| 1. |
- Campione, Nicolas E., et al.
(författare)
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A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods
- 2012
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Ingår i: BMC Biology. - : BioMed Central. - 1741-7007. ; 10, s. 60-
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundBody size is intimately related to the physiology and ecology of an organism. Therefore, accurate and consistent body mass estimates are essential for inferring numerous aspects of paleobiology in extinct taxa, and investigating large-scale evolutionary and ecological patterns in the history of life. Scaling relationships between skeletal measurements and body mass in birds and mammals are commonly used to predict body mass in extinct members of these crown clades, but the applicability of these models for predicting mass in more distantly related stem taxa, such as non-avian dinosaurs and non-mammalian synapsids, has been criticized on biomechanical grounds. Here we test the major criticisms of scaling methods for estimating body mass using an extensive dataset of mammalian and non-avian reptilian species derived from individual skeletons with live weights.ResultsSignificant differences in the limb scaling of mammals and reptiles are noted in comparisons of limb proportions and limb length to body mass. Remarkably, however, the relationship between proximal (stylopodial) limb bone circumference and body mass is highly conserved in extant terrestrial mammals and reptiles, in spite of their disparate limb postures, gaits, and phylogenetic histories. As a result, we are able to conclusively reject the main criticisms of scaling methods that question the applicability of a universal scaling equation for estimating body mass in distantly related taxa.ConclusionsThe conserved nature of the relationship between stylopodial circumference and body mass suggests that the minimum diaphyseal circumference of the major weight-bearing bones is only weakly influenced by the varied forces exerted on the limbs (that is, compression or torsion) and most strongly related to the mass of the animal. Our results, therefore, provide a much-needed, robust, phylogenetically corrected framework for accurate and consistent estimation of body mass in extinct terrestrial quadrupeds, which is important for a wide range of paleobiological studies (including growth rates, metabolism, and energetics) and meta-analyses of body size evolution.
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| 2. |
- Balakrishnan, Christopher N., et al.
(författare)
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Gene duplication and fragmentation in the zebra finch major histocompatibility complex
- 2010
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 8, s. 29-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Due to its high polymorphism and importance for disease resistance, the major histocompatibility complex (MHC) has been an important focus of many vertebrate genome projects. Avian MHC organization is of particular interest because the chicken Gallus gallus, the avian species with the best characterized MHC, possesses a highly streamlined minimal essential MHC, which is linked to resistance against specific pathogens. It remains unclear the extent to which this organization describes the situation in other birds and whether it represents a derived or ancestral condition. The sequencing of the zebra finch Taeniopygia guttata genome, in combination with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a highly divergent and diverse avian lineage, the passerines. Results: The zebra finch MHC exhibits a complex structure and history involving gene duplication and fragmentation. The zebra finch MHC includes multiple Class I and Class II genes, some of which appear to be pseudogenes, and spans a much more extensive genomic region than the chicken MHC, as evidenced by the presence of MHC genes on each of seven BACs spanning 739 kb. Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. MHC Class II regions are further characterized by high endogenous retroviral content. Lastly, we find strong evidence of selection acting on sites within passerine MHC Class I and Class II genes. Conclusion: The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a complete genome sequence. The apparent lack of synteny between TAP and the expressed MHC Class I locus is in fact reminiscent of a pattern seen in some mammalian lineages and may represent convergent evolution. Our analyses of the zebra finch MHC suggest a complex history involving chromosomal fission, gene duplication and translocation in the history of the MHC in birds, and highlight striking differences in MHC structure and organization among avian lineages.
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| 3. |
- Harraca, Vincent, et al.
(författare)
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Nymphs of the Common Bed Bug (Cimex lectularius) produce anti-aphrodisiac defence against conspecific males
- 2010
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background: Abdominal wounding by traumatic insemination and the lack of a long distance attraction pheromone set the scene for unusual sexual signalling systems. Male bed bugs (Cimex lectularius) mount any large, newly fed individual in an attempt to mate. Last instar nymphs overlap in size with mature females, which make them a potential target for interested males. However, nymphs lack the female's specific mating adaptations and may be severely injured by the abdominal wounding. We, therefore, hypothesized that nymphs emit chemical deterrents that act as an honest status signal, which prevents nymph sexual harassment and indirectly reduces energy costs for males. Results: Behavioural mating assays showed that males mount nymphs significantly shorter time compared to females, although initial mounting preference was the same. In support of our hypothesis, nymphs experienced the same percentage of mating with sperm transfer as females if they were unable to emit (E)-2-hexenal, (E)-2-octenal 4-oxo-(E)-2-hexenal and 4-oxo-(E)-2-octenal, from their dorsal abdominal glands. We report that the aldehydes and 4-oxo-(E)-2-hexenal are detected by olfactory receptor neurons housed in smooth and grooved peg sensilla, respectively, on the adult antennae, at biologically relevant concentrations. Behavioural experiments showed that application of 4-oxo-(E)-2-hexenal or the two aldehydes at a nymph-emitted ratio, to a male/female pair during mounting initiation, decreased mating frequency to a rate comparable to that of a male/nymph pair. Conclusions: By combining behavioural and sensory studies, we show that the nymph-specific alarm pheromone plays an important role in intra-specific communication in the common bed bug. Alarm pheromones are commonly looked upon as a system in predator/prey communication, but here we show that alarm pheromones may be used as multipurpose signals such as decreasing the risk of nymphal mating by males.
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| 4. |
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| 5. |
- Dantoft, Widad, et al.
(författare)
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The Oct1 homolog Nubbin is a repressor of NF-kappa B-dependent immune gene expression that increases the tolerance to gut microbiota
- 2013
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Background: Innate immune responses are evolutionarily conserved processes that provide crucial protection against invading organisms. Gene activation by potent NF-kappa B transcription factors is essential both in mammals and Drosophila during infection and stress challenges. If not strictly controlled, this potent defense system can activate autoimmune and inflammatory stress reactions, with deleterious consequences for the organism. Negative regulation to prevent gene activation in healthy organisms, in the presence of the commensal gut flora, is however not well understood. Results: We show that the Drosophila homolog of mammalian Oct1/POU2F1 transcription factor, called Nubbin (Nub), is a repressor of NF-kappa B/Relish-driven antimicrobial peptide gene expression in flies. In nub(1) mutants, which lack Nub-PD protein, excessive expression of antimicrobial peptide genes occurs in the absence of infection, leading to a significant reduction of the numbers of cultivatable gut commensal bacteria. This aberrant immune gene expression was effectively blocked by expression of Nub from a transgene. We have identified an upstream regulatory region, containing a cluster of octamer sites, which is required for repression of antimicrobial peptide gene expression in healthy flies. Chromatin immunoprecipitation experiments demonstrated that Nub binds to octamer-containing promoter fragments of several immune genes. Gene expression profiling revealed that Drosophila Nub negatively regulates many genes that are involved in immune and stress responses, while it is a positive regulator of genes involved in differentiation and metabolism. Conclusions: This study demonstrates that a large number of genes that are activated by NF-kappa B/Relish in response to infection are normally repressed by the evolutionarily conserved Oct/POU transcription factor Nub. This prevents uncontrolled gene activation and supports the existence of a normal gut flora. We suggest that Nub protein plays an ancient role, shared with mammalian Oct/POU transcription factors, to moderate responses to immune challenge, thereby increasing the tolerance to biotic stress.
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| 6. |
- Dekker, Teun
(författare)
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A carboxylesterase, Esterase-6, modulates sensory physiological and behavioral response dynamics to pheromone in Drosophila
- 2012
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Conclusions: Our study presents evidence that Est-6 plays a role in the physiological and behavioral dynamics of sex pheromone response in Drosophila males and supports a role of Est-6 as an odorant-degrading enzyme (ODE) in male antennae. Our results also expand the role of Est-6 in Drosophila biology, from reproduction to olfaction, and highlight the role of ODEs in insect olfaction.
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| 7. |
- Gabriel, Sofia I., et al.
(författare)
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Colonization, mouse-style
- 2010
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 8, s. 131-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Several recent papers, including one in BMC Evolutionary Biology, examine the colonization history of house mice. As well as background for the analysis of mouse adaptation, such studies offer a perspective on the history of movements of the humans that accidentally transported the mice.
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| 8. |
- Huminiecki, Lukasz, et al.
(författare)
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2R and remodeling of vertebrate signal transduction engine
- 2010
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 8, s. 146-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Whole genome duplication (WGD) is a special case of gene duplication, observed rarely in animals, where all genes duplicate simultaneously through polyploidisation. Two rounds of WGD (2R-WGD) occurred at the base of vertebrates, giving rise to an enormous wave of genetic novelty, but a systematic analysis of functional consequences of this event has not yet been performed. Results: We show that 2R-WGD affected overwhelming majority (74%) of signaling genes, in particular developmental pathways involving receptor tyrosine kinases, Wnt and TGF-beta ligands, GPCRs, and the apoptosis pathway. 2R-retained genes, in contrast to tandem duplicates, were enriched in protein interaction domains, and multifunctional signaling modules of Ras and MAP-kinase cascades. 2R-WGD had a fundamental impact on the cell-cycle machinery; redefined molecular building blocks of the neuronal synapse; and was formative for vertebrate brains. We investigated 2R-associated nodes in context of the human signaling network, as well as an inferred ancestral pre-2R (AP2R) network, and found that hubs (particularly involving negative regulations), were preferentially retained, with high-connectivity driving retention. Finally, microarrays and proteomics demonstrated a trend for gradual paralog expression divergence, independent of the duplication mechanism; but inferred ancestral expression states suggested preferential sub-functionalisation among 2R-ohnologs (2ROs). Conclusions: The 2R event left an indelible imprint on vertebrate signaling and cell-cycle. We show that 2R-WGD preferentially retained genes are associated with higher organismal complexity (e.g. locomotion, nervous system, morphogenesis), while genes associated with basic cellular functions (e.g. translation, replication, splicing, recombination; with the notable exception of cell-cycle) tended to be excluded. 2R-WGD set the stage for the emergence of key vertebrate functional novelties (such as complex brains, circulatory system, heart, bone, cartilage, musculature, and the adipose tissue). Full explanation of the impact of 2R on evolution, function, and the flow of information in vertebrate signaling networks is likely to have practical consequences for regenerative medicine, stem cell therapies, and cancer treatment.
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| 9. |
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| 10. |
- Tyo, Keith, 1979, et al.
(författare)
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Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress
- 2012
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 10:16, s. Art. no 16-
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe protein secretory pathway must process a wide assortment of native proteins for eukaryotic cells to function. As well, recombinant protein secretion is used extensively to produce many biologics and industrial enzymes. Therefore, secretory pathway dysfunction can be highly detrimental to the cell and can drastically inhibit product titers in biochemical production. Because the secretory pathway is a highly-integrated, multi-organelle system, dysfunction can happen at many levels and dissecting the root cause can be challenging. In this study, we apply a systems biology approach to analyze secretory pathway dysfunctions resulting from heterologous production of a small protein (insulin precursor) or a larger protein (α-amylase).ResultsHAC1-dependent and independent dysfunctions and cellular responses were apparent across multiple datasets. In particular, processes involving (a) degradation of protein/recycling amino acids, (b) overall transcription/translation repression, and (c) oxidative stress were broadly associated with secretory stress.ConclusionsApparent runaway oxidative stress due to radical production observed here and elsewhere can be explained by a futile cycle of disulfide formation and breaking that consumes reduced glutathione and produces reactive oxygen species. The futile cycle is dominating when protein folding rates are low relative to disulfide bond formation rates. While not strictly conclusive with the present data, this insight does provide a molecular interpretation to an, until now, largely empirical understanding of optimizing heterologous protein secretion. This molecular insight has direct implications on engineering a broad range of recombinant proteins for secretion and provides potential hypotheses for the root causes of several secretory-associated diseases.
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