Merit of integrating in situ transcriptomics and anatomical information for cell annotation and lineage construction in single-cell analyses of Populus

Cell type annotation and lineage construction are two of the most critical tasks conducted in the analyses of single-cell RNA sequencing (scRNA-seq). Four recent scRNA-seq studies of differentiating xylem propose four models on differentiating xylem development in Populus. The differences are mostly caused by the use of different strategies for cell type annotation and subsequent lineage interpretation. Here, we emphasize the necessity of using in situ transcriptomes and anatomical information to construct the most plausible xylem development model.

Human Thg1 displays tRNA-inducible GTPase activity

tRNA^His guanylyltransferase (Thg1) catalyzes the 3′-5′ incorporation of guanosine into position -1 (G-1) of tRNA^His. G-1 is unique to tRNA^His and is crucial for recognition by histidyl-tRNA synthetase (HisRS). Yeast Thg1 requires ATP for G-1 addition to tRNA^His opposite A73, whereas archaeal Thg1 requires either ATP or GTP for G-1 addition to tRNA^His opposite C73. Paradoxically, human Thg1 (HsThg1) can add G-1 to tRNAs^His with A73 (cytoplasmic) and C73 (mitochondrial). As N73 is immediately followed by a CCA end (positions 74–76), how HsThg1 prevents successive 3′-5′ incorporation of G-1/G-2/G-3 into mitochondrial tRNA^His (tRNA_m^His) through a template-dependent mechanism remains a puzzle. We showed herein that mature native human tRNA_m^His indeed contains only G-1. ATP was absolutely required for G-1 addition to tRNA_m^His by HsThg1. Although HsThg1 could incorporate more than one GTP into tRNA_m^Hisin vitro, a single-GTP incorporation prevailed when the relative GTP level was low. Surprisingly, HsThg1 possessed a tRNA-inducible GTPase activity, which could be inhibited by ATP. Similar activity was found in other high-eukaryotic dual-functional Thg1 enzymes, but not in yeast Thg1. This study suggests that HsThg1 may downregulate the level of GTP through its GTPase activity to prevent multiple-GTP incorporation into tRNA_m^His.

Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex

BACKGROUND

Yeast one-hybrid (Y1H) is a common technique for identifying DNA-protein interactions, and robotic platforms have been developed for high-throughput analyses to unravel the gene regulatory networks in many organisms. Use of these high-throughput techniques has led to the generation of increasingly large datasets, and several software packages have been developed to analyze such data. We previously established the currently most efficient Y1H system, meiosis-directed Y1H; however, the available software tools were not designed for processing the additional parameters suggested by meiosis-directed Y1H to avoid false positives and required programming skills for operation.

RESULTS

We developed a new tool named GateMultiplex with high computing performance using C++. GateMultiplex incorporated a graphical user interface (GUI), which allows the operation without any programming skills. Flexible parameter options were designed for multiple experimental purposes to enable the application of GateMultiplex even beyond Y1H platforms. We further demonstrated the data analysis from other three fields using GateMultiplex, the identification of lead compounds in preclinical cancer drug discovery, the crop line selection in precision agriculture, and the ocean pollution detection from deep-sea fishery.

CONCLUSIONS

The user-friendly GUI, fast C++ computing speed, flexible parameter setting, and applicability of GateMultiplex facilitate the feasibility of large-scale data analysis in life science fields.

Activation of Prp28 ATPase by phosphorylated Npl3 at a critical step of spliceosome remodeling

Splicing, a key step in the eukaryotic gene-expression pathway, converts precursor messenger RNA (pre-mRNA) into mRNA by excising introns and ligating exons. This task is accomplished by the spliceosome, a macromolecular machine that must undergo sequential conformational changes to establish its active site. Each of these major changes requires a dedicated DExD/H-box ATPase, but how these enzymes are activated remain obscure. Here we show that Prp28, a yeast DEAD-box ATPase, transiently interacts with the conserved 5' splice-site (5'SS) GU dinucleotide and makes splicing-dependent contacts with the U1 snRNP protein U1C, and U4/U6.U5 tri-snRNP proteins, Prp8, Brr2, and Snu114. We further show that Prp28's ATPase activity is potentiated by the phosphorylated Npl3, but not the unphosphorylated Npl3, thus suggesting a strategy for regulating DExD/H-box ATPases. We propose that Npl3 is a functional counterpart of the metazoan-specific Prp28 N-terminal region, which can be phosphorylated and serves as an anchor to human spliceosome.

Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells

Transcriptionally non-co-linear (NCL) transcripts can originate from trans-splicing (trans-spliced RNA; 'tsRNA') or cis-backsplicing (circular RNA; 'circRNA'). While numerous circRNAs have been detected in various species, tsRNAs remain largely uninvestigated. Here, we utilize integrative transcriptome sequencing of poly(A)- and non-poly(A)-selected RNA-seq data from diverse human cell lines to distinguish between tsRNAs and circRNAs. We identified 24,498 NCL events and found that a considerable proportion (20-35%) of them arise from both tsRNAs and circRNAs, representing extensive alternative trans-splicing and cis-backsplicing in human cells. We show that sequence generalities of exon circularization are also observed in tsRNAs. Recapitulation of NCL RNAs further shows that inverted Alu repeats can simultaneously promote the formation of tsRNAs and circRNAs. However, tsRNAs and circRNAs exhibit quite different, or even opposite, expression patterns, in terms of correlation with the expression of their co-linear counterparts, expression breadth/abundance, transcript stability, and subcellular localization preference. These results indicate that tsRNAs and circRNAs may play different regulatory roles and analysis of NCL events should take the joint effects of different NCL-splicing types and joint effects of multiple NCL events into consideration. This study describes the first transcriptome-wide analysis of trans-splicing and cis-backsplicing, expanding our understanding of the complexity of the human transcriptome.

Naturally occurring dual recognition of tRNAHis substrates with and without a universal identity element

The extra 5' guanine nucleotide (G-1) on tRNA^His is a nearly universal feature that specifies tRNA^His identity. The G-1 residue is either genome encoded or post-transcriptionally added by tRNA^His guanylyltransferase (Thg1). Despite Caenorhabditis elegans being a Thg1-independent organism, its cytoplasmic tRNA^His (CetRNA_n^His) retains a genome-encoded G-1. Our study showed that this eukaryote possesses a histidyl-tRNA synthetase (CeHisRS) gene encoding two distinct HisRS isoforms that differ only at their N-termini. Most interestingly, its mitochondrial tRNA^His (CetRNA_m^His) lacks G-1, a scenario never observed in any organelle. This tRNA, while lacking the canonical identity element, can still be efficiently aminoacylated in vivo. Even so, addition of G-1 to CetRNA_m^His strongly enhanced its aminoacylation efficiency in vitro. Overexpression of CeHisRS successfully bypassed the requirement for yeast THG1 in the presence of CetRNA_n^His without G-1. Mutagenesis assays showed that the anticodon takes a primary role in CetRNA^His identity recognition, being comparable to the universal identity element. Consequently, simultaneous introduction of both G-1 and the anticodon of tRNA^His effectively converted a non-cognate tRNA to a tRNA^His-like substrate. Our study suggests that a new balance between identity elements of tRNA^His relieves HisRS from the absolute requirement for G-1.

A novel synthetic-genetic-array-based yeast one-hybrid system for high discovery rate and short processing time

Eukaryotic gene expression is often tightly regulated by interactions between transcription factors (TFs) and their DNA cis targets. Yeast one-hybrid (Y1H) is one of the most extensively used methods to discover these interactions. We developed a high-throughput meiosis-directed yeast one-hybrid system using the Magic Markers of the synthetic genetic array analysis. The system has a transcription factor–DNA interaction discovery rate twice as high as the conventional diploid-mating approach and a processing time nearly one-tenth of the haploid-transformation method. The system also offers the highest accuracy in identifying TF–DNA interactions that can be authenticated in vivo by chromatin immunoprecipitation. With these unique features, this meiosis-directed Y1H system is particularly suited for constructing novel and comprehensive genome-scale gene regulatory networks for various organisms.

Adaptive transcription-splicing resynchronization upon losing an essential splicing factor

Essential genes form the core of a genome and are therefore thought to be indispensable for cellular viability. However, recent findings have challenged this notion in that cells may survive in the absence of some essential genes provided that relevant genetic modifiers are in existence. We therefore hypothesized that the loss of an essential gene may not always be fatefully detrimental; instead, it may pave the way towards genome evolution. We experimentally tested this hypothesis in the context of pre-messenger RNA splicing by evolving yeast cells harbouring a permanent loss of the essential splicing factor Prp28 in the presence of a genetic modifier. Here, we show that cellular fitness can be restored by compensatory mutations that alter either the splicing machinery per se or the Spt-Ada-Gcn5 acetyltransferase transcription co-activator complex in the cells with no Prp28. Biochemical and genetic analysis revealed that slowing down transcription compensates for splicing deficiency, which in turn boosts cellular fitness. In addition, we found that inefficient splicing also conversely decreases nascent RNA production. Taken together, our data suggest that transcription-splicing synchronization contributes to robustness in the gene-expression pathway and argue that the intrinsic interconnectivity within a biological system can be exploited for compensatory evolution and system re-optimization.

The conserved AU dinucleotide at the 5' end of nascent U1 snRNA is optimized for the interaction with nuclear cap-binding-complex

Splicing is initiated by a productive interaction between the pre-mRNA and the U1 snRNP, in which a short RNA duplex is established between the 5' splice site of a pre-mRNA and the 5' end of the U1 snRNA. A long-standing puzzle has been why the AU dincucleotide at the 5'-end of the U1 snRNA is highly conserved, despite the absence of an apparent role in the formation of the duplex. To explore this conundrum, we varied this AU dinucleotide into all possible permutations and analyzed the resulting molecular consequences. This led to the unexpected findings that the AU dinucleotide dictates the optimal binding of cap-binding complex (CBC) to the 5' end of the nascent U1 snRNA, which ultimately influences the utilization of U1 snRNP in splicing. Our data also provide a structural interpretation as to why the AU dinucleotide is conserved during evolution.

Candida albicans Hom6 is a homoserine dehydrogenase involved in protein synthesis and cell adhesion

BACKGROUND/PURPOSE

Candida albicans is a common fungal pathogen in humans. In healthy individuals, C. albicans represents a harmless commensal organism, but infections can be life threatening in immunocompromised patients. The complete genome sequence of C. albicans is extremely useful for identifying genes that may be potential drug targets and important for pathogenic virulence. However, there are still many uncharacterized genes in the Candida genome database. In this study, we investigated C. albicans Hom6, the functions of which remain undetermined experimentally.

METHODS

HOM6-deleted and HOM6-reintegrated mutant strains were constructed. The mutant strains were compared with wild-type in their growth in various media and enzyme activity. Effects of HOM6 deletion on translation were further investigated by cell susceptibility to hygromycin B or cycloheximide, as well as by polysome profiling, and cell adhesion to polystyrene was also determined.

RESULTS

C. albicans Hom6 exhibits homoserine dehydrogenase activity and is involved in the biosynthesis of methionine and threonine. HOM6 deletion caused translational arrest in cells grown under amino acid starvation conditions. Additionally, Hom6 protein was found in both cytosolic and cell-wall fractions of cultured cells. Furthermore, HOM6 deletion reduced C. albicans cell adhesion to polystyrene, which is a common plastic used in many medical devices.

CONCLUSION

Given that there is no Hom6 homologue in mammalian cells, our results provided an important foundation for future development of new antifungal drugs.

Modal analysis and efficient coupling of TE₀₁ mode in small-core THz Bragg fibers

We report a design of low-loss THz Bragg fibers with a core size on the order of wavelength that operates near the cutoff frequency of its TE01 mode. We also propose a broadband Y-type mode converter based on branched rectangular metallic waveguides to facilitate coupling between the TE01 mode of the Bragg fiber and the TEM mode in free space with 60% efficiency. Our fiber holds strong promise to facilitate beam-wave interaction in gyrotron for high-efficiency THz generation.

A population study of killer viruses reveals different evolutionary histories of two closely related Saccharomyces sensu stricto yeasts

Microbes have evolved ways of interference competition to gain advantage over their ecological competitors. The use of secreted killer toxins by yeast cells through acquiring double-stranded RNA viruses is one such prominent example. Although the killer behaviour has been well studied in laboratory yeast strains, our knowledge regarding how killer viruses are spread and maintained in nature and how yeast cells co-evolve with viruses remains limited. We investigated these issues using a panel of 81 yeast populations belonging to three Saccharomyces sensu stricto species isolated from diverse ecological niches and geographic locations. We found that killer strains are rare among all three species. In contrast, killer toxin resistance is widespread in Saccharomyces paradoxus populations, but not in Saccharomyces cerevisiae or Saccharomyces eubayanus populations. Genetic analyses revealed that toxin resistance in S. paradoxus is often caused by dominant alleles that have independently evolved in different populations. Molecular typing identified one M28 and two types of M1 killer viruses in those killer strains. We further showed that killer viruses of the same type could lead to distinct killer phenotypes under different host backgrounds, suggesting co-evolution between the viruses and hosts in different populations. Taken together, our data suggest that killer viruses vary in their evolutionary histories even within closely related yeast species.

Feedback Control of Snf1 Protein and Its Phosphorylation Is Necessary for Adaptation to Environmental Stress

Snf1, a member of the AMP-activated protein kinase family, plays a critical role in metabolic energy control in yeast cells. Snf1 activity is activated by phosphorylation of Thr-210 on the activation loop of its catalytic subunit; following activation, Snf1 regulates stress-responsive transcription factors. Here, we report that the level of Snf1 protein is dramatically decreased in a UBP8- and UBP10-deleted yeast mutant (ubp8Δ ubp10Δ), and this is independent of transcriptional regulation and proteasome-mediated degradation. Surprisingly, most Snf1-mediated functions, including glucose limitation regulation, utilization of alternative carbon sources, stress responses, and aging, are unaffected in this strain. Snf1 phosphorylation in ubp8Δ ubp10Δ cells is hyperactivated upon stress, which may compensate for the loss of the Snf1 protein and protect cells against stress and aging. Furthermore, artificial elevation of Snf1 phosphorylation (accomplished through deletion of REG1, which encodes a protein that regulates Snf1 dephosphorylation) restored Snf1 protein levels and the regulation of Snf1 activity in ubp8Δ ubp10Δ cells. Our results reveal the existence of a feedback loop that controls Snf1 protein level and its phosphorylation, which is masked by Ubp8 and Ubp10 through an unknown mechanism. We propose that this dynamic modulation of Snf1 phosphorylation and its protein level may be important for adaptation to environmental stress.

Functions of the DExD/H-box proteins in nuclear pre-mRNA splicing

In eukaryotes, many genes are transcribed as precursor messenger RNAs (pre-mRNAs) that contain exons and introns, the latter of which must be removed and exons ligated to form the mature mRNAs. This process is called pre-mRNA splicing, which occurs in the nucleus. Although the chemistry of pre-mRNA splicing is identical to that of the self-splicing Group II introns, hundreds of proteins and five small nuclear RNAs (snRNAs), U1, U2, U4, U5, and U6, are essential for executing pre-mRNA splicing. Spliceosome, arguably the most complex cellular machine made up of all those proteins and snRNAs, is responsible for carrying out pre-mRNA splicing. In contrast to the transcription and the translation machineries, spliceosome is formed anew onto each pre-mRNA and undergoes a series of highly coordinated reconfigurations to form the catalytic center. This amazing process is orchestrated by a number of DExD/H-proteins that are the focus of this article, which aims to review the field in general and to project the exciting challenges and opportunities ahead. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.

Mammalian α arrestins link activated seven transmembrane receptors to Nedd4 family e3 ubiquitin ligases and interact with β arrestins

The complement of fungal cell surface proteins is widely regulated by ubiquitination of membrane proteins, which results in their endocytosis and vacuolar degradation. For diverse fungal transporters, the specificity of ubiquitination is conferred by alpha arrestin adaptors, which recruit the Nedd4 family E3 ubiquitin ligase Rsp5. A recent study showed that one mammalian alpha arrestin also mediates ubiquitination and lysosomal trafficking of an activated plasma membrane receptor. Here we first screen all five widely-expressed human alpha arrestins for subcellular localization in ligand-stimulated and -unstimulated cells overexpressing the seven transmembrane receptor vasopressin 2. We then characterize the effects of alpha arrestins ARRDC3 and ARRDC4 upon activation of the seven transmembrane receptors vasopressin 2 and beta adrenergic 2. Using biochemical and imaging approaches, we show that ligand-activated receptors interact with alpha arrestins, and this results in recruitment of Nedd4 family E3 ubiquitin ligases and receptor ubiquitination - which are known to result in lysosomal trafficking. Our time course studies show these effects occur in the first 1-5 minutes after ligand activation, the same time that beta arrestins are known to have roles in receptor endocytic trafficking and kinase signaling. We tested the possibility that alpha and beta arrestins function coordinately and found co-immunoprecipitation and colocalization evidence to support this. Others recently reported that Arrdc3 knockout mice are lean and resistant to obesity. In the course of breeding our own Arrdc3-deficient mice, we observed two novel phenotypes in homozygotes: skin abnormalities, and embryonic lethality on normal chow diet, but not on high fat diet. Our findings suggest that alpha and beta arrestins function coordinately to maintain the optimal complement and function of cell surface proteins according to cellular physiological context and external signals. We discuss the implications of the alpha arrestin functions in fungi having evolved into coordinated alpha/beta arrestin functions in animals.

Accelerating effects of nonviable Staphylococcus aureus, its cell wall, and cell wall peptidoglycan

We have previously reported that local application of viable Staphylococcus aureus dramatically accelerates wound healing, but viable Staphylococcus epidermidis does not. Because the S. aureus effect occurred in the absence of infection and because the cell walls of the two bacterial species differ, we hypothesized that nonviable S. aureus, its cell wall, and its cell wall component(s) would accelerate healing. Nonviable S. aureus was prepared by chemical and physical means, and its cell wall and peptidoglycan was prepared from heat-killed cultures. In a large number of experiments, nonviable S. aureus (independent of the strain's protein A content), its cell wall, and peptidoglycan when instilled locally at the time of wounding each significantly increased the breaking strength of rat skin incisions (tested both in the fresh state and after formalin fixation). These agents also enhanced subcutaneous polyvinyl alcohol sponge reparative tissue collagen accumulation, generally by a factor of two. Histologic features of treated and control incisions were similar. In contrast, the reparative tissue of treated sponges contained more neutrophils, macrophages, capillaries, and collagen. These experimental data thus confirm our previous studies, as well as our hypothesis, and extend these observations of enhanced wound healing to specific fractions of the bacterial cell wall.

Molecular mechanisms underlying wound healing acceleration by Staphylococcus aureus peptidoglycan

Molecular mechanisms involved in wound healing acceleration by Staphylococcus aureus peptidoglycan were investigated with the use of polyvinyl alcohol sponges implanted under the dorsal skin of rats. Total collagen and RNA content and messenger RNA levels of alpha1(I) and alpha1(III) procollagen, transforming growth factor-beta1, and matrix metalloproteinase-1 were analyzed in saline solution- and S. aureus peptidoglycan-inoculated sponges at 4, 7, 14, and 21 days after implantation. S. aureus peptidoglycan-inoculated sponges on the fourth and seventh post-operative day were surrounded and penetrated by a thick capsule of reparative connective tissue. They were considerably heavier and contained more collagen and total RNA than saline solution-inoculated sponges. Histologically, the S. aureus peptidoglycan-inoculated sponges early on contained a denser infiltrate of polymorphonuclear cells than saline solution-inoculated sponges, and later fibroblasts, macrophages, collagen, and newly formed blood vessels were more abundant in the S. aureus peptidoglycan sponges. Matrix metalloproteinase-1 messenger RNA expression was elevated at 4 days in both sponge types. However, although matrix metalloproteinase-1 mRNA levels decreased to undetectable levels by 14 days in saline solution-inoculated sponges, they remained elevated throughout the 21-day study period in S. aureus peptidoglycan-inoculated sponges. No other significant differences in the parameters analyzed were detected. These results suggest that S. aureus peptidoglycan induces an accelerated but normal wound healing process in which the markedly increased early deposition of connective tissue is rapidly remodeled likely because of a sustained expression of matrix metalloproteinase-1.

Analysis of stress granule assembly in Schizosaccharomyces pombe

Stress granules (SGs) are cytoplasmic aggregates of RNA and proteins in eukaryotic cells that are rapidly induced in response to environmental stress, but are not seen in cells growing under favorable conditions. SGs have been primarily studied in mammalian cells. The existence of SGs in the fission yeast and the distantly related budding yeast was demonstrated only recently. In both species, they contain many orthologs of the proteins seen in mammalian SGs. In this study, we have characterized these proteins and determined their involvement in the assembly of fission yeast SGs, in particular, the homolog of human G3BP proteins. G3BP interacts with the deubiquitinating protease USP10 and plays an important role in the assembly of SGs. We have also identified Ubp3, an ortholog of USP10, as an interaction partner of the fission yeast G3BP-like protein Nxt3 and required for its stability. Under thermal stress, like their human orthologs, both Nxt3 and Ubp3 rapidly relocalize to cytoplasmic foci that contain the SG marker poly(A)-binding protein Pabp. However, in contrast to G3BP1 and USP10, neither deletion nor overexpression of nxt3(+) or ubp3(+) affected the assembly of fission yeast SGs as judged by the relocalization of Pabp. Similar results were observed in mutants defective in orthologs of SG components that are known to affect SG assembly in human and in budding yeast, such as ataxia-2 and TIA-like proteins. Together, our data indicate that despite similar protein compositions, the underlying molecular mechanisms for the assembly of SGs could be distinct between species.

H2B ubiquitylation is part of chromatin architecture that marks exon-intron structure in budding yeast

Background

The packaging of DNA into chromatin regulates transcription from initiation through 3' end processing. One aspect of transcription in which chromatin plays a poorly understood role is the co-transcriptional splicing of pre-mRNA.

Results

Here we provide evidence that H2B monoubiquitylation (H2BK123ub1) marks introns in Saccharomyces cerevisiae. A genome-wide map of H2BK123ub1 in this organism reveals that this modification is enriched in coding regions and that its levels peak at the transcribed regions of two characteristic subgroups of genes. First, long genes are more likely to have higher levels of H2BK123ub1, correlating with the postulated role of this modification in preventing cryptic transcription initiation in ORFs. Second, genes that are highly transcribed also have high levels of H2BK123ub1, including the ribosomal protein genes, which comprise the majority of intron-containing genes in yeast. H2BK123ub1 is also a feature of introns in the yeast genome, and the disruption of this modification alters the intragenic distribution of H3 trimethylation on lysine 36 (H3K36me3), which functionally correlates with alternative RNA splicing in humans. In addition, the deletion of genes encoding the U2 snRNP subunits, Lea1 or Msl1, in combination with an htb-K123R mutation, leads to synthetic lethality.

Conclusion

These data suggest that H2BK123ub1 facilitates cross talk between chromatin and pre-mRNA splicing by modulating the distribution of intronic and exonic histone modifications.

Efficient heating with a controlled microwave field

To uncover the intriguing non-thermal microwave effect, an experiment was conducted using an amplifier rather than an oscillator as the radiation source, which was injected into an applicator with strong electromagnetic field enhancement. The characteristics of the applicator are discussed and the enhancement of the microwave field is illustrated and explained. Thermal distribution is simulated based on the calculated microwave field profile. It was demonstrated that the proposed system heated a SiC susceptor to a temperature of 637 °C with the input power of 60 W. The reasons for such an efficient heating are discussed.

Genome-wide analysis of the cis-regulatory modules of divergent gene pairs in yeast

In budding yeast, approximately a quarter of adjacent genes are divergently transcribed (divergent gene pairs). Whether genes in a divergent pair share the same regulatory system is still unknown. By examining transcription factor (TF) knockout experiments, we found that most TF knockout only altered the expression of one gene in a divergent pair. This prompted us to conduct a comprehensive analysis in silico to estimate how many divergent pairs are regulated by common sets of TFs (cis-regulatory modules, CRMs) using TF binding sites and expression data. Analyses of ten expression datasets show that only a limited number of divergent gene pairs share CRMs in any single dataset. However, around half of divergent pairs do share a regulatory system in at least one dataset. Our analysis suggests that genes in a divergent pair tend to be co-regulated in at least one condition; however, in most conditions, they may not be co-regulated.

X-ray microfabrication and measurement of a terahertz mode converter

Mode converters are critical for frequency-tunable terahertz gyrotrons. This study reports the development of a broadband TE(02) mode converter centered at 0.2 THz. An octafeed sidewall coupling structure was employed and the mode purity was analyzed. The converter was built using the technique of x-ray microfabrication. The x rays irradiated on the SU-8 resist and generated a template of very high thickness of 1.295 mm. Pulse electroplating technique was used to deposit copper on the structure along the template. The parts then went through precise machining and the residual resist was removed via high-flux radical etching. A computer-aided diagnostic system was introduced to measure the performance of the converter. Results suggest that the frequency response of resistivity should be taken into consideration for the devices in terahertz region.

Comparison of photodegradative efficiencies and mechanisms of Victoria Blue R assisted by Nafion-coated and fluorinated TiO2 photocatalysts

The purposes of this research were to study the effects of two modified photocatalysts, Nafion-coated TiO(2) and fluorinated TiO(2), and photocatalytic degradation of Victoria Blue R in aqueous solution. Photocatalytic degradation of Victoria Blue R was accelerated by the modified photocatalysts. Bulk and surface characterizations of the resulting powders were carried out. Attachment of the anions to the TiO(2) surface using the Nafion-coated-TiO(2) possibly results in increased adsorption of the cationic dye, and the degradation rate is larger for the cationic dye. It was found that Victoria Blue R on the two illuminated TiO(2) surfaces underwent very different changes. To obtain a better understanding on the mechanistic details of this modified-TiO(2)-assisted photodegradation of the Victoria Blue R dye with UV irradiation, a large number of intermediates of the process were separated, identified, and characterized by a high-performance liquid chromatography-mass spectrometry technique. Several probable photodegradation pathways were proposed and discussed.

Roles of trans and cis variation in yeast intraspecies evolution of gene expression

Both cis and trans mutations contribute to gene expression divergence within and between species. We used Saccharomyces cerevisiae as a model organism to estimate the relative contributions of cis and trans variations to the expression divergence between a laboratory (BY) and a wild (RM) strain of yeast. We examined whether genes regulated by a single transcription factor (TF; single input module, SIM genes) or genes regulated by multiple TFs (multiple input module, MIM genes) are more susceptible to trans variation. Because a SIM gene is regulated by a single immediate upstream TF, the chance for a change to occur in its trans-acting factors would, on average, be smaller than that for a MIM gene. We chose 232 genes that exhibited expression divergence between BY and RM to test this hypothesis. We examined the expression patterns of these genes in a BY-RM coculture system and in a BY-RM diploid hybrid. We found that trans variation is far more important than cis variation for expression divergence between the two strains. However, because in 75% of the genes studied, cis variation has significantly contributed to expression divergence, cis change also plays a significant role in intraspecific expression evolution. Interestingly, we found that the proportion of genes with diverged expression between BY and RM is larger for MIM genes than for SIM genes; in fact, the proportion tends to increase with the number of transcription factors that regulate the gene. Moreover, MIM genes are, on average, subject to stronger trans effects than SIM genes, though the difference between the two types of genes is not conspicuous.

A targeted bypass screen identifies Ynl187p, Prp42p, Snu71p, and Cbp80p for stable U1 snRNP/Pre-mRNA interaction

To understand how DEXD/H-box proteins recognize and interact with their cellular substrates, we have been studying Prp28p, a DEXD/H-box splicing factor required for switching the U1 snRNP with the U6 snRNP at the precursor mRNA (pre-mRNA) 5' splice site. We previously demonstrated that the requirement for Prp28p can be eliminated by mutations that alter either the U1 snRNA or the U1C protein, suggesting that both are targets of Prp28p. Inspired by this finding, we designed a bypass genetic screen to specifically search for additional, novel targets of Prp28p. The screen identified Prp42p, Snu71p, and Cbp80p, all known components of commitment complexes, as well as Ynl187p, a protein of uncertain function. To examine the role of Ynl187p in splicing, we carried out extensive genetic and biochemical analysis, including chromatin immunoprecipitation. Our data suggest that Ynl187p acts in concert with U1C and Cbp80p to help stabilize the U1 snRNP-5' splice site interaction. These findings are discussed in the context of DEXD/H-box proteins and their role in vivo as well as the potential need for more integral U1-snRNP proteins in governing the fungal 5' splice site RNA-RNA interaction compared to the number of U1 snRNP proteins needed by metazoans.

Measurement of angular distributions of Drell-Yan dimuons in p+p interactions at 800 GeV/c

We report a measurement of the angular distributions of Drell-Yan dimuons produced using an 800 GeV/c proton beam on a hydrogen target. The polar and azimuthal angular distribution parameters have been extracted over the kinematic range 4.5<m micromicro<15 GeV/c2 (excluding the Upsilon resonance region), 0<p T <4 GeV/c, and 0<x F<0.8. The p+p angular distributions are similar to those of p+d, and both data sets are compared with models which attribute the cos2varphi distribution either to the presence of the transverse-momentum-dependent Boer-Mulders structure function h1 perpendicular to 1 or to QCD effects. The data indicate the need to include QCD effects before reliable information on the Boer-Mulders function can be extracted. The validity of the Lam-Tung relation in p+p Drell-Yan data is also tested.

High-power millimeter-wave rotary joint

The rotary joint is a useful microwave component that connects a fixed part to a rotatable part. This study systematically analyzes the effect of the discontinuity on the interface of a rotary joint for several waveguide modes. Simulation results indicate that the transmission of the TE(01) mode is independent of the geometry of the joint, and thus is ideal for such application. A rotary joint consisting of two identical TE(01) mode converters, clasped each other by a bearing, is designed, fabricated, and tested. Back-to-back transmission measurements exhibit an excellent agreement to the results of computer simulations. The measured optimum transmission is 97% with a 3 dB bandwidth of 8.5 GHz, centered at 35.0 GHz. The cold measurement shows that the results are independent of the angle of rotation. In addition, a high-power experiment is conducted. The just developed rotary joint can operate up to a peak input power of 210 W with a duty of 18%. The working principle, although demonstrated in the millimeter-wave region, can be applied up to the terahertz region where the joint gap is generally critical except for the operating TE(01) mode.

Measurement of Upsilon production for p + p and p + d interactions at 800 GeV/c

We report a high statistics measurement of Upsilon production with an 800 GeV/c proton beam on hydrogen and deuterium targets. The dominance of the gluon-gluon fusion process for Upsilon production at this energy implies that the cross section ratio, sigma(p+d-->Upsilon)/2sigma(p+p-->Upsilon), is sensitive to the gluon content in the neutron relative to that in the proton. Over the kinematic region 0<x(F)<0.6, this ratio is found to be consistent with unity, in striking contrast to the behavior of the Drell-Yan cross section ratio sigma(p+d)(DY)/2sigma(p+p)(DY). This result shows that the gluon distributions in the proton and neutron are very similar. The Upsilon production cross sections are also compared with the p+d and p+Cu cross sections from earlier measurements.

Effect of microwave annealing temperatures on lead zirconate titanate thin films

Lead zirconate titanate (Pb(1.1)(Zr(0.52)Ti(0.48))O(3)) thin films of thickness 260 nm on Pt/Ti/SiO(2)/Si substrates were densified by 2.45 GHz microwave annealing. The PZT thin films were annealed at various annealing temperatures from 400 to 700 °C for 30 min. X-ray diffraction showed that the pyrochlore phase was transformed to the perovskite phase at 450 °C and the film was fully crystallized. The secondary (again pyrochlore) phase was observed in the PZT thin films, which were annealed above 550 °C. The surface morphologies were changed above 550 °C of the PZT thin films due to the secondary phase. Higher dielectric constant (ε(r)) and lower dielectric loss coercive field (E(c)) were achieved for the 450 °C film than for the other annealed films.

Measurement of angular distributions of Drell-Yan dimuons in p+d interactions at 800 GeV/c

We report a measurement of the angular distributions of Drell-Yan dimuons produced using an 800 GeV/c proton beam on a deuterium target. The muon angular distributions in the dilepton rest frame have been measured over the kinematic range 4.5<m{mu mu}<15 GeV/c{2}, 0<p{T}<4 GeV/c, and 0<x{F}<0.8. No significant cos2phi dependence is found in these proton-induced Drell-Yan data, in contrast with the situation for pion-induced Drell-Yan data. The data are compared with expectations from models which attribute the cos2phi distribution to a QCD vacuum effect or to the presence of the transverse-momentum-dependent Boer-Mulders structure function h{1}{perpendicular}. Constraints on the magnitude of the sea-quark h{1}{perpendicular} structure functions are obtained.

Staphylococcus aureus peptidoglycan ameliorates cyclophosphamide-induced impairment of wound healing

Cyclophosphamide given systemically to rats leads to impaired wound healing, characterized by decreases in the inflammatory reaction, fibroplasia, neovascularization, reparative collagen accumulation, and wound breaking strength. In contrast, the local application of Staphylococcus aureus peptidoglycan at the time of wounding increases all of these processes in normal rats. Accordingly, we hypothesized that inoculation of S. aureus peptidoglycan into wounds of cyclophosphamide-treated rats would ameliorate the otherwise impaired healing. Dorsal bilateral skin incisions and subcutaneous implantation of polyvinyl alcohol sponges (two on each side) were performed on male Sprague-Dawley rats receiving either saline or cyclophosphamide (24 mg/kg) intraperitoneally at the time of operation, on postoperative days 1, 2, 3, 4 (for rats killed on postoperative day 7), and also on day 8 (for rats killed on postoperative day 14). The incisions on one side were inoculated at the time of closure with 0.2 ml of saline solution, and the incisions on the other side with 6 mg S. aureus peptidoglycan in 0.2 ml saline solution (860 microg/cm incision). The sponges were instilled with 0.1 ml saline solution on the saline solution-instilled incision side or with S. aureus peptidoglycan 0.5 mg/sponge) in 0.1 ml saline solution on the other side. In control rats receiving saline solution intraperitoneally, incisions treated with S. aureus peptidoglycan were significantly stronger than saline solution-treated incisions by a factor of 1.8 at 1 week (p < 0.001); at 2 weeks the increase was small and not significant. Cardiac blood leukocytes and platelets fell markedly (90%) in cyclophosphamide- treated rats, and there was a decrease in wound breaking strength of their saline-treated incisions at both 7 and 14 days compared with saline solution-treated incisions of control rats. S. aureus peptidoglycan treatment of the wounds completely prevented this effect at 7 days, and partially at 14 days. Polyvinyl alcohol sponge reparative tissue hydroxyproline, 7 days after surgery, was decreased in cyclophosphamide-treated rats; this was completely prevented by S. aureus peptidoglycan treatment of the sponges. Histologically, the inflammatory response to the wounding, influx of macrophages and fibroblasts, angiogenesis, and collagen accumulation were all reduced at day 7 and 14 after surgery in the sponge reparative tissue of cyclophosphamide- treated rats; this was prevented by S. aureus peptidoglycan treatment of the sponges. In conclusion, a single local application of S. aureus peptidoglycan ameliorates cyclophosphamide-impaired wound healing.

Single local instillation of nonviable Staphylococcus aureus or its peptidoglycan ameliorates glucocorticoid-induced impaired wound healing

An excess in glucocorticoid steroids, either from endogenous or exogenous sources, has been shown to inhibit wound repair. Key to this impairment is a diminution of the inflammatory response to wounding, fibroplasia, capillary formation, reparative tissue collagen accumulation, and wound breaking strength. Because a single local application at operation of nonviable Staphylococcus aureus or its peptidoglycan increases all of these processes in normal rats, we hypothesized that nonviable S. aureus and S. aureus peptidoglycan would each ameliorate glucocorticoid-induced impaired healing. Sprague-Dawley male rats aseptically received two 7 cm paravertebral skin incisions and underwent subcutaneous implantation of polyvinyl alcohol sponges. Two glucocorticoids were used: hydrocortisone, 8 mg intramuscularly, daily beginning 1 day before operation and continuing during the postoperative period; or a single dose of a long-acting preparation of methylprednisolone, 6 or 8 mg intramuscularly, on the day before operation. Controls received intramuscular injections of saline solution at the same respective times. At the time of the operation, one incision and the polyvinyl alcohol sponges on one side of the animal were instilled with saline solution while the incision and sponges on the opposite side were instilled with nonviable S. aureus (hydrocortisone study) or S. aureus peptidoglycan (two methylprednisolone studies). The data showed that, at postoperative day 7, the single local application at wounding of nonviable S. aureus or S. aureus peptidoglycan increased wound breaking strength in the control rats by factors of 1.6 in the hydrocortisone experiment and 1.4 and 1.6 in the methylprednisolone studies. These treatments prevented (in hydrocortisone-treated rats) or mitigated (in methylprednisolone-treated rats) the glucocorticoid-induced decrease in wound breaking strength. In addition, these treatments prevented the glucocorticoid-induced decreases in the inflammatory (largely mononuclear cells) response to wounding and in the accumulation within the polyvinyl alcohol sponge of reparative tissue fibroblasts, capillaries, and collagen.

MYBS: a comprehensive web server for mining transcription factor binding sites in yeast

Correct interactions between transcription factors (TFs) and their binding sites (TFBSs) are of central importance to gene regulation. Recently developed chromatin-immunoprecipitation DNA chip (ChIP-chip) techniques and the phylogenetic footprinting method provide ways to identify TFBSs with high precision. In this study, we constructed a user-friendly interactive platform for dynamic binding site mapping using ChIP-chip data and phylogenetic footprinting as two filters. MYBS (Mining Yeast Binding Sites) is a comprehensive web server that integrates an array of both experimentally verified and predicted position weight matrixes (PWMs) from eleven databases, including 481 binding motif consensus sequences and 71 PWMs that correspond to 183 TFs. MYBS users can search within this platform for motif occurrences (possible binding sites) in the promoters of genes of interest via simple motif or gene queries in conjunction with the above two filters. In addition, MYBS enables users to visualize in parallel the potential regulators for a given set of genes, a feature useful for finding potential regulatory associations between TFs. MYBS also allows users to identify target gene sets of each TF pair, which could be used as a starting point for further explorations of TF combinatorial regulation. MYBS is available at http://cg1.iis.sinica.edu.tw/~mybs/.

Variation in Bentgrass Susceptibility to Typhula incarnata and in Isolate Aggressiveness Under Controlled Environment Conditions

Typhula incarnata, the causal agent of gray snow mold, is an important winter pathogen of turfgrasses in the northern United States. The relative susceptibility of cultivars of three bent-grass species (creeping, colonial, and velvet bentgrass) to Typhula incarnata and the aggressiveness of 15 T. incarnata isolates obtained from infected turfgrasses on golf courses in Michigan, Minnesota, and Wisconsin were evaluated under controlled conditions. A hypersensitive type of resistance response to T. incarnata was not observed in any cultivar. Disease severity increased with higher inoculum concentration of T. incarnata. Colonization by gray snow mold gradually decreased with increasing plant age from 11 weeks after seeding in most cultivars tested, suggesting that age-related resistance was expressed over time. There were significant differences in disease severity among the three bentgrass species, particularly between tetraploid (creeping and colonial) and diploid (velvet) species, and among cultivars within each species, indicating varying levels of susceptibility to T. incarnata. All 15 isolates were pathogenic on bentgrass and were significantly different in aggressiveness, but aggressiveness was not related to geographic origin. Therefore, turfgrass breeders should be able to use one or a few virulent representative isolates of the pathogen to screen for resistance.

Rise and fall time behavior of the gyrotron backward-wave oscillator

The rise and fall time behavior of a pulsed microwave oscillator is a problem of academic interest. It is also of importance to radar and other applications because it can lead to phase and frequency jitters or even lock the entire pulse into an undesired mode. Here we present a study of the rise and fall time behavior in the gyrotron backward-wave oscillator (gyro-BWO). Single-mode simulations reveal that, during the rise and fall portions of the electron beam pulse, oscillation frequencies of the axial modes vary in such a way that their transit angles remain at the respective optimum values. Thus, axial mode competition and mode switching can readily take place in these transient stages. Time-dependent simulations demonstrate that, under both the gradual and instant turn-on conditions, the axial modes compete in a pattern governed by the characteristic asymmetry of the mode profiles. Other aspects of physics interest include the analysis and explanation of a resultant hysteresis effect between the rise and fall portions of the beam pulse. These understandings are expected to provide the basis for achieving a stable gyro-BWO operating at a single mode throughout the entire beam pulse.

Nuclear localization of poly(A)+ mRNA following siRNA reduction of expression of the mammalian RNA helicases UAP56 and URH49

UAP56 is a eukaryotic RNA helicase that is important for mRNA splicing and nuclear export. Although most eukaryotes have a single protein corresponding to UAP56, we have shown previously that in human and mouse cells there is a second protein, URH49, which is 90% identical to UAP56. Both proteins interact with the mRNA export factor Aly and both are able to rescue the loss of Sub2p (the yeast homolog of UAP56), suggesting that both proteins have similar functions. However, the two helicases have different expression profiles in different tissues and in growth-stimulated cells, which raises the possibility that they might be involved in the splicing and export of non-identical populations of mRNA. In the present study, we have used RNA interference to further explore the functions of these two helicases. Reducing the expression of either URH49 or UAP56 in HeLa cells had little effect on cell proliferation or expression of a co-transfected gene. However, analysis of poly(A)+ RNA localization by fluorescent in situ hybridization revealed a speckled pattern of RNA accumulation throughout the nucleus. Reducing the expression of both helicases resulted in a major reduction in reporter gene expression as well as cell death within 72 h. We also observed a more prominent speckled pattern of nuclear poly(A)+ RNA accumulation as well as reduced accumulation in the cytoplasmic compartment. These observations suggest that both helicases have essential but largely overlapping functions in the processing and export of mammalian mRNAs.

Transition of absolute instability from global to local modes in a gyrotron traveling-wave amplifier

The gyrotron traveling-wave amplifier employing the distributed-loss scheme is capable of very high gain and effective in suppressing the global absolute instabilities. This study systematically characterizes the local absolute instabilities and their transitional behavior. The local absolute instabilities are analyzed using a model that incorporates the penetration of the field from the copper section into the lossy section. The axial modes were characterized from the perspective of beam-wave interaction and were found to share many characteristics with the global modes. The transition from global modes to local modes as the distributed loss increases was demonstrated. The electron transit angle in the copper section, which determines the feedback criterion, governs the survivability of an oscillation. In addition, the oscillation thresholds predicted using this model are more accurate than those obtained using a simplified model.

Aggressiveness of Typhula ishikariensis Isolates to Cultivars of Bentgrass Species (Agrostis spp.) Under Controlled Environment Conditions

Speckled snow mold, caused by Typhula ishikariensis, is one of the most important Typhula snow molds in subarctic zones of the Northern Hemisphere. Nine isolates of three T. ishikariensis varieties (var. ishikariensis, var. canadensis, and var. idahoensis) isolated from infected turfgrasses on golf course fairways throughout Wisconsin were evaluated for their aggressiveness toward nine cultivars of three bentgrass species (three creeping, three colonial, and three velvet cultivars) under controlled environmental conditions. Speckled snow mold severity increased as inoculum concentration of T. ishikariensis was increased. In general, bentgrass susceptibility increased between 9 and 11 weeks after seeding but gradually decreased thereafter, suggesting expression of age-related resistance as plants matured. Significant differences in aggressiveness were detected within and among T. ishikariensis varieties. Significant interactions between T. ishikariensis varieties or isolates and bentgrass species were detected, but there was no interaction between pathogen isolates and bentgrass cultivars. Disease severity evaluations showed significant differences among bentgrass cultivars and species in their response to T. ishikariensis. Since bentgrass species exhibit differential responses to T. ishikariensis varieties, representative isolates of each variety should be employed for screening of bentgrass germplasm for resistance to speckled snow mold.

Dynamics of mode competition in the gyrotron backward-wave oscillator

The axial modes of the gyrotron backward-wave oscillator (gyro-BWO) each exhibit a distinctive asymmetry in axial field profile. As a result, and in sharp contrast to the behavior of the familiar resonator-based gyrotron oscillator, particle simulations of the gyro-BWO reveal a radically different pattern of mode competition in which a fast-growing and well-established mode is subsequently suppressed by a later-starting mode with a more favorable field profile. This is verified in a Ka-band experiment and the interaction dynamics are elucidated with a time-frequency analysis.

Exploring functional relationships between components of the gene expression machinery

Eukaryotic gene expression requires the coordinated activity of many macromolecular machines including transcription factors and RNA polymerase, the spliceosome, mRNA export factors, the nuclear pore, the ribosome and decay machineries. Yeast carrying mutations in genes encoding components of these machineries were examined using microarrays to measure changes in both pre-mRNA and mRNA levels. We used these measurements as a quantitative phenotype to ask how steps in the gene expression pathway are functionally connected. A multiclass support vector machine was trained to recognize the gene expression phenotypes caused by these mutations. In several cases, unexpected phenotype assignments by the computer revealed functional roles for specific factors at multiple steps in the gene expression pathway. The ability to resolve gene expression pathway phenotypes provides insight into how the major machineries of gene expression communicate with each other.

Absolute instabilities in a high-order-mode gyrotron traveling-wave amplifier

The absolute instability is a subject of considerable physics interest as well as a major source of self-oscillations in the gyrotron traveling-wave amplifier (gyro-TWT). We present a theoretical study of the absolute instabilities in a TE01 mode, fundamental cyclotron harmonic gyro-TWT with distributed wall losses. In this high-order-mode circuit, absolute instabilities arise in a variety of ways, including overdrive of the operating mode, fundamental cyclotron harmonic interactions with lower-order modes, and second cyclotron harmonic interaction with a higher-order mode. The distributed losses, on the other hand, provide an effective means for their stabilization. The combined configuration thus allows a rich display of absolute instability behavior together with the demonstration of its control. We begin with a study of the field profiles of absolute instabilities, which exhibit a range of characteristics depending in large measure upon the sign and magnitude of the synchronous value of the propagation constant. These profiles in turn explain the sensitivity of oscillation thresholds to the beam and circuit parameters. A general recipe for oscillation stabilization has resulted from these studies and its significance to the current TE01 -mode, 94-GHz gyro-TWT experiment at UC Davis is discussed.

RNA unwinding assay for DExD/H-box RNA helicases

The evolutionarily conserved DExD/H-box proteins are essential for all RNA-related biological processes. They are thought to modulate the structure and function of specific RNAs and/or ribonucleoprotein particles by using their intrinsic RNA-dependent ATPase activities to achieve the desired conformational changes. A number of DExD/H-box proteins have been shown to unwind short RNA duplexes in vitro, a hallmark of the so-called RNA helicases or unwindases. However, some are unable to do so, perhaps because of requirements for cofactors. Here, we present a "solid-state" method that may allow investigators to overcome such problems.

Ded1p, a conserved DExD/H-box translation factor, can promote yeast L-A virus negative-strand RNA synthesis in vitro

Viruses are intracellular parasites that must use the host machinery to multiply. Identification of the host factors that perform essential functions in viral replication is thus of crucial importance to the understanding of virus-host interactions. Here we describe Ded1p, a highly conserved DExD/H-box translation factor, as a possible host factor recruited by the yeast L-A double-stranded RNA (dsRNA) virus. We found that Ded1p interacts specifically and strongly with Gag, the L-A virus coat protein. Further analysis revealed that Ded1p interacts with the L-A virus in an RNA-independent manner and, as a result, L-A particles can be affinity purified via this interaction. The affinity-purified L-A particles are functional, as they are capable of synthesizing RNA in vitro. Critically, using purified L-A particles, we demonstrated that Ded1p specifically promotes L-A dsRNA replication by accelerating the rate of negative-strand RNA synthesis in vitro. In light of these data, we suggest that Ded1p may be a part of the long sought after activity shown to promote yeast viral dsRNA replication. This and the fact that Ded1p is also required for translating brome mosaic virus RNA2 in yeast thus raise the intriguing possibility that Ded1p is one of the key host factors favored by several evolutionarily related RNA viruses, including the human hepatitis C virus.