Perspectives of species identification by MALDI-TOF MS in monitoring - stability of proteomic fingerprints in marine epipelagic copepods

We analyzed robustness of species identification based on proteomic composition to data processing and intraspecific variability, specificity and sensitivity of species-markers as well as discriminatory power of proteomic fingerprinting and its sensitivity to phylogenetic distance. Our analysis is based on MALDI-TOF MS data from 32 marine copepod species coming from 13 regions (North and Central Atlantic and adjacent seas). A random forest (RF) model correctly classified all specimens to species level with only small sensitivity to data processing, demonstrating the strong robustness of the method. Compounds with high specificity showed low sensitivity i.e., identification was rather based on complex pattern-differences than on presence of single markers. Proteomic distance was not consistently related to phylogenetic distance. A species-gap in proteome composition appeared at 0.7 Euclidean distance when using only specimens from the same sample. When other regions or seasons were included, intra-specific variability increased, resulting in overlaps of intra- and inter-specific distance. Highest intra-specific distances (> 0.7) were observed between specimens from brackish and marine habitats i.e., salinity likely affects proteomic patterns. When testing library sensitivity of the RF model to regionality, strong misidentification was only detected between two congener pairs. Still, choice of reference library may have an impact on identification of closely related species and should be tested before routine application. We envision high relevance of this time- and cost-efficient method for future zooplankton monitoring as it provides not only in-depth taxonomic resolution for counted specimens but also add-on information e.g., on developmental stage or environmental conditions.

Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean

Species identification is pivotal in biodiversity assessments and proteomic fingerprinting by MALDI-TOF mass spectrometry has already been shown to reliably identify calanoid copepods to species level. However, MALDI-TOF data may contain more information beyond mere species identification. In this study, we investigated different ontogenetic stages (copepodids C1-C6 females) of three co-occurring Calanus species from the Arctic Fram Strait, which cannot be identified to species level based on morphological characters alone. Differentiation of the three species based on mass spectrometry data was without any error. In addition, a clear stage-specific signal was detected in all species, supported by clustering approaches as well as machine learning using Random Forest. More complex mass spectra in later ontogenetic stages as well as relative intensities of certain mass peaks were found as the main drivers of stage distinction in these species. Through a dilution series, we were able to show that this did not result from the higher amount of biomass that was used in tissue processing of the larger stages. Finally, the data were tested in a simulation for application in a real biodiversity assessment by using Random Forest for stage classification of specimens absent from the training data. This resulted in a successful stage-identification rate of almost 90%, making proteomic fingerprinting a promising tool to investigate polewards shifts of Atlantic Calanus species and, in general, to assess stage compositions in biodiversity assessments of Calanoida, which can be notoriously difficult using conventional identification methods.

Description of three new species of Bradyidius (Copepoda: Calanoida), the new aetideids from the deep Pacific Ocean, with notes on the genera Bradyidius and Aetideopsis

Three new aetideid species, Bradyidius abyssalis sp. nov., Bradyidius parabyssalis sp. nov., and B. kurilokamchaticus sp. nov. are described from female specimens collected near the seafloor in the abyss of the Pacific and Atlantic Oceans. Specimens of Bradyidius parabyssalis sp. nov. were obtained in both the Atlantic and Pacific Oceans (Argentine Basin, area of the Meteor Seamount and the Kurile-Kamchatka Trench). Bradyidius abyssalis sp. nov. was found only in the Atlantic Ocean, (Brazil and Guinea Basins and area of the Meteor Seamount) and Bradyidius kurilokamchaticus sp. nov. was recorded from the Kurile-Kamchatka Trench of the Pacific Ocean. Three new herein described Bradyidius species constitute the first documented records of the genus from the abyss of the World Ocean. In addition, three Bradyidius species from the Weddell Sea, the Atlantic Ocean and the Kurile-Kamchatka Trench, are briefly described without biological names due to their bad condition. Bradyidius parabyssalis sp. nov. and B. abyssalis sp. nov. are distinguished from all known congeners by the presence of 3 setae at the basis of the mandible and morphological details of the prosome posterior corners and P1. They show close resemblance to each other but differ in body size, rostrum structure, P4 coxa armament and length of the setae of the antennule ancestral segment I and the mandible basis. Bradyidius kurilokamchaticus sp. nov. shares with B. curtus Markhaseva, 1993, B. pacificus (Brodsky, 1950) and B. arnoldi Fleminger, 1957 a rostrum with non-divergent or parallel points, but differs from these species in the size, the well developed lateral spine on exopod segment 1, in the number of setae at the antenna exopod segment 1 and some morphological details of the prosome posterior corners. Characters that define the genus Bradyidius Giesbrecht, 1897 from Aetideopsis Sars, 1903, i.e. the shape of lateral spines of P1exopod segments 1 and 2; the endopod of P2 segmentation and the setation of the antennule ancestral segments XII, XV and XVII are discussed.

Proteomic fingerprinting facilitates biodiversity assessments in understudied ecosystems: A case study on integrated taxonomy of deep sea copepods

Accurate and reliable biodiversity estimates of marine zooplankton are a prerequisite to understand how changes in diversity can affect whole ecosystems. Species identification in the deep sea is significantly impeded by high numbers of new species and decreasing numbers of taxonomic experts, hampering any assessment of biodiversity. We used in parallel morphological, genetic, and proteomic characteristics of specimens of calanoid copepods from the abyssal South Atlantic to test if proteomic fingerprinting can accelerate estimating biodiversity. We cross-validated the respective molecular discrimination methods with morphological identifications to establish COI and proteomic reference libraries, as they are a pre-requisite to assign taxonomic information to the identified molecular species clusters. Due to the high number of new species only 37% of the individuals could be assigned to species or genus level morphologically. COI sequencing was successful for 70% of the specimens analysed, while proteomic fingerprinting was successful for all specimens examined. Predicted species richness based on morphological and molecular methods was 42 morphospecies, 56 molecular operational taxonomic units (MOTUs) and 79 proteomic operational taxonomic units (POTUs), respectively. Species diversity was predicted based on proteomic profiles using hierarchical cluster analysis followed by application of the variance ratio criterion for identification of species clusters. It was comparable to species diversity calculated based on COI sequence distances. Less than 7% of specimens were misidentified by proteomic profiles when compared with COI derived MOTUs, indicating that unsupervised machine learning using solely proteomic data could be used for quickly assessing species diversity.

Repositories for Taxonomic Data: Where We Are and What is Missing

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].

Description of Bradyetes paramatthei sp. nov. (Copepoda: Calanoida), a new aetideid species from the deep Pacific Ocean with notes on the genus Bradyetes

A new and rare aetideid species of the benthopelagic genus Bradyetes Farran, 1905 is described from female specimens collected near the seafloor from the abyss of the Pacific, Atlantic and Southern Oceans between 2000 and 2014. The new species, Bradyetes paramatthei sp. nov., is described from the Kurile-Kamchatka Trench (Pacific Ocean) and is additionally reported from the Angola and Guinea basins and from the Meteor Seamount of the Atlantic Ocean. Bradyetes paramatthei sp. nov. is related to the species B. matthei Johannessen, 1976, but differs in the shape of the prosome posterior corners, which are oval-rounded, and in the proximal segment of the antennal exopod, which is supplied with one seta. These two species are shown to constitute a separate species group within the genus Bradyetes. The other species group contains the remaining congeners including Bradyetes inermis Farran, 1905, for which morphological variability is discussed. Specimens of this species show diverse morphology and comprise 3 morphotypes distinguished by the P1, with a developed or absent lateral lobe , the P1 basal medial seta, which is either nude or supplied with setules, and by the different number of setae of the maxillule praecoxal arthrite.

Data storage and data re-use in taxonomy—the need for improved storage and accessibility of heterogeneous data

The ability to rapidly generate and share molecular, visual, and acoustic data, and to compare them with existing information, and thereby to detect and name biological entities is fundamentally changing our understanding of evolutionary relationships among organisms and is also impacting taxonomy. Harnessing taxonomic data for rapid, automated species identification by machine learning tools or DNA metabarcoding techniques has great potential but will require their review, accessible storage, comprehensive comparison, and integration with prior knowledge and information. Currently, data production, management, and sharing in taxonomic studies are not keeping pace with these needs. Indeed, a survey of recent taxonomic publications provides evidence that few species descriptions in zoology and botany incorporate DNA sequence data. The use of modern high-throughput (-omics) data is so far the exception in alpha-taxonomy, although they are easily stored in GenBank and similar databases. By contrast, for the more routinely used image data, the problem is that they are rarely made available in openly accessible repositories. Improved sharing and re-using of both types of data requires institutions that maintain long-term data storage and capacity with workable, user-friendly but highly automated pipelines. Top priority should be given to standardization and pipeline development for the easy submission and storage of machine-readable data (e.g., images, audio files, videos, tables of measurements). The taxonomic community in Germany and the German Federation for Biological Data are researching options for a higher level of automation, improved linking among data submission and storage platforms, and for making existing taxonomic information more readily accessible.

The phylogeny of Ryocalanoidea (Copepoda, Calanoida) based on morphology and a multi-gene analysis with a description of new ryocalanoidean species

Two new species of ryocalanoid copepods (Crustacea: Calanoida), Ryocalanus squamatus sp. nov. and Yrocalanus kurilensis sp. nov. are described together with a female of Ryocalanus infelix Tanaka, 1956, type species for the genus Ryocalanus Tanaka, 1956, from abyssal depths in the Kurile-Kamchatka trench. The new species can be assigned to the superfamily Ryocalanoidea based on the segmentation and armature of the swimming legs and the modification of the male right antennule. A new interpretation of the fusions of segments in the male right antennule of Ryocalanus shows the marked differences between the ryocalanoidean genera. The status of Ryocalanoidea within the Calanoida is discussed based on morphology and a first molecular multi-gene analysis with cytochrome oxidase subunit I, cytochrome b, nuclear ribosomal 18S and 28S rDNA and internal transcribed spacer 2. This analysis supports the close interrelationship between Ryocalanoidea and Spinocalanoidea. The monophyletic status of Ryocalanoidea could not be retrieved in the phylogenetic analysis, as specimens of Yrocalanus formed a clade within Spinocalanoidea. The inconclusive results between morphological and molecular analyses are discussed with a proposition to keep the current system until more males of taxa belonging to the Spinocalanoidea are discovered, as the male antennule plays a crucial role in the interpretation of relationships between Ryocalanoidea and Spinocalanoidea.

Reasoning about Topological and Cardinal Direction Relations Between 2-Dimensional Spatial Objects

Increasing the expressiveness of qualitative spatial calculi is an essential step towards meeting the requirements of applications. This can be achieved by combining existing calculi in a way that we can express spatial information using relations from multiple calculi. The great challenge is to develop reasoning algorithms that are correct and complete when reasoning over the combined information. Previous work has mainly studied cases where the interaction between the combined calculi was small, or where one of the two calculi was very simple. In this paper we tackle the important combination of topological and directional information for extended spatial objects. We combine some of the best known calculi in qualitative spatial reasoning, the RCC8 algebra for representing topological information, and the Rectangle Algebra (RA) and the Cardinal Direction Calculus (CDC) for directional information. We consider two different interpretations of the RCC8 algebra, one uses a weak connectedness relation, the other uses a strong connectedness relation. In both interpretations, we show that reasoning with topological and directional information is decidable and remains in NP. Our computational complexity results unveil the significant differences between RA and CDC, and that between weak and strong RCC8 models. Take the combination of basic RCC8 and basic CDC constraints as an example: we show that the consistency problem is in P only when we use the strong RCC8 algebra and explicitly know the corresponding basic RA constraints.

Histopathology and immunophenotype of the spleen during acute antibody-mediated rejection

Splenectomy has been reported to have a beneficial effect in treating Acute antibody-mediated rejection (ABMR). This reason for this often rapid and profound beneficial effect is not readily apparent from what is known about normal splenic immunoarchitecture. While the spleen is rich in mature B cells, it has not been noted to be a repository for direct antibody-secreting cells. We present a case of a Native American female who received a renal transplant and developed a severe episode of ABMR. The patient was initially refractory to both plasmapheresis and IVIG. The patient underwent an emergent splenectomy with almost immediate improvement in her renal function and a rapid drop in her DR51 antibodies. Immunohistochemical stains of the spleen demonstrated abundant clusters of CD138+ plasma cells (>10% CD138 cells as opposed to 1% CD138 cells as seen in traumatic controls). Though this is a single case, these findings offer a rationale for the rapid ameliorative effect of splenectomy in cases of antibody rejection. It is possible that the spleen during times of excessive antigenic stress may rapidly turn over B cells to active antibody-secreting cells or serve as a reservoir for these cells produced at other sites.

Haplotype analysis of the CD11 gene cluster in patients with chronic Helicobacter pylori infection and gastric ulcer disease

Helicobacter pylori infection leads to a broad spectrum of disease manifestations such as gastritis, ulcer disease, and even gastric carcinoma. The genetically determined immune response and subsequent inflammation influence the degree of mucosal damage. Adhesion molecules of the CD11 cluster play an important role in adherence of neutrophils to endothelial cells in inflammation. We conducted a haplotype-based analysis of the CD11 cluster in a sample of 315 patients with H. pylori infection and investigated associations with gastric erosions and ulcer disease. Twelve single nucleotide polymorphisms (SNPs) covering the genes CD11a, CD11b, and CD11c were genotyped by Taqman technology. Linkage disequilibrium (LD) was assessed within the CD11 cluster and haplotype case-control analysis was conducted. Sliding window haplotype analysis identified a haplotype consisting of the markers CD11c exon 15 and intron 31 associated with gastric ulcer disease. Patients carrying the haplotype GA bear a 2.4-fold increased risk. No significant associations of single markers with disease outcome were found. High-density LD mapping and mutation detection of CD11c in larger samples will be necessary to confirm our findings and identify the causative variant. Thus, we conclude that genetic variants in the CD11 cluster may play a role in the development of gastric ulcer in chronic H. pylori infection presumably by influencing leukocyte adhesion. The biological effect of genetic variants of CD11c in gastric inflammation needs further clarification.

Efficient Methods for Qualitative Spatial Reasoning

The theoretical properties of qualitative spatial reasoning in the RCC8 framework have been analyzed extensively. However, no empirical investigation has been made yet. Our experiments show that the adaption of the algorithms used for qualitative temporal reasoning can solve large RCC8 instances, even if they are in the phase transition region -- provided that one uses the maximal tractable subsets of RCC8 that have been identified by us. In particular, we demonstrate that the orthogonal combination of heuristic methods is successful in solving almost all apparently hard instances in the phase transition region up to a certain size in reasonable time.

Combination of flucloxacillin and gentamicin inhibits toxic shock syndrome toxin 1 production by Staphylococcus aureus in both logarithmic and stationary phases of growth

Production of exotoxins by staphylococci and streptococci may lead to the development of toxic shock syndrome (TSS). Because clindamycin inhibits exotoxin production, its use has been advocated for the treatment of TSS. However, the bacteriostatic action of clindamycin might be a disadvantage for the treatment of overwhelming infections. We investigated the effects of flucloxacillin and gentamicin on exotoxin production, because incubation with these antibiotics combines bactericidal action with protein synthesis inhibition. Staphylococcus aureus during the logarithmic and stationary phases of growth was incubated with either clindamycin, flucloxacillin, or a combination of flucloxacillin and gentamicin at concentrations of 2 or 10 times the MIC. In logarithmic-phase cultures clindamycin had a static effect on bacterial growth. After incubation with flucloxacillin, either alone or in combination with gentamicin, a rapid and large reduction in the number of viable bacteria was demonstrated. In stationary-phase cultures none of the antibiotics significantly changed the number of viable bacteria. TSS toxin 1 (TSST-1) production during logarithmic-phase growth was inhibited by > or =95% by all antibiotics. In stationary-phase cultures, clindamycin, flucloxacillin, and the combination of flucloxacillin and gentamicin inhibited TSST-1 production by 95, 30, and 75%, respectively, compared with the level of exotoxin production in the controls. The present results indicate that clindamycin inhibits TSST-1 production and exerts bacteriostatic activity in both bacterial growth phases. Because the combination of flucloxacillin and gentamicin combines the inhibition of exotoxin production with high bactericidal activity at least in logarithmic-phase cultures, it should be considered an alternative to clindamycin for the treatment of exotoxin-mediated diseases, especially in patients with overwhelming infections.

Pharmacological management of cancer pain. A guide for the health care professional

Cancer pain continues to remain a significant problem for oncology patients treated in both the university and the community setting. Nursing knowledge regarding pain management has advanced significantly in recent years. This article provides health care professionals with current factual information on cancer pain management. The information focuses on the emotional aspects of cancer pain, specific principles of analgesic management, opioid equianalgesics, multiple approaches to opioid administration, management of unwanted side effects, and a description of inappropriate drug therapies.