Biology subjects

Furmanek, T.

Publications and source records attributed to Furmanek, T..

5 recordsLinked to original sources

bioRxiv2022

Molecular mechanisms involved in Atlantic halibut (Hippoglossus hippoglossus) egg quality: impairments at transcription and protein folding levels induce inefficient protein and energy homeostasis during early development

BackgroundReproductive success and normal development in all animals are dependent on egg quality and developmental competence of the produced embryo. This study employed tandem mass tags labeling based liquid chromatography tandem mass spectrometry for egg proteomic profiling to investigate differences in the global proteome of good versus poor quality Atlantic halibut eggs at 1-cell stage post fertilization. ResultsA total of 115 proteins were found to be differentially abundant between good and poor quality eggs. Frequency distribution of these proteins revealed higher protein folding activity in good quality eggs in comparison to higher transcription and protein degradation activities in poor quality eggs (p < 0.05). Poor quality halibut eggs were significantly enriched with additional proteins related to mitochondrial structure and biogenesis (p < 0.05). The differential abundance of a selection of proteins was first confirmed at gene expression level using a transcriptomic approach followed by a targeted proteomic approach (parallel reaction monitoring based mass spectrometry) in biological samples obtained from two consecutive reproductive seasons. The findings of global proteome profiling, together with the validation of differential abundance of targeted proteins and their related genes, suggest impairments in protein and energy homeostasis which might be related to unfolded protein response and mitochondrial stress in poor quality eggs. Additional transmission electron microscopy studies were taken to assess potential differences in abundance and morphological integrity of mitochondria between good and poor quality eggs. Observations reveal poor quality eggs to contain significantly higher number of mitochondria with higher number of cristae. These mitochondria, however, are significantly smaller and have a more irregular shape than those found in high-quality eggs. Therewithal difference in mtDNA levels represented by mt-nd5 and mt-atp6 genomic DNA abundance in this study, were found to be not statistically significant (p > 0.05) between good and bad quality eggs at both 1 hpf and 24 hpf stages. ConclusionOverall evidence from this study indicate that poor quality eggs undergo impairments at both transcription and translation level leading to endoplasmic reticulum and mitochondrial deficiencies. Additional research may be required to expediate the details and the potential of these impairments occurring in different species. Nonetheless, this study will pave the way for future research and will help in acceleration of recent advances in the field of embryonic developmental competence of living organisms.

molecular biology↗

bioRxiv2021

Cardiac dysfunction affects eye development and vision by reducing supply of lipids in fish

Developing organisms are especially vulnerable to environmental stressors. We aimed to understand the underlying mechanisms of phenanthrene (Phe) and crude oil induced eye malformations. We exposed Atlantic haddock (Melanogrammus aeglefinus) embryos to a known L-type calcium channel blocker, nicardipine hydrochloride (Nic), and compared to early embryonic crude oil (Oil) and late embryonic Phe toxicity. All treatments lead to severe, eye, jaw and spinal deformities at early larval stages. At 3 days post hatching, larvae from all treatments and corresponding controls were dissected. Eyes, trunk, head and yolk sac were subjected to lipid profiling, and eyes were also subjected to transcriptomic profiling. Changes in lipid profiles and the transcriptome suggested that the dysfunctional and abnormal eyes in our treatments were due to both disruption of signaling pathways and insufficient supply of essential fatty acids and other nutrients form the yolk.

molecular biology↗

bioRxiv2021

The salmon louse genome: copepod features and parasitic adaptations.

Copepods encompass a range of ecological roles from parasites to phytoplankton grazers linking primary producers to higher trophic levels. Despite these important roles, copepod genome assemblies are scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod. We present the 695.4 Mbp L. salmonis genome assembly containing {approx}60% repetitive regions and 13081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics validated annotation and revealed a marked shift in gene expression after host attachment, including downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of peroxisomes, numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite large capacity to develop resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.

genomics↗

bioRxiv2020

Heterochiasmy facilitated the establishment of gsdf as a novel sex determining gene in Atlantic halibut

Atlantic Halibut (Hippoglossus hippoglossus) has a X/Y genetic sex determination system, but the sex determining factor is not known. We produced a high-quality genome assembly and identified parts of chromosome 13 as the Y chromosome due to sequence divergence between sexes and segregation of sex genotypes in pedigrees. Linkage analysis revealed that all chromosomes exhibit heterochiasmy, i.e. male- and female restricted meiotic recombination intervals (MRR/FRR). We show that FRR/MRR intervals differ in nucleotide diversity and repeat class content and that this is true also for other Pleuronectidae species. We further show that remnants of a Gypsy-like transposable element insertion on chr13 promotes early male specific expression of gonadal somatic cell derived factor (gsdf). Less than 4 MYA, this male-determining element evolved on an autosomal FRR segment featuring pre-existing male meiotic recombination barriers, thereby creating a Y chromosome. We propose that heterochiasmy may facilitate the evolution of genetic sex determination systems.

genomics↗

bioRxiv2020

ReCodLiver0.9: Overcoming challenges in genome-scale metabolic reconstruction of a non-model species

The availability of genome sequences, annotations and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in bacteria, archaea, and eukaryotes. When modeled using mathematical representations, a reconstruction can simulate underlying genotype-phenotype relationships. Accordingly, genome-scale models (GEMs) can be used to predict the response of organisms to genetic and environmental variations. A bottom-up reconstruction procedure typically starts by generating a draft model from existing annotation data on a target organism. For model species, this part of the process can be straightforward, due to the abundant organism-specific biochemical data. However, the process becomes complicated for non-model less-annotated species. In this paper, we present a draft liver reconstruction, ReCodLiver0.9, of Atlantic cod (Gadus morhua), a non-model teleost fish, as a practicable guide for cases with comparably few resources. Although the reconstruction is considered a draft version, we show that it already has utility in elucidating metabolic response mechanisms to environmental toxicants by mapping gene expression data of exposure experiments to the resulting model.Author summary Genome-scale metabolic models (GEMs) are constructed based upon reconstructed networks that are carried out by an organism. The underlying biochemical knowledge in such networks can be transformed into mathematical models that could serve as a platform to answer biological questions. The availability of high-throughput biological data, including genomics, proteomics, and metabolomics data, supports the generation of such models for a large number of organisms. Nevertheless, challenges arise for non-model species which are typically less annotated. In this paper, we discuss these challenges and possible solutions in the context of generation of a draft liver reconstruction of Atlantic cod (Gadus morhua). We also show how experimental data, here gene expression data, can be mapped to the resulting model to understand the metabolic response of cod liver to environmental toxicants.Competing Interest StatementThe authors have declared no competing interest.View Full Text

systems biology↗