Bioaerosol assessment in the library of Istanbul University and fungal flora associated with paper deterioration

Health problems in people who are in indoor environments with poor ventilation have resulted in an increase in the number of studies regarding air quality. Microorganisms and inferior indoor air-climatic conditions not only affect human health but also cause decay of invaluable materials present in libraries. Therefore, this study aimed to assess the culturable bioaerosol composition and concentration in the library of Istanbul University. The culturable fungal flora, a biodeterioration agent, of the damaged archival materials was also examined. The air was sampled for a year, as were the surfaces of 207 biologically damaged books. The fungal colonies’ range was between 235 and 1850 CFU/m³, and the bacterial colonies range between 270 and 1920 CFU/m³. This is the first volumetric record in Turkey. Although the microbial contamination was not very high, molds such as Aspergillus versicolor, Cladosporium sphaerospermum, Penicillium chrysogenum, Alternaria alternata, Chaetomium globosum, Aspergillus flavus, and Aspergillus ochraceus might cause harm to human beings or to books as biodeterioration agents. The highest amount of fungus was determined in Archive 3, which contained damaged books. The fungal species isolated from the air and books were essentially the same. Therefore, it is important to determine not only the numeric values but also the microbiological composition of fungal colonies because the variety of fungal species is indicative of a deterioration process in effect over a long period. The deterioration of books must be remedied.     

Characterization of a Trypanosoma cruzi genomic fragment complementary to several species-specific mRNAs but different from the spliced leader sequence

We have isolated a clone of Trypanosoma cruzi genomic DNA, lambda 3b2-5, which contains sequences that are reiterated in the genome. Northern blot analysis showed that clone 3b2-5 hybridizes to 1,200-5,000 bases different mRNA species. The number of mRNAs species hybridized to clone 3b2-5 exceeds its coding capacity showing that this clone carries sequences that are common to several mRNAs species and conserved in the poly A(+) RNA. These sequences are not homologous to the T. cruzi spliced leader sequence, since clone 3b2-5 does not hybridize to a synthetic 20 nucleotide complementary to the spliced leader sequence. Clone 3b2-5 does not hybridize to DNA and RNA from several genera of Trypanosomatidae and other Trypanosoma species indicating that it carries T. cruzi species-specific sequences.     

PCRless library mutagenesis via oligonucleotide recombination in yeast

The directed evolution of biomolecules with new functions is largely performed in vitro, with PCR mutagenesis followed by high-throughput assays for desired activities. As synthetic biology creates impetus for generating biomolecules that function in living cells, new technologies are needed for performing mutagenesis and selection for directed evolution in vivo. Homologous recombination, routinely exploited for targeted gene alteration, is an attractive tool for in vivo library mutagenesis, yet surprisingly is not routinely used for this purpose. Here, we report the design and characterization of a yeast-based system for library mutagenesis of protein loops via oligonucleotide recombination. In this system, a linear vector is co-transformed with single-stranded mutagenic oligonucleotides. Using repair of nonsense codons engineered in three different active-site loops in the selectable marker TRP1 as a model system, we first optimized the recombination efficiency. Single-loop recombination was highly efficient, averaging 5%, or 4.0×10(5) recombinants. Multiple loops could be simultaneously mutagenized, although the efficiencies dropped to 0.2%, or 6.0×10(3) recombinants, for two loops and 0.01% efficiency, or 1.5×10(2) recombinants, for three loops. Finally, the utility of this system for directed evolution was tested explicitly by selecting functional variants from a mock library of 1:10(6) wild-type:nonsense codons. Sequencing showed that oligonucleotide recombination readily covered this large library, mutating not only the target codon but also encoded silent mutations on either side of the library cassette. Together these results establish oligonucleotide recombination as a simple and powerful library mutagenesis technique and advance efforts to engineer the cell for fully in vivo directed evolution.     

A reliable DNA barcode reference library for the identification of the North European shelf fish fauna

Valid fish species identification is an essential step both for fundamental science and fisheries management. The traditional identification is mainly based on external morphological diagnostic characters, leading to inconsistent results in many cases. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for a valid identification of 93 North Atlantic fish species originating from the North Sea and adjacent waters, including many commercially exploited species. Neighbour‐joining analysis based on K2P genetic distances formed nonoverlapping clusters for all species with a ≥99% bootstrap support each. Identification was successful for 100% of the species as the minimum genetic distance to the nearest neighbour always exceeded the maximum intraspecific distance. A barcoding gap was apparent for the whole data set. Within‐species distances ranged from 0 to 2.35%, while interspecific distances varied between 3.15 and 28.09%. Distances between congeners were on average 51‐fold higher than those within species. The validation of the sequence library by applying BOLDs barcode index number (BIN) analysis tool and a ranking system demonstrated high taxonomic reliability of the DNA barcodes for 85% of the investigated fish species. Thus, the sequence library presented here can be confidently used as a benchmark for identification of at least two‐thirds of the typical fish species recorded for the North Sea.     

Monitoring microbial aeroflora using vegetable waste media: an ecological aspect

For isolation of aeromicroflora in ecologically different zones, a liquid vegetable waste, deproteinised leaf juice (DLJ) was used instead of usual media. DLJ samples from three different plants, cowpea (Vigna sinensis), turnip (Brassica campestris) and radish (Raphanus sativus), were used in order to determine their efficiency as potential growth media for different types of microbes. Four different ecological zones of West Bengal, India were selected to study the aeromicroflora. The zones were as follows: (i) densely populated and industrially polluted Calcutta (CAL); (ii) plateau region of western part of the state (WEST); (iii) Terai region of Northern Bengal (TER); (iv) sandy coastal zone of Midnapore district of Southern Bengal (SB). Each zone was subdivided into three subzones. The variation in population of fungi, bacteria and actinomycetes among these zones was studied. The relative abundance and species diversities of microbes were noted. The study indicates that pollution and ecological diversity both play important roles in controlling the above two factors.     

Phylogenesis of spermatogenesis in Annulipalpia caddisflies: An ultrastructural analysis on philopotamidae spermiogenesis

Characters currently used in phylogenetic analyses are insufficient for determining the status of several families of the order Trichoptera (caddisflies). Comparative spermatology can contribute to solving this problem. In the suborder Integripalpia, the sperm axoneme displays the pattern of 9 + 2 pairs of parallel microtubules found in many animal species. In the suborder Annulipalpia, however, axonemes bear remarkable aberrations. Consistently, in Chimarra florida (Philopotamidae, Annulipalpia) we found that the number of central microtubules varies from zero to four in axonemes of the spermatids and that spermatozoa lack axonemes. We propose that, similarly, the axoneme pattern became unstable in the Annulipalpia ancestor, from which branched two phylogenetic lines having different kinds of axoneme aberrations: (a) families in which the number of central microtubules of the axoneme exceeds two (e.g., Philopotamidae, Polycentropodidae) and (b) families in which the number of central microtubules of the axoneme does not exceed two (e.g., Hydropsychidae).     

Olive Knot Pathogen with Pronounced Epiphytic Lifestyle is not Present in Association to Leaf Surface of European Olive Across the Himalayas in Nepal

Pseudomonas savastanoi pv. savastanoi, the causal agent of olive knot disease, often switches from a saprophytic to a parasitic lifestyle only following natural or man‐made activities, that cause lesions on plant tissues. We investigated the possible presence of this pathogen on the phylloplane of 28 Italian olive cultivars, recently introduced to Nepal. Although a consistent number of bacterial species were found in association with leaf, there was no presence of olive knot pathogen across the study area. The results suggest that the introduction of a new plant species in a given area does not necessarily introduce the pathogen when the propagation materials are rigorously supervised for pathogen exclusion.     

RECENT ORNITHOLOGICAL PUBLICATIONS

Most of the books noted below are available for reference at the Alexander Library of the Edward Grey Institute of Field Ornithology, Department of Zoology, South Parks Road, Oxford; this library is open to BOU members, Monday to Friday (09.00–17.00 h); visitors are asked to write or telephone (01865 271143) in advance to ensure the library is open.
The library's aim is to build up a comprehensive collection of literature, so that it may be of maximum service to ornithologists. Its holdings include an extensive range of periodicals and a large number of reprints drawn from many sources; additional reprints of readers' papers are always most welcome. It has always greatly benefited from its close association with the BOU. For a number of years all journals received in exchange for Ibis have been deposited in the library, as also, through the generosity of reviewers, are most books sent for review.
In return, as a service to readers, the Recent Ornithological Publications section of Ibis is organized and edited by Dr J. Blakey, Dr M. L. Birch and Prof. C. M. Perrins of the Edward Grey Institute, with the help of a panel of contributors. They are always grateful for offers of further assistance with abstracting, especially with foreign language books and, likewise, offers to help compile the Recent Literature Supplement, in collaboration with the AOU and RAOU, are always welcome.     

RECENT ORNITHOLOGICAL PUBLICATIONS

Most of the books noted below are available for reference at the Alexander Library of the Edward Grey Institute of Field Orni-thology, Department of Zoology, South Parks Road, Oxford; this library is open to BOU members, Monday to Friday (09.00–17.00h); visitors are asked to write or telephone (01865271143) in advance to ensure the library is open.
The library's aim is to build up a comprehensive collection of literature, so that it may be of maximum service to ornitholo-gists. Its holdings include an extensive range of periodicals and a large number of reprints drawn from many sources; additional reprints of readers' papers are always most welcome. It has always greatly benefited from its close association with the BOU. For a number of years all journals received in exchange for Ibis have been deposited in the library. as also, through the generosity of reviewers, are most books sent for review.
In return, are a service to readers, the Recent Ornithological Publications section of Ibis is organized and edited by Dr J. Briskie, Dr. M. L. Birch and Prof C.M. Perrins ofthe Edward Grey Institute with the help of a panel of contributors. They are always grateful for offers of further assistance with reviews, especially with foreign language books and, likewise, offers to help compile the Recent Literature Supplement. in collabation with the AOU and the AOU and RAOU, are always welcome.     

Functional Characterization of Drosophila microRNAs by a Novel in Vivo Library

Animal microRNAs (miRNA) are implicated in the control of nearly all cellular functions. Due to high sequence redundancy within the miRNA gene pool, loss of most of these 21- to 24-bp long RNAs individually does not cause a phenotype. Thus, only very few miRNAs have been associated with clear functional roles. We constructed a transgenic UAS-miRNA library in Drosophila melanogaster that contains 180 fly miRNAs. This library circumvents the redundancy issues by facilitating the controlled misexpression of individual miRNAs and is a useful tool to complement loss-of-function approaches. Demonstrating the effectiveness of our library, 78 miRNAs induced clear phenotypes. Most of these miRNAs were previously unstudied. Furthermore, we present a simple system to create GFP sensors to monitor miRNA expression and test direct functional interactions in vivo. Finally, we focus on the miR-92 family and identify a direct target gene that is responsible for the specific wing phenotype induced by the misexpression of miR-92 family members.     

Random AT library: autonomously replicating sequence (ARS) activity of chemically synthesized random sequences for transformation of nonconventional yeast species

In a search for sequences that confer on bacterial plasmids the capacity of autonomous replication in yeast cells, we chemically synthesized polynucleotides 80 bp in length from an equimolar mixture of A and T. The random AT-polymer population, W80, was inserted into the plasmid YIp5-Kan1 (which carries the markers URA3 and G418(R), but does not replicate in yeast) and amplified in Escherichia coli. This library, representing 10 000 different AT sequences, was transformed into three species of yeast: Saccharomyces cerevisiae, Kluyveromyces lactis and Torulaspora delbrueckii. The aim was to evaluate the frequency, if any, of autonomously replicating sequences (ARSs) in the random sequences. A large number of transformants were obtained from each species. Many of them showed a stable transformed phenotype. Several W80 sequences were found many times for a given species, suggesting that each species preferred particular sequences for ARS function, although they are diverse in their primary sequence. In view of the high frequency and stability of the replicative plasmids found in the different hosts, this small random AT library may be conveniently used as a source of replicative gene vectors for genetic manipulation of many nonconventional yeast species, in place of searching for species-specific chromosomal ARSs.     

Patterns of ESS's. I

A matrix may have several evolutionarily stable strategies (ESS's). It is thus possible for different populations of a species to adopt a different ESS even when the pay-offs for the populations are the same. The occurrence of different strategies does not imply different circumstances. However, there are constraints upon the collection of supports of the ESS's (i.e. pattern) that any matrix can have. The best-known of these is that the support of one ESS cannot be contained in that of another and this gives bounds on the number of different patterns possible for n x n matrices. Other general constraints are presented here. The enumeration of the patterns for 3 x 3 and 4 x 4 matrices is completed and considerable progress made on 5 x 5 matrices where the number of (permutationally distinct, maximal) patterns exceeds 16.     

细胞dNTP库的稳态维持与基因组稳定性

作为DNA合成的重要前体,细胞中4种脱氧核糖核苷三磷酸(dATP、dTTP、dGTP和dCTP)是DNA复制、重组和修复所必需的原材料,而DNA的正确合成及其完整性则是基因组稳定性的重要体现,因此dNTP库状态的稳定对维持基因组的稳定进而保证细胞的稳定至关重要.从dNTP库的质量上讲,一些异质dNTP如氧化的dNTP掺...     

Across islands and continents,mammals are more successful invaders than birds

Many invasive species cause ecological or economic damage, and the fraction of introduced species that become invasive is an important determinant of the overall costs caused by invaders. According to the widely quoted tens rule, about 10% of all introduced species establish themselves and about 10% of these established species become invasive. Global taxonomic differences in the fraction of species becoming invasive have not been described. In a global analysis of mammal and bird introductions, I show that both mammals and birds have a much higher invasion success than predicted by the tens rule, and that mammals have a significantly higher success than birds. Averaged across islands and continents, 79% of mammals and 50% of birds introduced have established themselves and 63% of mammals and 34% of birds established have become invasive. My analysis also does not support the hypothesis that islands are more susceptible to invaders than continents, as I did not find a significant relationship between invasion success and the size of the island or continent to which the species were introduced. The data set used in this study has a number of limitations, e.g. information on propagule pressure was not available at this global scale, so understanding the mechanisms behind the observed patterns has to be postponed to future studies.     

TESTING ADAPTIVE RADIATION AND KEY INNOVATION HYPOTHESES IN SPIDERS

We combine statistical and phylogenetic approaches to test the hypothesis that adaptive radiation and key innovation have contributed to the diversity of the order Araneae. The number of unbalanced araneid clades (those whose species numbers differ by 90% or more) exceeds the number predicted by a null Markovian model. The current phylogeny of spider families contains 74 bifurcating nodes, of which 31 are unbalanced. As this is significantly more than the 14.8 expected unbalanced nodes, some of the diversity within the Araneae can be attributed to some deterministic cause (e.g., adaptive radiation). One of the more highly unbalanced (97%) bifurcations divides the orb-weaving spiders into the Deinopoidea and the larger Araneoidea. A simple statistical model shows that the inequality in diversity between the Deinopoidea and the Araneoidea is significant, and that it is associated with the replacement of primitive cribellar capture thread by viscous adhesive thread and a change from a horizontal to a vertical orb-web orientation. These changes improve an orb-web's ability to intercept and retain prey and expand the adaptive zone that orb-weaving spiders can occupy and are, therefore, considered to be “key innovations.”     

The art of observing rare protein species in proteomes with peptide ligand libraries

The present review deals with the use of combinatorial ligand libraries, composed by hexapeptides, in the capture and concentration of the low‐abundance proteome. This method, first reported in 2005, is compared with other current methodologies aimed at exploring the “deep proteome”, such as: depletion of high‐abundance proteins (especially in sera and cerebrospinal fluid) by individual or combined antibodies (up to 20 against the most abundant species); narrow (1‐pH‐unit) IPGs (zoom gels) and prefractionation with multicompartment electrolyzers or with Off‐Gel electrophoresis. The physico‐chemical properties of the hexapeptide library are also explored, namely in assessing the proper length of the baits and the behavior of shorter oligopeptides, down to capture elicited by single amino acids. A number of examples on the use of this library is given, such as the analysis of biological fluids (human sera, urine, bile, cerebrospinal fluid) and of cell lysates (platelets, red blood cells). In all cases, it was possible to detected from three to five times as many proteins as compared to control, untreated samples. Perhaps the most spectacular results were obtained with the erythrocyte proteome, where 1570 proteins could be identified in the “minority” proteome, representing only 2% of the total cell lysate. Another interesting area of application regards the concentration and detection of trace impurities contaminanting r‐DNA proteins meant for human consumption: several host proteins, never reported before, could be revealed for the first time. Other nonhuman samples are currently under investigation, such as egg‐white (where no less than 148 unique gene products could be identified), egg yolk (with 255 unique species) and latex from Hevea brasiliensis. It is anticipated that the ligand library could be a most useful tool for detecting biomarkers for different pathologies and for drug treatment. As a future outlook, one could envision the synthesis of specialized libraries able to capture given classes of proteins (e.g., phospho‐ and glyco‐proteins). Additionally, the library could be used in association with other techniques currently in vogue, such as zoom gels, Off‐Gels, and the like.     

9th Annual Symposium on Advances in Separation Science and Mass Spectrometry

Evaluation of: Di Girolamo F, Boschetti E, Chung MC, Guadagni F, Righetti PG. ‘Proteomineering’ or not? The debate on biomarker discovery in sera continues. J. Proteomics 74(5), 589–594 (2011).

The combinatorial peptide ligand library in association with mass spectrometry can greatly enhance the dynamic range of the analysis of low- and very low-abundance proteins constituting the vast majority of species in any sample. When compared with untreated samples, the increment in detection of low-abundance species appears to be at least fourfold. Recently, the combinatorial peptide ligand library has been challenged; however, it has been clearly demonstrated in the evaluated paper that the protocols for elution of the captured polypeptides make the difference. Therefore, the solid-phase ligand library made of hexapeptides remains a promising and unique tool for biomarker discovery.