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.].

Combining morphological and genomic evidence to resolve species diversity and study speciation processes of the Pallenopsis patagonica (Pycnogonida) species complex

BACKGROUND

Pallenopsis patagonica (Hoek, 1881) is a morphologically and genetically variable sea spider species whose taxonomic classification is challenging. Currently, it is considered as a species complex including several genetic lineages, many of which have not been formally described as species. Members of this species complex occur on the Patagonian and Antarctic continental shelves as well as around sub-Antarctic islands. These habitats have been strongly influenced by historical large-scale glaciations and previous studies suggested that communities were limited to very few refugia during glacial maxima. Therefore, allopatric speciation in these independent refugia is regarded as a common mechanism leading to high biodiversity of marine benthic taxa in the high-latitude Southern Hemisphere. However, other mechanisms such as ecological speciation have rarely been considered or tested. Therefore, we conducted an integrative morphological and genetic study on the P. patagonica species complex to i) resolve species diversity using a target hybrid enrichment approach to obtain multiple genomic markers, ii) find morphological characters and analyze morphometric measurements to distinguish species, and iii) investigate the speciation processes that led to multiple lineages within the species complex.

RESULTS

Phylogenomic results support most of the previously reported lineages within the P. patagonica species complex and morphological data show that several lineages are distinct species with diagnostic characters. Two lineages are proposed as new species, P. aulaeturcarum sp. nov. Dömel & Melzer, 2019 and P. obstaculumsuperavit sp. nov. Dömel, 2019, respectively. However, not all lineages could be distinguished morphologically and thus likely represent cryptic species that can only be identified with genetic tools. Further, morphometric data of 135 measurements showed a high amount of variability within and between species without clear support of adaptive divergence in sympatry.

CONCLUSIONS

We generated an unprecedented molecular data set for members of the P. patagonica sea spider species complex with a target hybrid enrichment approach, which we combined with extensive morphological and morphometric analyses to investigate the taxonomy, phylogeny and biogeography of this group. The extensive data set enabled us to delineate species boundaries, on the basis of which we formally described two new species. No consistent evidence for positive selection was found, rendering speciation in allopatric glacial refugia as the most likely model of speciation.

IL-6 protects enterocytes from hypoxia-induced apoptosis by induction of bcl-2 mRNA and reduction of fas mRNA

Interleukin-6 (IL-6) has been shown to rescue enterocytes from hypoxia-induced apoptosis when given orally following hemorrhagic shock. In vitro models using an intestinal epithelial cell line (IEC-6) cultured with lipopolysaccharide (LPS) under low O2 conditions, to mimic intestinal conditions, show that these cells also undergo apoptosis, which can be reduced by subsequent culture with IL-6. To examine further the mechanisms of rescue, we cultured normal rat intestinal epithelial cells (IEC-6) under both normoxic and hypoxic conditions and analyzed their responses to LPS and IL-6. We showed that IEC-6 expressed IL-6 receptor on its surface. Further, IEC-6 cells could be rescued from hypoxia-induced apoptosis by co-culture with IL-6. RNase protection assay (RPA) examination revealed that under hypoxic conditions, IEC-6 cells that were resistant to apoptosis showed reduced fas expression and increased bcl-2 expression after co-culture with LPS+IL-6.

Human neutrophil activation and increased adhesion by various resuscitation fluids

OBJECTIVE

To determine whether activated neutrophils play a major role in secondary tissue injury after resuscitation in trauma. We hypothesized that human neutrophil activation and adhesion vary, depending on the type and amount of resuscitation fluid used.

SETTING

University-based research facility.

SUBJECTS

Ten healthy adult volunteers.

DESIGN

Whole blood from volunteers was serially diluted in polypropylene tubes with various resuscitation fluids. Fluids tested were phosphate-buffered saline, normal saline, lactated Ringer's solution, dextran, hespan, 5% human albumin, 25% human albumin, 3.5% hypertonic saline, and 7.5% hypertonic saline. Neutrophil activation (intracellular oxidative burst activity with dichlorofluorescin diacetate staining) and adhesion (integrin cell surface expression of CD18) were measured with flow cytometry (fluorescence-activated cell sorting). Blood was diluted with hypertonic saline by controlling for sodium content equal to normal saline. dose-related increase in neutrophil oxidative burst activity as the result of dilution followed with crystalloid fluids and artificial colloids (dextran and hespan). The increase was 12-18 x baseline at the 75% dilution. The increase with 5% human albumin was only 2.2 x baseline, and 25% albumin did not demonstrate any increased intracellular activity. A similar significant increase in the neutrophil adhesion expression (CD18) occurred with artificial colloids (p<.05) and, to a lesser extent, with crystalloids, but not with albumin. Hypertonic saline caused a decrease in CD18 cell surface expression.

CONCLUSIONS

This study suggests that the neutrophil activation and adhesion may vary, depending on the type of resuscitative fluid used. All artificial resuscitative fluids may not be similar or innocuous, as demonstrated by the dose-related increase in neutrophil activation and adhesion.

Effects of neutrophils in rat luteal cells

Ovarian function may be modulated by cells of the immune system. We have investigated the role of neutrophils (polymorphonuclear leukocytes) on rat luteal cell function. Activated neutrophils inhibited LH-sensitive cAMP accumulation, which was dependent on neutrophil cell number. At a concentration of 10(6) neutrophils/ml and 10(5) luteal cells/ml, LH-stimulated cAMP accumulation was inhibited by 50%. The inhibitory effect of activated neutrophils was reversed by superoxide dismutase (SOD) and catalase. LH-stimulated progesterone production was also inhibited by activated neutrophils. Progesterone production by 10(5) luteal cells was inhibited approximately 20% in the presence of 10(6) activated neutrophils, and this inhibition was blocked by SOD and catalase. Conditioned medium from activated neutrophils also produced inhibitory effects on LH-stimulated cAMP accumulation and progesterone production, which could be reversed by SOD and catalase. The phosphodiesterase inhibitor isobutylmethylxanthine had no significant effect on the inhibition of cAMP accumulation by conditioned medium from activated neutrophils. Luteal cells loaded with a fluorescent indicator for determining intracellular reactive oxygen species (dichlorofluorescein diacetate) showed increased fluorescence in the presence of activated neutrophils. No increase in fluorescence occurred in the absence of neutrophils or in the presence of SOD and catalase. These studies demonstrate that reactive oxygen species produced by activated neutrophils can enter the luteal cell and cause antigonadotropic effects. Although the experimental model used in the present studies may not be truly physiological, the data demonstrate that neutrophils may play a role in functional and structural regression of the corpus luteum in the rat.

Malignant hyperthermia: nursing implications

This paper presents the pathophysiology, clinical symptoms, and a standard of care for the patient with MH. The information provided will assist the nurse in interpreting patient and technologic data to identify recurring episodes of MH, and prevent the negative outcomes associated with this syndrome.

Malignant hyperthermia: nursing implications

This paper presents the pathophysiology, clinical symptoms, and a standard of care for the patient with MH. The information provided will assist the nurse in interpreting patient and technologic data to identify recurring episodes of MH, and prevent the negative outcomes associated with this syndrome.