduiceps fulvofasciatus) from 13 of the 29 hosts based on three mitochondrial loci, and evaluated the relative importance of flyway differentiation (same host species has different lice along different flyways) and flyway homogenization (different host species have the same lice along the same flyway). We found no evidence for either process. Instead, the present, morphology‐based, taxonomy of the genus corresponds exactly to the gene‐based phylogeny, with all four included species monophyletic. Carduiceps zonarius is found both to inhabit a wider range of hosts than wing lice of the genus Lunaceps occurring on the same group of birds, and to occur on Calidris sandpipers of all sizes, both of which are unexpected for a body louse. The previously proposed family Esthiopteridae is found to be monophyletic with good support. The concatenated dataset suggests that the pigeon louse genus Columbicola may be closely related to the auk and diver louse genus Craspedonirmus. These two genera share some morphological characters with Carduiceps, but no support was obtained for grouping these three genera together. Based on mitochondrial data alone, the relationships among genera within this proposed family cannot be properly assessed, but some previously suggested relationships within this proposed family are confirmed.     

World revision of Dolichocolon Brauer & Bergenstamm (Diptera: Tachinidae: Exoristinae: Goniini)

The Palaeotropical goniine genus Dolichocolon Brauer & Bergenstamm is revised and analysed cladistically. Seventeen new species are described from Australia (Queensland, Northern Territory), Cameroon, China, the Democratic Republic of Congo, Ethiopia, Japan, Papua New Guinea, Senegal, Thailand, Uganda, Yemen, and Zimbabwe. The following new synonymy is proposed after direct comparison of primary types: Dolichocolon klapperichi Mesnil, 1967 = Dolichocolon orientale Townsend, 1927 syn. nov. A key to the 21 known species is presented. A cladistic analysis based on 36 morphological characters provides support for the monophyly of Dolichocolon. A sister‐group relationship is indicated between Dolichocolon and Kuwanimyia Townsend, whereas Dolichocolon chiangmaiensis sp. nov. from Thailand takes a position as sister group to all other Dolichocolon species. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 544–584.     

EMPIRE: a highly parallel semiempirical molecular orbital program: 2: periodic boundary conditions

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The Iberian Peninsula: ancient history of a hot spot of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi: Sironidae) diversity

The Iberian Peninsula represents a hot spot of cyphophthalmid (mite harvestman) disparity, with four of the eight genera currently recognized in the family Sironidae represented in the region – a generic diversity and morphological disparity not found in any other region of the World so far. From these, two genera (Iberosiro and Odontosiro) are monotypic, and are restricted to the western side of the peninsula. Parasiro is restricted to the north‐east region, from the Catalonian Coastal Ranges and both sides of the Eastern Pyrenees, in areas where the annual rainfall surpasses 1000 mm, and mostly restricted to areas with Paleozoic and Variscan rocks, with other species of the genus extending to Corsica, Sardinia, and the Italian Peninsula. A second species of the genus Paramiopsalis, Paramiopsalis eduardoi sp. nov. from Fragas do Eume, is described here along with a re‐diagnosis of the genus. Paramiopsalis species, together with Odontosiro, inhabit the north‐west corner of the Iberian Peninsula, an area with some of the highest recorded annual rainfall, and with Paleozoic rocks from the Iberian Massif or Variscan granitoid rocks. A phylogenetic analysis of the members of the family Sironidae using four molecular markers, despite not including all of the Iberian genera, clearly shows the non‐monophyly of the Iberian Cyphophthalmi, indicating that the Iberian Peninsula is home to multiple ancient lineages of mite harvestmen. The two Paramiopsalis species form a sister clade to the Balkan genus Cyphophthalmus, whereas Parasiro constitutes the first lineage of the sironids represented.