Real-space imaging of confined magnetic skyrmion tubes.

Magnetic skyrmions are topologically nontrivial particles with a potential application as information elements in future spintronic device architectures. While they are commonly portrayed as two dimensional objects, in reality magnetic skyrmions are thought to exist as elongated, tube-like objects extending through the thickness of the host material. The study of this skyrmion tube state (SkT) is vital for furthering the understanding of skyrmion formation and dynamics for future applications. However, direct experimental imaging of skyrmion tubes has yet to be reported. Here, we demonstrate the real-space observation of skyrmion tubes in a lamella of FeGe using resonant magnetic x-ray imaging and comparative micromagnetic simulations, confirming their extended structure. The formation of these structures at the edge of the sample highlights the importance of confinement and edge effects in the stabilisation of the SkT state, opening the door to further investigation into this unexplored dimension of the skyrmion spin texture.

The impact of combinatorial stress on the growth dynamics and metabolome of Burkholderia mesoacidophila demonstrates the complexity of tolerance mechanisms.

AIMS: The recently sequenced Burkholderia mesoacidophila (previously Pseudomonas mesoacidophila) is a soil organism and as such will be exposed to multiple concurrent stresses in the natural environment. The combinatorial stress potentially experienced by microbes in soil has not been investigated in detail. METHODS AND RESULTS: The impact of combinatorial stress on growth was investigated using tripartite variables-temperature, nutritional environment and either osmotic or oxidative stress. In nutritionally stringent conditions, increasing diamide concentration had no effect on growth while increasing H2 O2 concentration reduced both growth rate and maximum density. Metabolomic studies with oxidative stress revealed specific (unidentified) metabolites associated with diamide tolerance, and an overwhelming dominance of sugars and sugar alcohols in nutritionally stringent conditions with and without the additional stressor. CONCLUSIONS: Combinatorial stress tolerance is complex. Temperature had the greatest independent impact on growth, while the impact of the nutritional environment played a key role in oxidative stress tolerance. In nutritionally stringent conditions, the metabolome suggested different tolerance mechanisms for different types of oxidative stress. SIGNIFICANCE AND IMPACT OF THE STUDY: This work demonstrates the specificity of the stress response, and the need to consider multiple environmental factors to meaningfully investigate tolerance. Both environmental and clinical settings subject bacteria to combinatorial stress and this should be considered in the design of further studies.

The fungus that came in from the cold: dry rot's pre-adapted ability to invade buildings.

Many organisms benefit from being pre-adapted to niches shaped by human activity, and have successfully invaded man-made habitats. One such species is the dry rot fungus Serpula lacrymans, which has a wide distribution in buildings in temperate and boreal regions, where it decomposes coniferous construction wood. Comparative genomic analyses and growth experiments using this species and its wild relatives revealed that S. lacrymans evolved a very effective brown rot decay compared to its wild relatives, enabling an extremely rapid decay in buildings under suitable conditions. Adaptations in intracellular transport machineries promoting hyphal growth, and nutrient and water transport may explain why it is has become a successful invader of timber in houses. Further, we demonstrate that S. lacrymans has poor combative ability in our experimental setup, compared to other brown rot fungi. In sheltered indoor conditions, the dry rot fungus may have limited encounters with other wood decay fungi compared to its wild relatives. Overall, our analyses indicate that the dry rot fungus is an ecological specialist with poor combative ability against other fungi.

Interdependence of Primary Metabolism and Xenobiotic Mitigation Characterizes the Proteome of Bjerkandera adusta during Wood Decomposition.

The aim of the current work was to identify key features of the fungal proteome involved in the active decay of beechwood blocks by the white rot fungus Bjerkandera adusta at 20°C and 24°C. A combination of protein and domain analyses ensured a high level of annotation, which revealed that while the variation in the proteins identified was high between replicates, there was a considerable degree of functional conservation between the two temperatures. Further analysis revealed differences in the pathways and processes employed by the fungus at the different temperatures, particularly in relation to nutrient acquisition and xenobiotic mitigation. Key features showing temperature-dependent variation in mechanisms for both lignocellulose decomposition and sugar utilization were found, alongside differences in the enzymes involved in mitigation against damage caused by toxic phenolic compounds and oxidative stress.IMPORTANCE This work was conducted using the wood decay fungus B. adusta, grown on solid wood blocks to closely mimic the natural environment, and gives greater insight into the proteome of an important environmental fungus during active decay. We show that a change in incubation temperature from 20°C to 24°C altered the protein profile. Proteomic studies in the field of white-rotting basidiomycetes have thus far been hampered by poor annotation of protein databases, with a large proportion of proteins simply with unknown function. This study was enhanced by extensive protein domain analysis, enabling a higher level of functional assignment and greater understanding of the proteome composition. This work revealed a strong interdependence of the primary process of nutrient acquisition and specialized metabolic processes for the detoxification of plant extractives and the phenolic breakdown products of lignocellulose.

KLF2 mutation is the most frequent somatic change in splenic marginal zone lymphoma and identifies a subset with distinct genotype.

To characterise the genetics of splenic marginal zone lymphoma (SMZL), we performed whole exome sequencing of 16 cases and identified novel recurrent inactivating mutations in Kruppel-like factor 2 (KLF2), a gene whose deficiency was previously shown to cause splenic marginal zone hyperplasia in mice. KLF2 mutation was found in 40 (42%) of 96 SMZLs, but rarely in other B-cell lymphomas. The majority of KLF2 mutations were frameshift indels or nonsense changes, with missense mutations clustered in the C-terminal zinc finger domains. Functional assays showed that these mutations inactivated the ability of KLF2 to suppress NF-κB activation by TLR, BCR, BAFFR and TNFR signalling. Further extensive investigations revealed common and distinct genetic changes between SMZL with and without KLF2 mutation. IGHV1-2 rearrangement and 7q deletion were primarily seen in SMZL with KLF2 mutation, while MYD88 and TP53 mutations were nearly exclusively found in those without KLF2 mutation. NOTCH2, TRAF3, TNFAIP3 and CARD11 mutations were observed in SMZL both with and without KLF2 mutation. Taken together, KLF2 mutation is the most common genetic change in SMZL and identifies a subset with a distinct genotype characterised by multi-genetic changes. These different genetic changes may deregulate various signalling pathways and generate cooperative oncogenic properties, thereby contributing to lymphomagenesis.

PRKACA mediates resistance to HER2-targeted therapy in breast cancer cells and restores anti-apoptotic signaling.

Targeting HER2 with antibodies or small molecule inhibitors in HER2-positive breast cancer leads to improved survival, but resistance is a common clinical problem. To uncover novel mechanisms of resistance to anti-HER2 therapy in breast cancer, we performed a kinase open reading frame screen to identify genes that rescue HER2-amplified breast cancer cells from HER2 inhibition or suppression. In addition to multiple members of the MAPK (mitogen-activated protein kinase) and PI3K (phosphoinositide 3-kinase) signaling pathways, we discovered that expression of the survival kinases PRKACA and PIM1 rescued cells from anti-HER2 therapy. Furthermore, we observed elevated PRKACA expression in trastuzumab-resistant breast cancer samples, indicating that this pathway is activated in breast cancers that are clinically resistant to trastuzumab-containing therapy. We found that neither PRKACA nor PIM1 restored MAPK or PI3K activation after lapatinib or trastuzumab treatment, but rather inactivated the pro-apoptotic protein BAD, the BCl-2-associated death promoter, thereby permitting survival signaling through BCL-XL. Pharmacological blockade of BCL-XL/BCL-2 partially abrogated the rescue effects conferred by PRKACA and PIM1, and sensitized cells to lapatinib treatment. These observations suggest that combined targeting of HER2 and the BCL-XL/BCL-2 anti-apoptotic pathway may increase responses to anti-HER2 therapy in breast cancer and decrease the emergence of resistant disease.

A hyperthermal energy ion beamline for probing hot electron chemistry at surfaces.

An ultrahigh vacuum ion beamline and chamber have been assembled to produce hyperthermal (<400 eV) energy ions for studying hot electron chemistry at surfaces. The specific design requirements for this modified instrument were chosen to enable the exposure of a metal-oxide-semiconductor (MOS) device to monoenergtic, well-collimated beams of alkali ions while monitoring both the scattered beam flux and the device characteristics. Our goal is to explore the role that hot electrons injected toward the MOS device surface play in the neutralization of scattered ions. To illustrate the functionality of our system, we present energy-resolved spectra for Na+, K+, and Cs+ ions scattered from the surface of a Ag(001) single crystal for a range of incident energies. In addition, we show MOS device current-voltage characteristics measured in situ in a new rapid-turnaround load lock and sample translation stage.

Changes in mitotic rate and GFAP expression in the primary olfactory axis of streptozotocin-induced diabetic rats.

Many diabetic individuals develop anosmia but the mechanism(s) causing the dysfunction in the olfactory system is (are) unknown. Glial fibrillary acidic protein expression is reduced in diabetic retinopathy and is also reduced, with unknown consequences, in other brain regions of diabetic rats. We used immunohistochemistry and immunoblotting from untreated control and streptozotocin-induced type 1 (insulin dependent) diabetic rats to investigate main olfactory epithelial mitotic rate and glial fibrillary acidic protein expression in the lamina propria of the sensory epithelium and in the olfactory bulb. Numbers of bromodeoxyuridine-positive cells were significantly lower in the diabetic sensory epithelium compared to non-diabetic controls. Immunohistochemical observations suggested a qualitative difference in glial fibrillary acidic protein expression in both regions examined especially in the olfactory bulb external plexiform layer and the lamina propria. Immunoblot analysis confirmed that the diabetic olfactory bulb and lamina propria expressed less glial fibrillary acidic protein compared to the non-diabetic control group. The lower expression levels in the olfactory bulb external plexiform layer suggested by immunohistochemistry do not reflect a change in the number of astrocytes since the numbers of S100B(+) cells were not different between the two groups.

Learning preferences and learning styles: a study of Wessex general practice registrars.

BACKGROUND: Experienced trainers know that individual registrars react very differently to identical learning experiences generated during the year in practice. This divergence reflects differences in registrars' learning styles. Only one study of United Kingdom (UK) general practitioners' learning styles has been undertaken. Learning style theory predicts that matching learning preference with learning style will enhance learning. This paper researches for the first time the evidence in the setting of UK general practice. AIM: To determine, for the general practice registrars within the Wessex Region, the nature of their learning preferences and learning styles and correlations between them. DESIGN OF STUDY: A descriptive confidential postal questionnaire survey. SETTING: Fifty-seven registrars identified in the Wessex Region with a minimum experience of six months in general practice. METHOD: The questionnaire gathered demographic data (sex, age, experience in general practice, years post-registration, and postgraduate qualifications). Learning preferences were elicited using a six-point Likert scale for learning experiences. The Honey and Mumford Learning Style Questionnaire (LSQ) elicited the registrars' learning styles. A second questionnaire was sent to non-responders. RESULTS: The response rate was 74%. Registrars report that interactive learning with feedback is preferred, but more passive learning formats remain valued. A wide range of learning style scores was found. The Honey and Mumford LSQ mean scores fell within the reflector-theorist quadrant. Evidence for correlations between learning preferences and learning styles was also found, in particular for the multiple choice question and audit components of summative assessment. CONCLUSION: A wide range of registrar learning styles exists in Wessex, and initial correlations are described between learning preferences and learning styles as predicted by style theory. This work sets the stage for a shared understanding and use of learning style theory to enhance professional learning throughout a GP's career. More research is needed in this domain.

foxD5a, a Xenopus winged helix gene, maintains an immature neural ectoderm via transcriptional repression that is dependent on the C-terminal domain.

Xenopus foxD5a, the full-length fork head gene previously described as a PCR fragment (XFLIP), is first detectable at stage II of oogenesis. Low-abundance maternal transcripts are localized to the animal hemisphere of the cleavage embryo, and protein can be translocated to the nucleus prior to the onset of zygotic transcription. Zygotic expression is strongest in the presumptive neural ectoderm at gastrula and neural plate stages, but there is minor paraxial mesodermal expression during primary gastrulation that becomes significant in the tail bud during secondary gastrulation. Expression of foxD5a in animal cap explants induces elongation and expression of mesodermal, neural-inducing, and early neural-specifying genes, indicating a role in dorsal axis formation. Zygotic foxD5a expression is induced strongly by siamois, moderately by cerberus, weakly by Wnt8 and noggin, and not by chordin in animal cap explants. Expression of foxD5a in whole embryos has differential dorsal and ventral effects. Ventral mRNA injection induces partial secondary axes composed of expanded mesodermal and epidermal tissues, but does not induce ectopic neural tissues. Dorsal mRNA injection causes hypertrophy of the neural plate and expansion of early neural genes (sox3 and otx2), but this is not the result of increased proliferation or expanded neural-inducing mesoderm. The neural plate appears to be maintained in an immature state because otx2 expression is expanded and expression of en2, Krox20, proneural genes (Xnrgn1, neuroD) and a neural differentiation gene (n-tubulin) is repressed in foxD5a-expressing cells. These results indicate that foxD5a maintains an undifferentiated neural ectoderm after neural induction. Expression of foxD5a constructs fused with the engrailed repressor domain or with the VP16 activation domain demonstrates that FoxD5a acts as a transcriptional repressor in axis formation and neural plate expansion. Deletion constructs indicate that this activity requires the C-terminal domain of the protein.

Prefrontal cortex neurons reflecting reports of a visual illusion.

When a small, focally attended visual stimulus and a larger background frame shift location at the same time, the frame's new location can affect spatial perception. For horizontal displacements on the order of 1--2 degrees, when the frame moves more than the attended stimulus, human subjects may perceive that the attended stimulus has shifted to the right or left when it has not done so. However, that misapprehension does not disable accurate eye movements to the same stimulus. We trained a rhesus monkey to report the direction that an attended stimulus had shifted by making an eye movement to one of the two report targets. Then, using conditions that induce displacement illusions in human subjects, we tested the hypothesis that neuronal activity in the prefrontal cortex (PF) would reflect the displacement directions reported by the monkey, even when they conflicted with the actual displacement, if any, of the attended stimulus. We also predicted that these cells would have directional selectivity for movements used to make those reports, but not for similar eye movements made to fixate the attended stimulus. A population of PF neurons showed the predicted properties, which could not be accounted for on the basis of either eye-movement or frame-shift parameters. This activity, termed report-related, began approximately 150 ms before the onset of the reporting saccade. Another population of PF neurons showed greater directional selectivity for saccadic eye movements made to fixate the attended stimulus than for similar saccades made to report its displacement. In view of the evidence that PF functions to integrate inputs and actions occurring at different times and places, the present findings support the idea that such integration involves movements to acquire response targets, directly, as well as actions guided by less direct response rules, such as perceptual reports.

c-MYC induces mammary tumorigenesis by means of a preferred pathway involving spontaneous Kras2 mutations.

Although the process of mammary tumorigenesis requires multiple genetic events, it is unclear to what extent carcinogenesis proceeds through preferred secondary pathways following a specific initiating oncogenic event. Similarly, the extent to which established mammary tumors remain dependent on individual mutations for maintenance of the transformed state is unknown. Here we use the tetracycline regulatory system to conditionally express the human c-MYC oncogene in the mammary epithelium of transgenic mice. MYC encodes a transcription factor implicated in multiple human cancers. In particular, amplification and overexpression of c-MYC in human breast cancers is associated with poor prognosis, although the genetic mechanisms by which c-MYC promotes tumor progression are poorly understood. We show that deregulated c-MYC expression in this inducible system results in the formation of invasive mammary adenocarcinomas, many of which fully regress following c-MYC deinduction. Approximately half of these tumors harbor spontaneous activating point mutations in the ras family of proto-oncogenes with a strong preference for Kras2 compared with Hras1. Nearly all tumors lacking activating ras mutations fully regressed following c-MYC deinduction, whereas tumors bearing ras mutations did not, suggesting that secondary mutations in ras contribute to tumor progression. These findings demonstrate that c-MYC-induced mammary tumorigenesis proceeds through a preferred secondary oncogenic pathway involving Kras2.

Transcription factors of the anterior neural plate alter cell movements of epidermal progenitors to specify a retinal fate.

The embryonic progenitors that give rise to the vertebrate retina acquire their cell fate identity through a series of transitions that ultimately determine their final, differentiated retinal cell fates. In Xenopus, these transitions have been broadly defined as competence, specification, and determination. The expression of several transcription factors within the anterior neural plate at the time when the presumptive eye field separates from other neural derivatives suggests that these genes function to specify competent embryonic progenitors toward a retinal fate. In support of this, we demonstrate that some transcription factors expressed in the anterior neural ectoderm and/or presumptive eye field (otx2, pax6, and rx1) change the fate of competent, ventral progenitors, which normally do not contribute to the retina, from an epidermal to a retinal fate. Furthermore, the expression of these factors changes the morphogenetic movements of progenitors during gastrulation, causing ventral cells to populate the native anterior neural plate. In addition, we experimentally demonstrate that the efficacy of pax6 to specify retinal cells depends on the position of the affected cell relative to the field of neural induction. Thereby, otx2, pax6, and rx1 mediate early steps of retinal specification, including the regulation of morphogenetic cell movements, that are dependent on the level of neural-inductive signaling.

Xenopus Six1 gene is expressed in neurogenic cranial placodes and maintained in the differentiating lateral lines.

Six genes are homeobox-containing transcription factors, many of which are expressed in head structures. We isolated a full-length cDNA of a previously unknown Xenopus member of this family. It shares a high sequence homology with mouse and human Six1, which during development are expressed in mesoderm and muscle. In contrast, XSix1 is prominently expressed in all neurogenic cephalic placodes and lateral line primordia from neurula to tadpole stages. The neurons derived from these placodes do not express XSix1, but the lateral line mechanoreceptors maintain expression. XSix1 is weakly expressed in muscle later in development.

A model that accounts for activity prior to sensory inputs and responses during matching-to-sample tasks.

Neural network models were examined during delayed matching-to-sample tasks (DMS), and neurons in a monkey's prefrontal cortex were studied during the performance of comparable tasks. In DMS, various input stimuli follow a sample stimulus, and an output should occur whenever the sample reappears. Our previous models have been restricted to certain kinds of inputs, outputs, and temporal patterns. Here, we generalized the models by training them on both spatial and nonspatial inputs, spatial and nonspatial outputs, and both fixed and variable interstimulus intervals. Two versions of DMS were presented to both the model and the monkey, both involving nonspatial samples: (1) Two stimuli simultaneously appeared at a variable interval after the sample; and (2) A series of single stimuli appeared at fixed intervals after the sample. Both versions required identical spatial responses, reflecting the direction (left or right) of the matching stimulus relative to a central origin. Thus, these two versions of DMS involved the same samples, memory, and responses, but established different response contexts. Our analysis focused on unit activity prior to stimuli, as well as that prior to responses, termed anticipatory and response-related activity, respectively. In both the model and the monkey, anticipatory activity occurred only for fixed interstimulus intervals. In the model, we could determine that anticipatory activity acted either like a filter to suppress inappropriate responses or it served to enhance the network's general readiness to respond. As for response-related activity, units in both the model and the monkey showed directional selectivity and had a strong dependence on response context. In the model, we could show that this activity contributed both to the suppression of inappropriate responses and to the generation of correct ones. None of the model's hidden units contributed exclusively to computing the direction of match output. Instead, their response-related activity contributed to the computation of both the match decision and the correct response direction.

Squamous cell carcinoma of the external auditory canal: an evaluation of a staging system.

OBJECTIVE: The study was conducted to review a staging system proposed by the University of Pittsburgh for temporal bone cancer and to evaluate survival status according to stage, treatment, and certain prognostic factors. STUDY DESIGN: The study was a retrospective case review. SETTING: The study was conducted at a tertiary care medical center and specialty hospital. PATIENTS: Thirty-two patients with primary squamous cell carcinoma of the external auditory canal were studied. INTERVENTION: All patients underwent surgery of the temporal bone. Radiotherapy was given depending on tumor stage and histopathologic findings. MAIN OUTCOME MEASURES: The 2-year survival rates of patients undergoing surgical resection with or without adjuvant radiotherapy. RESULTS: The 2-year survival rates for primary squamous cell carcinoma of the temporal bone were as follows: T1 lesions 100%, T2 80%, T3 50%, and T4 7%. Survival for T3 tumors was 75% with postoperative radiotherapy, compared with 0% with surgery alone. CONCLUSIONS: The 2-year survival data directly correlated with the staging system. The use of adjuvant radiotherapy increased survival rate in patients with a T3 lesion.

Intrinsic bias and lineage restriction in the phenotype determination of dopamine and neuropeptide Y amacrine cells.

Blastomere lineages are differentially biased to produce different neurotransmitter subtypes of amacrine cells (Huang and Moody, 1995, 1997,). To elucidate when this bias is acquired, we examined amacrine lineages at different early developmental times. Our experiments demonstrate that the bias to express dopamine and neuropeptide Y amacrine fates involves several steps before the formation of the definitive optic cup. At cleavage stages, a retinal progenitor that contributes large numbers of cells is already biased to produce its normal repertoire of dopamine amacrine cells, as revealed by transplantation to a new location, whereas the amacrine fate of a progenitor that contributes fewer cells is modified by its new position. At neural plate stages, not all retinal progenitors are multipotent. Nearly one-half populate only the inner nuclear layer and are enriched in amacrine cells. During early optic vesicle stages, an appropriate mitotic tree is required for dopamine and neuropeptide Y, but not serotonin, amacrine cell clusters to form. Thus, the acquisition of amacrine fate bias involves intrinsic maternal factors at cleavage, fate restriction in the neural plate, and specified mitotic patterns in the optic vesicle. At each of these steps only a subset of the embryonic retinal progenitors contributing to amacrine subtypes is biased; the remaining progenitors maintain multipotency. Thus, from the earliest embryonic stages, progenitors of the retina are a dynamic mosaic. This is the first experimental demonstration of amacrine fate decisions that occur during early embryonic periods in advance of the events described in the later, committed retina.