Timing major conflict between mitochondrial and nuclear genes in species relationships of Polygonia butterflies (Nymphalidae: Nymphalini)

<p>Abstract</p> <p>Background</p> <p>Major conflict between mitochondrial and nuclear genes in estimating species relationships is an increasingly common finding in animals. Usually this is attributed to incomplete lineage sorting, but recently the possibility has been raised that hybridization is important in generating such phylogenetic patterns. Just how widespread ancient and/or recent hybridization is in animals and how it affects estimates of species relationships is still not well-known.</p> <p>Results</p> <p>We investigate the species relationships and their evolutionary history over time in the genus <it>Polygonia </it>using DNA sequences from two mitochondrial gene regions (COI and ND1, total 1931 bp) and four nuclear gene regions (EF-1α, wingless, GAPDH and RpS5, total 2948 bp). We found clear, strongly supported conflict between mitochondrial and nuclear DNA sequences in estimating species relationships in the genus <it>Polygonia</it>. Nodes at which there was no conflict tended to have diverged at the same time when analyzed separately, while nodes at which conflict was present diverged at different times. We find that two species create most of the conflict, and attribute the conflict found in <it>Polygonia satyrus </it>to ancient hybridization and conflict found in <it>Polygonia oreas </it>to recent or ongoing hybridization. In both examples, the nuclear gene regions tended to give the phylogenetic relationships of the species supported by morphology and biology.</p> <p>Conclusion</p> <p>Studies inferring species-level relationships using molecular data should never be based on a single locus. Here we show that the phylogenetic hypothesis generated using mitochondrial DNA gives a very different interpretation of the evolutionary history of <it>Polygonia </it>species compared to that generated from nuclear DNA. We show that possible cases of hybridization in <it>Polygonia </it>are not limited to sister species, but may be inferred further back in time. Furthermore, we provide more evidence that Haldane's effect might not be as strong a process in preventing hybridization in butterflies as has been previously thought.</p

Structure determination and thermodynamic stabilization of an engineered protein-protein complex

The interaction between two 6 kDa proteins has been investigated. The studied complex of micromolar affinity (Kd) consists of the Z domain derived from staphylococcal protein A and the related protein ZSPA-1, belonging to a group of binding proteins denoted affibody molecules generated via combinatorial engineering of the Z domain. Affibody-target protein complexes are good model systems for structural and thermodynamic studies of protein-protein interactions. With the Z:ZSPA-1 pair as a starting point, we determined the solution structure of the complex and carried out a preliminary characterization of ZSPA-1. We found that the complex contains a rather large (ca. 1600 Å2) interaction interface with tight steric and polar/nonpolar complementarity. The structure of ZSPA-1 in the complex is well-ordered in a conformation that is very similar to that of the Z domain. However, the conformation of the free ZSPA-1 is best characterized by comparisons with protein molten globules. It shows a reduced secondary structure content, aggregation propensity, poor thermal stability, and binds the hydrophobic dye ANS. This molten globule state of ZSPA-1 is the native state in the absence of the Z domain, and the ordered state is only adopted following a stabilization that occurs upon binding. A more extensive characterization of ZSPA-1 suggested that the average topology of the Z domain is retained in the molten globule state but that it is represented by a multitude of conformations. Furthermore, the molten globule state is only marginally stable, and a significant fraction of ZSPA-1 exists in a completely unfolded state at room temperature. A complete thermodynamic characterization of the Z:ZSPA-1 pair suggests that the stabilization of the molten globule state to an ordered three helix structure in the complex is associated with a significant conformational entropy penalty that might influence the binding affinity negatively and result in an intermediate-affinity (µM) binding protein. This can be compared to a dissociation constant of 20-70 nM for the complex Z:Fc of IgG where Z uses the same binding surface as in Z:ZSPA-1. Structure analyses of Z in the free and bound state reveal an induced fit response upon complex formation with ZSPA-1 where a conformational change of several side chains in the binding surface increases the accessible surface area with almost 400 Å2 i.e. almost half of the total interaction surface in the complex. Two cysteine residues were introduced at specific positions in ZSPA-1 for five mutants in order to stabilize the conformation of ZSPA-1 by disulfide bridge formation. The mutants were thermodynamically characterized and the binding affinity of one mutant showed an improvement by more than a factor of ten. The improvement of the introduced cysteine bridge correlates with an increase in binding enthalpy rather than with entropy. Further analysis of the binding entropy suggests that the conformational entropy change in fact is reduced but its favorable contribution is opposed by a less favorable desolvation enthalpy change. These studies illustrate the structural and thermodynamic complexity of protein-protein interactions, but also that this complexity can be dissected and understood. In this study, a comprehensive characterization of the ZSPA-1 affibody has gained insight into the intricate mechanisms involved in complex formation. These theories were supported by the design of a ZSPA-1 mutant with improved binding affinity.QC 2010092

Molecular dataset for phylogenetic analysis of the butterfly subfamily Satyrinae (Nymphalidae)

<p>Molecular dataset for species in the butterfly subfamily Satyrinae. There are three gene blocks: Cytochrome oxidase I (COI), elongation factor 1 (EF1a) and wingless.</p> <p>This dataset was used in the study:</p> <p> </p> <p>Peña, C., N. Wahlberg, E. Weingartner, U. Kodandaramaiah, S. Nylin, A.V.L. Freitas & A.V.Z. Brower. 2006. Higher level phylogeny of Satyrinae butterflies (Lepidoptera: Nymphalidae) based on DNA sequence data. Molecular Phylogenetics and Evolution 40(1): 29-49. doi:10.1016/j.ympev.2006.02.007</p

Identification of proteins that specifically recognize and bind protofibrillar aggregates of amyloid-β

Protofibrils of the 42 amino acids long amyloid-beta peptide are transient pre-fibrillar intermediates in the process of peptide aggregation into amyloid plaques and are thought to play a critical role in the pathology of Alzheimer's disease. Hence, there is a need for research reagents and potential diagnostic reagents for detection and imaging of such aggregates. Here we describe an in vitro selection of Affibody molecules that bind to protofibrils of A beta(42)cc, which is a stable engineered mimic of wild type A beta(42) protofibrils. Several binders were identified that bind A beta(42)cc protofibrils with low nanomolar affinities, and which also recognize wild type A beta(42) protofibrils. Dimeric head-to-tail fusion proteins with subnanomolar binding affinities, and very slow dissociation off-rates, were also constructed. A mapping of the chemical properties of the side chains onto the Affibody scaffold surface reveals three distinct adjacent surface areas of positively charged surface, nonpolar surface and a polar surface, which presumably match a corresponding surface epitope on the protofibrils. The results demonstrate that the engineered A beta(42)cc is a suitable antigen for directed evolution of affinity reagents with specificity for wild type A beta(42) protofibrils

Pituitary Metastases : A Nationwide Study on Current Characteristics with Special Reference to Breast Cancer

Objective To investigate the contemporary presentation of pituitary metastases. Patients Thirty-eight patients diagnosed with pituitary metastases from 1996 to 2018 in Sweden. Methods Pituitary metastases were confirmed by histopathology (n = 27) or considered highly likely according to radiological findings, including rapid tumor progression (n = 11). Medical records were reviewed and sellar images reexamined centrally. Results Breast and lung cancers were the most common primary tumors, in 45% and 21% of patients, respectively. Sixty-seven percent of breast cancers overexpressed human epidermal growth factor receptor 2 (HER2); 53% of pituitary metastases from breast cancers appeared ≥10 years after diagnosis of the primary tumor. At presentation, 71% appeared to have ACTH deficiency, 65% had TSH deficiency, and 26% had diabetes insipidus. Fatigue, nausea/vomiting, loss of appetite, weight loss, myalgia, and/or arthralgia were reported in 47% of patients with morning cortisol <100 nmol/L vs 23% with cortisol ≥200 nmol/L. Sixteen patients had visual field defects, and eight had diplopia. Intrasellar and suprasellar tumor growth was the most frequent finding. Initially, a pituitary adenoma was considered the etiology in 18% of patients. Radiotherapy, pituitary surgery, and chemotherapy were used in 68%, 68%, and 11% of patients, respectively. One and 2 years after diagnosis of pituitary metastases, 50% and 26% of patients were alive. Conclusion Pituitary metastases may be mistaken for pituitary adenomas and can appear late, especially in breast cancer. Breast cancers overexpressing HER2 seem prone to metastasize to the pituitary. Hypocortisolism may be misdiagnosed as cancer-related malaise. An increased awareness of pituitary metastases and undiagnosed pituitary failure can improve management in these patients

Bergslagen : Arbetsplatser och bostäder under hundra år

Denna skrift utgör resultatet av Arkitekturskolans studier läsåret 1978-79. Att redigera manuskripten visade sig arbets­krävande och har också dragit ut på tiden. Att vissa av de uppgifter som lämnas inte är helt aktuella spelar ändå inte så stor roll - tyngdpunkten i framställningen ligger på det his­toriska materialet och de långa tidsperspektiven. Arbetet inleds med en demografisk översikt över ett brett bäl­te tvärs över Mellansverige från Värmland till Upplandskusten. Där antyds utvecklingens huvudriktning både i Bergslagens gam­la kärnområden och i yttre zoner av delvis annan karaktär. Därefter följer åtta från varandra fristående kapitel som dock alla har ett gemensamt mål, att granska och analysera bebyg­gelseu.tvecklingen inom ett tydligt avgränsat område. Konkre­tion och åskådlighet har eftersträvats - därför har också stor möda nedlagts på bildmaterialet i form av kartor, ritningar och foton. Valet av undersökningsobjekt har gjorts av förfat­tarna själva, som också utformat sina avsnitt självständigt.Denna bok är en rapport från Konsthögskolans arkitekturskola. Boken består av åtta från varandra fristående studier, författade av elever vid arkitekturskolan och grundade på omfattande fältarbeten. Ett äldre skede i Bergslagens arbetsliv före­träds av en undersökning om två bergsmansbyar, Stimmerbo och Älvhyttan, och hur de utvecklats in i nutiden. Storindustrins byggnads verksamhet under ett sekel exemplifieras med nuvarande SKF Steels anläggningar i Hofors. En tyngdpunkt i skriften utgörs av redogörelser för fyra större samhällens växt sedan slutet av 1800-talet: Fagersta, Grängesberg, Hofors och Smedjebacken. I två avslutande kapitel behandlas ett par mindre orter, båda starkt präglade av industrinedläggning­ar, Fredriksberg och Ställberg.</p

Cometin is a novel neurotrophic factor that promotes neurite outgrowth and neuroblast migration in vitro and supports survival of spiral ganglion neurons in vivo

AbstractNeurotrophic factors are secreted proteins responsible for migration, growth and survival of neurons during development, and for maintenance and plasticity of adult neurons. Here we present a novel secreted protein named Cometin which together with Meteorin defines a new evolutionary conserved protein family. During early mouse development, Cometin is found exclusively in the floor plate and from E13.5 also in dorsal root ganglions and inner ear but apparently not in the adult nervous system. In vitro, Cometin promotes neurite outgrowth from dorsal root ganglion cells which can be blocked by inhibition of the Janus or MEK kinases. In this assay, additive effects of Cometin and Meteorin are observed indicating separate receptors. Furthermore, Cometin supports migration of neuroblasts from subventricular zone explants to the same extend as stromal cell derived factor 1a. Given the neurotrophic properties in vitro, combined with the restricted inner ear expression during development, we further investigated Cometin in relation to deafness. In neomycin deafened guinea pigs, two weeks intracochlear infusion of recombinant Cometin supports spiral ganglion neuron survival and function. In contrast to the control group receiving artificial perilymph, Cometin treated animals retain normal electrically-evoked brainstem response which is maintained several weeks after treatment cessation. Neuroprotection is also evident from stereological analysis of the spiral ganglion. Altogether, these studies show that Cometin is a potent new neurotrophic factor with therapeutic potential