Ana­tomy and De­vel­op­mental Bio­logy

We study developmental interactions:

  • Regulation of the morphogenesis of three-dimensional anatomical structures
  • Development of the immune system and early host-microbe interactions
  • Epigenetic regulation of blood cell differentiation

The research in developmental interactions is led by professor Antti Iivanainen. University lecturer Juha Laakkonen studies macroscopic anatomy utilizing silicone cast models. We have also studied host-microbe interactions in bovine mastitis and the differentiation potential of circulating stem cells.

We also provide the following equipment to be used by researchers:

3D-modeling and radiographic imaging uncovers novel information on spatial skeletal development and its disorders. Our main interests at present are canine hipdysplasia and lumbosacral transitional vertebrae. We also study the genetic aspect of these diseases in close collaboration with Professor Hannes Lohi and his canine genetics research group.

Hip dysplasia (HD) is the most common canine developmental musculoskeletal disorder. HD severely compromises animal welfare as it is often painful and may cause severe disability or lead to euthanasia at a young age. The genetic background of HD is poorly characterized. Also, the diagnostic methods vary between countries.

Lumbosacral transitional vertebrae (LTV) manifest as one or several abnormal vertebrae in the lumbosacral spine. The transitional vertebrae bear the characteristics of both lumbar and sacral vertebrae. The associated changes may be symmetrical or asymmetrical. In the most severe form, a single sacral vertebra has adopted a lumbar phenotype or vice versa. This developmental disorder predisposes to degenerative changes in the lumbosacral spine, which can cause lower back pain or even paralysis of the hind limbs. LTV is known to cause unilateral hipdysplasia in cases with unilateral sacralization of the seventh lumbar vertebra.

Image: 3D model of canine pelvis produced with Slicer. Left: normal canine pelvis, middle: dysplastic hips with osteophyte formation, right: asymmetrical structural change in the lumbosacral spine.

Additional information on the website for canine genetic studies: hip dysplasia and lumbosacral transitional vertebrae.


Koiran lantio 3-d



Mammals have adopted varying strategies for the production of B lymphocytes and the enormous antibody repertoire that is critical to the immune defense. In ruminants, the germline repertoire of immunoglobulin genes is much smaller than in humans and mice, and therefore they are traditionally though to use additional methods for diversifying the preimmune repertoire. Whereas humans and mice produce B lymphocytes in the bone marrow, ruminants largely utilize a large mass of lymphoid follicles in the wall of the small intestine, the ileal Peyer’s patch.

We have shown that in cattle, new B lymphocytes are generated primarily in the fetal period. They are originally generated in the bone marrow, where the immunoglobulin genes are built from several alternative segments just like in humans and mice. We also showed that the bovine germline immunoglobulin repertoire indeed is very small in comparison to these other species. The repertoire is however expanded due to the expression of the terminal deoxynucleotidyl transferase (TdT) already at the fetal period, adding or removing nucleotides in the joints of the gene segments.

From the bone marrow, immature B cells migrate to the ileal Peyer’s patch, where they proliferate massively. Meanwhile, the immunoglobulin genes are rapidly mutated. In humans and mice, this somatic hypermutation occurs during postnatal immune responses to infections. In cattle, however, the hypermutation starts already during the fetal development. Fetal cattle expresses the same hypermutating enzyme, activation-induced cytidine deaminase (AICDA or AID), that that is used after birth to reshape and target the repertoire against specific antigens during the immune response.

Image: immunofluorescence staining of bovine fetal lymph node. B cells in red, T cells in green and TdT expression in white.

Immunofluoresenssivärjäys naudan sikiön imusolmukkeesta



The maternal microbiota influences the fetal development of the immune system, although previously the fetus was thought to develop in a sterile uterine environment. However, the exact mechanisms and actual physiological effects are still unknown. 

We study the development and immunological impact of the prenatal microbiota in cattle and other domestic animals. This is a readily accessible and especially interesting model for these studies. Microbes are especially important for nutrition in ruminants. Ruminants also generate their B lymphocytes in the intestine, rather than in the bone marrow. The fetal development in large domestic animals proceeds in a similar timescale as in humans, allowing the maturation of intestinal microbiota and associated immune responses. We have previously shown that in cattle, somatic hypermutation of immunoglobulins with antigen-driven signatures starts already in the fetus. Our recent research indicates that microbial DNA can be detected in the bovine intestine already at the moment of birth. 

In this project, we characterize the prenatal microbiota quantitatively and qualitatively by modern genomic sequence-driven and traditional culture-based methods, and analyze the fetal immune responses and host-microbe interactions. We will also compare the prenatal microbial colonization across mammalian species with different placental structure and permeability.

The project provides new knowledge on prenatal host-microbe interactions, and how they shape the early development of the immune system. The prenatal microbiota may prime the immune system for effective protection, and could induce tolerance for commensal microbes. The ability to distinguish between intestinal commensals and dangerous pathogens is one of the most critical aspects of a functional immune system, yet still poorly understood. Failure to tolerate commensals results in pathological immune responses such as inflammatory bowel diseases.

The research also has major implications in modern farm animal husbandry. The substantial early mortality in intestinal infections and the risks associated with the globally massive antibiotic use call for new prevention strategies. Rational design of such measures requires thorough understanding of early host-microbe interactions and of the fetal effects of manipulations of the maternal microbiota.

Our recent article on the early bovine intestinal microbiota:

Alipour MJ, Jalanka J, Pessa-Morikawa T, Kokkonen T, Satokari R, Hynönen U, Iivanainen A, Niku M (2018) The composition of the perinatal intestinal microbiota in cattle. Sci Rep.8(1):10437. doi: 10.1038/s41598-018-28733-y.

Open Access:

Summary of the results:


DNA methylation is an important regulator of gene expression. When methyl groups are added to the cytosine bases in the regulatory regions of a gene, the gene is usually silenced. Methylation patterns change during cellular differentiation, when genes are switched on and off. Perturbed methylation is associated with cancer.

We investigate poorly understood mechanisms removing DNA methylation. We focus on erythroid differentiation, where methylation changes occur during the activation of hemoglobin expression, and when the fetal hemoglobin (HBG) changes to the adult type (HBA). We use a human erythroleukemia cell line which can be induced to erythroid differentiation, and the modern CRISPR genome modification technology to effectively switch off genes of interest in these cells. We also investigate the regulation of hemoglobin switching in cattle, which (like humans) has a specific fetal hemoglobin, in contrast to mice.

We use rapidly setting silicone materials to study the macroanatomy of wild and domesticated animals. Collecting morphological data on wild animals is important for the documentation of evolutionary changes. As soft tissue structures are more difficult to harvest and preserve than skeletons, we have prepared silicone models of the respiratory tracts of the lynx and the Saimaa ringed seal as well the structures in the multi-part stomach of an Asian rat variety to aid in research. These models are a great help in both academic research and teaching, where they can be used to illustrate various soft tissue structures. The silicone models can also be used as models in 3D digital imaging, which our discipline has used to study the structures of cow udders and as an illustration for teaching purposes.


Silicone models



Laakkonen, J., Kankaanpää, T., Corfe, I., Jernvall, J., Soveri, T., Keovichit, K. & Hugot, J-P. (2014). Gastrointestinal and dental morphology of herbivorous mammals: where does the Laotian rock rat fit? Annales Zoologici Fennici. 51, 153-161. [Open Access full text]

Laakkonen, J. Jernvall, J. 2016. Macroscopic anatomy of the Saimaa ringed seal(Phoca hispida saimensis) lower respiratory tract. Anatomical Record. In Press.

Vesterinen, H.M., Corfe, I.J., Sinkkonen, V., Iivanainen, A., Jernvall, J., and Laakkonen, J. (2015). Teat morphology characterization with 3D imaging. Anat. Rec. Hoboken NJ 2007 298, 1359–1366.  [PubMed]

Mastitis is the economically most significant infectious disease in dairy cows. Streptococcus uberis and several Staphylococcus species are common pathogens. We use molecular and cell biological, microbiological and bioinformatics methods to investigate the pathogenic mechanisms of mastitis and how the common pathogens resist the host defense.