Long Non-Coding RNAs and Their "Discrete" Contribution to IBD and Johne's Disease-What Stands out in the Current Picture? A Comprehensive Review

Non-coding RNAs (ncRNA) have paved the way to new perspectives on the regulation of gene expression, not only in biology and medicine, but also in associated fields and technologies, ensuring advances in diagnostic means and therapeutic modalities. Critical in this multistep approach are the associations of long non-coding RNA (lncRNA) with diseases and their causal genes in their networks of interactions, gene enrichment and expression analysis, associated pathways, the monitoring of the involved genes and their functional roles during disease progression from one stage to another. Studies have shown that Johne's Disease (JD), caused by Mycobacterium avium subspecies partuberculosis (MAP), shares common lncRNAs, clinical findings, and other molecular entities with Crohn's Disease (CD). This has been a subject of vigorous investigation owing to the zoonotic nature of this condition, although results are still inconclusive. In this review, on one hand, the current knowledge of lncRNAs in cells is presented, focusing on the pathogenesis of gastrointestinal-related pathologies and MAP-related infections and, on the other hand, we attempt to dissect the associated genes and pathways involved. Furthermore, the recently characterized and novel lncRNAs share common pathologies with IBD and JD, including the expression, molecular networks, and dataset analysis results. These are also presented in an attempt to identify potential biomarkers pertinent to cattle and human disease phenotypes.

Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1)

Natural Resistance-Associated Macrophage Proteins are a family of transmembrane divalent metal ion transporters, with important implications in life of both bacteria and mammals. Among them, the Solute Carrier family 11 member A1 (SLC11A1) has been implicated with susceptibility to infection by Mycobacterium avium subspecies paratuberculosis (MAP), potentially causing Crohn's disease in humans and paratuberculosis (PTB) in ruminants. Our previous research had focused on sequencing the mRNA of the caprine slc11a1 gene and pinpointed polymorphisms that contribute to caprine SLC11A1's susceptibility to infection by MAP in PTB. Despite its importance, little is known on the structural/dynamic features of mammalian SLC11A1 that may influence its function under normal or pathological conditions at the protein level. In this work we studied the structural architecture of SLC11A1 in Capra hircus and Bos taurus through molecular modeling, molecular dynamics simulations in different, functionally relevant configurations, free energy calculations of protein-metal interactions and sequence conservation analysis. The results of this study propose a three dimensional structure for SLC11A1 with conserved sequence and structural features and provide hints for a potential mechanism through which divalent metal ion transport is conducted. Given the importance of SLC11A1 in susceptibility to PTB, this study provides a framework for further studies on the structure and dynamics of SLC11A1 in other organisms, to gain 3D structural insight into the macromolecular arrangements of SLC11A1 but also suggesting a potential mechanism which divalent metal ion transport is conducted.

Effect of β-lactoglobulin gene polymorphism, lactation stage and breed on milk traits in Chios and Karagouniko sheep breeds

The animal selection with favourable phenotypes of the past has been, currently, replaced by the genotype selection on quantitative traits, assisted by the expanding molecular techniques in the context of livestock improvement. In this study, the c.112T>C polymorphism in exon II of β-lactoglobulin (β-LG) gene was investigated in Karagouniko and Chios sheep breeds by using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP), and possible associations with milk traits were examined. In total, 125 blood DNA samples were isolated for PCR-RFLP analysis and the respective 217 milk samples′ composition profile was obtained. The goodness of fit test to Hardy-Weinberg equilibrium (HWE) for β-LG genotypes was estimated and associations found between β-LG genotypes and raw milk composition. Two alleles and three genotypes were observed (AA, AB and BB) in both breeds, and Chios breed significantly deviated (P≤0.05) from Hardy-Weinberg equilibrium (HWE). Conclusively, linear mixed model analysis on samples, from both breeds collectively, showed significant effects of β-LG genotype on lactose percentage and somatic cell count (SCC), lactation stage on daily milk yield and protein, while the breed effect was significant only on daily milk yield.

Epigenetics and inheritance of phenotype variation in livestock

Epigenetic inheritance plays a crucial role in many biological processes, such as gene expression in early embryo development, imprinting and the silencing of transposons. It has recently been established that epigenetic effects can be inherited from one generation to the next. Here, we review examples of epigenetic mechanisms governing animal phenotype and behaviour, and we discuss the importance of these findings in respect to animal studies, and livestock in general. Epigenetic parameters orchestrating transgenerational effects, as well as heritable disorders, and the often-overlooked areas of livestock immunity and stress, are also discussed. We highlight the importance of nutrition and how it is linked to epigenetic alteration. Finally, we describe how our understanding of epigenetics is underpinning the latest cancer research and how this can be translated into directed efforts to improve animal health and welfare.

Epigenetics and inheritance of phenotype variation in livestock

Epigenetic inheritance plays a crucial role in many biological processes, such as gene expression in early embryo development, imprinting and the silencing of transposons. It has recently been established that epigenetic effects can be inherited from one generation to the next. Here, we review examples of epigenetic mechanisms governing animal phenotype and behaviour, and we discuss the importance of these findings in respect to animal studies, and livestock in general. Epigenetic parameters orchestrating transgenerational effects, as well as heritable disorders, and the often-overlooked areas of livestock immunity and stress, are also discussed. We highlight the importance of nutrition and how it is linked to epigenetic alteration. Finally, we describe how our understanding of epigenetics is underpinning the latest cancer research and how this can be translated into directed efforts to improve animal health and welfare.

Energy balance-dependent regulation of ovine glucose 6-phosphate dehydrogenase protein isoform expression

G6PDH is the rate-limiting enzyme of the pentose phosphate pathway and one of the principal source of NADPH, a major cellular reductant. Importantly, in ruminant's metabolism the aforementioned NADPH provided, is utilized for de novo fatty acid synthesis. Previous work of cloning the ovine (Ovis aries) og6pdh gene has revealed the presence of two cDNA transcripts (og6pda and og6pdb), og6pdb being a product of alternative splicing not similar to any other previously reported.¹ In the current study the effect of energy balance in the ovine G6PDH protein expression was investigated, shedding light on the biochemical features and potential physiological role of the oG6PDB isoform. Changes in energy balance leads to protein expression changes in both transcripts, to the opposite direction and not in a proportional way. Negative energy balance was not in favor of the presence of any particular isoform, while both protein expression levels were not significantly different (P > 0.05). In contrast, at the transition point from negative to positive and on the positive energy balance, there is a significant increase of oG6PDA compared with oG6PDB protein expression (P < 0.001). Both oG6PDH protein isoforms changed significantly toward the positive energy balance. oG6PDA is escalating, while oG6PDB is falling, under the same stimulus (positive energy balance alteration). This change is also positively associated with increasing levels in enzyme activity, 4 weeks post-weaning in ewes’ adipose tissue. Furthermore, regression analysis clearly demonstrated the linear correlation of both proteins in response to the WPW, while energy balance, enzyme activity, and oG6PDA relative protein expression follow the same escalating trend; in contrast, oG6PDB relative protein expression falls in time, similar to both transcripts accumulation pattern, as reported previously.²

Gene therapy for chronic relapsing experimental allergic encephalomyelitis using cells expressing a novel soluble p75 dimeric TNF receptor

In a murine relapsing experimental allergic encephalomyelitis (EAE) model, gene therapy to block TNF was investigated with the use of a retroviral dimeric p75 TNF receptor (dTNFR) construct. To effectively produce these TNF inhibitors in vivo, a conditionally immortalized syngeneic fibroblast line was established, using a temperature-sensitive SV40 large T Ag-expressing retrovirus. These cells were subsequently infected with a retrovirus expressing soluble dTNFR. CNS-injected cells could be detected 3 mo after transplantation and were shown to produce the transgene product by immunocytochemistry and ELISA of tissue fluids. These levels of dTNFR protein were biologically active and could significantly ameliorate both acute and relapsing EAE. This cell-based gene-vector approach is ideal for delivering proteins to the CNS and has particular relevance to the control of inflammatory CNS disease.

Amelioration of collagen-induced arthritis and suppression of interferon-gamma, interleukin-12, and tumor necrosis factor alpha production by interferon-beta gene therapy

OBJECTIVE

To investigate the therapeutic effects and possible mechanisms of action of constitutive expression of interferon-beta (IFNbeta) by syngeneic fibroblasts from DBA/1 mice in the collagen-induced arthritis (CIA) model.

METHODS

Immortalized embryonic DBA/1 fibroblasts were infected with a retrovirus expressing murine IFNbeta. IFNbeta-expressing fibroblasts were then implanted intraperitoneally into mice immunized with bovine type II collagen. The effect of IFNbeta on paw swelling, anticollagen antibody levels, IgG1/IgG2a isotype profiles, arthritis score, histologic joint damage, and cytokine secretion from lymph node cells and from bone marrow-derived macrophages was assessed.

RESULTS

A single injection of IFNbeta-secreting fibroblasts was sufficient to prevent arthritis or to ameliorate existing disease. Thus, IFNbeta reduced the clinical score and paw swelling irrespective of whether the injection was administered before or after disease onset in treated mice, compared with that in the untreated control group (P < 0.05). Histologic findings in the IFNbeta-treated mice were markedly less severe than in the control group (P < 0.001). This effect was accompanied by a decrease in total anticollagen IgG levels, a decrease in anticollagen IgG2a, and an increase in IgG1. In vitro, supernatants from these engineered fibroblasts inhibited collagen-induced interferon-gamma secretion from lymph node cells, and reduced the levels of tumor necrosis factor alpha and interleukin-12 produced by lipopolysaccharide/IFNgamma-treated bone marrow-derived macrophages. This effect was specific, since it was reversed with anti-IFNbeta polyclonal antibodies.

CONCLUSION

These results indicate that IFNbeta, which is currently used as a treatment for relapsing, remitting multiple sclerosis, is a potent immunomodulatory and antiinflammatory cytokine in CIA and should be considered for the treatment of rheumatoid arthritis.

Action spectrum of light-harvesting-II precursor apoprotein transcript accumulation and coordinated translation

In an attempt to ascertain that the phytochrome chromoproteins do indeed constitute the photoreceptor involved in light-harvesting-II-apoprotein-transcript accumulation and the synchronization of the endogenous circadian clock [Tavladoraki, P., Kloppstech, K. & Argyroudi-Akoyunoglou, J. H. (1989) Plant Physiol. (Bethesda) 90, 665-672], we studied the action spectrum of Cab transcription in 9-10-day-old etiolated Phaseolus vulgaris leaves. Transcript accumulation was detected by hybridization experiments or immunoprecipitation of the in-vitro translation products, obtained from isolated leaf poly(A)-rich mRNA species. It was found that the accumulation of the precursor-light-harvesting-II-apoprotein mRNA depends highly on the wavelength of light exposure, the action spectrum of its accumulation being closely correlated with the absorption spectrum of the red-absorbing phytochrome form (Pr); the reversal by far-red light of the light-induced Cab-mRNA accumulation depends also on wavelength of light exposure, used prior to far red for activation of transcription; the action spectrum thus obtained resembles the difference absorption spectrum of the purified phytochrome protein (delta A Pr-Pfr). In addition, immunoblot analysis of total lithium-dodecyl-sulphate-solubilized protein extracts of leaves showed that the appearance of the mature light-harvesting-II apoprotein in etiolated leaves previously exposed to a light pulse of equal dose but varying wavelength, closely follows the pattern of its transcript accumulation and the action spectrum of protochlorophyllide photoconversion. Thus, translation of the protein in vivo, as monitored by the steady level of the protein appearing in Western blots, is closely coordinated with the accumulation of its transcript, the action spectrum of both processes closely resembling the absorption spectrum of phytochrome. The results suggest that phytochrome is involved in photoreception mediating Cab-gene transcription in 9-10-day-old etiolated bean leaves and that Cab transcription, appearance of the mature protein and stabilization of the apoprotein in thylakoids by the chlorophyll formed during the light pulse are in close coordination.