Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic reconstruction based on COI reshuffles the taxonomy of hyalosphenid shelled (testate) amoebae and reveals the convoluted evolution of shell plate shapes

Species diversity in most protistan groups has been underestimated. Many morpho‐species are in fact complexes that require detailed morphometric studies to be discriminated. However, which traits can be used for species descriptions remains in many cases unclear. The testate amoeba genus Quadrulella produces self‐secreted, siliceous plates with a very characteristic square shape—such plates were assumed to be synapomorphic of the genus. Here we demonstrate that Quadrulella symmetrica (the most common Holarctic species) is not monophyletic. Square plate size and arrangement, test size and general shape are efficient criteria for species discrimination. Based on morphology and sequence data, we describe Quadrulella variabilis sp. nov. from Switzerland, and Quadrulella madibai sp. nov. from South Africa, and confirm the validity of Q. alata. The former species Q. subcarinata does not belong to the genus Quadrulella. We therefore transfer this species to the new genus Mrabella gen. nov. Our results show that hyalosphenids presenting siliceous square shell plates do not form a monophyletic clade. Several possible hypotheses about the origins of square plates are discussed. Additionally, this comprehensive phylogenetic analysis of the family Hyalospheniidae confirms that the genus Nebela is paraphyletic and needs to be divided into genera based on general shell shape: Nebela sensu stricto, Longinebela gen. nov., Planocarina gen. nov., Gibbocarina gen. nov., Cornutheca gen. nov. and Mrabella gen. nov.
Localisation of corneal epithelial progenitors and characterization of cell-cell interactions in the human limbal stem cell niche

The cornea, the transparent tissue located at the front of the eye, is a highly specialized tissue that transmits and refracts light onto the retina. Maintenance of the corneal epithelium relies on a population of limbal epithelial stem cells (LESCs) that maintain transparency of the ocular surface that is essential for vision. Despite great advances in our understanding of ocular stem cell biology over the last decade, the exact location of the LESC niche remains unclear. After observing a high population of basal epithelial cells expressing stem cell markers within the previously identified limbal crypts (LC), the first aim of this study was to demonstrate by in vitro clonal analysis that these structures provide a niche for the resident LESCs. High-resolution transmission electron microscopy has been further used to image the basal epithelial layer at the limbus. Cells with morphology consistent with stem cells were present within the basal layer of the limbal crypts but not within the basal layer of non-crypt limbal biopsies. Moreover, LESCs appeared proximal to limbal stromal cell extensions that suggested a possible route for direct cell-to-cell interaction. These observations were further confirmed by serial block-face scanning electron microscopy that revealed, for the first time, direct epithelial-stromal interactions in the LESC niche whereas limbal melanocytes maintained the LESC apically. In order to assess the role of limbal melanocytes (hLM) as niche cells for the maintenance of LESC, a novel co-culture system was developed in which hLM were used as a feeder layer for the expansion of limbal epithelial cells in vitro. Interestingly, hLM had the ability to support the clonal growth of LECs that maintained stem cell-like characteristics in 2D and 3D tissue equivalents. Taken together, these observations suggest an important role for melanocytes as niche cells in the native human limbal crypts.
Response of Running Shoot tips of Strawberry (Fragaria x ananasa) for in vitro Propagation in Kurdistan Region of Iraq

Strawberry (Fragaria x ananasa) is grown for its excellent food and nutritional value in many parts of the world. The main objective of this study was to optimize an efficient, reliable and economical protocol for In vitro propagation of strawberry plants. The effect of BAP (6-Benzyl amino purine) alone or combined with (Gibberellic acid, Kinetin, IBA) and the effects of TDZ (Thidiazuron) on shoot proliferation of strawberry (Fragaria x ananasa) has been evaluated. It has been noticed that 2.0 mgl-1 BAP combination with 0.25 mgl-1 IBA able to generate the maximum number of shoots / explants (6.375) with high shoot length ( 0.675 cm) and high leaves number /explants (19.0). On the other hand, presence of 1.5 mgl-1 of TDZ in the nutrient medium increased the shoot number/explants to (7.335) as compared to BAP treatments. The proliferated shoots were subjected to full strength MS media supplemented with 0.75 mgl-1 IAA give the optimal ratio of rooting. Survived rooted plantlets were acclimatized gradually and successfully transferred under greenhouse conditions for hardening.
Taxonomic resolution and treatment effects – alone and combined – can mask significant biodiversity reductions

ABSTRACT Taxonomic resolution or uncertainty poses an important problem in biodiversity research. Assessment of biodiversity at the species level is most informative and preferred, but requires effort and expertise. Alternatively, researchers often bin species into higher taxa because they are unable to recognize them, or to save money and time. Here we analyse, by simulation and analytical modelling, the combined effects of dose-dependent mortality and taxonomic binning on biodiversity indices for a fictitious community of organisms. We asked (1) how binning species in a sample into higher taxa significantly affects biodiversity measures, and (2) whether dose-dependent mortality effects, alone or in combination with taxonomic uncertainty, are duly captured by classic biodiversity indices. Our study shows that haphazard binning into various taxonomic levels is legitimate and preferable to orderly binning (all taxa binned at the same level), because it provides the best resolution. We further show that binning will regularly obscure statistical detection of biodiversity differences, if only due to scaling of mean and variance. Also, treatment effects in combination with taxonomic uncertainty can introduce estimation biases of at times complex nonlinear and non-intuitive nature under any taxonomic resolution scenario, potentially including relative increases in the biodiversity index when intuitively decreases would be expected. We recommend being specific about the expected qualitative and quantitative effects of any treatment or natural comparison before formulating a hypothesis regarding biodiversity reductions. Our theoretical study should aid in this endeavour. EDITED BY Isabelle Durance
Nouvelles espèces d'Henneguya Thélohan, 1895 (Myxozoa, Myxosporea) parasites des poissons marins du Sénégal : Etude en microscopie photonique et électronique

Huit nouvelles especes de Myxosporidies du genre Henneguya sont decrites chez des poissons des cotes senegalaises. H. brachideuteri sp. n. vit dans le coeur de Brachydeuterus auritus. L'ultrastructure de sa sporogenese et de ses spores est analogue a celle de toutes les especes du genre. H. joalensis sp. nov. infeste les reins de Cephalopholis taeniops. H. kayarensis sp. nov. parasite le foie de Galeoides decadactylus. H. lutjani sp. nov. infeste les branchies de Lutjanus agennes. H. mbourensis sp. nov. vit dans les reins de Dentex canariensis. H. ouakamensis sp. nov. parasite les branchies et le coeur de Mugil cephalus. H. priacanthi sp. nov. a ete rencontre sur les branchies de Priacanthus arenatus et H. yoffensis sp. nov. parasite les branchies et le coeur de Sparus caeruleostictus.
A Review of Field Lysimeter Studies to Describe the Environmental Fate of Pesticides

A brief review is presented for the use of soil lysimeters in studying transpiration, evapotranspiration, moisture, and nutrient movement in earlier times and pesticide dissipation and movement, and mass-balance of pesticide dissipation in more recent times. The important factors needed to understand research findings and to model pesticide dissipation such as key soil and site characteristics, climatic conditions, and the methods involved are discussed. Several case studies carried out by Ciba and North Carolina State University are discussed and current developments in soil column field lysimeters are presented.
Micropropagation of Pacific Dogwood

daho's population of Pacific dogwood (Cornus nuttallii Audubon) has declined. Propagation of disease-resistant clones would be useful to horticulturists and conservation biologists. In intro-derived microshoots, incubated for 1 month on woody plant medium supplemented with 6.04 mm calcium gluconate and 4.44 μM benzyladenine, produced an average of 3.1 axillary microshoots per explant. Up to 62% of the elongated microshoots had rooted ex vitro 5 weeks following a 4.5%IBA talc dip. Pantlets resumed shoot growth within 2 months of acclimatization, and 70% survived after 1 year. This protocol is more rapid and efficient than propagation by layering or rooting the difficult-to-root stem cuttings of this species
Going, going, gone? Loss of genetic diversity in two critically endangered Australian freshwater fishes, Scaturiginichthys vermeilipinnis and Chlamydogobius squamigenus, from Great Artesian Basin springs at Edgbaston, Queensland, Australia

Artesian springs are particularly sensitive freshwater ecosystems, characterized by specialized flora and fauna which, owing to their isolation, are often endemic. Thus, protection of spring habitats and endemic spring biota is important for biodiversity conservation, particularly because human impacts such as invasive species, habitat destruction, and fragmentation can have such devastating effects. This study investigated the mitochondrial DNA (mtDNA) genetic diversity and structure of two critically endangered (IUCN) freshwater fish species: red-finned blue-eye Scaturiginichthys vermeilipinnis, and Edgbaston goby Chlamydogobius squamigenus, with the aim of assisting management agencies to establish relocated populations that conserve the genetic integrity and evolutionary potential of both species. 2862 bp from multiple mtDNA genes were amplified from 111 red-finned blue-eye individuals (17 from the 1990s and 94 from 2010), and a 660 bp segment of mtDNA cytochrome b was amplified from 111 Edgbaston goby individuals (from 2010). In total, 14 concatenated mtDNA haplotypes were identified in red-finned blue-eye and three cytb haplotypes were identified in Edgbaston goby. Overall assessment of the genetic diversity and structure of the endemic fish fauna from the Edgbaston springs revealed low levels of diversity in both species and a loss of haplotypes in red-finned blue-eye over time. In addition, both species displayed significant genetic structure: at the spring scale for red-finned blue-eye and at the spring group scale for Edgbaston goby. It is concluded that without the appropriate management of relocated populations, such as considering genetic structure and diversity and selecting high quality habitats, these species are at a severe risk of losing evolutionary potential and becoming extinct. This study provides a valuable example for conservation managers of the contribution that population genetic studies can make regarding the adaptive management of endangered species. Copyright © 2016 John Wiley & Sons, Ltd.
Complete plastid genome sequences of Coreanomecon hylomeconoides Nakai (Papaveraceae), a Korea endemic genus

Abstract The plastid genome (plastome) sequences from the monotypic endemic genus of Korea, Coreanomecon hylomeconoides Nakai, were completed in this study (NCBI No. KT274030). The complete plastome size was 158,824 bp in length, containing a pair of 26,685 bp inverted repeat (IR), which were separated by a large and small single copy (LSC, SSC) region of 86,916 bp and 18,538 bp, respectively. The overall GC contents were 38.8%. The plastome contained 112 genes, including protein-coding genes, 30 tRNA genes, 4 rRNA genes. Sixteen genes contained one intron and two genes had two introns. Phylogenetic analysis revealed that C. hylomeconoides was sister group of Papaver somniferum with 100% support value.
Insertional Mutagenesis of Chlamydomonas reinhardtii

[Abstract] The unicellular microalga Chlamydomonas reinhardtii (C. reinhardtii) has been used as a reference model for numerous fields of research. Principle research areas are eukaryotic flagellar structure and function, basal bodies (centrioles), cell-cell recognition, cell cycle control, chloroplast biogenesis, phototaxis, nonphotochemical quenching, and especially photosynthesis for C. reinhardtii can grow in the dark on an organic carbon (e.g., acetate), and thus provides advantages over land plants (Harris, 2001; Peers et al., 2009). C. reinhardtii has a short life cycle, a sequenced genome (Merchant et al., 2007), and a growing molecular toolbox for forward and reverse genetic studies, including transformation protocols, gene silencing (Kim and Cerutti, 2009; Molnar et al., 2009), and fluorescent protein-tag (Rasala et al., 2013). There are two commonly used methods for C. reinhardtii transformation – electroporation and glass bead agitation. Electroporation is normally restricted to strains with cell wall, as it kills cell-wall-deficient strains effectively if without careful handling of osmosis. Electroporation also requires special instruments such as electroporator and cuvettes. In contrast, glass bead agitation uses simple lab equipment. The mild shear created by agitation in the presence of glass bead allows cell-wall-deficient strains to take up DNA. If glass bead method is to be applied to cell-wall strains, cells need to be treated with autolysin (http://www.chlamy.org/methods/autolysin.html) to partially lyse the wall components. A pitfall of both methods is that the DNAs are often shortened by nuclease once entering the cells, making the downstream PCR-based genotyping of insertion site rather difficult. Here I describe an improved design of insertional mutagenesis used in (Tsai et al., 2014), and the transformation protocol using glass bead as previously described in (Kindle, 1990) with minor modification. The putative mutants can be selected by autotrophic or antibiotic resistance markers, and the disrupted loci can be mapped by methods such as plasmid rescue (Peers et al., 2009) and SiteFinding PCR (Tan et al., 2005).
Review of the Indo-Pacific Flasherwrasses of the genus Paracheilinus (Perciformes: Labridae), with descriptions of three new species

The Indo-Pacific labrid fish genus Paracheilinus now contains 20 species. Most of the currently known species inhabit the mega-diverse East Indian region including Paracheilinus angulatus, P. carpenteri, P. cyaneus, P. filamentosus, P. flavianalis, P. lineopunctatus, P. nursalim, P. rennyae, P. togeanensis, P. walton, as well as three recent discoveries described as new species herein. Five species are known from the Red Sea and Indian Ocean, including P. attenuatus (Seychelles and Kenya), P. hemitaeniatus (Madagascar and South Africa), P. mccoskeri (Kenya, Comoro Islands and Arabian Gulf to Andaman Sea), P. octotaenia (Red Sea), and P. piscilineatus (Mauritius). The remaining two species, P. bellae and P. rubricaudalis, are mainly confined to Micronesia/Marshall Islands and PNG/Fiji/Vanuatu, respectively. Members of the genus are typically distinguished on the basis of their caudal-fin and dorsal-fin shapes, the presence or absence of elongate filamentous dorsal-fin rays, and, in particular, the color of terminal-phase (TP) males, including their dramatic nuptial-display patterns. Paracheilinus paineorum n. sp. is described from 8 specimens, 43.1–70.0 mm SL, collected in Indonesia (southwestern Flores, Sulawesi, Nusa Penida, East Borneo, and Seribu Islands) in depths of 10–65 m. It is closely related to the allopatric P. filamentosus and P. xanthocirritus n. sp. , differing mainly in coloration (particularly the bright red dorsal-fin markings) and larger maximum size (to at least 70 mm SL). Paracheilinus xanthocirritus n. sp. is described from 12 specimens, 33.9–49.3 mm SL, collected in the South China Sea at the Anambas Islands of Indonesia and Brunei in depths of 15–25 m. In contrast to the closely related P. paineorum n. sp. , TP males of this species have a mostly yellow dorsal fin lacking red markings. The two new species further differ from P. filamentosus by having a narrower interorbital and a shorter caudal peduncle. A third new species, Paracheilinus alfiani, n.
Fruit rot of sweet cherries and raspberries caused by Penicillium crustosum and Mucor piriformis in South Patagonia, Argentina

Abstract Cherries and raspberries are important fruit crops in Patagonia, Argentina. A high proportion (50%) of raspberry production is organic certified and sold for fresh and frozen domestic markets. Due to post-harvest rot diseases, cherries and raspberries from Patagonia are kept in cold storage for a short period of time. During the storage season of 2012–2013, fruit rot samples were obtained from conventional and organic sweet cherry and raspberry orchards in the Andean zone of Central Patagonia. Penicillium crustosum and Mucor piriformis were isolated from both types of production systems and identified through morphological and molecular analysis; their pathogenicity was confirmed based on their virulence (incidence and severity). To our knowledge, this is the first report confirming Penicillium crustosum and Mucor piriformis causing post-harvest disease on cherries and raspberries in Argentina, and it contributes to expanding the knowledge on emerging pathogens.
Post‐settlement ecological changes in the forests of the Great Lakes National Parks

National parks of the United States seek to preserve the natural and cultural heritage of the United States, yet parks in the eastern and Midwestern United States were established after periods of human settlement and disturbance. In the Great Lakes region, fire and windfall originally dominated as disturbance agents, driving dynamics in prairies, savannas, and in many forested ecosystems. However, fire suppression over the last century has radically lengthened fire return intervals. Additionally, widespread logging, slash burning, mining, and agricultural settlement successively shifted the dominant forms of land use, greatly altering these forests. From 2008 to 2014, the National Park Service's Great Lakes Inventory and Monitoring Program surveyed vegetation in nine Great Lakes National Parks. We compared these surveys with data derived from the mid- to late-1800s Public Land Survey (PLS) to assess shifts in forest composition. Community composition has changed dramatically since the mid-19th century. Preferred timber species (e.g., Pinus strobus and Tsuga canadensis) and fire-adapted species (e.g., Quercus macrocarpa and Pinus banksiana) have declined across the region, while aspen (Populus spp.) and/or maple (Acer spp.) have consistently increased. Ordinations reveal both these general trends and substantial divergence in composition within particular parks since the PLS. Past logging practices and mesification following fire suppression account for most general trends across the region, while local differences in edaphic conditions, ungulate herbivory, and disturbance regimes account for many park-to-park differences. Understanding how these factors, alone and in combination, have affected forests in these parks provides both a picture of regional forest dynamics and tools that improve our ability to manage these parks. Continuing to monitor forest vegetation in these parks will allow us to test our understanding of forest dynamics and to use these parks as the “land laboratories” that Leopold envisioned.
Evaluation of different insecticides against green semilooper, Thysanoplusia orichalcea (Fab.) in soybean ecosystem

A field study was conducted during Kharif season 2014-15 to determine the efficacy of different insecticides against semilooper Thysanoplusia orichalcea (Fab.) in soybean ecosystem in the insectory premises of Agricultural Entomology Section, College of Agriculture Nagpur. Least cumulative average number larvae (0.05/mrl) was recorded in treatment of Fenvalerate 20 EC @ 0.50 ml/l (T 7 ) found to be superior compared to other treatments. The next effective treatments were emamectin benzoate 5 SG @ 0.3 g/ l (T 6 : 0.06/mrl) and also in Spinosad 45 SC @ 0.25 ml/l (T 3 :0.07/mrl), Indoxacarb 15.8 EC @ 0.60 ml/l (T 5 :0.08/mrl) found to be at par with T 6 and T 3 . However, the treatment Neem Oil 2 per cent (T 2 ) recorded 0.78 larvae/mrl. Whereas, NSE @ 5 per cent (T 1 :0.95/mrl) and Beauveria bassiana 1x10 8 CFU @ 4 g/l (T 4 :0.99/mrl) were found to be least effective in reducing larval population/mrl. Maximum mean larval population (1.48/mrl) was recorded in control (Water spray; T 8 ). Fenvalerate 20 EC @ 0.50 ml/l, Indoxacarb 15.8 EC @ 0.60 ml/l, Spinosad 45 SC @ 0.25 ml/l were found to be most effective treatments which recorded highest yield of 21.05 q/ha, 20.10 q/ha and 19.02 q/ha, respectively. From the seed production point of view Fenvalerate 20 EC @ 0.50 ml/l, Indoxacarb 15.8 EC @ 0.60 ml/l, Spinosad 45 SC @ 0.25 ml/l were most effective in recording highest yield.
New record of two cymothoid isopods (Crustacea: Malacostraca: Isopoda) from South Korea

E) and Gageo­do Island (34°02 ′ N, 125° 07 ′ E) in South Korea, respectively. They were preserved directly in 95% ethyl alcohol after collection. All exam­ ined specimens were deposited in the National Institute of Biological Resources (NIBR) and Inha University, South Korea. The specimens were transferred to glycerin for dis­ section and then examined and dissected under a stereo­ microscope (Model SZX­7; Olympus, Tokyo, Japan). Figures of dissected appendages were obtained by light microscopy with attached drawing tube (Model DM 2500; Leica, X50­630, Wetzlar, Germany). Figures of the whole body were obtained using the drawing tube at­ to a stereomicroscope (Olympus SZX­12, Tokyo, Two marine isopods, Elaphognathia sugashimaensis (Nunomura, 1981) and Metacirolana shijikiensis Nunomura, 2008, have been reported for the first time in South Korea. Specimens of E. sugashimaensis and M. shijikiensis were collected using light traps from Yeongdeok­gun and Gageo­do Island in South Korea, respectively. The genera Elaphognathia Monod, 1926 and Metacirolana Kussakin, 1979 are new to South Korea. In this paper, we provide descriptions of diagnostic characteristics and illustrations of their morphologies. Additionally, the partial sequences of mitochondrial cytochrome c oxidase subunit 1 ( CO1 ) of two species are provided as molecular characteristics.
Potential of molecular marker analysis for variety identification in processed tobacco

We describe the assessment of random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers for the fingerprinting and identification of cultivated tobacco varieties. Two DNA extractionand purification methods were found to be suitable for fingerprinting analysis on different types of processed tobacco leaf. RAPD markers revealed low levels of polymorphism between the varieties tested and were not reproducibly found in cured tobacco leaves. Conversely, a total of 33 polymorphic AFLP markers could be identified upon the analysis of green leaf of four commercial tobacco varieties using six primer combinations. In addition, the AFLP pattern of cured and green leaf of the same variety was comparable. These results confirm the superiority of AFLP over RAPD techniques in plant variety fingerprinting and open interesting possibilities for post-harvest variety identification in cured tobacco and other processed agricultural crops.