Igor Babiak

Nord University | HIBO · Faculty of Biosciences and Aquaculture

Studies in non-teleost vertebrates have found microRNAs (miRNAs) to be essential for proper gonadal development. However, comparatively little is known about their role during gonadal development in teleost fishes. So far in zebrafish, a model teleost, transcript profiling throughout gonadal development has not been established because of a tiny si...

Environmental temperature has serious implications in life cycle of aquatic ectotherms. Understanding the molecular mechanisms of temperature acclimation and adaptation of marine organisms is of the uttermost importance for ecology, fisheries, and aquaculture, as it allows modeling the effects of global warming on population dynamics. Regulatory mo...

MicroRNAs (miRNAs) are transcriptional and posttranscriptional regulators involved in nearly all known biological processes in distant eukaryotic clades. Their discovery and functional characterization have broadened our understanding of biological regulatory mechanisms in animals and plants. They show both evolutionary conserved and unique feature...

No information exists on the identification of primordial germ cells (PGCs) in the superorder Protacanthopterygii, which includes the Salmonidae family and Atlantic salmon (Salmo salar L.), one of the most commercially important aquatic animals worldwide. In order to identify salmon PGCs, we cloned the full-length cDNA of vasa, dead end (dnd), and...

Zebrafish are an important model species in developmental biology. However, their potential in reproductive biology research has yet to be realized. In this study, we established See-Thru-Gonad zebrafish, a transparent line with fluorescently labeled germ cells visible throughout the life cycle, validated its gonadal development features, and demon...

RNAs originating from mitochondrial genomes are abundant in transcriptomic datasets produced by high-throughput sequencing technologies, primarily in short-read outputs. Specific features of mitochondrial small RNAs (mt-sRNAs), such as non-templated additions, presence of length variants, sequence variants, and other modifications, necessitate the...

Group I introns are mobile genetic elements encoding self-splicing ribozymes. Group I introns in nuclear genes are restricted to ribosomal DNA of eukaryotic microorganisms. For example, the myxomycetes, which represent a distinct protist phylum with a unique life strategy, are rich in nucleolar group I introns. We analyzed and compared 75 group I i...

The available zebrafish genotyping protocols do not provide the most accurate results, mainly due to the use of electrophoresis gels. Single nucleotide polymorphisms, insertions, deletions and point mutations are most accurately detected by sequencing. Here, we describe a high accuracy and scalable single-day protocol to detect zebrafish mutants by...

Nuclear group I introns are restricted to the ribosomal DNA locus where they interrupt genes for small subunit and large subunit ribosomal RNAs at conserved sites in some eukaryotic microorganisms. Here, the myxomycete protists are a frequent source of nuclear group I introns due to their unique life strategy and a billion years of separate evoluti...

In spotted wolffish Anarhichas minor aquaculture, cryopreservation is used to secure sperm availability throughout the entire spawning season. Under current protocols, sperm is cryopreserved in 0.5-mL straws. This implies thawing a considerable number of straws for insemination with cryopreserved sperm. In this work, we scale up the spotted wolffis...

Studying biology of sperm provides valuable information to optimize artificial reproduction and is crucial for sustainable aquaculture. Here, we investigated morphology of spermatozoon in Atlantic cod (Gadus morhua) using transmission and scanning electron microscopy. Furthermore, spermatozoa motility kinetics at different osmolalities were studied...

Gamma radiation produces DNA instability and impaired phenotype. Previously, we observed negative effects on phenotype, DNA methylation, and gene expression profiles, in offspring of zebrafish exposed to gamma radiation during gametogenesis. We hypothesize that previously observed effects are accompanied with changes in the expression profile of no...

During zebrafish development, an early type of rRNA is gradually replaced by a late type that is substantially different in sequence. We applied RiboMeth-seq to rRNA from developmental stages for profiling of 2’-O-Me, to learn if changes in methylation pattern were a component of the shift. We compiled a catalogue of 2’-O-Me sites and cognate box C...

Sequencing datasets available in public repositories are already high in number, and their growth is exponential. Raw sequencing data files constitute a substantial portion of these data, and they need to be pre-processed for any downstream analyses. The removal of adapter sequences is the first essential step. Tools available for the automated det...

The origin and contribution of seminal plasma RNAs into the whole semen RNA repertoire are poorly known, frequently being overlooked or neglected. In this study, we used high-throughput sequencing and RT-qPCR to profile microRNA (miRNA) constituents in the whole semen, as well as in fractionated spermatozoa and seminal plasma of Atlantic salmon (Sa...

Zebrafish is a well-recognized organism for investigating vertebrate development and human diseases. However, the data on zebrafish proteome are scarce, particularly during embryogenesis. This is mostly due to the overwhelming abundance of egg yolk proteins, which tend to mask the detectable presence of less abundant proteins. We developed an effic...

Background: Zebrafish is a well-recognised organism for investigating vertebrate development and human diseases. However, the data on zebrafish proteome are scarce, particularly during embryogenesis. This is mostly due to the overwhelming abundance of egg yolk proteins, which tend to mask the detectable presence of less abundant proteins. Results:...

Zebrafish is a well-established model organism for the investigation of development of vertebrates. Multiple genomics and transcriptomics studies have been performed to analyse zebrafish embryonic development in recent years. However, quantitative proteomics studies of early embryo remained unexplored. Previous proteomics analysis of early embryo w...

Biological functions of micro RNAs (miRNAs) in the early stages of vertebrate development remain largely unknown. In zebrafish, miRNA miR-92a-3p is abundant in the germ cells throughout gonadal development, as well as in ovulated oocytes. Previously, we demonstrated that inhibition of miR-92a-3p in mature ovaries resulted in developmental arrest at...

Background The origin and contribution of seminal plasma RNAs into the whole semen RNA repertoire are poorly known, frequently being overlooked or neglected. Virtually nothing is known about seminal plasma RNAs in fish, including small RNAs, which have regulatory functions in gonadal development. Results In this study, we profiled microRNA (miRNA)...

Zebrafish is a well-characterized model organism for the investigation of development of vertebrates. Proteome profile of zebrafish has high similarity to human, making it an attractive model for the study of human diseases. Genomic and transcriptomic resources on the development of zebrafish embryo are relatively well established, yet the proteomi...

Background Early development of an oviparous organism is based on maternally stocked structural, nutritional and regulatory components. These components influence the future developmental potential of an embryo, which is referred to as egg quality. Until zygotic genome activation, translational activity in a fish early embryo is limited to parental...

Zebrafish is an excellent and well-recognised organism for investigating vertebrate development. Its proteome is apparently highly similar to that of humans, which makes the zebrafish an attractive model of human diseases. Although genomic and transcriptomic data on zebrafish embryonic development are well established, data on the proteome are scar...

Zebrafish is an excellent and well-recognized organism for investigating vertebrate development. Its proteome is apparently highly similar to that of humans, which makes the zebrafish an attractive model of human diseases. Although genomic and transcriptomic data on zebrafish embryonic development are well established, data on the proteome are scar...

In many fish species, the immune system is significantly constrained by water temperature. In spite of its critical importance in protecting the host against pathogens, little is known about the influence of embryonic incubation temperature on the innate immunity of fish larvae. Zebrafish (Danio rerio) embryos were incubated at 24, 28 or 32 °C unti...

To our knowledge, there is no report on microRNA (miRNA) expression and their target analysis in relation to the type of the first feed and its effect on the further growth of fish. Atlantic cod (Gadus morhua) larvae have better growth and development performance when fed natural zooplankton as a start-feed, as compared with those fed typical aquac...

Modern out-of-season egg production in Atlantic salmon (Salmo salar) increases the risk of postovulatory aging (POA) of oocytes. Postovulatory aging is known to influence oocyte quality in salmonids, but reliable tests for POA are lacking in Atlantic salmon egg production. To address this problem, we have collected oocytes from the same 20 Atlantic...

A method to mitigate or possibly eliminate reproduction in farmed fish is highly demanded. The existing approaches have certain applicative limitations. So far, no immunization strategies affecting gonadal development in juvenile animals have been developed. We hypothesized that autoimmune mechanisms, occurring spontaneously in a number of diseases...

Background Commercial Atlantic halibut (Hippoglossus hippoglossus) farming is restricted by variable oocyte quality, slow growth, and early maturation of male fish. Maternally transferred components regulate early developmental processes; therefore, they have an effect on the future viability of the embryo. Using a newly developed Agilent 10 k cust...

The notion that the circadian rhythm is exclusively regulated by a central clock has been challenged by the discovery of peripheral oscillators. These peripheral clocks are known to have a direct influence on the biological processes in a tissue or cell. In fish, several peripheral clocks respond directly to light, thus raising the hypothesis of au...

The classical notion of a centralized clock that governs circadian rhythmicity has been challenged with the discovery of peripheral oscillators that enable organisms to cope with daily changes in their environment. The present study aimed to identify the molecular clock components in Atlantic cod (Gadus morhua) and to investigate their daily gene e...

The role of sex steroid regulation in gonadal maturation is a very complex process that is far from being fully understood. Hence, we have investigated seasonal changes in gonadal expression of estrogen receptors (ERs) in Atlantic cod (Gadus morhua L.), a batch spawner, throughout annual reproductive cycle. Three nuclear ER partial cDNA sequences (...

Significant efforts have been made to elucidate factors affecting egg quality in fish. Recently, we have shown that eggs originating from wild broodstock (WB) of Atlantic cod (Gadus morhua L.) are of superior quality to those derived from farmed broodstock (FB), and this is associated with differences in the chemical composition of egg yolk. Howeve...

microRNAs (miRNAs) are implicated in regulation of many cellular processes. miRNAs are processed to their mature functional form in a step-wise manner by multiple proteins and cofactors in the nucleus and cytoplasm. Many miRNAs are conserved across vertebrates. Mature miRNAs have recently been characterized in Atlantic halibut (Hippoglossus hippogl...

pre-miRNA alignment. The conserved pre-miRNA sequence alignment (5′–3′) among teleosts. In cases of undiscovered miRNAs in teleosts, mammalian pre-miRNA orthologs were used. In addition to full Atlantic halibut precursor miRNAs, partial pre-miRNA sequences of Atlantic halibut are also aligned to teleosts ortholog. Highlighted bold sequences represe...

Amplified fragments of Atlantic halibut miR-430 target genes using RACE-PCR. (PDF)

A) 3'UTR oligo sequences; B) 454 genome sequence of the miR-430 cluster and pre-miR-10 and pre-miR-196; and C), RACE-PCR sequences of miR-430 transcripts from pooled samples of different developmental stages of Atlantic halibut (see Materials and Methods). Bold and highlighted letters indicate pre-miRNAs. (PDF)

Hairpin structures predicted from Atlantic halibut sequenced genome data using srnaloop. The sequence centroid secondary structure and minimum free energy in kcal/mol are depicted. (DOC)

miRNA target prediction in Atlantic halibut using miRanda and RNAHybrid. Bold font indicates miRNA consensus between the two algorithms. (XLS)

Variation in oocyte quality affects sustainability of finfish aquaculture products including Atlantic halibut (Hippoglossus hippoglossus L.). To have an insight into role of major egg yolk constituents in the oocyte quality, egg fatty acid (FA), amino acid (AA) and folate contents were related to normal blastomere symmetry, and fertilization and ha...

The study aimed at improving the protocol for cryopreservation of Atlantic cod sperm. Five diluents, four cryoprotectants, two time intervals between thawing and activation of spermatozoa, and two sperm collection times prior to freezing were tested for their effect on post‐thaw motility and fertilization ability. Minimum sufficient sperm:egg ratio...

We investigated the profiles of 25 genes involved in apoptosis (bcl-x2, casp3, casp8, ccar1, mcl1, and tpt1), immunity (bty, cathl, ifng, il1b, il6, il8, il10, lyzg, and tfa), oxidative stress (cat, gpx4, gsh-px, hsp70, hsp90a, and sod1), and stress axis (crh, pomc, grl1, and mlr) during Atlantic cod development and compared the mRNA transcript lev...

Primordial germ cells (PGCs), progenitors of gametes, are specified very early in embryonic development and undergo an active migration to the site where the future gonads will form. While the developmental pattern of PGCs during embryogenesis has been documented in few model teleost fishes, there is currently no information available for any repre...

The role of miRNA in fish sexual development is not elucidated yet. We profiled miRNAs in gonads and brains of Atlantic halibut using SOLiD sequencing technology. We found tissue- and sexually dimorphic expression of several miRNAs, including miR-29a, miR-34, miR-143, miR-145, miR-202-3p, miR-451, and miR-2188. miR-9 and miR-202 were abundant in br...

The effects of cryopreservation on the viability, morphology and capability of spermatozoa in Atlantic cod, Gadus morhua L., were studied. The sperm was cryopreserved in straws using Hanks' balanced salt solution, hens' egg yolks and glycerol in the vapor of liquid nitrogen. Straws of cryopreserved sperm were stored in liquid nitrogen and thawed in...

We investigated the effect of two commercial nucleotide products (NT1 and NT2), administered through live feed, on growth and stress tolerance of Atlantic cod larvae. Expression of genes related to muscle growth (igf-1, igf1r, igf-2, fst, fgf6, myod, and myhc) and nucleotide metabolism (uox, hprt, ndk, and uck) was evaluated during larval developme...

The Atlantic cod (Gadus morhua) is an important natural resource for northern societies and is now also considered to be a promising candidate for aquaculture. In recent years, much effort has been directed towards the development of genomic tools, and genome initiatives for Atlantic cod have been established. Despite the growing attention devoted...

Farming of Atlantic cod, Gadus morhua L., has been facing several challenges lately. Biological issues such as differences in egg quality and lack of high quality larvae are considered as prominent limiting factors. The aim of this study was to compare fertilization and hatching rates, incidence of malformed larvae at hatching, larval viability (hi...

MicroRNAs (miRNAs) play a major role in animal ontogenesis. Size variants of miRNAs, isomiRs, are observed along with the main miRNA types, but their origin and possible biological role are uncovered yet. Developmental profiles of miRNAs have been reported in few fish species only and, to our knowledge, differential expressions of isomiRs have not...

IsomiR occurrence during early development of Atlantic halibut. All miRNAs having ≥ 0.01% truncation/s or addition/s in 5' and/or 3' ends are listed. The percentage of both template and non-template nucleotide changes (A, U, C, and G) are shown as percentage of total reads of a given miRNA.

Cloned miRNA sequences and their frequency. Indentified conserved miRNAs using cloning technique and their frequencies. Nucleotide mismatches (green), additions (blue) or modifications (red) are found in some miRNAs.

Size distribution of mapped reads in Atlantic halibut deep sequencing data. Reads mapped to different databases: A) mitochondrial transcripts, rRNA, tRNA, other non-coding RNA; B) miRBase 16 and C) Atlantic halibut ESTs. The size distribution of mapped reads for each database is given.

Identified conserved miRNAs. All identified conserved Atlantic halibut miRNAs along with miRBase name, nucleotide sequences and read counts for each investigated developmental stages are given. Lower case letters indicate mismatches comparing to references.

miRNA diversity during early development of Atlantic halibut. The number of different types of miRNAs identified during 8 stages of Atlantic halibut development; increasing as the development progressed.

Read counts for 8 developmental stages of Atlantic halibut. The total number of raw sequence reads obtained from SOLiD sequencing and the number of usable reads for each developmental stage is given.

Production of all-female Atlantic halibut (Hippoglossus hippoglossus L.) is desirable for the industry because of sexual growth dimorphism existing in this species. The first step towards establishing monosex all-female cohorts is to produce sex-reversed females (neo-males). The objective of this study was to test the efficiency of an aromatase inh...

The Atlantic cod, Gadus morhua, is one of the most important species for commercial fisheries and a promising candidate for aquaculture. Precocious sexual maturation of males is one of the major issues compromising large scale production. The potential approaches to this problem include production of all female populations. Consequently, the object...

Rainbow trout homogametic males, (XX or YY sex genotype), can be obtained, respectively, through masculinisation of genetic females or induced androgenesis. Aim of this study was to compare reproductive potential of neo-males (XX) and super-males (YY) with heterogametic males (XY). We measured spermatozoa motility parameters, sperm concentrati...

Rainbow trout homogametic males, (XX or YY sex genotype), can be obtained, respectively, through masculinisation of genetic females or induced androgenesis. Aim of this study was to compare reproductive potential of neo-males (XX) and super-males (YY) with heterogametic males (XY). We measured spermatozoa motility parameters, sperm concentration, o...

There is a lack of biomarkers or indices that can be used to predict the quality of fish semen samples following the freezing and thawing cycle. In the present study, a series of semen indices were tested to assess if they could accurately forecast the cryopreservation potential of Atlantic cod (Gadus morhua) semen. Fresh and frozen-thawed sperm ac...