Transport signatures of symmetry protection in 1D Floquet topological insulators

Time-periodic external drives have emerged as a powerful tool to artificially create topological phases of matter. Prime examples are Floquet topological insulators (FTIs), where a gapped bulk supports in-gap edge states, protected against symmetry-preserving local perturbations. Similar to an ordinary static topological insulator, the robustness of an edge state in a one-dimensional (1D) FTI shows up as a pinning of its quasienergy level, but now inside one of two distinct bulk gaps. Here we propose a scheme for probing this unique feature by observing transport characteristics of a 1D finite-sized FTI attached to external leads. We present predictions for transmission spectra using a nonequilibrium Green's function approach. Our analysis covers FTIs with time-independent and periodically driven boundary perturbations which either preserve or break the protecting chiral symmetry.

Measurement Quench in Many-Body Systems

Measurement is one of the key concepts which discriminates classical and quantum physics. Unlike classical systems, a measurement on a quantum system typically alters it drastically as a result of wave function collapse. Here we suggest that this feature can be exploited for inducing quench dynamics in a many-body system while leaving its Hamiltonian unchanged. Importantly, by doing away with dedicated macroscopic devices for inducing a quench-using instead the indispensable measurement apparatus only-the protocol is expected to be easier to implement and more resilient against decoherence. By way of various case studies, we show that our scheme also has decisive advantages beyond reducing decoherence-for spectroscopy purposes and probing nonequilibrium scaling of critical and quantum impurity many-body systems.

Loschmidt Echo Revivals: Critical and Noncritical

A quantum phase transition is generally thought to imprint distinctive characteristics on the nonequilibrium dynamics of a closed quantum system. Specifically, the Loschmidt echo after a sudden quench to a quantum critical point-measuring the time dependence of the overlap between initial and time-evolved states-is expected to exhibit an accelerated relaxation followed by periodic revivals. We here introduce a new exactly solvable model, the extended Su-Schrieffer-Heeger model, the Loschmidt echo of which provides a counterexample. A parallell analysis of the quench dynamics of the three-site spin-interacting XY model allows us to pinpoint the conditions under which a periodic Loschmidt revival actually appears.

A systematic search strategy identifies cubilin as independent prognostic marker for renal cell carcinoma

BACKGROUND

There is an unmet clinical need for better prognostic and diagnostic tools for renal cell carcinoma (RCC).

METHODS

Human Protein Atlas data resources, including the transcriptomes and proteomes of normal and malignant human tissues, were searched for RCC-specific proteins and cubilin (CUBN) identified as a candidate. Patient tissue representing various cancer types was constructed into a tissue microarray (n = 940) and immunohistochemistry used to investigate the specificity of CUBN expression in RCC as compared to other cancers. Two independent RCC cohorts (n = 181; n = 114) were analyzed to further establish the sensitivity of CUBN as RCC-specific marker and to explore if the fraction of RCCs lacking CUBN expression could predict differences in patient survival.

RESULTS

CUBN was identified as highly RCC-specific protein with 58% of all primary RCCs staining positive for CUBN using immunohistochemistry. In venous tumor thrombi and metastatic lesions, the frequency of CUBN expression was increasingly lost. Clear cell RCC (ccRCC) patients with CUBN positive tumors had a significantly better prognosis compared to patients with CUBN negative tumors, independent of T-stage, Fuhrman grade and nodal status (HR 0.382, CI 0.203-0.719, P = 0.003).

CONCLUSIONS

CUBN expression is highly specific to RCC and loss of the protein is significantly and independently associated with poor prognosis. CUBN expression in ccRCC provides a promising positive prognostic indicator for patients with ccRCC. The high specificity of CUBN expression in RCC also suggests a role as a new diagnostic marker in clinical cancer differential diagnostics to confirm or rule out RCC.

Loss of ASRGL1 expression is an independent biomarker for disease-specific survival in endometrioid endometrial carcinoma

OBJECTIVE

For endometrial carcinoma, prognostic stratification methods do not satisfactorily identify patients with adverse outcome. Currently, histology, tumor grade and stage are used to tailoring surgical treatment and to determine the need for adjuvant treatment. Low-risk patients are not considered to require adjuvant therapy or staging lymphadenectomy. For patients with intermediate or high risk, some guidelines recommend tailoring adjuvant treatment according to additional negative prognostic factors. Our objective was to evaluate the biomarker potential of the ASRGL1 protein in endometrial carcinoma.

METHODS

Using The Human Protein Atlas (www.proteinatlas.org), the l-asparaginase (ASRGL1) protein was identified as an endometrial carcinoma biomarker candidate. ASRGL1 expression was immunohistochemically evaluated with an extensively validated antibody on two independent endometrial carcinoma cohorts (n=229 and n=286) arranged as tissue microarrays. Staining results were correlated with clinical features.

RESULTS

Reduced expression of ASRGL1, defined as <75% positively stained tumor cells, was significantly associated with poor prognosis and reduced disease-specific survival in endometrioid endometrial adenocarcinoma (EEA). In multivariate analysis the hazard ratios for disease-specific survival were 3.55 (95% CI=1.10-11.43; p=0.003) and 3.23 (95% CI=1.53-6.81; p=0.002) in the two cohorts, respectively. Of the 48 cases with Grade 3 Stage I tumor all disease-related deaths were associated with low ASRGL1 expression.

CONCLUSIONS

Loss of ASRGL1 in EEA is a powerful biomarker for poor prognosis and retained ASRGL1 has a positive impact on survival. ASRGL1 immunohistochemistry has potential to become an additional tool for prognostication in cases where tailoring adjuvant treatment according to additional prognostic factors besides grade and stage is recommended.

Dynamics of transcriptome evolution in the model eukaryote Neurospora

Mounting evidence indicates that changes in the transcriptome contribute significantly to the phenotypic differentiation of closely related species. Nonetheless, further genome-wide studies, spanning a broad range of organisms, are needed to decipher the factors driving transcriptome evolution. The model Neurospora (Ascomycota) comprises a simple system for empirically studying the evolutionary dynamics of the transcriptome. Here, we studied the evolution of gene expression in Neurospora crassa and Neurospora tetrasperma and show that patterns of transcriptome evolution are connected to genome evolution, tissue type and sexual identity (mating types, mat A and mat a) in these eukaryotes. Based on the comparisons of inter- and intraspecies expression divergence, our data reveal that rapid expression divergence is more apt to occur in sexual/female (SF) than vegetative/male (VM) tissues. In addition, interspecies gene expression and protein sequence divergence were strongly correlated for SF, but not VM, tissue. A correlation between transcriptome and protein evolution parallels findings from certain animals, but not yeast, and add support for the theory that expression evolution differs fundamentally among multicellular and unicellular eukaryotes. Finally, we found that sexual identity in these hermaphroditic Neurospora species is connected to interspecies expression divergence in a tissue-dependent manner: rapid divergence occurred for mat A- and mat a-biased genes from SF and VM tissues, respectively. Based on these findings, it is hypothesized that rapid interspecies transcriptome evolution is shifting the mating types of Neurospora towards distinct female and male phenotypes, that is, sexual dimorphism.

An order parameter for impurity systems at quantum criticality

A quantum phase transition may occur in the ground state of a system at zero temperature when a controlling field or interaction is varied. The resulting quantum fluctuations which trigger the transition produce scaling behaviour of various observables, governed by universal critical exponents. A particularly interesting class of such transitions appear in systems with quantum impurities where a non-extensive term in the free energy becomes singular at the critical point. Curiously, the notion of a conventional order parameter that exhibits scaling at the critical point is generically missing in these systems. Here we explore the possibility to use the Schmidt gap, which is an observable obtained from the entanglement spectrum, as an order parameter. A case study of the two-impurity Kondo model confirms that the Schmidt gap faithfully captures the scaling behaviour by correctly predicting the critical exponent of the dynamically generated length scale at the critical point.

So far, the notion of the order parameter for impurity quantum phase transitions has been missing. Using a two-impurity Kondo model, Bayat et al. show that the Schmidt gap obtained from the entanglement spectrum may serve as a nonlocal order parameter for a quantum impurity system at criticality.

Membranous expression of podocalyxin-like protein is an independent factor of poor prognosis in urothelial bladder cancer

BACKGROUND

Membranous expression of the anti-adhesive glycoprotein podocalyxin-like (PODXL) has previously been found to correlate with poor prognosis in several major cancer forms. Here we examined the prognostic impact of PODXL expression in urothelial bladder cancer.

METHODS

Immunohistochemical PODXL expression was examined in tissue microarrays with tumours from two independent cohorts of patients with urothelial bladder cancer: n=100 (Cohort I) and n=343 (Cohort II). The impact of PODXL expression on disease-specific survival (DSS; Cohort II), 5-year overall survival (OS; both cohorts) and 2-year progression-free survival (PFS; Cohort II) was assessed.

RESULTS

Membranous PODXL expression was significantly associated with more advanced tumour (T) stage and high-grade tumours in both cohorts, and a significantly reduced 5-year OS (unadjusted HR=2.25 in Cohort I and 3.10 in Cohort II, adjusted HR=2.05 in Cohort I and 2.18 in Cohort II) and DSS (unadjusted HR=4.36, adjusted HR=2.70). In patients with Ta and T1 tumours, membranous PODXL expression was an independent predictor of a reduced 2-year PFS (unadjusted HR=6.19, adjusted HR=4.60) and DSS (unadjusted HR=8.34, adjusted HR=7.16).

CONCLUSION

Membranous PODXL expression is an independent risk factor for progressive disease and death in patients with urothelial bladder cancer.

Entanglement probe of two-impurity Kondo physics in a spin chain

We propose that real-space properties of the two-impurity Kondo model can be obtained from an effective spin model where two single-impurity Kondo spin chains are joined via an Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction between the two impurity spins. We then use a density matrix renormalization group approach, valid in all ranges of parameters, to study its features using two complementary quantum-entanglement measures, the negativity and the von Neumann entropy. This nonperturbative approach enables us to uncover the precise dependence of the spatial extent ξ(K) of the Kondo screening cloud with the Kondo and RKKY couplings. Our results reveal an exponential suppression of the Kondo temperature T(K)~1/ξ(K) with the size of the effective impurity spin in the limit of large ferromagnetic RKKY coupling, a striking display of "Kondo resonance narrowing" in the two-impurity Kondo model. We also show how the antiferromagnetic RKKY interaction produces an effective decoupling of the impurities from the bulk already for intermediate strengths of this interaction, and, furthermore, exhibit how the non-Fermi liquid quantum critical point is signaled in the quantum entanglement between various parts of the system.

High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer

PURPOSE

In this study, we investigated the prognostic impact of human RBM3 expression in colorectal cancer using tissue microarray-based immunohistochemical analysis.

EXPERIMENTAL DESIGN

One polyclonal antibody and four monoclonal anti-RBM3 antibodies were generated and epitope mapped using two different methods. Bacterial display revealed five distinct epitopes for the polyclonal antibody, while the four mouse monoclonal antibodies were found to bind to three of the five epitopes. A peptide suspension bead array assay confirmed the five epitopes of the polyclonal antibody, while only one of the monoclonal antibodies could be mapped using this approach. Antibody specificity was confirmed by Western blotting and immunohistochemistry, including siRNA-mediated knock-down. Two of the antibodies (polyclonal and monoclonal) were subsequently used to analyze RBM3 expression in tumor samples from two independent colorectal cancer cohorts, one consecutive cohort (n=270) and one prospectively collected cohort of patients with cancer of the sigmoid colon (n=305). RBM3-expression was detected, with high correlation between both antibodies (R=0.81, p<0.001).

RESULTS

In both cohorts, tumors with high nuclear RBM3 staining had significantly prolonged the overall survival. This was also confirmed in multivariate analysis, adjusted for established prognostic factors.

CONCLUSION AND CLINICAL RELEVANCE

These data demonstrate that high tumor-specific nuclear expression of RBM3 is an independent predictor of good prognosis in colorectal cancer.

Arabidopsis thaliana TERMINAL FLOWER2 is involved in light-controlled signalling during seedling photomorphogenesis

Plants respond to changes in the environment by altering their growth pattern. Light is one of the most important environmental cues and affects plants throughout the life cycle. It is perceived by photoreceptors such as phytochromes that absorb light of red and far-red wavelengths and control, for example, seedling de-etiolation, chlorophyll biosynthesis and shade avoidance response. We report that the terminal flower2 (tfl2) mutant, carrying a mutation in the Arabidopsis thaliana HETEROCHROMATIN PROTEIN1 homolog, functions in negative regulation of phytochrome dependent light signalling. tfl2 shows defects in both hypocotyl elongation and shade avoidance response. Double mutant analysis indicates that mutants of the red/far-red light absorbing phytochrome family of plant photoreceptors, phyA and phyB, are epistatic to tfl2 in far-red and red light, respectively. An overlap between genes regulated by light and by auxin has earlier been reported and, in tfl2 plants light-dependent auxin-regulated genes are misexpressed. Further, we show that TFL2 binds to IAA5 and IAA19 suggesting that TFL2 might be involved in regulation of phytochrome-mediated light responses through auxin action.

Genome-wide selection on codon usage at the population level in the fungal model organism Neurospora crassa

Many organisms exhibit biased codon usage in their genome, including the fungal model organism Neurospora crassa. The preferential use of subset of synonymous codons (optimal codons) at the macroevolutionary level is believed to result from a history of selection to promote translational efficiency. At present, few data are available about selection on optimal codons at the microevolutionary scale, that is, at the population level. Herein, we conducted a large-scale assessment of codon mutations at biallelic sites, spanning more than 5,100 genes, in 2 distinct populations of N. crassa: the Caribbean and Louisiana populations. Based on analysis of the frequency spectra of synonymous codon mutations at biallelic sites, we found that derived (nonancestral) optimal codon mutations segregate at a higher frequency than derived nonoptimal codon mutations in each population; this is consistent with natural selection favoring optimal codons. We also report that optimal codon variants were less frequent in longer genes and that the fixation of optimal codons was reduced in rapidly evolving long genes/proteins, trends suggestive of genetic hitchhiking (Hill-Robertson) altering codon usage variation. Notably, nonsynonymous codon mutations segregated at a lower frequency than synonymous nonoptimal codon mutations (which impair translational efficiency) in each N. crassa population, suggesting that changes in protein composition are more detrimental to fitness than mutations altering translation. Overall, the present data demonstrate that selection, and partly genetic interference, shapes codon variation across the genome in N. crassa populations.

Generation of monospecific antibodies based on affinity capture of polyclonal antibodies

A method is described to generate and validate antibodies based on mapping the linear epitopes of a polyclonal antibody followed by sequential epitope-specific capture using synthetic peptides. Polyclonal antibodies directed towards four proteins RBM3, SATB2, ANLN, and CNDP1, potentially involved in human cancers, were selected and antibodies to several non-overlapping epitopes were generated and subsequently validated by Western blot, immunohistochemistry, and immunofluorescence. For all four proteins, a dramatic difference in functionality could be observed for these monospecific antibodies directed to the different epitopes. In each case, at least one antibody was obtained with full functionality across all applications, while other epitope-specific fractions showed no or little functionality. These results present a path forward to use the mapped binding sites of polyclonal antibodies to generate epitope-specific antibodies, providing an attractive approach for large-scale efforts to characterize the human proteome by antibodies.

Evolution of synonymous codon usage in Neurospora tetrasperma and Neurospora discreta

Neurospora comprises a primary model system for the study of fungal genetics and biology. In spite of this, little is known about genome evolution in Neurospora. For example, the evolution of synonymous codon usage is largely unknown in this genus. In the present investigation, we conducted a comprehensive analysis of synonymous codon usage and its relationship to gene expression and gene length (GL) in Neurospora tetrasperma and Neurospora discreta. For our analysis, we examined codon usage among 2,079 genes per organism and assessed gene expression using large-scale expressed sequenced tag (EST) data sets (279,323 and 453,559 ESTs for N. tetrasperma and N. discreta, respectively). Data on relative synonymous codon usage revealed 24 codons (and two putative codons) that are more frequently used in genes with high than with low expression and thus were defined as optimal codons. Although codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous codon usage in these genomes. We also report that GL (coding sequences [CDS]) was inversely associated with optimal codon usage at each gene expression level, with highly expressed short genes having the greatest frequency of optimal codons. Optimal codon frequency was moderately higher in N. tetrasperma than in N. discreta, which might be due to variation in selective pressures and/or mating systems.

Edge dynamics in a quantum spin Hall state: effects from Rashba spin-orbit interaction

We analyze the dynamics of the helical edge modes of a quantum spin Hall state in the presence of a spatially nonuniform Rashba spin-orbit (SO) interaction. A randomly fluctuating Rashba SO coupling is found to open a scattering channel which causes localization of the edge modes for a weakly screened electron-electron (e-e) interaction. A periodic modulation of the SO coupling, with a wave number commensurate with the Fermi momentum, makes the edge insulating already at intermediate strengths of the e-e interaction. We discuss implications for experiments on edge state transport in a HgTe quantum well.

Phylogenetic and biological species diversity within the Neurospora tetrasperma complex

The objective of this study was to explore the evolutionary history of the morphologically recognized filamentous ascomycete Neurospora tetrasperma, and to reveal the genetic and reproductive relationships among its individuals and populations. We applied both phylogenetic and biological species recognition to a collection of strains representing the geographic and genetic diversity of N. tetrasperma. First, we were able to confirm a monophyletic origin of N. tetrasperma. Furthermore, we found nine phylogenetic species within the morphospecies. When using the traditional broad biological species recognition all investigated strains of N. tetrasperma constituted a single biological species. In contrast, when using a quantitative measurement of the reproductive success, incorporating characters such as viability and fertility of offspring, we found a high congruence between the phylogenetic and biological species recognition. Taken together, phylogenetically and biologically defined groups of individuals exist in N. tetrasperma, and these should be taken into account in future studies of its life history traits.

Tunneling between edge states in a quantum spin Hall system

We analyze a quantum spin Hall device with a point contact connecting two of its edges. The contact supports a net spin tunneling current that can be probed experimentally via a two-terminal resistance measurement. We find that the low-bias tunneling current and the differential conductance exhibit scaling with voltage and temperature that depend nonlinearly on the strength of the electron-electron interaction.

A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members

The homeodomain leucine zipper (HD-Zip) genes encode transcription factors that have diverse functions in plant development and have often been implicated in stress adaptation. The HD-Zip genes are the most abundant group of homeobox (HB) genes in plants and do not occur in other eukaryotes. This paper describes the complete annotation of the HD-Zip families I, II and III from rice and compares these gene families with Arabidopsis in a phylogeny reconstruction. Orthologous pairs of rice and Arabidopsis HD-Zip genes were predicted based on neighbour joining and maximum parsimony (MP) trees with support of conserved intron-exon organization. Additionally, a number of HD-Zip genes appeared to be unique to rice. Searching of EST and cDNA databases and expression analysis using RT-PCR showed that 30 out of 31 predicted rice HD-Zip genes are expressed. Most HD-Zip genes were broadly expressed in mature plants and seedlings, but others showed more organ specific patterns. Like in Arabidopsis and other dicots, a subset of the rice HD-Zip I and II genes was found to be regulated by drought stress. We identified both drought-induced and drought-repressed HD-Zip genes and demonstrate that these genes are differentially regulated in drought-sensitive versus drought-tolerant rice cultivars. The drought-repressed HD-Zip family I gene, Oshox4, was selected for promoter-GUS analysis, showing that drought-responsiveness of Oshox4 is controlled by the promoter and that Oshox4 expression is predominantly vascular-specific. Loss-of-function analysis of Oshox4 revealed no specific phenotype, but overexpression analysis suggested a role for Oshox4 in elongation and maturation processes.

Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation

In previous time-resolved microarray-based expression profiling, we identified 32 genes encoding putative transcription factors, signaling components, and unknown proteins that are rapidly and robustly induced by phytochrome (phy)-mediated light signals. Postulating that they are the most likely to be direct targets of phy signaling and to function in the primary phy regulatory circuitry, we examined the impact of targeted mutations in these genes on the phy-induced seedling deetiolation process in Arabidopsis thaliana. Using light-imposed concomitant inhibition of hypocotyl and stimulation of cotyledon growth as diagnostic criteria for normal deetiolation, we identified three major mutant response categories. Seven (22%) lines displayed statistically significant, reciprocal, aberrant photoresponsiveness in the two organs, suggesting disruption of normal deetiolation; 13 (41%) lines displayed significant defects either unidirectionally in both organs or in hypocotyls only, suggesting global effects not directly related to photomorphogenic signaling; and 12 (37%) lines displayed no significant difference in photoresponsiveness from the wild type. Potential reasons for the high proportion of rapidly light-responsive genes apparently unnecessary for the deetiolation phenotype are discussed. One of the seven disrupted genes displaying a significant mutant phenotype, the basic helix-loop-helix factor-encoding PHYTOCHROME-INTERACTING FACTOR3-LIKE1 gene, was found to be necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related PSEUDO-RESPONSE REGULATOR9 gene, indicating a regulatory function in the early phy-induced transcriptional network.

A homeodomain leucine zipper gene from Craterostigma plantagineum regulates abscisic acid responsive gene expression and physiological responses

A subset of homeodomain leucine zipper proteins (HDZip) play a role in regulating adaptation responses including developmental adjustment to environmental cues in plants. Here we report the structural and functional characterisation of a dehydration responsive nuclear-targeted HDZip transcriptional regulator, CpHB-7. DNA-protein interaction studies suggest that CDeT6-19, a known ABA and dehydration responsive dehydrin gene, is a potential target gene of CpHB-7 in the desiccation-tolerant plant Craterostigma plantagineum. Transgenic plants that ectopically express CpHB-7 display reduced sensitivity towards ABA during seed germination and stomatal closure. Expression analysis reveals that genes with induced or repressed expression in CpHB-7 ectopic expression lines are either mostly repressed or induced by ABA, drought or salt treatment respectively, thus demonstrating that CpHB-7 modifies ABA-responsive gene expression as a negative regulator. CpHB-7 gene expression is also linked to early organ development, leading to the suggestion that CpHB-7 is functionally similar to the Arabidopsis transcription factor, ATHB-6.

Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii

Coccidioides posadasii is a dimorphic fungal pathogen that grows as a filamentous saprobe in the soil and as endosporulating spherules within the host. To identify genes specific to the pathogenic phase of Co. posadasii, we carried out a large-scale study of gene expression in two isolates of the species. From the sequenced Co. posadasii genome, we chose 1,000 open reading frames to construct a 70-mer microarray. RNA was recovered from both isolates at three life-cycle phases: hyphae, presegmented spherules, and spherules releasing endospores. Comparative hybridizations were conducted in a circuit design, permitting comparison between both isolates at all three life-cycle phases, and among all life-cycle phases for each isolate. By using this approach, we identified 92 genes that were differentially expressed between pathogenic and saprobic phases in both fungal isolates, and 43 genes with consistent differential expression between the two parasitic developmental phases. Genes with elevated expression in the pathogenic phases of both isolates included a number of genes that were involved in the response to environmental stress as well as in the metabolism of lipids. The latter observation is in agreement with previous studies demonstrating that spherules contain a higher proportion of lipids than saprobic phase tissue. Intriguingly, we discovered statistically significant and divergent levels of gene expression between the two isolates profiled for 64 genes. The results suggest that incorporating more than one isolate in the experimental design offers a means of categorizing the large collection of candidate genes that transcriptional profiling typically identifies into those that are strain-specific and those that characterize the entire species.

Entanglement scaling in the one-dimensional Hubbard model at criticality

We derive exact expressions for the local entanglement entropy epsilon in the ground state of the one-dimensional Hubbard model at a quantum phase transition driven by a change in magnetic field h or chemical potential mu. The leading divergences of delta epsilon/delta h and delta epsilon/delta mu are shown to be directly related to those of the zero-temperature spin and charge susceptibilities. Logarithmic corrections to scaling signal a change in the number of local states accessible to the system as it undergoes the transition.

Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships

Members of the homeodomain leucine zipper (HDZip) family of transcription factors are present in a wide range of plants, from mosses to higher plants, but not in other eukaryotes. The HDZip genes act in developmental processes, including vascular tissue and trichome development, and several of them have been suggested to be involved in the mediation of external signals to regulate plant growth. The Arabidopsis (Arabidopsis thaliana) genome contains 47 HDZip genes, which, based on sequence criteria, have been grouped into four different classes: HDZip I to IV. In this article, we present an overview of the class I HDZip genes in Arabidopsis. We describe their expression patterns, transcriptional regulation properties, duplication history, and phylogeny. The phylogeny of HDZip class I genes is supported by data on the duplication history of the genes, as well as the intron/exon patterning of the HDZip-encoding motifs. The HDZip class I genes were found to be widely expressed and partly to have overlapping expression patterns at the organ level. Further, abscisic acid or water deficit treatments and different light conditions affected the transcript levels of a majority of the HDZip I genes. Within the gene family, our data show examples of closely related HDZip genes with similarities in the function of the gene product, but a divergence in expression pattern. In addition, six HDZip class I proteins tested were found to be activators of gene expression. In conclusion, several HDZip I genes appear to regulate similar cellular processes, although in different organs or tissues and in response to different environmental signals.

Measuring Luttinger liquid correlations from charge fluctuations in a nanoscale structure

We suggest an experiment to study Luttinger liquid behavior in a one-dimensional nanostructure, avoiding the usual complications associated with transport measurements. The proposed setup consists of a quantum box, biased by a gate voltage, and side coupled to a quantum wire by a point contact. Close to the degeneracy points of the Coulomb blockaded box, and in the presence of a magnetic field sufficiently strong to spin polarize the electrons, the setup can be described as a Luttinger liquid interacting with an effective Kondo impurity. Using exact nonperturbative techniques, we predict that the differential capacitance of the box will exhibit distinctive Luttinger liquid scaling with temperature and gate voltage.

Parental tracking in the postfire wood decay ascomycete Daldinia loculata using highly variable nuclear gene loci

The origin of the male and female gametes involved in fertilization events within a local population of the postfire wood decay ascomycete Daldinia loculata was investigated by genotyping the mycelia growing in the wood and the sexual ascospores, using three highly variable nuclear gene loci. The study was conducted in a geographically isolated burned forest site in southern Sweden. An intensive sampling was performed by collecting stromata containing ascospores and wood samples containing mycelia. In total, from 32 mapped burned birches, cultures of 22 haploid genets from decayed wood and six ascospores from each of 19 stromata were isolated and analysed. In 80% of the investigated burned branches, only one genet was found. From the analysis of the ascospore genotypes, we detected 30 fertilization events and 60% of them were the result of mating between conidia (clonal propagules) acting as male gametes and the genets in the branches representing the female gametes. The male parents producing the conidia were detected within the same local population as the female parents in 27% of the fertilization events and originated either from the same branch or from different trees located at 0.5-36 m away from the female parents. In 33% of the fertilization events, conidia originated from three male parents that were not found within the local population sampled. These parents could be anywhere inside or outside the sampled area. For the remaining fertilization events, we could not rule out the ascospores or the conidia as fertilizing propagules. No strong evidence for fertilization by recombinant propagules (ascospores) was detected in this study. The pyrophilous insect species associated with conidia of D. loculata are suggested to be essential vectors for the realization of the sexual cycle of this fungal species. By feeding on the conidia and flying between nearby trees inhabiting wood decay mycelia, these insects allow the transfer of conidia and therefore the opposite mating types to meet within a localized burned forest site.

The Arabidopsis thaliana homeobox gene ATHB5 is a potential regulator of abscisic acid responsiveness in developing seedlings

ATHB5 is a member of the homeodomain-leucine zipper (HDZip) transcription factor gene family of Arabidopsis thaliana. In this report we show that increased expression levels of ATHB5 in transgenic Arabidopsis plants cause an enhanced sensitivity to the inhibitory effect of abscisic acid (ABA) on seed germination and seedling growth. Consistent with this finding we demonstrate in northern blot experiments that the ABA-responsive gene RAB18 is hyperinduced by ABA in transgenic overexpressor lines as compared to the wild type. Northern blot and promoter-GUS fusion analyses show that ATHB5 gene transcription is initiated rapidly after the onset of germination and localized primarily to the hypocotyl of germinating seedlings. Moreover, analysis of ATHB5 gene expression during post-germinative growth in different ABA response mutants shows that ATHB5 gene activity is down-regulated in the abil-1, abi3-1 and abi5-1 mutant lines, but not in abi2-1 or abi4-1. The identification of a T-DNA insertion mutant line of ATHB5 is described and no phenotypic alterations could be discerned, suggesting that ATHB5 may act redundantly with other HDZip genes. Taken together, these data suggest that ATHB5 is a positive regulator of ABA-responsiveness, mediating the inhibitory effect of ABA on growth during seedling establishment.

Kondo resonance in a mesoscopic ring coupled to a quantum dot: exact results for the Aharonov-Bohm-Casher effects

We study the persistent currents induced by both the Aharonov-Bohm and Aharonov-Casher effects in a one-dimensional mesoscopic ring coupled to a sidebranch quantum dot at Kondo resonance. For privileged values of the Aharonov-Bohm-Casher fluxes, the problem can be mapped onto an integrable model, exactly solvable by a Bethe ansatz. In the case of a pure magnetic Aharonov-Bohm flux, we find that the presence of the quantum dot has no effect on the persistent current. In contrast, the Kondo resonance interferes with the spin-dependent Aharonov-Casher effect to induce a current which, in the strong-coupling limit, is independent of the number of electrons in the ring.

Genetic differentiation in Eurasian populations of the postfire ascomycete Daldinia loculata

The genetic population structure of the postfire ascomycete Daldinia loculata was studied to test for differentiation on a continental scale. Ninety-six samples of spore families, each comprising mycelia from six to 10 spores originating from single perithecia, were sampled from one Russian and six Fennoscandian forest sites. Allelic distribution was assayed for six nuclear gene loci by restriction enzyme analyses of polymerase chain reaction (PCR)-amplified gene fragments. In addition, the full sequence of the gene fragment was analysed for a subset of haploid single-ascospore isolates in a multiallelic approach. A third data set was generated by using arbitrary-primed PCR with the core sequence of the phage M13 as primer. Although there was a reduction in heterozygosity in the total population from what would have been expected at random mating, the levels of genetic differentiation among the Eurasian subpopulations of D. loculata were low. All subpopulations were found to be in Hardy-Weinberg equilibrium and gametic equilibrium was observed between all investigated nuclear gene loci. The results obtained by the different markers were consistent; we confirmed low levels of genetic differentiation among the Eurasian subpopulations of D. loculata. The differentiation did not increase with distance; the Russian subpopulation, sampled more than 7000 km from the Fennoscandian subpopulations, was only moderately differentiated from the others (FST = 0.00-0.14). In contrast, one of the Swedish populations was the most highly differentiated from the others, with FST and GST values of 0.10-0.16. The results suggest that D. loculata consists of a long-lived background Eurasian population of latent mycelia in nonburned forests, established by sexual ascospores dispersed from scattered burned forest sites. Local differentiation is probably due to founder effects of populations in areas with low fire frequency. A tentative life cycle of D. loculata is presented.

Sugar-dependent alterations in cotyledon and leaf development in transgenic plants expressing the HDZhdip gene ATHB13

ATHB13 is a new member of the homeodomain leucine zipper (HDZip) transcription factor family of Arabidopsis thaliana. Constitutive high-level expression of the ATHB13 cDNA in transgenic plants results in altered development of cotyledons and leaves, specifically in plants grown on media containing metabolizable sugars. Cotyledons and leaves of sugar-grown transgenic plants are more narrow and the junction between the petiole and the leaf blade less distinct, as compared to the wild type. High-level expression of ATHB13 affects cotyledon shape by inhibiting lateral expansion of epidermal cells in sugar-treated seedlings. Experiments with non-metabolizable sugars indicate that the alteration in leaf shape in the ATHB13 transgenics is mediated by sucrose sensing. ATHB13 further affects a subset of the gene expression responses of the wild-type plant to sugars. The expression of genes encoding beta-amylase and vegetative storage protein is induced to higher levels in response to sucrose in the transgenic plants as compared to the wild type. The expression of other sugar-regulated genes examined is unaffected by ATHB13. These data suggest that ATHB13 may be a component of the sucrose-signalling pathway, active close to the targets of the signal transduction.

DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro

Homeodomain-leucine zipper (HDZip) proteins constitute a large family of transcription factors apparently unique to plants. In this report we characterize the DNA-binding and dimerization preferences in vitro of class I HDZip proteins. Using gel-exclusion chromatography and in vitro protein binding assays we demonstrate that the HDZip class I protein ATHB5 forms a homodimeric complex in solution. Consistent with this finding we have demonstrated the sequence-specific interaction of ATHB5 with a 9 bp pseudopalindromic DNA sequence, CAATNATTG, composed of two half-sites overlapping at a central position, by use of a PCR-assisted binding-site selection assay and competitive EMSA experiments. A majority of other known members of HDZip class I interacted with similar DNA sequences, but differed in their preference for A/T versus G/C in the central position of the binding site. Selective heterodimerization in vitro was demonstrated between ATHB5 and different class I HDZip proteins. Heterodimer formation between class I HDZip proteins is of potential functional significance for the integration of information from different signalling pathways in the control of plant development.

Two-species reaction-diffusion system with equal diffusion constants: anomalous density decay at large times

We study a two-species reaction-diffusion model where A+A-->, A+B-->, and B+B-->, with annihilation rates lambda(0), delta(0)>lambda(0), and lambda(0), respectively. The initial particle configuration is taken to be randomly mixed with mean densities n(A)(0)>n(B)(0), and with the two species A and B diffusing with the same diffusion constant. A field-theoretic renormalization group analysis suggests that, contrary to expectation, the large-time density of the minority species decays at the same rate as the majority when d</=2. Monte Carlo data support the field theory prediction in d=1, while in d=2 the logarithmically slow convergence to the large-time asymptotics makes a numerical test difficult.

The LAMB1 gene from the clubmoss, Lycopodium annotinum, is a divergent MADS-box gene, expressed specifically in sporogenic structures

Transcription factors encoded by the large MADS-box gene family have important developmental functions in angiosperms, the flowering plants. Mutations in certain MADS-box genes are known to cause homeotic alterations in floral organ identity, and the establishment of floral organ identity is the most well-studied developmental process in which MADS-box genes are known to function. Our interest is in the potential connection between the duplication history of this gene family and the evolutionary origin of the structures that the different MADS-box genes developmentally regulate in plants. Previous studies have demonstrated that the origin of the MADS-box genes that control floral organ identity predate the evolutionary origin of the flower itself, since gymnosperms have genes that are orthologous to angiosperm floral homeotic MADS-box genes, whereas ferns appear to lack such genes. Here we report on the isolation of a MADS-box gene from Lycopodium annotinum, which belongs to the clubmosses, the phylogenetic sister group to other vascular plants. The gene, LAMB1, in the sporophyte is expressed exclusively in the reproductive structure, the strobilus, during sporogenesis. LAMB1 is similar to other plant MADS-box genes in that it contains a MADS-box as well as a second conserved element, a K-box. However, it differs in length and in exon/intron structure in the region between the MADS- and K-box, and also in the length and structure of the C-terminal region. A phylogenetic analysis indicates that LAMB1 is not closely related to other plant-type MADS-box genes, and may represent one of the basal branches in the phylogenetic tree of plant MADS-box genes.