Organization and connectivity of premotor interneurons in the mouse spinal cord

Movement is the final behavioral output of neuronal activity in the spinal cord. In all vertebrates, motor neurons are grouped into motor neuron pools, the functional units innervating individual muscles. Spinal interneurons receive a variety of inputs from the brain, cerebellum and sensory afferents, process this information and as the final outcome, the information reaches the motor neurons that control the activation of the innervated muscles. For generation of movement, precise activation of distinct motor neuron pools at the right moment in time is crucial and this precision is possible due to the cohorts of spinal interneurons, connected with specificity to distinct motor neuron pools that regulate motor neuronal activity. How premotor circuits connect to distinct motor neuron pools with specificity is poorly understood and represented a main question of my PhD thesis work. In my thesis, I present the results of my studies on connectivity of premotor interneuron populations to specific motor neuron pools in two layers - as general distribution patterns specific to control the regulation of particular muscles and by closer examination of the connection specificity of one class of the spinal pre-motor interneurons, the cholinergic partition cells. One significant part of this project was to develop a tool that allowed studying the pre-motor interneurons innervating defined motor neuron pools. For this purpose, I have adapted a novel rabies virus based tool (Wickersham et al. (2007b)) for mono- transsynaptic tracing of neuronal circuits in the spinal cord in vivo. I was successful in establishing an anatomical rabies-virus based connectivity assay in early postnatal mice in order to study the connectivity scheme of premotor neurons, the neuronal cohorts monosynaptically connected to motor neurons. The main parts of my thesis focus on: 1) motor neuron pools connectivity with premotor interneurons that appear to be widely-distributed when analysed at the segmental level, yet group into stereotypic populations, and differing for pools innervating functionally-distinct muscles; 2) local or segmental distribution of interneurons depending on their molecular identity; 3) specificity of the connectivity of cholinergic partition cells involved in the regulation of motor neuron excitability - this subpopulation of premotor interneurons segregate into ipsilaterally and bilaterally projecting populations, the latter exhibiting preferential connections to equivalent motor neuron pools bilaterally. A minor part of my thesis is devoted to the connectivity of the spinal pre-motor interneurons in α2-chimaerin mutant mice. Data presented in this part are preliminary and this project needs continuation, but the results begin to provide insight into the function of the α2-chimaerin molecule in the axon guidance and perhaps connectivity process of the bilaterally projecting subclass of partition cells and a dorsal subgroup of premotor interneurons. I demonstrate that the distribution of cholinergic partition cells connected to a particular motor neuron pool is different in α2-chimaerin mutant mice than in the wild-type mice. I also show that the distribution pattern of ectopic bilaterally projecting premotor interneurons in α2-chimaerin mutant mice what concerns the dorsal population of premotor interneurons. These studies of premotor interneurons visualize the widespread but precise nature of connectivity with motor neuron pools, reveal exquisite synaptic specificity for bilaterally projecting cholinergic partition cells and show the importance of the α2-chimaerin molecule in axon guidance and connectivity processes for the establishment of the appropriate premotor circuits in the spinal cord

Undirected singing rate as a non-invasive tool for welfare monitoring in isolated male zebra finches

Research on the songbird zebra finch (Taeniopygia guttata) has advanced our behavioral, hormonal, neuronal, and genetic understanding of vocal learning. However, little is known about the impact of typical experimental manipulations on the welfare of these birds. Here we explore whether the undirected singing rate can be used as an indicator of welfare. We tested this idea by performing a post hoc analysis of singing behavior in isolated male zebra finches subjected to interactive white noise, to surgery, or to tethering. We find that the latter two experimental manipulations transiently but reliably decreased singing rates. By contraposition, we infer that a high-sustained singing rate is suggestive of successful coping or improved welfare in these experiments. Our analysis across more than 300 days of song data suggests that a singing rate above a threshold of several hundred song motifs per day implies an absence of an acute stressor or a successful coping with stress. Because singing rate can be measured in a completely automatic fashion, its observation can help to reduce experimenter bias in welfare monitoring. Because singing rate measurements are non-invasive, we expect this study to contribute to the refinement of the current welfare monitoring tools in zebra finches.Fil: Yamahachi, Homare. Universitat Zurich; SuizaFil: Zai, Anja T.. Universitat Zurich; SuizaFil: Tachibana, Ryosuke O.. Universitat Zurich; SuizaFil: Stepien, Anna E.. Universitat Zurich; SuizaFil: Rodrigues, Diana I.. Universitat Zurich; SuizaFil: Cavé Lopez, Sophie. Universitat Zurich; SuizaFil: Lorenz, Corinna. Universite Paris Saclay; Francia. Universitat Zurich; SuizaFil: Arneodo, Ezequiel Matías. Universitat Zurich; Suiza. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Giret, Nicolas. Universite Paris Saclay; FranciaFil: Hahnloser, Richard H. R.. Universitat Zurich; Suiz

Metabolomic profiles of hepatocellular carcinoma in a European prospective cohort

Background: Hepatocellular carcinoma (HCC), the most prevalent form of liver cancer, is difficult to diagnose and has limited treatment options with a low survival rate. Aside from a few key risk factors, such as hepatitis, high alcohol consumption, smoking, obesity, and diabetes, there is incomplete etiologic understanding of the disease and little progress in identification of early risk biomarkers. Methods: To address these aspects, an untargeted nuclear magnetic resonance metabolomic approach was applied to pre-diagnostic serum samples obtained from first incident, primary HCC cases (n = 114) and matched controls (n = 222) identified from amongst the participants of a large European prospective cohort. Results: A metabolic pattern associated with HCC risk comprised of perturbations in fatty acid oxidation and amino acid, lipid, and carbohydrate metabolism was observed. Sixteen metabolites of either endogenous or exogenous origin were found to be significantly associated with HCC risk. The influence of hepatitis infection and potential liver damage was assessed, and further analyses were made to distinguish patterns of early or later diagnosis. Conclusion: Our results show clear metabolic alterations from early stages of HCC development with application for better etiologic understanding, prevention, and early detection of this increasingly common cancer.This work was supported by the French National Cancer Institute (L’Institut National du Cancer; INCA; grant number 2009-139; PI: M. Jenab). AF received financial support (BDI fellowship) from the Centre National de la Recherche Scientifique (CNRS) and Bruker Biospin. The coordination of EPIC is financially supported by the European Commission (DG-SANCO) and the International Agency for Research on Cancer. The national cohorts are supported by Danish Cancer Society (Denmark); Ligue Contre le Cancer, Institut Gustave Roussy, Mutuelle Générale de l’Education Nationale, and Institut National de la Santé et de la Recherche Médicale (INSERM) (France); Deutsche Krebshilfe, Deutsches Krebsforschungszentrum (DKFZ), and Federal Ministry of Education and Research (Germany); Hellenic Health Foundation (Greece); Italian Association for Research on Cancer (AIRC), National Research Council, Associazione Italiana per la Ricerca sul Cancro-AIRC-Italy, and AIRE-ONLUS Ragusa, AVIS Ragusa, Sicilian Government (Italy); Dutch Ministry of Public Health, Welfare and Sports (VWS), Netherlands Cancer Registry (NKR), LK Research Funds, Dutch Prevention Funds, Dutch ZON (Zorg Onderzoek Nederland), World Cancer Research Fund (WCRF), and Statistics Netherlands (the Netherlands); European Research Council (ERC; grant number ERC-2009-AdG 232997) and Nordforsk, and Nordic Center of Excellence Programme on Food, Nutrition and Health (Norway); Health Research Fund (FIS), Regional Governments of Andalucía, Asturias, Basque Country, Murcia (No. 6236) and Navarra, and ISCIII RETIC (RD06/0020) (Spain); Swedish Cancer Society, Swedish Scientific Council, and Regional Government of Skåne and Västerbotten (Sweden); Cancer Research UK, Medical Research Council, Stroke Association, British Heart Foundation, Department of Health, Food Standards Agency, and Wellcome Trust (UK)

Circulating bilirubin levels and risk of colorectal cancer: serological and Mendelian randomization analyses

Abstract: Background: Bilirubin, a byproduct of hemoglobin breakdown and purported anti-oxidant, is thought to be cancer preventive. We conducted complementary serological and Mendelian randomization (MR) analyses to investigate whether alterations in circulating levels of bilirubin are associated with risk of colorectal cancer (CRC). We decided a priori to perform analyses separately in men and women based on suggestive evidence that associations may differ by sex. Methods: In a case-control study nested in the European Prospective Investigation into Cancer and Nutrition (EPIC), pre-diagnostic unconjugated bilirubin (UCB, the main component of total bilirubin) concentrations were measured by high-performance liquid chromatography in plasma samples of 1386 CRC cases and their individually matched controls. Additionally, 115 single-nucleotide polymorphisms (SNPs) robustly associated (P < 5 × 10−8) with circulating total bilirubin were instrumented in a 2-sample MR to test for a potential causal effect of bilirubin on CRC risk in 52,775 CRC cases and 45,940 matched controls in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), the Colon Cancer Family Registry (CCFR), and the Colorectal Transdisciplinary (CORECT) study. Results: The associations between circulating UCB levels and CRC risk differed by sex (Pheterogeneity = 0.008). Among men, higher levels of UCB were positively associated with CRC risk (odds ratio [OR] = 1.19, 95% confidence interval [CI] = 1.04–1.36; per 1-SD increment of log-UCB). In women, an inverse association was observed (OR = 0.86 (0.76–0.97)). In the MR analysis of the main UGT1A1 SNP (rs6431625), genetically predicted higher levels of total bilirubin were associated with a 7% increase in CRC risk in men (OR = 1.07 (1.02–1.12); P = 0.006; per 1-SD increment of total bilirubin), while there was no association in women (OR = 1.01 (0.96–1.06); P = 0.73). Raised bilirubin levels, predicted by instrumental variables excluding rs6431625, were suggestive of an inverse association with CRC in men, but not in women. These differences by sex did not reach formal statistical significance (Pheterogeneity ≥ 0.2). Conclusions: Additional insight into the relationship between circulating bilirubin and CRC is needed in order to conclude on a potential causal role of bilirubin in CRC development

SummarizeBlasteDNAEnvironmentSepASVs

Perl script summarizes blast results. For each sequence it makes a string containing all the species hits that had the lowest e value for that query. Script removes hits with % identity of query cover < 90. Script also prints if an ASV had no BLAST results or if all e values were equal to the minimum. Returns a table with columns: Sample, Species (String of lowest e value hits), N ASVs, N reads, Proportion of reads, Sequence name (from sample results file)

Primer trimming script

Perl script trims primers and removes sequences with spacer primers that are incorrect (likely index hops). Script cycles through results folders, and puts results in a separate folder for DADA2 merging

MorphVeDNASummarizeErrMoreCons

Script compares morphological results to eDNA results. Removes ASVs < than the max error calculated from positive controls. Requires eDNA results input, SppStatus.txt, and INMorph.txt