TreeView: an application to display phylogenetic trees on personal computers

Revision of the systematics of the Polystomoidinae (Platyhelminthes, Monogenea, Polystomatidae) with redefinition of Polystomoides Ward, 1917 and Uteropolystomoides Tinsley, 2017

Polystomatids are platyhelminth parasites that infect mainly amphibians and freshwater turtles. For more than seven decades, chelonian polystomes were classified into three genera according to the number of hamuli, i.e. absent for Neopolystoma, one pair for Polystomoidella and two pairs for Polystomoides. Following re-examination of morphological characters, seven new genera were erected the past six years, namely Apaloneotrema, Aussietrema, Fornixtrema, Manotrema, Pleurodirotrema, Uropolystomoides and Uteropolystomoides. However, the polyphyly of Neopolystoma and Polystomoides on the one hand, and the nested position of Uteropolystomoides within a clade encompassing all Neopolystoma and Polystomoides spp. on the other, still raised questions about the validity of these genera. We therefore re-examined several types, paratypes and voucher specimens, and investigated the molecular phylogeny of polystomes sampled from the oral cavity of North American turtles to re-evaluate their systematic status. We show that all Polystomoides Ward, 1917, sensu Du Preez et al., 2022, Neopolystoma Price, 1939, sensu Du Preez et al., 2022 and Uteropolystomoides Tinsley, 2017 species, display vaginae that are peripheral and extend well beyond the intestine. We thus reassign all species of the clade to Polystomoides and propose nine new combinations; however, although Uteropolystomoides is nested within this clade, based on its unique morphological features, we propose to keep it as a valid taxon. Polystomoides as redefined herein groups all polystome species infecting either the oral cavity or the urinary bladder of cryptodires, with peripheral vaginae and with or without two pairs of small hamuli. Uteropolystomoides nelsoni (Du Preez & Van Rooyen 2015), originally described from Pseudemys nelsoni Carr is now regarded as Uteropolystomoides multifalx (Stunkard, 1924) n. comb. infecting three distinct Pseudemys species of North America.

First Report of Aphelenchoides Bicaudatus (Imamura, 1931) Filipjev and Schuurmans Stekhoven, 1941 Associated with Grass in South Africa

Aphelenchoides bicaudatus associated with grass in South Africa was identified morphologically and molecularly. This population is characterized by a body length of 409 - 529 μm, a stylet length of 9.5 - 13 μm, a post-vulval uterine sac of 45 - 50 μm, and the characteristic tail bifurcated at the end with one prong longer than the other. Molecular analyses based on the 18S and ITS rDNA data confirmed the primary morphological identification of the A. bicaudatus species. The obtained phylogenetic trees revealed a close positioning of the South African population to other representatives of A. bicaudatus with the maximum (1.00) posterior probability value. Principal component analysis (PCA) also indicated a variation within the populations of A. bicaudatus. This is the first report of A. bicaudatus from South Africa.

Identification of a new species of Ixodes Latreille, 1795 (Acari: Ixodidae), parasite of hog badgers (Carnivora: Mustelidae) in China

Ixodes hunanensis n. sp. (Acari: Ixodidae), is identified based on the morphological characteristics and molecular biological analyses of males and females ex hog badger, Arctonyx collaris Cuvier (Carnivora: Mustelidae) from China. Adults of this new species are similar to those of other species of the subgenus Pholeoixodes Schulze, 1942, from which they can be distinguished by the shape of basis capituli, development of cornua, size of porose areas, shape, and size of spurs on coxae and phylogenetic analyses of the cox1 and 16S rRNA sequences.

Vetinformatics from functional genomics to drug discovery: Insights into decoding complex molecular mechanisms of livestock systems in veterinary science

Having played important roles in human growth and development, livestock animals are regarded as integral parts of society. However, industrialization has depleted natural resources and exacerbated climate change worldwide, spurring the emergence of various diseases that reduce livestock productivity. Meanwhile, a growing human population demands sufficient food to meet their needs, necessitating innovations in veterinary sciences that increase productivity both quantitatively and qualitatively. We have been able to address various challenges facing veterinary and farm systems with new scientific and technological advances, which might open new opportunities for research. Recent breakthroughs in multi-omics platforms have produced a wealth of genetic and genomic data for livestock that must be converted into knowledge for breeding, disease prevention and management, productivity, and sustainability. Vetinformatics is regarded as a new bioinformatics research concept or approach that is revolutionizing the field of veterinary science. It employs an interdisciplinary approach to understand the complex molecular mechanisms of animal systems in order to expedite veterinary research, ensuring food and nutritional security. This review article highlights the background, recent advances, challenges, opportunities, and application of vetinformatics for quality veterinary services.

B cell lymphoma 6A regulates immune development and function in zebrafish

BCL6A is a transcriptional repressor implicated in the development and survival of B and T lymphoctyes, which is also highly expressed in many non-Hodgkin’s lymphomas, such as diffuse large B cell lymphoma and follicular lymphoma. Roles in other cell types, including macrophages and non-hematopoietic cells, have also been suggested but require further investigation. This study sought to identify and characterize zebrafish BCL6A and investigate its role in immune cell development and function, with a focus on early macrophages. Bioinformatics analysis identified a homologue for BCL6A (bcl6aa), as well as an additional fish-specific duplicate (bcl6ab) and a homologue for the closely-related BCL6B (bcl6b). The human BCL6A and zebrafish Bcl6aa proteins were highly conserved across the constituent BTB/POZ, PEST and zinc finger domains. Expression of bcl6aa during early zebrafish embryogenesis was observed in the lateral plate mesoderm, a site of early myeloid cell development, with later expression seen in the brain, eye and thymus. Homozygous bcl6aa mutants developed normally until around 14 days post fertilization (dpf), after which their subsequent growth and maturation was severely impacted along with their relative survival, with heterozygous bcl6aa mutants showing an intermediate phenotype. Analysis of immune cell development revealed significantly decreased lymphoid and macrophage cells in both homozygous and heterozygous bcl6aa mutants, being exacerbated in homozygous mutants. In contrast, the number of neutrophils was unaffected. Only the homozygous bcl6aa mutants showed decreased macrophage mobility in response to wounding and reduced ability to contain bacterial infection. Collectively, this suggests strong conservation of BCL6A across evolution, including a role in macrophage biology.

Orthohantaviruses in Reservoir and Atypical Hosts in the Czech Republic: Spillover Infection and Indication of Virus-Specific Tissue Tropism

Orthohantaviruses (genus Orthohantavirus) are a diverse group of viruses that are closely associated with their natural hosts (rodents, shrews, and moles). Several orthohantaviruses cause severe disease in humans. Central and western Europe are areas with emerging orthohantavirus occurrences. In our study, several orthohantaviruses, including the pathogenic Kurkino virus (KURV), were detected in their natural hosts trapped at several study sites in the Czech Republic. KURV was detected mainly in its typical host, the striped field mouse (Apodemus agrarius). Nevertheless, spillover infections were also detected in wood mice (Apodemus sylvaticus) and common voles (Microtus arvalis). Similarly, Tula virus (TULV) was found primarily in common voles, and events of spillover to rodents of other host species, including Apodemus spp., were recorded. In addition, unlike most previous studies, different tissues were sampled and compared to assess their suitability for orthohantavirus screening and possible tissue tropism. Our data suggest possible virus-specific tissue tropism in rodent hosts. TULV was most commonly detected in the lung tissue, whereas KURV was more common in the liver, spleen, and brain. Moreover, Seewis and Asikkala viruses were detected in randomly found common shrews (Sorex araneus). In conclusion, we have demonstrated the presence of human-pathogenic KURV and the potentially pathogenic TULV in their typical hosts as well as their spillover to atypical host species belonging to another family. Furthermore, we suggest the possibility of virus-specific tissue tropism of orthohantaviruses in their natural hosts. IMPORTANCE Orthohantaviruses (genus Orthohantavirus, family Hantaviridae) are a diverse group of globally distributed viruses that are closely associated with their natural hosts. Some orthohantaviruses are capable of infecting humans and causing severe disease. Orthohantaviruses are considered emerging pathogens due to their ever-increasing diversity and increasing numbers of disease cases. We report the detection of four different orthohantaviruses in rodents and shrews in the Czech Republic. Most viruses were found in their typical hosts, Kurkino virus (KURV) in striped field mice (Apodemus agrarius), Tula virus (TULV) in common voles (Microtus arvalis), and Seewis virus in common shrews (Sorex araneus). Nevertheless, spillover infections of atypical host species were also recorded for KURV, TULV, and another shrew-borne orthohantavirus, Asikkala virus. In addition, indications of virus-specific patterns of tissue tropism were observed. Our results highlight the circulation of several orthohantaviruses, including KURV, which is pathogenic to humans, among rodents and shrews in the Czech Republic.

A new study of Nagrajomyces: with two new species proposed and taxonomic status inferred by phylogenetic methods

Nagrajomyces (incertae sedis, Ascomycota) is a monotypic genus with a previously unknown systematic position. In this report, two new species are proposed, Nagrajomycesfusiformis and Nagrajomyceslaojunshanensis. These new taxa are proposed based on morphological characteristics evident via light microscopy and molecular data. Multi-locus phylogenetic analyses (ITS rDNA, nrLSU rDNA, RPB2, and TEF1-α) show that specimens recently collected in Yunnan Province, China are closely related to Gnomoniaceae. Both new species and known species were discovered repeatedly in their asexual developmental form exclusively on twigs of Rhododendron spp. (Ericaceae). This indicates a host specificity of Nagrajomyces spp. for species of Rhododendron.

Genetic and Cross Neutralization Analyses of Coxsackievirus A16 Circulating in Taiwan from 1998 to 2021 Suggest Dominant Genotype B1 can Serve as Vaccine Candidate

Coxsackievirus A16 (CVA16) is well known for causing hand-foot-and-mouth disease (HFMD) and outbreaks were frequently reported in Taiwan in the past twenty years. The epidemiology and genetic variations of CVA16 in Taiwan from 1998 to 2021 were analyzed in this study. CVA16 infections usually occurred in early summer and early winter, and showed increased incidence in 1998, 2000-2003, 2005, 2007-2008, and 2010 in Taiwan. Little or no CVA16 was detected from 2017 to 2021. CVA16 infection was prevalent in patients between 1 to 3 years old. A total of 69 isolates were sequenced. Phylogenetic analysis based on the VP1 region showed that CVA16 subgenotype B1 was dominantly isolated in Taiwan from 1998 to 2019, and B2 was identified only from isolates collected in 1999 and 2000. There was a high frequency of synonymous mutations in the amino acid sequences of the VP1 region among CVA16 isolates, with the exception of position 145 which showed positive selection. The recombination analysis of the whole genome of CVA16 isolates indicated that the 5'-untranslated region and the non-structural protein region of CVA16 subgenotype B1 were recombined with Coxsackievirus A4 (CVA4) and enterovirus A71 (EVA71) genotype A, respectively. The recombination pattern of subgenotype B2 was similar to B1, however, the 3D region was similar to EVA71 genotype B. Cross-neutralization among CVA16 showed that mouse antisera from various subgenotypes viruses can cross-neutralize different genotype with high neutralizing antibody titers. These results suggest that the dominant CVA16 genotype B1 can serve as a vaccine candidate for CVA16.

Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

Turnip mosaic virus (TuMV), an important pathogen that causes mosaic diseases in vegetable crops worldwide, belongs to the genus Potyvirus of the family Potyviridae. Previously, the areas of genetic variation, population structure, timescale, and migration of TuMV have been well studied. However, the codon usage pattern and host adaptation analysis of TuMV is unclear. Here, compositional bias and codon usage of TuMV were performed using 184 non-recombinant sequences. We found a relatively stable change existed in genomic composition and a slightly lower codon usage choice displayed in TuMV protein-coding sequences. Statistical analysis presented that the codon usage patterns of TuMV protein-coding sequences were mainly affected by natural selection and mutation pressure, and natural selection was the key influencing factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) revealed that TuMV genes were strongly adapted to Brassica oleracea from the present data. Similarity index (SiD) analysis also indicated that B. oleracea is potentially the preferred host of TuMV. Our study provides the first insights for assessing the codon usage bias of TuMV based on complete genomes and will provide better advice for future research on TuMV origins and evolution patterns.

Relationship between Phenolic Compounds and Antioxidant Activity in Berries and Leaves of Raspberry Genotypes and Their Genotyping by SSR Markers

The red raspberry is one of the world’s most popular berries. The main direction of its breeding has switched to nutritional quality, and the evaluation of raspberry germplasm for antioxidant content and activity is very important. As berries, raspberry leaves contain valuable bioactive compounds, but the optimal time for their collection is unknown. We evaluated 25 new breeding lines and standard raspberry cultivars for their polyphenolic content and antioxidant capacity. The antioxidant activity of berries correlated better with the content of total phenolics (0.88 and 0.92) and flavonoids (0.76 and 0.88) than with anthocyanins (0.37 and 0.66). Two breeding lines were significantly superior to the standard cultivars and can be used in further breeding. Leaves collected in three phenological phases of the raspberry contained more phenolics (5.4-fold) and flavonoids (4.1-fold) and showed higher antioxidant activities (2.4-fold in FRAP assay, 2.2-fold in ABTS) than berries. The optimal time for harvesting raspberry leaves is the fruit ripening stage, with exceptions for some cultivars. Genetic diversity analysis using microsatellite (SSR) markers from flavonoid biosynthesis genes divided the genotypes into five clusters, generally in agreement with their kinships. The relationship between genetic data based on metabolism-specific SSR markers and the chemical diversity of cultivars was first assessed. The biochemical and genetic results show a strong correlation (0.78). This study is useful for further the improvement of raspberry and other berry crops.

Two new forest pathogens in Phaeolus (Polyporales, Basidiomycota) on Chinese coniferous trees were confirmed by molecular phylogeny

Phaeolus schweinitzii (Fr.) Pat. was originally described in Europe and is considered a common forest pathogen on conifers in the Northern Hemisphere. Our molecular phylogeny based on samples from China, Europe, and North America confirms that P. schweinitzii is a species complex, including six taxa. P. schweinitzii sensu stricto has a distribution in Eurasia; the samples from Northeast and Southwest China are distantly related to P. schweinitzii sensu stricto, and two new species are described after morphological, phylogenetic, and geographical analyses. The species growing on Larix, Picea, and Pinus in Northeast China is described as Phaeolus asiae-orientalis. Another species mostly occurring on Pinus yunnanensis in Southwest China is Phaeolus yunnanensis. In addition, three taxa distributed in North America differ from P. schweinitzii sensu stricto. Phaeolus tabulaeformis (Berk.) Pat. is in Southeast North America, “P. schweinitzii-1” in Northeast North America, and “P. schweinitzii-2” in western North America.

Molecular Character of Mylonchulus hawaiiensis and Morphometric Differentiation of Six Mylonchulus (Nematoda; Order: Mononchida; Family: Mylonchulidae) Species Using Multivariate Analysis

Mononchida members are predatory nematodes with the potential to reduce the number of plant-parasitic nematodes in the soil. During a survey on Mononchida in Iran, several populations of Mylonchulus were recovered from various localities. A population of M. hawaiiensis was studied using 18S rDNA. The phylogenetic analysis using Bayesian inference placed the sequenced M. hawiinesis (OP210758) together with other M. hawaiiensis from Japan (AB361438-AB361442) with a 1.00 posterior probability support. In addition, morphological differences between six Mylonchulus (Nematoda; order: Mononchida; Family: Mylonchulidae) populations were investigated in Iran using discriminant analyses (DA), PERMANOVA, and principal coordinate analysis (PCoA). The purpose was to evaluate the efficacy of PCoA and DA in separating the Mylonchulus species, namely M. sigmaturus, M. paitensis, M. lacustris, M. brachyuris, M. kermaninesis, and M. hawaiiensis. To achieve this, 16 morphometric measurements (body length, a, b, c, c′, V, G1, G2, buccal cavity length, buccal cavity width, dorsal tooth apex, dorsal tooth length, neck length, amphid from anterior end, rectum, and tail length) were made on 160 specimens. The analysis of variance showed that all features were significantly different among the species, except a, b, and the amphid position from the anterior end and tail length. The stepwise discriminant analysis revealed that body length, tail length, neck length, and c′ value were the four most discriminating variables useful to distinguish clearly the six species of Mylonchulus. The variables with strong discriminatory power correctly classified 98.87% of individuals from Iran’s sample of known Mylonchulus species. The results provide a morphometric basis for effectively distinguishing Mylonchulus species.

Morphology, Phenotype, and Molecular Identification of Clinical and Environmental Fusarium solani Species Complex Isolates from Malaysia

Fusarium infections in humans (fusariosis) and in economically important plants involve species of several Fusarium species complexes. Species of the Fusarium solani species complex (FSSC) are the most frequent cause of human fusariosis. The FSSC comprises more than 60 closely related species that can be separated into three major clades by multi-locus sequence typing (MLST) using translation elongation factor 1-alpha (TEF1-α) and RNA polymerase II (RPB2) DNA sequences. The MLST nomenclature for clade 3 of the FSSC assigns numbers to species types (e.g., FSSC 2) and lowercase letters to identify unique haplotypes. The aim of this study was to analyse the genotypic and phenotypic characteristics of 15 environmental and 15 clinical FSSC isolates from Malaysia. MLST was used for the genotypic characterisation of FSSC isolates from various locations within Malaysia, which was complemented by their morphological characterisation on potato dextrose and carnation leaf agar. MLST identified eight different FSSC species: thirteen Fusarium keratoplasticum (i.e., FSSC 2), six Fusarium suttonianum (FSSC 20), five Fusarium falciforme (FSSC 3+4), two Fusarium cyanescens (FSSC 27), and one each of Fusarium petroliphilum (FSSC 1), Fusarium waltergamsii (FSSC 7), Fusarium sp. (FSSC 12), and Fusarium striatum (FSSC 21). Consistent with previous reports from Malaysia, most (11 of 15) clinical FSSC isolates were F. keratoplasticum and the majority (9 of 15) of environmental isolates were F. suttonianum (5) or F. falciforme (4) strains. The taxonomic relationships of the isolates were resolved phylogenetically. The eight Fusarium species also showed distinct morphological characteristics, but these were less clearly defined and reached across species boundaries. Although TEF1-α and RPB2 sequences were sufficient for the species identification of most FSSC isolates, a more precise MLST scheme needs to be established to reliably assign individual isolates of the species-rich FSSC to their geographically-, epidemiologically-, and host-associated sub-lineages.

Population genetics reveals divergent lineages and ongoing hybridization in a declining migratory fish species complex

Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression of two species of anadromous fish with contrasting life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at thirteen microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species A. alosa, which disperses greater distances compared to the iteroparous species, A. fallax. Individuals caught at sea were assigned at the river level for A. fallax and at the region level for A. alosa. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species and lineages involved historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence for contemporary hybridization and bidirectional introgression due to gene flow between both species and lineages. Moreover, our results support the existence of at least one distinct species in the Mediterrannean sea: A. agone in Golfe du Lion area, and another divergent lineage in Corsica. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species' populations and their hybridization should be carefully considered while implementing conservation programs.

Phylogeny and pathogenicity of Colletotrichum lindemuthianum causing anthracnose of Phaseolus vulgaris cv. Bhaderwah-Rajmash from northern Himalayas, India

With an annual loss of up to 100%, anthracnose caused by Colletotrichum is one of the most devastating diseases of common beans (Phaseolus vulgaris L.). Due to few distinctive morphological characters, Colletotrichum species are frequently misidentified. In India, several Colletotrichum species have been reported as pathogens of Phaseolus species, but none had previously been validated by means of molecular tools. In this study, we studied Colletotrichum strains from common beans cv. Bhaderwah-Rajmash from the northern Himalayas of India based on both morphological and DNA sequence data of six loci, namely ITS, gapdh, chs-1, his3, act, tub2. The strains were identified as C. lindemuthianum that belongs to the C. orbiculare species complex. Representative C. lindemuthianum strains tested on Phaseolus vulgaris cv. Bhaderwah-Rajmash were pathogenic and exhibited variation in symptomology and disease progression. By identifying the causal agent, we provided substantial information to develop the best control strategies for anthracnose of Phaseolus vulgaris from the northern Himalayas of India.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03216-0.

Taxonomy and Multi-Gene Phylogeny of Poroid Panellus (Mycenaceae, Agaricales) With the Description of Five New Species From China

Panellus is an Agaricales genus with both lamellate and poroid hymenophore. The poroid species are readily overlooked because of their tiny basidiocarps. The Chinese samples of poroid Panellus are studied, and five species, namely Panellus alpinus, Panellus crassiporus, Panellus longistipitatus, Panellus minutissimus, and Panellus palmicola are described as new species based on morphology and molecular phylogenetic analyses inferred from an nrITS dataset and a multi-gene dataset (nrITS + nrLSU + mtSSU + nrSSU + tef1). Panellus alpinus is characterized by its round to ellipsoid pores measuring 4-6 per mm and oblong ellipsoid basidiospores measuring 4.8-6 μm × 2.8-3.6 μm; P. crassiporus differs from other poroid species in the genus by the irregular pores with thick dissepiments and globose basidiospores measuring 8-9.8 μm × 6.9-8 μm; P. longistipitatus is distinguished by its long stipes, pyriform cheilocystidia, and broadly ellipsoid to subglobose basidiospores measuring 7-9.8 μm × 5-7 μm; P. minutissimus is characterized by its tiny and gelatinous basidiocarps, 5-20 pores per basidiocarp, and ellipsoid basidiospores measuring 6-8 μm × 3.2-4.2 μm; P. palmicola is characterized by its round pores measuring 2-4 per mm, the presence of acerose basidioles, and globose basidiospores measuring 7-9.5 μm × 6.2-8.2 μm. An identification key to 20 poroid species of Panellus is provided.

Comprehensive treatise of Hevansia and three new genera Jenniferia, Parahevansia and Polystromomyces on spiders in Cordycipitaceae from Thailand

Collections of pathogenic fungi found on spiders from Thailand were selected for a detailed taxonomic study. Morphological comparison and phylogenetic analyses of the combined ITS, LSU, tef1, rpb1 and rpb2 sequence data indicated that these specimens formed new independent lineages within the Cordycipitaceae, containing two new genera occurring on spiders, i.e. Jenniferia gen. nov. and Polystromomyces gen. nov. Two new species in Jenniferia, J.griseocinerea sp. nov. and J.thomisidarum sp. nov., are described. Two strains, NHJ 03510 and BCC 2191, initially named as Akanthomycescinereus (Hevansiacinerea), were shown to be part of Jenniferia. By including sequences of putative Hevansia species from GenBank, we also revealed Parahevansia as a new genus with the ex-type strain NHJ 666.01 of Pa.koratensis, accommodating specimens previously named as Akanthomyceskoratensis (Hevansiakoratensis). One species of Polystromomyces, Po.araneae sp. nov., is described. We established an asexual-sexual morph connection for Hevansianovoguineensis (Cordycipitaceae) with ex-type CBS 610.80 and proposed a new species, H.minuta sp. nov. Based on characteristics of the sexual morph, Hevansia and Polystromomyces share phenotypic traits by producing stipitate ascoma with fertile terminal heads; however, they differ in the shape and colour of the stipes. Meanwhile, Jenniferia produces non-stipitate ascoma with aggregated superficial perithecia forming a cushion. A new morphology of ascospores in Jenniferia is described, illustrated and compared with other species in Cordycipitaceae.

Genomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soil

Municipal landfills are known for methane production and a source of nitrate pollution leading to various environmental issues. Therefore, this niche was selected for the isolation of one-carbon (C1) utilizing bacteria with denitrifying capacities using anaerobic enrichment on nitrate mineral salt medium supplemented with methanol as carbon source. Eight axenic cultures were isolated of which, isolate AAK/M5 demonstrated the highest methanol removal (73.28%) in terms of soluble chemical oxygen demand and methane removal (41.27%) at the expense of total nitrate removal of 100% and 33% respectively. The whole genome characterization with phylogenomic approach suggested that the strain AAK/M5 could be assigned to Pseudomonas aeruginosa with close neighbours as type strains DVT779, AES1M, W60856, and LES400. The circular genome annotation showed the presence of complete set of genes essential for methanol utilization and complete denitrification process. The study demonstrates the potential of P. aeruginosa strain AAK/M5 in catalysing methane oxidation thus serving as a methane sink vis-à-vis utilization of nitrate. Considering the existence of such bacteria at landfill site, the study highlights the need to develop strategies for their enrichment and designing of efficient catabolic activity for such environments.

Current genetic structure of European vendace Coregonus albula (L.) populations in Latvia after multiple past translocations

The European vendace Coregonus albula (L.), also known as the European cisco, is a widespread fish species in northern Europe, often regarded as an example of a glacial relict. It is an economically valuable fish and has been artificially propagated in Latvia since 1900. Despite past translocations of larvae and fry and its current protection status, it can be found in only 15 Latvian lakes. We used nine microsatellite markers to study vendace populations from nine Latvian lakes. A higher mean allelic richness and private allelic richness in Lake Riču suggest that this population may be indigenous. Three complementary clustering methods revealed similar grouping into three distinct genetic groups. According to the results, European vendace populations in the Latvian lakes studied may currently be a mixture of several other populations after multiple translocations.

Analysis of genetic diversity among Onobrychis accessions with high agronomic performance by simple sequence repeat (SSR) markers

BACKGROUND

Onobrychis viciifolia Scop. is a short-lived perennial cool-season legume used for forage production. It is a common native species in Asia Minor, especially in Turkey, the districts of the Caucasus, and the Caspian fringes. It can grow well in a broad range of climatic and soil types found in Asia, Europe, and North America. It is a non-bloating crop, making it suitable for use in both hay and pasture.

METHODS AND RESULTS

The aim was to assess the diversity of the 83 sainfoin genotypes selected based on their high agronomic performance from a germplasm collection evaluated in the experimental field of Tekirdag Namik Kemal University, Turkey. Ten nuclear simple sequence repeat (nSSR) primers (OVK036, OVK046, OVK094, OVK101, OVK125, OVK161, OVK174, OVM033, OVM061, and OVM125) were used in the study. All nSSR loci were found to be polymorphic and totally 92 alleles were detected. The mean observed number of alleles per locus was calculated as 9.2. Among the genetic diversity parameters, Shannon Index (I = 0.375), unbiased genetic diversity value (uh = 0.243), and mean polymorphic information content (PIC = 0.240) were calculated. The genetic distance value varied between 0.43 and 0.95. Based on the dendrogram built by the UPGMA clustering method using genetic distance values, it was observed that the studied sainfoin genotypes were divided into two main clusters, whereas the STRUCTURE analysis results had high support for three clusters.

CONCLUSIONS

The results obtained from this study provide important information on the genetic structures of the studied sainfoin genotypes and their genetic relationship. Therefore acquired genetic data will be useful in designing more efficient polycross nurseries, allowing open pollination of best performing and genetically diverse genotypes in the isolated conditions, which will increase genetic gain in sainfoin breeding programs.

Taxonomy and an Updated Phylogeny of Anomoloma (Amylocorticiales, Basidiomycota)

Anomoloma is a cosmopolitan poroid wood-decaying genus, belonging to the Amylocorticiales. During a study on polypores, two new species of Anomoloma were found in Eurasia, and they are described as A. denticulatum and A. eurasiaticum. To examine the phylogenetic relationships among species of Anomoloma, we analyzed nuclear ribosomal sequence data from the ITS regions and the LSU gene. The result demonstrates that A. denticulatum and A. eurasiaticum are independent species that belong to the Anomoloma genus. Both new species share the principal characteristics of the genus, but Anomoloma denticulatum is characterized by extensive white rhizomorphs spreading under the whole fruiting body, angular pores measuring 1–2 per mm, distinctly lacerate to dentate dissepiments and basidiospores of 3.5–4.3 × 2–2.5 μm. Anomoloma eurasiaticum is characterized by bearing plenty of large crystals on the mycelia and growth on Picea in high altitude areas. A key to the accepted species of Anomoloma worldwide is provided.

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

Narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV), which belong to the genus Potyvirus of the family Potyviridae, cause significant losses in the ornamental value and quality of narcissus. Several previous studies have explored the genetic diversity and evolution rate of narcissus viruses, but the analysis of the synonymous codons of the narcissus viruses is still unclear. Herein, the coat protein (CP) of three viruses is used to analyze the viruses’ phylogeny and codon usage pattern. Phylogenetic analysis showed that NYSV, NDV and NLSYV isolates were divided into five, three and five clusters, respectively, and these clusters seemed to reflect the geographic distribution. The effective number of codon (ENC) values indicated a weak codon usage bias in the CP coding region of the three narcissus viruses. ENC-plot and neutrality analysis showed that the codon usage bias of the three narcissus viruses is all mainly influenced by natural selection compared with the mutation pressure. The three narcissus viruses shared the same best optimal codon (CCA) and the synonymous codon prefers to use codons ending with A/U, compared to C/G. Our study shows the codon analysis of different viruses on the same host for the first time, which indicates the importance of the evolutionary-based design to control these viruses.

Photobiont Diversity in Lichen Symbioses From Extreme Environments

Fungal–algal relationships—both across evolutionary and ecological scales—are finely modulated by the presence of the symbionts in the environments and by the degree of selectivity and specificity that either symbiont develop reciprocally. In lichens, the green algal genus Trebouxia Puymaly is one of the most frequently recovered chlorobionts. Trebouxia species-level lineages have been recognized on the basis of their morphological and phylogenetic diversity, while their ecological preferences and distribution are still only partially unknown. We selected two cosmopolitan species complexes of lichen-forming fungi as reference models, i.e., Rhizoplaca melanophthalma and Tephromela atra, to investigate the diversity of their associated Trebouxia spp. in montane habitats across their distributional range worldwide. The greatest diversity of Trebouxia species-level lineages was recovered in the altitudinal range 1,000–2,500 m a.s.l. A total of 10 distinct Trebouxia species-level lineages were found to associate with either mycobiont, for which new photobionts are reported. One previously unrecognized Trebouxia species-level lineage was identified and is here provisionally named Trebouxia “A52.” Analyses of cell morphology and ultrastructure were performed on axenically isolated strains to fully characterize the new Trebouxia “A52” and three other previously recognized lineages, i.e., Trebouxia “A02,” T. vagua “A04,” and T. vagua “A10,” which were successfully isolated in culture during this study. The species-level diversity of Trebouxia associating with the two lichen-forming fungi in extreme habitats helps elucidate the evolutionary pathways that this lichen photobiont genus traversed to occupy varied climatic and vegetative regimes.

Colletotrichum Spp. Diversity Between Leaf Anthracnose and Crown Rot From the Same Strawberry Plant

Leaf anthracnose (LA) and anthracnose crown rot (ACR) represent serious fungal diseases that pose significant threats to strawberry production. To characterize the pathogen diversity associated with above diseases, 100 strawberry plants, including varieties of "Hongjia," "Zhangji," and "Tianxianzui," were sampled from Jiande and Zhoushan, the primary plantation regions of Zhejiang province, China. A total of 309 Colletotrichum isolates were isolated from crown (150 isolates) and leaves (159 isolates) of affected samples. Among these, 100 isolates obtained from the plants showing both LA and CR symptoms were selected randomly for further characterization. Based on the morphological observations combined with phylogenetic analysis of multiple genes (ACT, ITS, CAL, GAPDH, and CHS), all the 100 tested isolates were identified as C. gloeosporioides species complex, including 91 isolates of C. siamense, 8 isolates of C. fructicola causing both LA and ACR, and one isolate of C. aenigma causing ACR. The phenotypic characteristics of these isolated species were investigated using the BIOLOG phenotype MicroArray (PM) and a total of 950 different metabolic phenotype were tested, showing the characteristics among these isolates and providing the theoretical basis for pathogenic biochemistry and metabolism. The pathogenicity tests showed that even the same Colletotrichum species isolated from different diseased tissues (leaves or crowns) had significantly different pathogenicity toward strawberry leaves and crown. C. siamense isolated from diseased leaves (CSLA) was more aggressive than C. siamense isolated from rotted crown (CSCR) during the infection on "Zhangji" leaves. Additionally, C. fructicola isolated from affected leaf (CFLA) caused more severe symptoms on the leaves of four strawberry varieties compared to C. fructicola isolated from diseased crown (CFCR). For crown rot, the pathogenicity of CSCR was higher than that of CSLA.

Use of Investigator 24plex GO! to analyse allele frequencies of 21 autosomal STRs in the population of Veracruz state, Mexico

BackgroundMexican population databases for autosomal STRs are scarce, and no previous studies have been performed with the Qiagen Investigator 24plex GO! Aim: To analyse the frequency of 21 autosomal short tandem repeat (STR) loci and forensic parameters in individuals from Veracruz state, Mexico. Subjects and methods: A total of 234 unrelated individuals were analysed with the Investigator 24plex GO! Kit, which includes the following autosomal STRs: TH01, D3S1358, vWA, D21S11, TPOX, D1S1656, D12S391, SE33, D10S1248, D22S1045, D19S433, D8S133879, D2S1338, D2S441, D18S51, FGA, D16S539, CSF1PO, D13S317, D5S818, and D7S820. Allele frequencies, forensic parameters, and relationships with neighbouring Mexican populations were estimated. Results: The STRs analysed were in Hardy-Weinberg Equilibrium (HWE). The combined matching probability and combined PE were 1.5266 E-24 and 0.999999988711, respectively. The D18S51 and SE33 loci presented the highest Ho (0.8974 and 0.8932) and PE (0.7902 and 0.7815), respectively. The highest PIC (0.9337) and PD (0.9894) values corresponded to SE33. Conversely, D22S1045 had the lowest PIC and PE (0.5533 y 0.3546, respectively). A population cluster among southern Mexican populations, which included non-differentiation between Guerrero and Veracruz states was detected. Conclusion: The forensic efficacy of the 21 STRs analysed by the Investigator 24plex GO! Kit was evaluated in the Veracruz state. Moreover, new population clusters that have not been yet been described and are related to geographic regions were identified, and these are in agreement with previously reported ancestral differences.

Natural Diversity and Phylogeny of Asian Red-Cheeked Squirrels (Rodentia, Sciuridae, Dremomys) in Eastern Indochina

Abstract

Based on new molecular data for mitochondrial (Cyt b) and nuclear (IRBP, RAG1) genes, as well as an extensive analysis of morphological material, we accessed actual species taxonomy and relationships among Asian red-cheeked squirrels Dremomys distributed in eastern Indochina and southern China. Phylogenetic analyses demonstrated that Asian red-cheeked squirrels, which are currently attributed to D. rufigenis, are not homogenic but instead consisted of two independent species-level clades—northern and south-central. The latter clade was additionally subdivided into two highly divergent clades based on Cyt b gene phylogeny. In spite of multidimensional statistics approach applied (PCA) only minor cranial differences were found between populations of study what lay a basis to treat it as cryptic species. Based on our findings, red-cheeked squirrels inhabit northern Vietnam and southern China, which are usually attributed to D. rufigenis, should be treated as distinct genetic species D. ornatus Thomas, 1914. In ones turn, based on its peculiar external morphology we can attribute the specimens from southern and central Vietnam to D. rufigenis proper and treat them as D. rufigenisfuscus Bonhote, 1907 and D. r. laomache Bonhote, 1921, respectively.

Narcissus Plants: A Melting Pot of Potyviruses

Our paper presents detailed evolutionary analyses of narcissus viruses from wild and domesticated Narcissus plants in Japan. Narcissus late season yellows virus (NLSYV) and narcissus degeneration virus (NDV) are major viruses of Narcissus plants, causing serious disease outbreaks in Japan. In this study, we collected Narcissus plants showing mosaic or striped leaves along with asymptomatic plants in Japan for evolutionary analyses. Our findings show that (1) NLSYV is widely distributed, whereas the distribution of NDV is limited to the southwest parts of Japan; (2) the genomes of NLSYV isolates share nucleotide identities of around 82%, whereas those of NDV isolates are around 94%; (3) three novel recombination type patterns were found in NLSYV; (4) NLSYV comprises at least five distinct phylogenetic groups whereas NDV has two; and (5) infection with narcissus viruses often occur as co-infection with different viruses, different isolates of the same virus, and in the presence of quasispecies (mutant clouds) of the same virus in nature. Therefore, the wild and domesticated Narcissus plants in Japan are somewhat like a melting pot of potyviruses and other viruses.

Fourteen New Species of Foliar Colletotrichum Associated with the Invasive Plant Ageratinaadenophora and Surrounding Crops

Ageratina adenophora is one of the most invasive weeds in China. Following an outbreak in Yunnan in the 1960s, A. adenophora has been spreading in Southwest China at tremendous speed. Previous research indicated A. adenophora contained many Colletotrichum species as endophytes. In this study, we investigated the diversity of Colletotrichum in healthy and diseased leaves of the invasive plant A. adenophora and several surrounding crops in Yunnan, Guangxi, and Guizhou provinces in China, and obtained over 1000 Colletotrichum strains. After preliminary delimitation using the internal transcribed spacer region (ITS) sequences, 44 representative strains were selected for further study. Their phylogenetic positions were determined by phylogenetic analyses using combined sequences of ITS, actin (ACT), chitin synthase (CHS-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and beta-tubulin (TUB2). Combined with morphological characteristics, 14 new Colletotrichum species were named as C. adenophorae, C. analogum, C. cangyuanense, C. dimorphum, C. gracile, C. nanhuaense, C. nullisetosum, C. oblongisporum, C. parvisporum, C. robustum, C. simulanticitri, C. speciosum, C. subhenanense, and C. yunajiangense.

A Case Study of the Morphological and Molecular Variation within a Ciliate Genus: Taxonomic Descriptions of Three Dysteria Species (Ciliophora, Cyrtophoria), with the Establishment of a New Species

Three Dysteria species, D. crassipes Claparède & Lachmann, 1859; D. brasiliensis Faria et al., 1922; and D. paracrassipes n. sp., were collected from subtropical coastal waters of the East China Sea, near Ningbo, China. The three species were studied based on their living morphology, infraciliature, and molecular data. The new species D. paracrassipes n. sp. is very similar to D. crassipes in most morphological features except the preoral kinety, which is double-rowed in the new species (vs. single-rowed in D. crassipes). The difference in the small ribosomal subunit sequences (SSU rDNA) between these two species is 56 bases, supporting the establishment of the new species. The Ningbo population of D. crassipes is highly similar in morphology to other known populations. Nevertheless, the SSU rDNA sequences of these populations are very different, indicating high genetic diversity and potentially cryptic species. Dysteria brasiliensis is cosmopolitan with many described populations worldwide and four deposited SSU rDNA sequences. The present work supplies morphological and molecular information from five subtropical populations of D. brasiliensis that bear identical molecular sequences but show significant morphological differences. The findings of this study provide an opportunity to improve understanding of the morphological and genetic diversity of ciliates.

The dopamine transporter gene SLC6A3: multidisease risks

The human dopamine transporter gene SLC6A3 has been consistently implicated in several neuropsychiatric diseases but the disease mechanism remains elusive. In this risk synthesis, we have concluded that SLC6A3 represents an increasingly recognized risk with a growing number of familial mutants associated with neuropsychiatric and neurological disorders. At least five loci were related to common and severe diseases including alcohol use disorder (high activity variant), attention-deficit/hyperactivity disorder (low activity variant), autism (familial proteins with mutated networking) and movement disorders (both regulatory variants and familial mutations). Association signals depended on genetic markers used as well as ethnicity examined. Strong haplotype selection and gene-wide epistases support multimarker assessment of functional variations and phenotype associations. Inclusion of its promoter region's functional markers such as DNPi (rs67175440) and 5'VNTR (rs70957367) may help delineate condensate-based risk action, testing a locus-pathway-phenotype hypothesis for one gene-multidisease etiology.

Endophytic Colletotrichum Species from Aquatic Plants in Southwest China

Colletotrichum species are plant pathogens, saprobes, and endophytes in many economically important hosts. Many studies have investigated the diversity and pathogenicity of Colletotrichum species in common ornamentals, fruits, and vegetables. However, Colletotrichum species occurring in aquatic plants are not well known. During the investigation of the diversity of endophytic fungi in aquatic plants in southwest China, 66 Colletotrichum isolates were obtained from aquatic plants there, and 26 of them were selected for sequencing and analyses of actin (ACT), chitin synthase (CHS-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the internal transcribed spacer (ITS) region, and β-tubulin (TUB2) genomic regions. Based on morphological characterization and multi-locus phylogenetic analyses, 13 Colletotrichum species were recognized, namely, C. baiyuense sp. nov., C. casaense sp. nov., C. demersi sp. nov., C. dianense sp. nov., C. fructicola, C. garzense sp. nov., C. jiangxiense, C. karstii, C. philoxeroidis sp. nov., C. spicati sp. nov., C. tengchongense sp. nov., C. vulgaris sp. nov., C. wuxuhaiense sp. nov. Two species complexes, the C. boninense species complex and C. gloeosporioides species complex, were found to be associated with aquatic plants. Pathogenicity tests revealed a broad diversity in pathogenicity and aggressiveness among the eight new Colletotrichum species.

New species in Aciculosporium, Shimizuomyces and a new genus Morakotia associated with plants in Clavicipitaceae from Thailand

Three new fungal species in the Clavicipitaceae (Hypocreales, Ascomycota) associated with plants were collected in Thailand. Morphological characterisation and phylogenetic analyses based on multi-locus sequences of LSU, RPB1 and TEF1 showed that two species belong to Aciculosporium and Shimizuomyces. Morakotia occupies a unique clade and is proposed as a novel genus in Clavicipitaceae. Shimizuomyces cinereus and Morakotia fusca share the morphological characteristic of having cylindrical to clavate stromata arising from seeds. Aciculosporium siamense produces perithecial plates and occurs on a leaf sheath of an unknown panicoid grass.

The re-description of Synoecnemahirsutum Timm, 1959 (Synoecneminae, Ungellidae, Drilonematoidea) from a pheretimoid earthworm in Vietnam with the analysis of its phylogenetic relationships

Synoecnemahirsutum Timm, 1959 (Ungellidae, Drilonematoidea), found in the body cavity of the pheretimoid earthworm at the border of Laos and Vietnam, was re-described and illustrated. The mitochondrial genome of S.hirsutum obtained with Illumina HiSeq sequencing is the first annotated mitochondrial genome as a representative of the superfamily Drilonematoidea. The phylogeny inferred from the analysis of 12 mitochondrial genes has shown some similarity of S.hirsutum with a cephalobid Acrobeloidesvarius.

The role of Leishmania GP63 in the modulation of innate inflammatory response to Leishmania major infection

Leishmaniasis is a disease caused by the protozoan parasite Leishmania and is known to affect millions of individuals worldwide. In recent years, we have established the critical role played by Leishmania zinc-metalloprotease GP63 in the modulation of host macrophage signalling and functions, favouring its survival and progression within its host. Leishmania major lacking GP63 was reported to cause limited infection in mice, however, it is still unclear how GP63 may influence the innate inflammatory response and parasite survival in an in vivo context. Therefore, we were interested in analyzing the early innate inflammatory events upon Leishmania inoculation within mice and establish whether Leishmania GP63 influences this initial inflammatory response. Experimentally, L. major WT (L. majorWT), L. major GP63 knockout (L. majorKO), or L. major GP63 rescue (L. majorR) were intraperitoneally inoculated in mice and the inflammatory cells recruited were characterized microscopically and by flow cytometry (number and cell type), and their infection determined. Pro-inflammatory markers such as cytokines, chemokines, and extracellular vesicles (EVs, e.g. exosomes) were monitored and proteomic analysis was performed on exosome contents. Data obtained from this study suggest that Leishmania GP63 does not significantly influence the pathogen-induced inflammatory cell recruitment, but rather their activation status and effector function. Concordantly, internalization of promastigotes during early infection could be influenced by GP63 as fewer L. majorKO amastigotes were found within host cells and appear to maintain in host cells over time. Collectively this study provides a clear analysis of innate inflammatory events occurring during L. major infection and further establish the prominent role of the virulence factor GP63 to provide favourable conditions for host cell infection.

The dinucleotide composition of sugarcane mosaic virus is shaped more by protein coding regions than by host species

Sugarcane mosaic virus (SCMV), which belongs to the Potyvirus genus of the family Potyviridae, causes mosaic diseases in canna, sugarcane and maize worldwide. Previously, the genetic variations, timescale, codon usage patterns and host adaptions of SCMV were determined. However, the dinucleotide composition and the dinucleotide bias from hosts or the protein coding regions of the virus have yet to be investigated. In this study, comprehensive analyses of the dinucleotide composition and dinucleotide bias from hosts, lineages and protein coding regions of SCMV were performed using 131 complete genomic sequences. We found that UpG and CpA were largely overrepresented while UpA, CpC, and CpG were largely underrepresented in the polyprotein and 11 protein coding region data sets. SCMV dinucleotide composition bias is more strongly dependent on the protein coding regions than on hosts. A weak association between the dinucleotide composition and SCMV lineages was also observed. Our analysis provides a novel perspective on the molecular evolutionary mechanisms of SCMV and may provide a better understanding of future research on the origin and evolutionary patterns of SCMV.

 Azygosporus gen. nov., a synapmorphic clade in the family Ancylistaceae

The fungal genus Conidiobolus sensu lato was delimited into four genera based on morphology and phylogeny. However, the taxonomic placement of C.parvus has not been determined until now. Here, we show that C.parvus belongs to a distinct lineage based on mitochondrial (mtSSU) and nuclear (TEF1 and nrLSU) phylogenetic analyses. Phylogenetic analyses further revealed a new species as sister to C.parvus. We identified a synapomorphy uniting these lineages (azygospore production) that was not observed in other allied genera of the family Ancylistaceae, and erected a new genus Azygosporusgen. nov. for this monophyletic group, with a new combination, A.parvuscomb. nov. as the type species. Within Azygosporus, the novel species A.macropapillatussp. nov. was introduced from China based on morphological characteristics and molecular evidence, which is characterized by its prominent basal papilla, in comparison to other closely related species, measuring 7.5–10.0×5.0–10.0 µm. Our study resolved the phylogenetic placement of C.parvus and improved the taxonomic system of the Ancylistaceae family.

Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic

Scallion mosaic virus (ScaMV) belongs to the turnip mosaic virus phylogenetic group of potyvirus and is known to infect domestic scallion plants (Allium chinense) in China and wild Japanese garlic (Allium macrostemon Bunge) in Japan. Wild Japanese garlic plants showing asymptomatic leaves were collected from different sites in Japan during 2012–2015. We found that 73 wild Japanese garlic plants out of 277 collected plants were infected with ScaMV, identified by partial genomic nucleotide sequences of the amplified RT-PCR products using potyvirus-specific primer pairs. Sixty-three ScaMV isolates were then chosen, and those full genomic sequences were determined. We carried out evolutionary analyses of the complete polyprotein-coding sequences and four non-recombinogenic regions of partial genomic sequences. We found that 80% of ScaMV samples have recombination-like genome structure and identified 12 recombination-type patterns in the genomes of the Japanese ScaMV isolates. Furthermore, we found two non-recombinant-type patterns in the Japanese population. Because the wild plants and weeds may often serve as reservoirs of viruses, it is important to study providing the exploratory investigation before emergence in the domestic plants. This is possibly the first epidemiological and evolutionary study of a virus from asymptomatic wild plants.

Pre-steady-state Kinetic Analysis of Amino Acid Transporter SLC6A14 Reveals Rapid Turnover Rate and Substrate Translocation

SLC6A14 (solute carrier family 6 member 14) is an amino acid transporter, driven by Na⁺ and Cl⁻ co-transport, whose structure, function, and molecular and kinetic mechanism have not been well characterized. Its broad substrate selectivity, including neutral and cationic amino acids, differentiates it from other SLC6 family members, and its proposed involvement in nutrient transport in several cancers suggest that it could become an important drug target. In the present study, we investigated SLC6A14 function and its kinetic mechanism after expression in human embryonic kidney (HEK293) cells, including substrate specificity and voltage dependence under various ionic conditions. We applied rapid solution exchange, voltage jumps, and laser photolysis of caged alanine, allowing sub-millisecond temporal resolution, to study SLC6A14 steady state and pre-steady state kinetics. The results highlight the broad substrate specificity and suggest that extracellular chloride enhances substrate transport but is not required for transport. As in other SLC6 family members, Na⁺ binding to the substrate-free transporter (or conformational changes associated with it) is electrogenic and is likely rate limiting for transporter turnover. Transient current decaying with a time constant of <1ms is also observed after rapid amino acid application, both in forward transport and homoexchange modes, indicating a slightly electrogenic, but fast and not rate-limiting substrate translocation step. Our results, which are consistent with kinetic modeling, suggest rapid transporter turnover rate and substrate translocation with faster kinetics compared with other SLC6 family members. Together, these results provided novel information on the SLC6A14 transport cycle and mechanism, expanding our understanding of SLC6A14 function.

Global Studies of the Host-Parasite Relationships between Ectoparasitic Mites of the Family Syringophilidae and Birds of the Order Columbiformes

The quill mites belonging to the family Syringophilidae (Acari: Prostigmata: Cheyletoidea) are obligate ectoparasites of birds. They inhabit different types of the quills, where they spend their whole life cycle. In this paper, we conducted a global study of syringophilid mites associated with columbiform birds. We examined 772 pigeon and dove individuals belonging to 112 species (35% world fauna) from all zoogeographical regions (except Madagascan) where Columbiformes occur. We measured the prevalence (IP) and the confidence interval (CI) for all infested host species. IP ranges between 4.2 and 66.7 (CI 0.2-100). We applied a bipartite analysis to determine host-parasite interaction, network indices, and host specificity on species and whole network levels. The Syringophilidae-Columbiformes network was composed of 25 mite species and 65 host species. The bipartite network was characterized by a high network level specialization H2' = 0.93, high nestedness N = 0.908, connectance C = 0.90, and high modularity Q = 0.83, with 20 modules. Moreover, we reconstructed the phylogeny of the quill mites associated with columbiform birds on the generic level. Analysis shows two distinct clades: Meitingsunes + Psittaciphilus, and Peristerophila + Terratosyringophilus.

Paramecium bursaria—A Complex of Five Cryptic Species: Mitochondrial DNA COI Haplotype Variation and Biogeographic Distribution

Ciliates are a diverse protistan group and many consist of cryptic species complexes whose members may be restricted to particular biogeographic locations. Mitochondrial genes, characterized by a high resolution for closely related species, were applied to identify new species and to distinguish closely related morphospecies. In the current study, we analyzed 132 sequences of COI mtDNA fragments obtained from P. bursaria species collected worldwide. The results allowed, for the first time, to generate a network of COI haplotypes and demonstrate the relationships between P. bursaria strains, as well as to confirm the existence of five reproductively isolated haplogroups. The P. bursaria haplogroups identified in the present study correspond to previously reported syngens (R1, R2, R3, R4, and R5), thus we decided to propose the following binominal names for each of them: P. primabursaria, P. bibursaria, P. tribursaria, P. tetrabursaria, and P. pentabursaria, respectively. The phylogeographic distribution of P. bursaria species showed that P. primabursaria and P. bibursaria were strictly Eurasian, except for two South Australian P. bibursaria strains. P. tribursaria was found mainly in Eastern Asia, in two stands in Europe and in North America. In turn, P. tetrabursaria was restricted to the USA territory, whereas P. pentabursaria was found in two European localities.

Discovery proteomics defines androgen-regulated glycoprotein networks in prostate cancer cells, as well as putative biomarkers of prostatic diseases

Supraphysiologic androgen (SPA) inhibits cell proliferation in prostate cancer (PCa) cells by transcriptional repression of DNA replication and cell-cycle genes. In this study, quantitative glycoprotein profiling identified androgen-regulated glycoprotein networks associated with SPA-mediated inhibition of PCa cell proliferation, and androgen-regulated glycoproteins in clinical prostate tissues. SPA-regulated glycoprotein networks were enriched for translation factors and ribosomal proteins, proteins that are known to be O-GlcNAcylated in response to various cellular stresses. Thus, androgen-regulated glycoproteins are likely to be targeted for O-GlcNAcylation. Comparative analysis of glycosylated proteins in PCa cells and clinical prostate tissue identified androgen-regulated glycoproteins that are differentially expressed prostate tissues at various stages of cancer. Notably, the enzyme ectonucleoside triphosphate diphosphohydrolase 5 was found to be an androgen-regulated glycoprotein in PCa cells, with higher expression in cancerous versus non-cancerous prostate tissue. Our glycoproteomics study provides an experimental framework for characterizing androgen-regulated proteins and glycoprotein networks, toward better understanding how this subproteome leads to physiologic and supraphysiologic proliferation responses in PCa cells, and their potential use as druggable biomarkers of dysregulated AR-dependent signaling in PCa cells.

Antarctolichenia onofrii gen. nov. sp. nov. from Antarctic Endolithic Communities Untangles the Evolution of Rock-Inhabiting and Lichenized Fungi in Arthoniomycetes

Microbial endolithic communities are the main and most widespread life forms in the coldest and hyper-arid desert of the McMurdo Dry Valleys and other ice-free areas across Victoria Land, Antarctica. There, the lichen-dominated communities are complex and self-supporting assemblages of phototrophic and heterotrophic microorganisms, including bacteria, chlorophytes, and both free-living and lichen-forming fungi living at the edge of their physiological adaptability. In particular, among the free-living fungi, microcolonial, melanized, and anamorphic species are highly recurrent, while a few species were sometimes found to be associated with algae. One of these fungi is of paramount importance for its peculiar traits, i.e., a yeast-like habitus, co-growing with algae and being difficult to propagate in pure culture. In the present study, this taxon is herein described as the new genus Antarctolichenia and its type species is A. onofrii, which represents a transitional group between the free-living and symbiotic lifestyle in Arthoniomycetes. The phylogenetic placement of Antarctolichenia was studied using three rDNA molecular markers and morphological characters were described. In this study, we also reappraise the evolution and the connections linking the lichen-forming and rock-inhabiting lifestyles in the basal lineages of Arthoniomycetes (i.e., Lichenostigmatales) and Dothideomycetes.

Identification of Signaling Pathways for Early Embryonic Lethality and Developmental Retardation in Sephs1-/- Mice

Selenophosphate synthetase 1 (SEPHS1) plays an essential role in cell growth and survival. However, the underlying molecular mechanisms remain unclear. In the present study, the pathways regulated by SEPHS1 during gastrulation were determined by bioinformatical analyses and experimental verification using systemic knockout mice targeting Sephs1. We found that the coagulation system and retinoic acid signaling were most highly affected by SEPHS1 deficiency throughout gastrulation. Gene expression patterns of altered embryo morphogenesis and inhibition of Wnt signaling were predicted with high probability at E6.5. These predictions were verified by structural abnormalities in the dermal layer of Sephs1^−/− embryos. At E7.5, organogenesis and activation of prolactin signaling were predicted to be affected by Sephs1 knockout. Delay of head fold formation was observed in the Sephs1^−/− embryos. At E8.5, gene expression associated with organ development and insulin-like growth hormone signaling that regulates organ growth during development was altered. Consistent with these observations, various morphological abnormalities of organs and axial rotation failure were observed. We also found that the gene sets related to redox homeostasis and apoptosis were gradually enriched in a time-dependent manner until E8.5. However, DNA damage and apoptosis markers were detected only when the Sephs1^−/− embryos aged to E9.5. Our results suggest that SEPHS1 deficiency causes a gradual increase of oxidative stress which changes signaling pathways during gastrulation, and afterwards leads to apoptosis.

Taxonomy and Phylogeny of the Favolaschia calocera Complex (Mycenaceae) with Descriptions of Four New Species

Favolaschia calocera was originally described from Madagascar, and reported to have a worldwide distribution. In the current study, samples of the Favolaschia calocera from Central America, Australia, China, Kenya, Italy, New Zealand, and Thailand were analyzed by using both morphological and molecular methods. Phylogenetic analyses were based on the internal transcribed spacer (ITS) dataset, and the combined five-locus dataset of ITS, large subunit nuclear ribosomal RNA gene (nLSU), the small subunit mitochondrial rRNA gene (mt-SSU), the small subunit of nuclear ribosomal RNA gene (nu-SSU), and the translation elongation factor 1α (TEF1). Our study proves that Favolaschia calocera is a species complex, and six species are recognized in the complex including four new species. Three new species F. brevibasidiata, F. brevistipitata, and F. longistipitata from China; and one new species F. minutissima from Asia. In addition, Favolaschia claudopus (Singer) Q.Y. Zhang & C. Dai, earlier treated as a variety of Favolaschia calocera R. Heim, were raised to species rank. Illustrated descriptions of these five new taxa are given. An identification key and a comparison of the characteristics of species in the Favolaschia calocera complex are provided.

Taxonomy and Phylogeny of the Dileptid Ciliate Genus Paradileptus (Protista: Ciliophora), With a Brief Review and Redescriptions of Two Species Isolated From a Wetland in Northern China

Members of the genus Paradileptus are apex predators in microbial food webs. They are often encountered in freshwater biotopes and have been used in research on water quality monitoring and ecology. Nevertheless, our understanding of the biodiversity of Paradileptus, especially its ecological and genetic diversities, is very poor which hinders our ability to understand the ecosystem services it provides. The present study gives a detailed account of two Chinese populations of Paradileptus elephantinus and P. conicus including their living morphology, infraciliature, and molecular phylogenies based on 18S, 5.8S, and ITS ribosomal DNA sequences. The phylogenetic relationships between these two species and other rhynchostomatians are investigated. We also explore the potential contribution of differentiation of the proboscis (e.g., extrusomes, dorsal brush, and differentiated kineties) to niche partitioning and speciation in Paradileptus. The global distribution of Paradileptus is summarized based on published data. Finally, a key to the identification of the valid species of Paradileptus is provided.