A new species of the genus <Emphasis Type="Italic">Xanthorhoe</Emphasis> (Lepidoptera,Geometridae, Larentiinae) from the Urals and Western Siberia

A new geometrid-moth species, Xanthorhoe pseudoannotinata, is described. It is similar to X. annotinata in the coloration and wing pattern, but differs in structure of the costa of the valva, presence of 9 or 10 spines at the base of the aedeagal vesica of the male, large oval and trapezoid-like ostium, and short conic ductus bursae of the female. The holotype is deposited at the Siberian Zoological Museum, Institute of Animal Systematics and Ecology (Novosibirsk, Russia), the paratypes, at the same museum and in the Finnish Museum of Natural History (Helsinki, Finland).     

Image Quality Improvement in Adaptive Optics Scanning Laser Ophthalmoscopy Assisted Capillary Visualization Using B-spline-based Elastic Image Registration

Purpose

To investigate the effect of B-spline-based elastic image registration on adaptive optics scanning laser ophthalmoscopy (AO-SLO)-assisted capillary visualization.

Methods

AO-SLO videos were acquired from parafoveal areas in the eyes of healthy subjects and patients with various diseases. After nonlinear image registration, the image quality of capillary images constructed from AO-SLO videos using motion contrast enhancement was compared before and after B-spline-based elastic (nonlinear) image registration performed using ImageJ. For objective comparison of image quality, contrast-to-noise ratios (CNRS) for vessel images were calculated. For subjective comparison, experienced ophthalmologists ranked images on a 5-point scale.

Results

All AO-SLO videos were successfully stabilized by elastic image registration. CNR was significantly higher in capillary images stabilized by elastic image registration than in those stabilized without registration. The average ratio of CNR in images with elastic image registration to CNR in images without elastic image registration was 2.10 ± 1.73, with no significant difference in the ratio between patients and healthy subjects. Improvement of image quality was also supported by expert comparison.

Conclusions

Use of B-spline-based elastic image registration in AO-SLO-assisted capillary visualization was effective for enhancing image quality both objectively and subjectively.     

Recent Emergence of a Chytrid Fungal Pathogen in California Cascades Frogs (<Emphasis Type="Italic">Rana cascadae</Emphasis>)

The pathogenic fungus Batrachochytrium dendrobatidis (Bd) has been associated with global amphibian declines, but it is often difficult to discern the relative importance of Bd as a causal agent in declines that have already occurred. Retrospective analyses of museum specimens have allowed researchers to associate the timing of Bd arrival with the timing of past amphibian declines. Cascades frogs (Rana cascadae) have experienced dramatic declines in northern California, but it is not clear whether the onset of these declines corresponds to the arrival of Bd. We used quantitative real-time PCR assays of samples collected from museum specimens to determine historical Bd prevalence in the northern California range of Cascades frogs. We detected Bd in 13 of 364 (3.5%) Cascades frog specimens collected between 1907 and 2003, with the first positive result from 1978. A Bayesian analysis suggested that Bd arrived in the region between 1973 and 1978, which corresponds well with the first observations of declines in the 1980s.     

A new quality management perspective for biodiversity conservation and research: Investigating Biospecimen Reporting for Improved Study Quality (BRISQ) and the Standard PRE-analytical Code (SPREC) using Natural History Museum and culture collections as case studies

The aims of this paper are to debate and raise awareness about the use of systematic, interconnected approaches for biodiversity collection curation by exploring the multi-disciplinary relevance of quality management tools developed by clinical biobanks. An appraisal of their best practices indicated the need for improved sample and process chain annotation as a significant number of historical collections used in medical research were of inadequate quality. This stimulated the creation of a new discipline, biospecimen science to develop quality management tools for clinical biobanks, two of which, Biospecimen Reporting for Improved Study Quality (BRISQ) and the Standard PRE-analytical Code (SPREC) report critical information about samples and process chain variables. Unprecedented advances in molecular-genetic and in silico technologies applied across the tree of life require international conservation networks to generate and share knowledge. This is used in biodiversity and systematics research, and to address the accelerating loss of species, including the sustainable use of bioresources. This review investigates the application of BRISQ and SPREC for biodiversity research and conservation using natural history, museum and living culture collections as case studies. The distinction between preservation and conservation is discussed with regard to process and storage treatments and how they impact on the usability of biospecimens and cultures. We conclude: (i) more rigorous approaches are needed for the quality management of biospecimens, bioresources and their associated sample and processing data to assure their fitness-for-purpose; and (ii) biospecimen science tools developed by clinical biobanks can be adapted to future-proof the quality of biodiversity collections and the reliability of molecular data generated from their use.     

The structure of biogenic habitat and epibiotic assemblages associated with the global invasive kelp <Emphasis Type="Italic">Undaria pinnatifida</Emphasis> in comparison to native macroalgae

Kelp forests dominate temperate and polar rocky coastlines and represent critical marine habitats because they support elevated rates of primary and secondary production and high biodiversity. A major threat to the stability of these ecosystems is the proliferation of non-native species, such as the Japanese kelp Undaria pinnatifida (‘Wakame’), which has recently colonised natural habitats in the UK. We quantified the abundance and biomass of U. pinnatifida on a natural rocky reef habitat over 10 months to make comparisons with three native canopy-forming brown algae (Laminaria ochroleuca, Saccharina latissima, and Saccorhiza polyschides). We also examined the biogenic habitat structure provided by, and epibiotic assemblages associated with, U. pinnatifida in comparison to native macroalgae. Surveys conducted within the Plymouth Sound Special Area of Conservation indicated that U. pinnatifida is now a dominant and conspicuous member of kelp-dominated communities on natural substrata. Crucially, U. pinnatifida supported a structurally dissimilar and less diverse epibiotic assemblage than the native perennial kelp species. However, U. pinnatifida-associated assemblages were similar to those associated with Saccorhiza polyschides, which has a similar life history and growth strategy. Our results suggest that a shift towards U. pinnatifida dominated reefs could result in impoverished epibiotic assemblages and lower local biodiversity, although this could be offset, to some extent, by the climate-driven proliferation of L. ochroleuca at the poleward range edge, which provides complex biogenic habitat and harbours relatively high biodiversity. Clearly, greater understanding of the long-term dynamics and competitive interactions between these habitat-forming species is needed to accurately predict future biodiversity patterns.     

Phenotypic and phylogenetic characterization of actinomycetes isolated from <Emphasis Type="Italic">Lasius niger</Emphasis> and <Emphasis Type="Italic">Formica cunicularia</Emphasis> ants

Multiple actinomycete strains were isolated from two ant species, Lasius niger and Formica cunicularia, and their phenotypic properties and phylogenetic position were studied. Partial sequencing of 16S rRNA assigned the greater part of them to the genus Streptomyces, but only one belonged to Nocardia. However, some isolates had significant color and morphological differences from their closest phylogenetic relatives. The abundance and biodiversity of actinomycete communities isolated from L. niger ants greatly exceeded those found for F. cunicularia. All of the actinomycetes associated with F. cunicularia ants demonstrated cellulolytic activity, but only one had such ability among the strains associated with black ants.     

Magnetic microbubble-mediated ultrasound-MRI registration based on robust optical flow model

Background

As a dual-modality contrast agent, magnetic microbubbles (MMBs) can not only improve contrast of ultrasound (US) image, but can also serve as a contrast agent of magnetic resonance image (MRI). With the help of MMBs, a new registration method between US image and MRI is presented.

Methods

In this method, MMBs were used in both ultrasound and magnetic resonance imaging process to enhance the most important information of interest. In order to reduce the influence of the speckle noise to registration, semi-automatic segmentations of US image and MRI were carried out by using active contour model. After that, a robust optical flow model between US image segmentation (floating image) and MRI segmentation (reference image) was built, and the vector flow field was estimated by using the Coarse-to-fine Gaussian pyramid and graduated non-convexity (GNC) schemes.

Results

Qualitative and quantitative analyses of multiple group comparison experiments showed that registration results using all methods tested in this paper without MMBs were unsatisfactory. On the contrary, the proposed method combined with MMBs led to the best registration results.

Conclusion

The proposed algorithm combined with MMBs contends with larger deformation and performs well not only for local deformation but also for global deformation. The comparison experiments also demonstrated that ultrasound-MRI registration using the above-mentioned method might be a promising method for obtaining more accurate image information.

     

Association between expression levels and growth trait-related SNPs located in promoters of the <Emphasis Type="Italic">MC4R</Emphasis> and <Emphasis Type="Italic">MSTN</Emphasis> genes in <Emphasis Type="Italic">Spinibarbus hollandi</Emphasis>

Melanocortin 4 receptor: (MC4R) and Myostatin (MSTN) are two important growth trait-related genes in animals. In this study, we showed that two SNPs, MC4R-719A>G and MSTN-519C>T, found in the promoters of the MC4R and MSTN genes, respectively, are both associated with growth traits in Spinibarbus hollandi. Furthermore, we observed that there were significant associations between the expression levels of the MC4R and MSTN genes and these two growth trait-related SNPs. The expression level of MC4R gene in brain was lower in GG genotype fish with extremely high growth performance than that in AA genotype fish with extremely low growth performance. Expression level of the MSTN gene in muscle was lower in TT genotype fish with extremely high growth performance than that in CC and CT genotype fish with lower growth performance. The results indicated that these SNPs located in the promoters of MC4R and MSTN are associated with growth-related traits through modification of gene expression levels. The MSTN and MC4R SNPs may have useful application in effective marker-assisted selection aimed to increase output in S. hollandi.     

Cell-by-Cell Alignment of Repeated Specular Microscopy Images from the Same Eye

Purpose

Modern specular microscopes (SM) robustly depict the same central area of the corneal endothelium at different time points through a built-in fixation light. However, repeated image acquisitions slightly shift and rotate because of minute changes in head position in the chin and forehead rest. This prevents the manual retrieval of individual corneal endothelial cells (CECs) in repeated measurements because SM images usually lack obvious landmarks. We devised and validated an image registration algorithm that aligns SM images from the same eye to make corresponding CECs coincide.

Methods

We retrospectively selected 27 image pairs for the presence of significant image overlap. Each image pair had been recorded on the same day and of the same eye. We applied our registration method in each image pair. Two observers independently validated, by means of alternation flicker, that the image pairs had been correctly aligned. We also repeatedly applied our registration method on unrelated image pairs by randomly drawing images and making certain that the images did not originate from the same eye. This was done to assess the specifity of our method.

Results

All automated registrations of the same-day and same-eye image pairs were accurate. However, one single image incorrectly failed to trigger the non-match diagnosis twice in 81 registration attempts between unrelated images. As it turned out, this particular image depicted only 73 CECs. The average number of CECs was 253 (range 73–393).

Conclusion

Repeated non-contact SM images can be automatedly aligned so that the corresponding CECs coincide. Any successful alignment can be considered as proof of the retrieval of identical CECs as soon as at least 100 CEC centroids have been identified. We believe our method is the first to robustly confirm endothelial stability in individual eyes.     

A first insight into the intestinal microbiota of snow trout (<Emphasis Type="Italic">Schizothorax zarudnyi</Emphasis>)

This study addresses the biodiversity profile of bacterial community in the intestinal lumen and mucosa of snow trout fish by applying 16S rRNA gene 454-pyrosequencing. A total of 209,106 sequences with average length 689 (±53) were filtered, denoised, trimmed, and then sorted into OTUs based on 97 % sequence similarity using the USEARCH software pipeline. Bacteria representing 10 phyla were found in the samples investigated. Fimicutes ribotypes were present in intestinal-mucosa and lumen in all fish and often dominated the libraries (average 43 and 38 %, respectively). Proteobacteria were also prevalent, but at a lower relative abundance, at 22 and 29 % in mucosa and lumen, respectively. The autochthonous microbiota was dominated by sequences belonging to the Bacilli (mean sequence abundance 24 %), in particular the Lactobacillaceae, with Lactobacillus and Pediococcous being the most abundant genera. Fewer Bacilli (mean sequence abundance 22 %) and Actinobacteria (2 %) were present in the lumen, and allochthonous communities consisted of a more even split among the bacterial classes, with increases in sequences assigned to members of the γ-Proteobacteria (16 %) and Fusobacteriia (8 %). The principal bacterial genera recorded in the lumen belonged to the lactic acid bacteria group, Cetobacterium, Clostridium and Synechococcus. Results obtained suggest that the lumen and mucosal layer of the snow trout intestine may host different microbial communities. Moreover, both regions harbour a diverse microbiome with a greater microbial diversity in the intestinal mucus compared with the luminal communities of the fish. Many of these microbes might be of high physiological relevance for the fish and may play key roles in the functioning of its gut.     

Random subwindows and extremely randomized trees for image classification in cell biology

Background

With the improvements in biosensors and high-throughput image acquisition technologies, life science laboratories are able to perform an increasing number of experiments that involve the generation of a large amount of images at different imaging modalities/scales. It stresses the need for computer vision methods that automate image classification tasks.

Results

We illustrate the potential of our image classification method in cell biology by evaluating it on four datasets of images related to protein distributions or subcellular localizations, and red-blood cell shapes. Accuracy results are quite good without any specific pre-processing neither domain knowledge incorporation. The method is implemented in Java and available upon request for evaluation and research purpose.

Conclusion

Our method is directly applicable to any image classification problems. We foresee the use of this automatic approach as a baseline method and first try on various biological image classification problems.

     

Registration Error and Intensity Similarity Based Label Fusion for Segmentation

Background

Label fusion is a core step of Multi-Atlas Segmentation (MAS), which has a decisive effect on segmentation results. Although existed strategies using image intensity or image shape to fuse labels have got acceptable results, there is still necessity for further performance improvement. Here, we propose a new label fusion strategy, which considers the joint information of intensity and registration quality.

Estimation de la distensibilité aortique à partir de séquences d’images de résonance magnétique « steady-state free-precession » et « contraste de phase »

Objective

To investigate the accuracy in the estimation of the aortic lumen area and distensibility obtained from Steady-State Free-Precession (SSFP) and Phase Contrast (PC) MR sequences.

Subjects and methods

Systolic and diastolic aortic lumen of the ascending and descending aorta of 50 subjects, collected with both acquisition sequences, were extracted using a 2D + t automated segmentation method.

Results

While the statistical study indicated very similar lumen areas for SSFP and PC data (slope = 1, r = 0.99), the corresponding distensibility values were less correlated (r = 0.54). Comparison between distensibility values in the ascending and descending aorta and study of these values with aging indicated a greater coherence with expected physiological behavior of the aorta when using SSFP images.

Discussion

Flow artifacts were more severe in PC images and could explain the better results obtained when using SSFP sequences.

Conclusion

A more accurate local assessment of the aortic stiffness is obtained from SSFP image sequences than from PC image sequences.     

Direct impact of invasive bivalve (<Emphasis Type="Italic">Sinanodonta woodiana</Emphasis>) parasitism on freshwater fish physiology: evidence and implications

Direct and potentially damaging effects of invasive alien species can remain unnoticed or insufficiently quantified, resulting in a lack of stakeholder awareness. We report for the first time that parasitic larvae (glochidia) of the invasive freshwater mussel Sinanodonta (Anodonta) woodiana (Unionidae, Bivalvia) cause an unexpected reduction in the condition factor of parasitized native fish species. The reduction in the body mass and condition factor of experimentally infested European chub (Squalius cephalus) was associated with changes in several physiological parameters measured in host fish plasma. Ion concentrations (potassium, chloride) and enzymes activities (aspartate aminotransferase, alanine aminotransferase, lactate dehydrogenase, alkaline phosphatase) were significantly affected; hence, the results reveal the complex effects of non-native glochidia on the homeostasis of the individually tested fish. Changes in host physiology and condition status were recorded also in environmentally relevant infestation intensities (mean of 3.02 ± 0.51 glochidia g^?1). Despite intensive concern regarding the negative biodiversity and ecosystem impacts of the adult stage of S. woodiana among conservationists and natural resource managers, potential effects of its larval stage have been neglected until now. Because fish hosts are an obligatory part of the reproductive cycle of the mussel and the main vector for spreading, documentation of this direct and easily quantifiable impact on fish has great potential to influence the key community of stakeholders in fisheries and aquaculture sectors and to serve as a strong motivating factor for invasive species control. We argue for more careful consideration of potential multiple life-stage effects of S. woodiana and of other invasive alien species as well, as different life stages can have highly specific impacts and corresponding relevance for key stakeholder groups.     

<Emphasis Type="Italic">Anoplodiscus</Emphasis> Sonsino, 1890 (Monogenea: Anoplodiscidae): a new Australian species,and the first African record from South African hosts

Species of Anoplodiscus Sonsino, 1890 were previously only known from host members of Sparidae. A new species, Anoplodiscus hutsonae n. sp. is proposed for museum specimens originally collected from species of Scolopsis Cuvier (Nemipteridae) off Heron Island and Lizard Island, Australia. Additionally, Anoplodiscus tai Ogawa, 1994 is synonymised with Anoplodiscus cirrusspiralis Roubal, Armitage & Rohde, 1983 due to a lack of support for differential characters, and Anoplodiscus richiardii is considered a species inquirenda. Anoplodiscus cirrusspiralis causes visible lesions on the skin and fins of its host, and may also contribute to poor food conversion rates in sparid aquaculture. Anoplodiscus cirrusspiralis has been recorded from cultured sparids in Australia, Japan, South Africa, and South Korea, and was implicated as a disease agent in fish from the former two countries. However, the discovery of A. cirrusspiralis on Chrysoblephus gibbiceps (Valenciennes), Ch. laticeps (Valenciennes) and Cymatoceps nasutus (Castelnau) in South Africa, ?Pagrus major (Temminck & Schlegel) in South Korea, and P. auratus (Forster) in Australia, New Zealand and Japan suggests that this species may have a wide distribution and low host-specificity within the Sparidae. In South Africa, A. cirrusspiralis was first encountered on a morbid C. nasutus and Ch. gibbiceps from two public aquaria in 2009 (Two Oceans Aquarium, Cape Town and uShaka Sea World, Durban, respectively). Additional material was collected from C. laticeps kept at an abalone farm in Hermanus that originated from Struisbaai on the South African south coast. Anoplodiscus cirrusspiralis is redescribed from the South African specimens. This is the first record of a member of Anoplodiscidae Tagliani, 1912 from Africa.     

Tropical biodiversity loss and people – A brief review

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Massive anthropogenic land use changes are taking place in the tropics. These changes have not only jeopardized native biodiversity but also people. Environmental apathy, corruption, poor natural resource governance, poverty and lack of conservation funding remain formidable challenges for conservation biologists. Any meaningful success in tropical conservation will, hence, need active collaboration by the civil society, biologists, social scientists, lawyers, funding agencies, national and multinational corporations, governments and non-governmental organizations. Concerted research efforts are urgently needed to understand the imperiled tropical biodiversity.     

Invasion of the Fungal Pathogen <Emphasis Type="Italic">Batrachochytrium dendrobatidis</Emphasis> on California Islands

Batrachochytrium dendrobatidis (Bd), an amphibian fungal pathogen, has infected >500 species and caused extinctions or declines in >200 species worldwide. Despite over a decade of research, little is known about its invasion biology. To better understand this, we conducted a museum specimen survey (1910–1997) of Bd in amphibians on 11 California islands and found a pattern consistent with the emergence of Bd epizootics on the mainland, suggesting that geographic isolation did not prevent Bd invasion. We propose that suitable habitat, host diversity, and human visitation overcome isolation from the mainland and play a role in Bd invasion.     

Rediscovery of type material of the bioerosional trace fossil <Emphasis Type="Italic">Talpina</Emphasis> von Hagenow, 1840 and its ichnotaxonomic implications

Friedrich von Hagenow is renowned for his seminal inventory of the diverse invertebrate fauna from the lower Maastrichtian chalk (Upper Cretaceous) of the Isle of Rügen, Germany. Tragically, his immense collection at Stettin (today Szczecin, Poland) was almost completely destroyed during World War II, including the type material of hundreds of species established by him during the first half of the 19th century. Seven belemnite specimens from his collection rediscovered at the Museum für Naturkunde Berlin, as well as 14 belemnites traced at the Museum für Mineralogie und Geologie at the Senckenberg Naturhistorische Sammlungen Dresden, include syntypes of four Talpina ichnospecies, labelled T. ramosa, T. solitaria, T. foliacea and T. sentiformis. To document this material, a new ‘digital cylinder seal technique’ was applied. The rediscovered material allows lectotype designations for T. ramosa and T. solitaria (now Trypanites solitarius), whereas T. foliacea and T. sentiformis, which where not formally published by von Hagenow, are regarded as nomina nuda. As a consequence, the non-topotypical neotypes of T. ramosa and T. solitaria, as designated by Ehrhard Voigt in 1972, are obsolete.     

Assemblage-level effects of the introduced peacock hind (<Emphasis Type="Italic">Cephalopholis argus</Emphasis>) on Hawaiian reef fishes

The peacock hind Cephalopholis argus (family Serranidae), locally known as ‘roi’, was introduced from French Polynesia to Hawaii in the mid-twentieth century as a food fish. However, because of its association with ciguatera fish poisoning, it is rarely fished for food. Previous research indicates that roi could have a negative impact on native reef fish assemblages because of their high densities and prey consumption rates. However, it is unclear whether roi add to the cumulative mortality of prey (predation hypothesis), or whether predation is instead compensatory (doomed surplus hypothesis). This study experimentally assessed the effects of roi on reef fish populations through a long-term (5.5 year) predator removal experiment. A Before-After-Control-Impact study design was used to assess changes in fish assemblages following the removal of roi on 1.3 ha of patch reef. Increases in the density of prey-sized fish (<15 cm TL) were observed 18 months after roi removal. However, those effects did not translate into sustained increases in prey. While increases in potential competitors, wrasses (family Labridae), particularly the piscivorous ringtail wrasse Oxycheilinus unifasciatus, were observed on roi-free reefs, the fish assemblage did not diverge substantially in composition. Native reef fish appeared to resist the potential negative impacts of predation by roi, possibly through a refuge in size for some fish families. Management to protect intact fish assemblage size-structure could serve to bolster native resistance to invading species. In considering the threats facing coral reefs, and the possible solutions, roi removal alone will not likely replenish native fishery resources.     

Development of subfossil <Emphasis Type="Italic">Daphnia</Emphasis> and <Emphasis Type="Italic">Chaoborus</Emphasis> assemblages in relation to progressive acidification and fish community alterations in SW Sweden

Dated sediment cores from acidified and fishless Lake Gaffeln and Lake Härsvatten, SW Sweden, were analyzed for Daphnia ephippia and Chaoborus mandibles to test whether acidification history and fish extirpations could be reconstructed in a paleo-study using these easily identifiable animal remains. According to monitoring data fish were lost in both lakes from the 1950s to the 1970s. Progressive acidification prior to monitoring was confirmed by a gradual decrease and eventual loss of Daphnia ephippia in both study lakes during the first half of the twentieth century. In Lake Gaffeln mandibles of C. obscuripes appeared immediately after fish loss in 1973, and the regular presence of this species confirmed the succeeding fishless state of this lake. In Lake Härsvatten sediments C. obscuripes appeared only recently, i.e. three decades after fish extirpation, showing that the absence of C. obscuripes mandibles is not a trustworthy indicator of fish presence. Hence, the appearance of C. obscuripes was not temporally related to fish loss but confirmed the present fishless condition. Known historical presence of cyprinid fish in Lake Gaffeln was confirmed by a significantly higher proportion of fragmented mandibles of C. flavicans compared to the historically cyprinid-free Lake Härsvatten. In addition, both lake profiles displayed zero-proportions of fragmented mandibles during fishless periods. We conclude that acidification history and fish extirpations can be inferred by integrated studies on subfossil Daphnia ephippia and Chaoborus mandibles. However, during extreme ultra-oligotrophic conditions in acidified clear-water lakes subfossil Chaoborus mandibles may be too scarce to infer fish absence/presence.