Spectropolarimetric investigation of the propagation of magnetoacoustic waves and shock formation in sunspot atmospheres

Velocity oscillations in sunspot umbrae have been measured simultaneously in two spectral lines: the photospheric Silicon I 10827 A line and the chromospheric Helium I 10830 A multiplet. From the full Stokes inversion of temporal series of spectropolarimetric observations we retrieved, among other parameters, the line of sight velocity temporal variations at photospheric and chromospheric heights. Chromospheric velocity oscillations show a three minute period with a clear sawtooth shape typical of propagating shock wave fronts. Photospheric velocity oscillations have basically a five minute period, although the power spectrum also shows a secondary peak in the three minute band which has proven to be predecessor for its chromospheric counterpart. The derived phase spectra yield a value of the atmospheric cut-off frequency around 4 mHz and give evidence for the upward propagation of higher frequency oscillation modes. The phase spectrum has been reproduced with a simple model of linear vertical propagation of slow magneto-acoustic waves in a stratified magnetized atmosphere that accounts for radiative losses through Newton's cooling law. The model explains the main features in the phase spectrum, and allows us to compute the theoretical time delay between the photospheric and chromospheric signals, which happens to have a strong dependence on frequency. We find a very good agreement between this and the time delay obtained directly from the cross-correlation of photospheric and chromospheric velocity maps filtered around the 6 mHz band. This allows us to infer that the 3-minute power observed at chromospheric heights comes directly from the photosphere by means of linear wave propagation, rather than from non-linear interaction of 5-minute (and/or higher frequency) modes.Comment: aastex preprint, 32 pages, 12 figure

openBIS: a flexible framework for managing and analyzing complex data in biology research

<p>Abstract</p> <p>Background</p> <p>Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.</p> <p>Results</p> <p>We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.</p> <p>Conclusions</p> <p>openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.</p

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

The nematode Caenorhabditis elegans is a popular model system in genetics, not least because a majority of human disease genes are conserved in C. elegans. To generate a comprehensive inventory of its expressed proteome, we performed extensive shotgun proteomics and identified more than half of all predicted C. elegans proteins. This allowed us to confirm and extend genome annotations, characterize the role of operons in C. elegans, and semiquantitatively infer abundance levels for thousands of proteins. Furthermore, for the first time to our knowledge, we were able to compare two animal proteomes (C. elegans and Drosophila melanogaster). We found that the abundances of orthologous proteins in metazoans correlate remarkably well, better than protein abundance versus transcript abundance within each organism or transcript abundances across organisms; this suggests that changes in transcript abundance may have been partially offset during evolution by opposing changes in protein abundance

Citizen science and online data: Opportunities and challenges for snake ecology and action against snakebite

The secretive behavior and life history of snakes makes studying their biology, distribution, and the epidemiology of venomous snakebite challenging. One of the most useful, most versatile, and easiest to collect types of biological data are photographs, particularly those that are connected with geographic location and date-time metadata. Photos verify occurrence records, provide data on phenotypes and ecology, and are often used to illustrate new species descriptions, field guides and identification keys, as well as in training humans and computer vision algorithms to identify snakes. We scoured eleven online and two offline sources of snake photos in an attempt to collect as many photos of as many snake species as possible, and attempt to explain some of the inter-species variation in photograph quantity among global regions and taxonomic groups, and with regard to medical importance, human population density, and range size. We collected a total of 725,565 photos—between 1 and 48,696 photos of 3098 of the world's 3879 snake species (79.9%), leaving 781 “most wanted” species with no photos (20.1% of all currently-described species as of the December 2020 release of The Reptile Database). We provide a list of most wanted species sortable by family, continent, authority, and medical importance, and encourage snake photographers worldwide to submit photos and associated metadata, particularly of “missing” species, to the most permanent and useful online archives: The Reptile Database, iNaturalist, and HerpMapper.ISSN:2590-171

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Nucgenotypesaelleni_griveaudi_islands

Individual genotypes for all 10 microsatellite loci, in Arlequin forma

Dloop_aell_grivesamplingsites

Description of haplotype sequences and haplotype composition of each sampled populatio

Mapsamplingsites

Geographic location of sampling sites and island

Out of Southeast Asia: A new species of thick-thumbed bat (Chiroptera: Vespertilionidae: Glischropus) from Meghalaya, north-eastern India

Saikia, Uttam, Ruedi, Manuel, Csorba, Gabor (2022): Out of Southeast Asia: A new species of thick-thumbed bat (Chiroptera: Vespertilionidae: Glischropus) from Meghalaya, north-eastern India. Zootaxa 5154 (3): 355-364, DOI: 10.11646/zootaxa.5154.3.

Two Mitochondrial Barcodes for one Biological Species: The Case of European Kuhl's Pipistrelles (Chiroptera).

The Kuhl's pipistrelle (Pipistrellus kuhlii) is a Western Palaearctic species of bat that exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages. We examined here two lineages occurring in Western Europe, and used both mitochondrial and nuclear markers to measure degrees of genetic isolation between bats carrying them. The sampling focused on an area of strict lineage sympatry in Switzerland but also included bats from further south, in North Africa. All individuals were barcoded for the COI gene to identify their mitochondrial lineages and five highly polymorphic microsatellite loci were used to cluster them according to their nuclear genotypes. Despite this low number of nuclear markers, all North African nuclear genotypes were grouped in a highly distinct subpopulation when compared with European samples sharing the same mitochondrial barcodes. The reverse situation prevailed in Switzerland where bats carrying distinct barcodes had similar nuclear genotypes. There was a weak east/west nuclear structure of populations, but this was independent of mitochondrial lineages as bats carrying either variant were completely admixed. Thus, the divergent mitochondrial barcodes present in Western Europe do not represent cryptic species, but are part of a single biological species. We argue that these distinct barcodes evolved in allopatry and came recently into secondary contact in an area of admixture north of the Alps. Historical records from this area and molecular dating support such a recent bipolar spatial expansion. These results also highlight the need for using appropriate markers before claiming the existence of cryptic species based on highly divergent barcodes