Single cell RNA-sequencing and RNA-tomography of the avian embryo extending body axis.

Introduction: Vertebrate body axis formation initiates during gastrulation and continues within the tail bud at the posterior end of the embryo. Major structures in the trunk are paired somites, which generate the musculoskeletal system, the spinal cord-forming part of the central nervous system, and the notochord, with important patterning functions. The specification of these different cell lineages by key signalling pathways and transcription factors is essential, however, a global map of cell types and expressed genes in the avian trunk is missing. Methods: Here we use high-throughput sequencing approaches to generate a molecular map of the emerging trunk and tailbud in the chick embryo. Results and Discussion: Single cell RNA-sequencing (scRNA-seq) identifies discrete cell lineages including somites, neural tube, neural crest, lateral plate mesoderm, ectoderm, endothelial and blood progenitors. In addition, RNA-seq of sequential tissue sections (RNA-tomography) provides a spatially resolved, genome-wide expression dataset for the avian tailbud and emerging body, comparable to other model systems. Combining the single cell and RNA-tomography datasets, we identify spatially restricted genes, focusing on somites and early myoblasts. Thus, this high-resolution transcriptome map incorporating cell types in the embryonic trunk can expose molecular pathways involved in body axis development.

Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus.

BACKGROUND: The Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary. RESULTS: Using a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11 Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate. CONCLUSION: Because of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits.

Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches.

The epithelial lining of the small intestine consists of multiple cell types, including Paneth cells and goblet cells, that work in cohort to maintain gut health. 3D in vitro cultures of human primary epithelial cells, called organoids, have become a key model to study the functions of Paneth cells and goblet cells in normal and diseased conditions. Advances in these models include the ability to skew differentiation to particular lineages, providing a useful tool to study cell type specific function/dysfunction in the context of the epithelium. Here, we use comprehensive profiling of mRNA, microRNA and long non-coding RNA expression to confirm that Paneth cell and goblet cell enrichment of murine small intestinal organoids (enteroids) establishes a physiologically accurate model. We employ network analysis to infer the regulatory landscape altered by skewing differentiation, and using knowledge of cell type specific markers, we predict key regulators of cell type specific functions: Cebpa, Jun, Nr1d1 and Rxra specific to Paneth cells, Gfi1b and Myc specific for goblet cells and Ets1, Nr3c1 and Vdr shared between them. Links identified between these regulators and cellular phenotypes of inflammatory bowel disease (IBD) suggest that global regulatory rewiring during or after differentiation of Paneth cells and goblet cells could contribute to IBD aetiology. Future application of cell type enriched enteroids combined with the presented computational workflow can be used to disentangle multifactorial mechanisms of these cell types and propose regulators whose pharmacological targeting could be advantageous in treating IBD patients with Crohn's disease or ulcerative colitis.

Pre-reproductive isolation as a consequence of allopatric differentiation between populations of Drosophila melanogaster.

While pre-reproductive isolations are more and more frequently described between closely related species or within species, very little is known about their conditions of emergence. In Brazzaville, two populations (Kronenbourg and Loua) of Drosophila melanogaster show a premating isolation. Two hypotheses were proposed to explain such a situation: a local sympatric differentiation or an allopatric divergence followed by a secondary contact. A microsatellite analysis, using markers on all chromosomes, strongly suggests that the Kronenbourg population has a European origin. Therefore, the allopatric divergence between Kronenbourg and Loua populations is probably responsible for the sexual isolation observed today in sympatry, after a recent introduction of a European propagule in Brazzaville.

Microspatial structure of Drosophila melanogaster populations in Brazzaville: evidence of natural selection acting on morphometrical traits.

Two genetically distinct habitat races of Drosophila melanogaster coexist in Brazzaville (Congo). One is the typical field type of Afrotropical populations, the other mainly breeds in beer residues in breweries. These two populations differ in their ethanol tolerance, in their allelic frequencies at several enzyme and microsatellite loci and in the composition of their cuticular hydrocarbons. The brewery population is quite similar to European temperate populations with regard to all these traits. Previous investigations of two morphological traits (ovariole number and sternopleural bristle number) failed to detect any difference between the two habitat races. Here we investigated other morphological traits (wing and thorax length, thorax pigmentation and female abdomen pigmentation). The reaction norms of these traits according to growth temperature were compared in the two Afrotropical habitat races and in a French temperate population. As expected, the French population was very different from the field African population: as a general rule, the brewery population (Kronenbourg) was intermediate in several aspects between the other two. We conclude that the strong selective forces that maintain the genetic divergence between the two habitat races also act on morphometrical traits, and the possible selective mechanisms are discussed.

Reproductive isolation in natural populations of Drosophila melanogaster from Brazzaville (Congo).

The aim of this work is to analyze the homogamy previously detected between two natural populations of Drosophila melanogaster from Brazzaville. It is shown that mating isolation was still maintained under laboratory conditions 10 years after the populations samples were trapped. Isolation seemed to be due mainly to premating isolation and we checked for any suggestion of post-mating mortality of hybrids. Pre-mating isolation was not symmetrical, and significant chi2 values were found in 3/4 possible 3-way mating choice experiments. The only exception involved a male from the countryside and two females (one from each population) for which no significant mating preference was detected. Mortality of hybrids was intermediate between those of the parental strains showing a clear maternal effect and the existence of partial dominance. Major differences in the cuticular hydrocarbons were also found and they could account for the isolation. These findings in populations from African breweries indicate that they are closely related to European ones, suggesting that this phenomenon is not a case of sympatric speciation, but probably attributable to the reintroduction of an allopatric population.

[Generalized gas gangrene infection with rhabdomyloysis following cholecystectomy]. / Generalisierte Gasbrand-infektion mit Rhabdomyolyse nach Cholezystektomie.

We report a rare case of spontaneously developing generalised gas gangrene with massive rhabdomyolysis after a cholecystectomy and drainage of a hepatic abscess. On preoperative physical examination the patient appeared severely ill and was icteric and oliguric. Laboratory evaluation showed signs of systemic inflammation, elevated lactate levels, evidence of disseminated intravascular coagulation (DIC), and increased levels of serum creatine kinase (CK) activity. Abdominal ultrasound and endoscopic retrograde cholangiography showed a gallbladder perforation and a hepatic abscess. Cholecystectomy and drainage of the abscess was performed immediately and without technical problems. After postoperative admission to the intensive care unit, the patient showed evidence of generalised myonecrosis with subcutaneous gas formation and acute renal failure. Initially, there were few other signs of systemic toxicity; the patient was not hypotensive and the pulmonary gas exchange was normal. Within hours diffuse swelling of his right leg developed with cutaneous gangrene and a compartment syndrome. After fasciectomy and extensive surgical debridement, uncontrollable bleeding due to DIC developed from the fasciectomy site, which finally required exarticulation of the leg at the hip joint. At this point, multiple organ failure including severe adult respiratory distress syndrome was present. Two days after cholecystectomy, the patient died from hypoxic cardiocirculatory failure. Clostridium perfringens was repeatedly isolated from the wounds. Besides gas gangrene, the differential diagnosis of such infections includes localised clostridial cellulitis, nonclostridial anaerobic cellulitis caused by mixed aerobes and anaerobes, and type I or type II necrotising fasciitis. Patients with systemic necrotising infections should be treated with broad-spectrum antimicrobial regimens (penicillin G, 3rd generation cephalosporins, clindamycin, and aminoglycosides). An otherwise unexplained elevation of serum CK activity in the presence of acute cholecystitis may suggest haematologic spread of an aggressive myolytic agent and the beginning of myonecrosis. This should prompt immediate surgical exploration after establishing broad-spectrum antibiotic coverage. The role of hyperbaric oxygen treatment in this situation remains to be established. If hyperbaric oxygen is to be employed, it should neither delay surgical exploration nor jeopardize the patient with the hazards of an interhospital transport.