Life history,distribution and molecular phylogenetics of the Upward-Mouth Spikefish Atrophacanthus japonicus (Teleostei: Tetraodontiformes: Triacanthodidae)

Ninety-six juvenile specimens (37–54 mm standard length; L_S) of the rarely collected Upward-Mouth Spikefish Atrophacanthus japonicus (Triacanthodidae) were obtained from the stomachs of three Yellowfin Tuna Thunnus albacares collected off Guam in the Mariana Islands in the central Pacific Ocean. These specimens extend the range of A. japonicus eastward into Oceania. We review the systematic characters of the monotypic genus Atrophacanthus and present colour photographs of freshly collected specimens. The diet of the juvenile specimens of A. japonicus consisted of thecosome pteropods and foraminiferans. We present a range map of A. japonicus based on all known specimens and show that specimen size is related to whether specimens were collected in the pelagic zone or on the bottom. Our results support that, compared to all other Triacanthodidae, A. japonicus has an unusually extended pelagic larval and juvenile period, up to 54 mm L_S, before settling to the bottom as adults. Lastly, we provide a multilocus phylogeny addressing the phylogenetic placement of Atrophacanthus based on eight of 11 triacanthodid genera and six genetic markers. Our results reveal that Atrophacanthus is the sister group of Macrorhamphosodes and they provide new insights about the evolutionary history of the family.     

BRAF Mutation Analysis of Fine-Needle Aspiration Biopsies of Papillary Thyroid Carcinoma: Impact on Diagnosis and Prognosis

Objective: The BRAF V600E mutation has been associated with aggressive disease in papillary thyroid carcinoma (PTC). Molecular testing has been proposed as a useful adjunct to cytology in the diagnosis of malignancy and for tailoring clinical management. The aims of our study were to evaluate the BRAF mutational status using archived fine-needle aspiration biopsy (FNAB) material from patients with long-term follow-up and to correlate it with the original cytology diagnosis, clinicopathological stage at surgery, and prognosis. Study Design: FNAB material from 52 cases of PTC, with a mean follow-up of 8.4 years, was used in this study. DNA was extracted from archival cytology slides. Mutation analysis was performed by standard sequencing and locked nucleic acid-PCR/sequencing. Results: The BRAF V600E mutation was present in 46% of cases, but it was absent in all FNABs diagnosed originally as atypical and in 14 of 17 suspicious cases. Recurrence was significantly more frequent (p = 0.006) in cases with BRAF mutations and 54% of these cases presented with stage 2 or higher. Conclusion: The BRAF V600E mutation is associated with a higher pathological stage at surgery and a higher rate of recurrence. BRAF mutation analysis did not provide a significant increase in the accuracy of thyroid FNABs diagnosed as suspicious or atypical in our institution.     

Implementing team‐based learning in the life sciences: A case study in an online introductory level evolution and biodiversity course

Team‐Based Learning (TBL) is a pedagogical tool that has great potential to develop student engagement, accountability, and equity in the online classroom. TBL is rooted in evidence‐based educational theories and practices that underlie many active learning approaches such as self‐testing, team discussion, and application of knowledge. The use of these approaches is associated with better student performance, retention, and sense of belonging in the classroom, aspects that are often reported to be especially lacking in online courses. Here, we describe how we implemented TBL in a face‐to‐face and an online introductory level evolution and biodiversity course. We implemented TBL in the face‐to‐face course (~200 students) starting in 2018 and in the online course (~30 students) starting in the summer of 2019. We used several online applications to facilitate the transition to an online platform such as Simbio, Slack, VoiceThread, Articulate 360, and Teammates. Our experiences using TBL approaches in the online course have been rewarding, and students are engaged and accountable for their learning and performed well in the course. Our goal is to provide an example of how we designed a life science course using TBL approaches and transitioned the course to an online environment. With the current switch to remote instruction and online learning, we recommend the use of TBL as a course design approach that can improve the students’ online learning experience.     

Habitat disturbance modifies dominance,coexistence, and competitive interactions in tropical ant communities

1. Interspecific competition is a major structuring principle in ecological communities. Despite their prevalence, the outcome of competitive interactions is hard to predict, highly context-dependent, and multiple factors can modulate such interactions. 2. We tested predictions concerning how competitive interactions are modified by anthropogenic habitat disturbance in ground-foraging ant assemblages inhabiting fragmented Inter-Andean tropical dry forests in southwestern Colombia, and investigated ant assemblages recruiting to baits in 10 forest fragments exposed to varying level of human disturbance. 3. Specifically, we evaluated how different components of competitive interactions (patterns of species co-occurrence, resource partitioning, numerical dominance, and interspecific trade-offs between discovery and dominance competition) varied with level of habitat disturbance in a human-dominated ecosystem. 4. Multiple lines of evidence suggest that the role of competitive interactions in structuring ground-foraging ant communities at baits varied with respect to habitat disturbance. As disturbance increased, community structure was more likely to exhibit random co-occurrence patterns, higher levels of monopolization of food resources by dominant ants, and disproportionate dominance of a single species, the little fire ant (Wasmannia auropunctata). At a regional scale, we found evidence for a trade-off between dominance and discovery abilities of the 15 most common species at baits. 5. Together, these results suggest that human disturbance modifies the outcome of competitive interactions in ground-foraging ant assemblages and may promote dominant species that reduce diversity and coexistence in tropical ecosystems.     

The direct and ecological costs of an ant-plant symbiosis

How strong is selection for cheating in mutualisms? The answer depends on the type and magnitude of the costs of the mutualism. Here we investigated the direct and ecological costs of plant defense by ants in the association between Cordia nodosa, a myrmecophytic plant, and Allomerus octoarticulatus, a phytoecious ant. Cordia nodosa trees produce food and housing to reward ants that protect them against herbivores. For nearly 1 year, we manipulated the presence of A. octoarticulatus ants and most insect herbivores on C. nodosa in a full-factorial experiment. Ants increased plant growth when herbivores were present but decreased plant growth when herbivores were absent, indicating that hosting ants can be costly to plants. However, we did not detect a cost to ant colonies of defending host plants against herbivores. Although this asymmetry in costs suggests that the plants may be under stronger selection than the ants to cheat by withholding investment in their partner, the costs to C. nodosa are probably at least partly ecological, arising because ants tend scale insects on their host plants. We argue that ecological costs should favor resistance or traits other than cheating and thus that neither partner may face much temptation to cheat.     

Activities of Phosphoenolpyruvate Carboxylase and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase in Leaves and Fruit Pericarp Tissue of Different Coffee (Coffea sp.) Genotypes

In order to study photosynthetic characteristics, phosphoenolpyruvate carboxylase (PEPC) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO) activities as well as soluble protein and chlorophyll contents were determined in leaf and fruit pericarp samples from diverse coffee genotypes (Coffea arabica cv. Colombia, Caturra, Caturra Erecta, San Pacho, Tipica, C. stenophylla, C. eugenioides, C. congensis, C. canephora, C. canephora cv. Arabusta, C. arabica cv. Caturra×C. canephora and Hibrido de Timor. We found a slightly higher PEPC activity in fruit pericarp than in leaves, while RuBPCO activity was much lower in pericarp than leaf tissue. Partial purification of PEPC and RuBPCO was carried out from leaves of C. arabica cv. Caturra and Michaelis-Menten kinetics for RuBPCO (K_m CO₂ = 5.34 µM), (K_m RuBP = 9.09 µM) and PEPC (K_m PEP = 19.5 µM) were determined. Leaf tissues of Colombia, Hibrido de Timor, and Caturra consistently showed higher content of protein [55.4–64.4 g kg^–1 (f.m.)] than San Pacho, C. stenophylla, Tipica, Caturra Erecta, and Caturra×C. canephora [25.6–36.9 g kg^–1 (f.m.)] and C. canephora cv. Arabusta, Borbon, C. congensis, C. eugenioides, and C. canephora [16.1–21.1 g kg^–1 (f.m.)].     

Deep annotation of mouse iso-miR and iso-moR variation

With a dataset of more than 600 million small RNAs deeply sequenced from mouse hippocampal and staged sets of mouse cells that underwent reprogramming to induced pluripotent stem cells, we annotated the stem-loop precursors of the known miRNAs to identify isomoRs (miRNA-offset RNAs), loops, non-preferred strands, and guide strands. Products from both strands were readily detectable for most miRNAs. Changes in the dominant isomiR occurred among the cell types, as did switches of the preferred strand. The terminal nucleotide of the dominant isomiR aligned well with the dominant off-set sequence suggesting that Drosha cleavage generates most miRNA reads without terminal modification. Among the terminal modifications detected, most were non-templated mono- or di-nucleotide additions to the 3'-end. Based on the relative enrichment or depletion of specific nucleotide additions in an Ago-IP fraction there may be differential effects of these modifications on RISC loading. Sequence variation of the two strands at their cleavage sites suggested higher fidelity of Drosha than Dicer. These studies demonstrated multiple patterns of miRNA processing and considerable versatility in miRNA target selection.     

Activation of apoptosis, but not necrosis, during Mycobacterium tuberculosis infection correlated with decreased bacterial growth: role of TNF-alpha, IL-10, caspases and phospholipase A2

Monocyte/macrophage cell death is an important event during mycobacterial infection. To get insights about the influence of mononuclear phagocyte maturation in this event we compared the response to Mycobacterium tuberculosis (Mtb) infection of fresh isolated monocytes and monocyte-derived macrophages (MDM) from healthy tuberculin positive individuals. Both monocytes and MDM underwent apoptosis, however, there was a higher numbers of apoptotic macrophages with active Caspases 8 and 9. We also compared Mtb-induced cell death in U937 pro-monocytes and PMA-differentiated cells (U937D). In response to Mtb infection, U937D cells underwent apoptosis and promonocytes both apoptosis and necrosis. There were high number of U937D cells producing TNF-α and high number of IL-10⁺ promonocytes. These evidences suggest that U937 could be a valid model to study the mechanisms that rule Mtb-induced cell death. Experiments with the cell line and fresh isolated mononuclear cells with pharmacological inhibitors showed that induction of necrosis involved calcium and cAMP signals resulting in IL-10 production. Necrosis also correlated with Caspase 3, PLA2 activity and bacterial growth. In U937D cells and monocytes from healthy donors there was activation of calcium, TNF-α and Caspase 8 activation and decreased bacterial load. Understanding the mechanisms that control the dichotomy events between apoptosis and necrosis/oncosis associated with cell maturity might open new strategies to better control the course of mycobacterial infections.