Diversity of Biomphalaria spp. freshwater snails and associated mollusks in areas with schistosomiasis risk, using molecular and spatial analysis tools

The Middle Paranapanema River region of São Paulo, Brazil is home to significant diversity of Biomphalaria species and is very vulnerable to health and environmental impacts such as schistosomiasis. This study updates freshwater malacological surveys for ecosystems in one portion of the Middle Paranapanema River Basin, with emphasis on the genus Biomphalaria. Snails were collected from 114 distinct bodies of water between 2015 and 2018. Biomphalaria specimens were identified according to morphological and molecular characteristics, while animals in other genera (Drepanotrema, Lymnaea, Melanoides, Physa and Pomacea) were identified solely according to shell characteristics. A geographic information system was used to update intermediate host colonization sites and consequently assist in identifying probable hotspots for intermediate hosts of schistosomiasis. The sequences of the COI gene relating to the DNA barcode stretch were tested for similarity against sequences found in GenBank, for monophyly through Maximum Likelihood phylogenetic inference, and analyzed in ABDG, bPTP and GMYC for the delimitation of putative species. Of the 10,722 snails collected, 86.7% were in the Planorbidae family (75.5% Biomphalaria and 11.2% Drepanotrema) and 13.3% were other non-Planorbidae species (Lymnaea, Melanoides, Physa and Pomacea). The taxonomic COI reference sequences in the NCBI nucleotide database used for DNA sequence comparison, and phylogenetic analysis used to test the monophyly of the groups, resulted in more reliable taxonomic units than delimitation of the COI sequences in MOTUs using statistical taxonomic models. Analysis of the species distribution shows that B. glabrata and B. tenagophila are heterogeneously distributed in the study area. B. glabrata colonizes only five water bodies, in the study area, most of them in Ourinhos, while B. tenagophila predominates in water bodies in Ipaussu. Contrasting with this, B. straminea, B. occidentalis and B. peregrina are evenly distributed throughout the study area.

Geosmithia species associated with fir-infesting beetles in Poland

<em>Geosmithia</em> species (Ascomycota: Hypocreales) are common ectosymbionts of scolytine bark and ambrosia beetles that feed on coniferous and deciduous trees in different forest ecosystems. <em>Geosmithia morbida</em> is the canker pathogen that causes extensive mortality of <em>Juglans nigra</em>. Because little is known regarding the <em>Geosmithia</em> species on European silver fir (<em>Abies alba</em>), we have investigated the diversity and abundance of these fungi associated with insects infesting European silver fir in Poland. Samples associated with eight beetle species were collected from three fir forests. Fungi were isolated from beetles and galleries. Isolates were identified based on morphological characteristics, DNA sequence comparison for three gene regions (ITS, ßT, TEF1-α), and phylogenetic analyses. <em>Geosmithia</em> was detected in 33% of the total 531 beetle samples obtained from <em>A. alba</em>. Two undescribed species of <em>Geosmithia</em> were distinguished, <em>Geosmithia</em> sp. 9 and <em>Geosmithia</em> sp. 16. Associations of <em>Pityokteines</em> spp. with <em>Geosmithia</em> fungi were recorded for the first time. <em>Pityokteines vorontzowi</em> and <em>Pityophthorus pityographus</em> appear to be regular vectors for <em>Geosmithia</em> sp. 9 and <em>Geosmithia</em> sp. 16, respectively. <em>Pityokteines curvidens</em> and <em>Cryphalus piceae</em> were associated with <em>Geosmitha</em> sp. 9 at lower frequencies.

Use of Fuzzy Set Theory in DNA Sequence Comparison and Amino Acid Classification

This chapter describes the use of fuzzy set theory and intuitionistic fuzzy set theory in DNA sequence comparison. It also shows an indirect application of fuzzy set theory in comparing protein sequences. In fact, protein sequences consist of 20 amino acids. The chapter shows how such amino acids can be classified in six different groups. These groups are obtained purely from theoretical considerations. These are entirely different from the known groups of amino acids based on biological considerations. Also it is known how these classified groups of amino acids help in protein sequence comparison. The results of comparison differ as the groups differ in number and their compositions. Naturally it is expected that newer results of comparison will come out from such newer classified groups of amino acids obtained theoretically. Thus fuzzy set theory is also useful in protein sequence comparison.

Ophiostomatoid fungi isolated from fallen shoots of Scots pine pruned by Tomicus species in Poland

Ophiostomatoid fungi are known to be associated with <em>Tomicus</em> spp. on <em>Pinus sylvestris</em>. However, very little is actually known about the fungi present in the pine shoots damaged by these insects. The aim of this study was to survey species of <em>Ophiostoma</em> s.lato associated with fallen shoots of Scots pine pruned by <em>Tomicus</em> spp. in Poland. The study was conducted in four pure Scots pine stands in southern and south-western part of the country. Fungi were identified based on morphology and DNA sequence comparison for two gene (the ITS rDNA region and ß–tubulin). In total, 64 isolates obtained, represent seven species of ophiostomatoid fungi, including their asexual states of the genera. Two of them, <em>Ophiostoma</em> sp. 1 and <em>Sporothrix</em> sp. 1 probably represent new taxa. All species were found at very low frequencies. Among them, <em>Ophiostoma minus, Ophiostoma</em> sp. 1 and <em>Sporothrix</em> sp. 1 were the most frequently isolated, with a frequency of 2.0%. Occasionally, isolated species included <em>Leptographium piriforme, Ophiostoma canum, Ophiostoma floccosum</em> and <em>Grosmannia cucullata</em>-like. Association of species of Ophiostoma s. lato with <em>Tomicus</em> spp. and the taxonomic status of two new species are discussed.

DNA sequence comparison based on Tabular Representation

DNA sequence comparison remains as one of the critical steps in the analysis of phylogenetic relationships between species. In order to get quantitative comparison, we want to devise an algorithm that would use the tabular representation of DNA sequences. The tabular approach of representation captures the essence of the base composition and distribution of the sequence. In this contribution, we take the tabular notation for DNA sequences and then these tables are compared to find the similarity/dissimilarity measure of the sequences. We have developed algorithms for comparing DNA sequences. These programs help us to search similar segments of sequences, calculate similarity scores and identify repetitions based on local sequence similarity. There are two approaches: one is to find the exact similarity and another is to find the measurement for similarity. The first approach is more sensitive, which can be used to search DNA sequence similarities only if complete matches occurred and can compare exactly similar sequences only. This approach violates if a single mismatch for any base character appears so it is not a general solution. To find the miss matches along with the matches we have suggested another approach which compiles the information matrix based on matches and miss matches. This approach is quiet general in terms of sequences which have a large fragment common with less no of dissimilar base characters. This alternate approach includes an additional step in the calculation of the similarity score that denotes multiple regions of similarity between sequences. For both these approaches computer programs are prepared and tested on data sets. These programs can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. In addition, these programs have been generalized to allow comparison of DNA sequences based on a variety of alternative scoring matrices. We have been developing tools for the analysis of protein The method is very simple and fast, and it can be used to analyze both short and long DNA sequences. The utility of this method is tested on the several sequences of species and the results are consistent with that reported.