An extensive allelic series of Drosophila kae1 mutants reveals diverse and tissue-specific requirements for t6A biogenesis

N⁶-threonylcarbamoyl-adenosine (t6A) is one of the few RNA modifications that is universally present in life. This modification occurs at high frequency at position 37 of most tRNAs that decode ANN codons, and stabilizes cognate anticodon–codon interactions. Nearly all genetic studies of the t6A pathway have focused on single-celled organisms. In this study, we report the isolation of an extensive allelic series in the Drosophila ortholog of the core t6A biosynthesis factor Kae1. kae1 hemizygous larvae exhibit decreases in t6A that correlate with allele strength; however, we still detect substantial t6A-modified tRNAs even during the extended larval phase of null alleles. Nevertheless, complementation of Drosophila Kae1 and other t6A factors in corresponding yeast null mutants demonstrates that these metazoan genes execute t6A synthesis. Turning to the biological consequences of t6A loss, we characterize prominent kae1 melanotic masses and show that they are associated with lymph gland overgrowth and ectopic generation of lamellocytes. On the other hand, kae1 mutants exhibit other phenotypes that reflect insufficient tissue growth. Interestingly, whole-tissue and clonal analyses show that strongly mitotic tissues such as imaginal discs are exquisitely sensitive to loss of kae1, whereas nonproliferating tissues are less affected. Indeed, despite overt requirements of t6A for growth of many tissues, certain strong kae1 alleles achieve and sustain enlarged body size during their extended larval phase. Our studies highlight tissue-specific requirements of the t6A pathway in a metazoan context and provide insights into the diverse biological roles of this fundamental RNA modification during animal development and disease.     

Identification of antigenic linear peptides in the soil-transmitted helminth and Schistosoma mansoni proteome

The scientific community identified non stool-based biomarkers as the way forward to support soil-transmitted helminth (STH; Ascaris lumbricoides, Trichuris trichiura and the hookworms Ancylostoma duodenale and Necator americanus) and schistosome (S. mansoni and S. haematobium) deworming programs. This support is needed in making the decision of whether or not to stop preventive chemotherapy intervention efforts and to ultimately transition towards a post-intervention surveillance phase. We applied a two-step micro-array approach to identify antigenic linear epitopes in the STH and S. mansoni proteomes. In a first experiment, we identified antigenic peptides by applying sera from 24 STH and/or S. mansoni infected Ethiopian children on a high-density peptide microarray containing 3.3 million peptides derived from the complete STH and S. mansoni proteomes. A second array experiment with 170,185 peptides that were recognized in the first array was designed to identify non-specific antibody reactivity by applying sera from 24 healthy individuals from Belgium (a non-endemic country). From this array testing cascade, several peptides were identified for STH but none of them appeared to be unique for one species. We therefore concluded that for STH, none of the peptides revealed to be sufficiently sensitive or species specific. For S. mansoni, some promising peptides were identified prompting future investigation. Based on these results, it is unlikely that linear epitopes would be highly useful in detecting species-specific antibody responses to STH in endemic communities. For S. mansoni, one particular peptide of the micro-exon gene 12 (MEG-12) protein deserves further research. In addition, this study emphasizes the need of well-characterized biobanks for biomarker discovery, particularly when the integration of multiple disease programs is envisioned.     

Current status of American mink Neovison vison in Great Britain: a review of the evidence for a population decline

1. The American mink Neovison vison in Great Britain is an invasive alien species, with significant impacts on native prey species. There have been suggestions that populations of mink in Britain have declined since the 1990s.
2. Three nationwide data sets include data on mink distribution and abundance. Scat surveys and the National Game Bag Census suggest population declines, but the latter does not take account of survey effort (which may also have declined) and the former is misleading because there is evidence that mink change their marking behaviour in the presence of otters Lutra lutra. National Biodiversity Network data suggest an increase in mink numbers, but this can be explained by a concomitant increase in mammal recording.
3. Although intra-guild competition between invasive mink and native otters is likely, there is no evidence that otters have caused a decline in mink numbers. There is little information on the impact of disease, or exposure to rodenticides, on wild mink – both warrant further attention. Eradication efforts can have an impact on mink populations, but currently neither implementation nor monitoring is sufficient to generate effects throughout Great Britain or to assess the impact of cumulative local and regional efforts.
4. We conclude that it is not possible, on the basis of currently available data for Great Britain, to ascertain the status of mink or assess the underlying trend in their population. We stress the importance of collaboration, coordination, and record keeping (and sharing) in future, proper interpretation of existing data, and the use of alternative data sources. We call for greater, and better, effort in both mink management and monitoring of management in Great Britain.

     

Early post-metamorphic,Carboniferous blastoid reveals the evolution and development of the digestive system in echinoderms

Inferring the development of the earliest echinoderms is critical to uncovering the evolutionary assembly of the phylum-level body plan but has long proven problematic because early ontogenetic stages are rarely preserved as fossils. Here, we use synchrotron tomography to describe a new early post-metamorphic blastoid echinoderm from the Carboniferous (approx. 323 Ma) of China. The resulting three-dimensional reconstruction reveals a U-shaped tubular structure in the fossil interior, which is interpreted as the digestive tract. Comparisons with the developing gut of modern crinoids demonstrate that crinoids are an imperfect analogue for many extinct groups. Furthermore, consideration of our findings in a phylogenetic context allows us to reconstruct the evolution and development of the digestive system in echinoderms more broadly; there was a transition from a straight to a simple curved gut early in the phylum''s evolution, but additional loops and coils of the digestive tract (as seen in crinoids) were not acquired until much later.     

Movements and Site Fidelity of two Juvenile Fish Species Using Surf Zone Nursery Habitats Along The Southeastern North Carolina Coast

We examined the extent of movements of juvenile Florida pompano, Trachinotus carolinus, and gulf kingfish, Menticirrhus littoralis, along an open ocean beach. Fishes were collected by seine at three sites along Masonboro Island and Carolina Beach, NC between 7 June and 7 July 1995. All specimens 40 mm standard length (SL) were tagged with coded wire tags and released at the capture sites. Between 7 July and 9 August and on 15–16 September Masonboro Island and northern Carolina Beach were surveyed for tagged fish. A controlled tag mortality/retention study was conducted for both species. Overall, 1569 Florida pompano (40–135 mm SL) were tagged. Sixty-one (3.9%) of these were recaptured, and only eight moved away from the original tagging sites. The largest movements by two Florida pompano were 2.1 and 10.5 km. Many fish remained at their original tagging sites for 21–27 days. Of 488 gulf kingfish (36–158 mm SL) tagged, 16 (3.3%) were recaptured. Gulf kingfish also exhibited little movement away from tagging sites during the study, with individuals remaining at original tagging sites up to 21 days. Stock size estimates for Florida pompano ranged from 3354 to 4670 among the tagging sites, with densities ranging from 1.9 to 2.6 fish m^–2. The remarkable site fidelity exhibited by these two species suggests that resources were not limiting or that predation pressure was not high enough to cause large scale movements during the study. This implies that local disturbances could impact behavior or survival of juvenile fishes in the surf zone.     

Factors affecting escape behaviour in moulting Greylag Geese Anser anser

The escape behaviour of flightless greylag geese Anser anser has been studied at a Danish moult site. In more than 40% of escapes, a stimulus could not be discerned, suggesting some importance of inaccurate risk assessment among the geese. Quasi-predator stimuli, for example gull alarms and helicopters, were also important and caused 31–43 and 5–13% of escapes, respectively. Geese were, however, displaced in less than 5% of encounters with these stimuli. Each escape prevented geese from feeding for 19 min on average, and hence, the cost of escapes was high. This, the low in-situ predation risk, and the partly distant and not directly threatening nature of the stimuli may have weakened the response of the geese. During the main moult period the geese were, nevertheless, more susceptible to quasi-predator stimuli than before moult—the probability of escape per 15 min period was 0.16–0.22 during moult and 0 before moult. The probability of escapes among moulting geese, which formed large cohesive flocks, was, furthermore, significantly enhanced with increasing flock size. It is possible large flocks were better at detecting quasi-predator stimuli, or simply that there was a greater risk of signals from flock members being misinterpreted. Thus in terms of maintaining uninterrupted foraging it was concluded that an individual would incur extra cost by joining large flocks during the moult period.     

CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines

Chinese hamster ovary (CHO) cell lines are widely used in industry for biological drug production. During cell culture development, considerable effort is invested to understand the factors that greatly impact cell growth, specific productivity and product qualities of the biotherapeutics. While high-throughput omics approaches have been increasingly utilized to reveal cellular mechanisms associated with cell line phenotypes and guide process optimization, comprehensive omics data analysis and management have been a challenge. Here we developed CHOmics, a web-based tool for integrative analysis of CHO cell line omics data that provides an interactive visualization of omics analysis outputs and efficient data management. CHOmics has a built-in comprehensive pipeline for RNA sequencing data processing and multi-layer statistical modules to explore relevant genes or pathways. Moreover, advanced functionalities were provided to enable users to customize their analysis and visualize the output systematically and interactively. The tool was also designed with the flexibility to accommodate other types of omics data and thereby enabling multi-omics comparison and visualization at both gene and pathway levels. Collectively, CHOmics is an integrative platform for data analysis, visualization and management with expectations to promote the broader use of omics in CHO cell research.     

A parasitoid wasp of Drosophila employs preemptive and reactive strategies to deplete its host’s blood cells

The wasps Leptopilina heterotoma parasitize and ingest their Drosophila hosts. They produce extracellular vesicles (EVs) in the venom that are packed with proteins, some of which perform immune suppressive functions. EV interactions with blood cells of host larvae are linked to hematopoietic depletion, immune suppression, and parasite success. But how EVs disperse within the host, enter and kill hematopoietic cells is not well understood. Using an antibody marker for L. heterotoma EVs, we show that these parasite-derived structures are readily distributed within the hosts’ hemolymphatic system. EVs converge around the tightly clustered cells of the posterior signaling center (PSC) of the larval lymph gland, a small hematopoietic organ in Drosophila. The PSC serves as a source of developmental signals in naïve animals. In wasp-infected animals, the PSC directs the differentiation of lymph gland progenitors into lamellocytes. These lamellocytes are needed to encapsulate the wasp egg and block parasite development. We found that L. heterotoma infection disassembles the PSC and PSC cells disperse into the disintegrating lymph gland lobes. Genetically manipulated PSC-less lymph glands remain non-responsive and largely intact in the face of L. heterotoma infection. We also show that the larval lymph gland progenitors use the endocytic machinery to internalize EVs. Once inside, L. heterotoma EVs damage the Rab7- and LAMP-positive late endocytic and phagolysosomal compartments. Rab5 maintains hematopoietic and immune quiescence as Rab5 knockdown results in hematopoietic over-proliferation and ectopic lamellocyte differentiation. Thus, both aspects of anti-parasite immunity, i.e., (a) phagocytosis of the wasp’s immune-suppressive EVs, and (b) progenitor differentiation for wasp egg encapsulation reside in the lymph gland. These results help explain why the lymph gland is specifically and precisely targeted for destruction. The parasite’s simultaneous and multipronged approach to block cellular immunity not only eliminates blood cells, but also tactically blocks the genetic programming needed for supplementary hematopoietic differentiation necessary for host success. In addition to its known functions in hematopoiesis, our results highlight a previously unrecognized phagocytic role of the lymph gland in cellular immunity. EV-mediated virulence strategies described for L. heterotoma are likely to be shared by other parasitoid wasps; their understanding can improve the design and development of novel therapeutics and biopesticides as well as help protect biodiversity.