bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation of mutations that act in trans to alter expression from a yeast hsp70 promoter.
Authors: Findly R C , Alavi H , Platt T
Published: September 2015

Transcription of SSA1 (formerly YG100), a member of the hsp70 gene family in Saccharomyces cerevisiae, increases dramatically upon heat shock. An expression vector in which the promoter of SSA1 is fused to the Escherichia coli galactokinase gene (galK) was constructed and transformed into a galactokinase-deficient yeast strain. The transformants grew on galactose at 23 degrees C, but increased expression of the SSA1-galK fusion gene inhibited growth of cells on galactose at 37 degrees C. Selection for survivors under nonpermissive conditions yielded a class of mutants, termed HSR (for heat shock regulation), which showed reduced levels of expression of the hsp70-galK gene fusion as determined by measurement of galactokinase activity. Similar effects on beta-galactosidase activity were obtained when an SSA1-lacZ fusion vector was introduced into the mutants, suggesting action in trans through the SSA1 promoter. Analysis of Northern (RNA) blots demonstrated that the reduction in expression was a result of decreased mRNA levels for the fusion gene. In addition, mRNA levels of the endogenous SSA1 gene are reduced in an HSR mutant. Genetic analysis has shown that these mutations act in trans and affect both transcription from the SSA1 promoter and turnover of the fusion transcript. These are the first trans-acting mutations known to affect directly the transcriptional regulation and transcript stability of heat shock genes in eucaryotes.
Structural characterization of Dictyostelium discoideum prespore-specific gene D19 and of its product, cell surface glycoprotein PsA.
Authors: Early A E , Williams J G , Meyer H E , Por S B , Smith E , Williams K L , Gooley A A
Published: September 2015

The Dictyostelium discoideum cell surface antigen PsA is a glycoprotein which first appears in the multicellular stage soon after tip formation and is selectively expressed on prespore cells. The D19 gene encodes an mRNA sequence which is highly enriched in prespore over prestalk cells in the slug stage. We have determined 81 amino acid residues of N-terminal sequence from immunoaffinity-purified PsA protein and shown this sequence to be identical to the predicted sequence of the D19 gene. There are several short repeat elements close to the C terminus, and unequal crossing-over within these is proposed to account for the size polymorphism observed in PsA protein isolated from different D. discoideum strains. The repeats are proline rich and show similarity to the C-terminal region of the D. discoideum cell adhesion molecule, contact sites A. The extreme C terminus, which is also homologous to contact sites A, is characteristic of proteins attached to the plasma membrane via a glycosyl-phosphatidylinositol link. We have marked the PsA gene by insertion of an oligonucleotide encoding an epitope of the human c-myc protein. A construct containing this gene and 990 base pairs of 5'-flanking region directed correct temporal and spatial mRNA accumulation. We found the marked PsA protein, detected with the human c-myc antibody, to be correctly localized on the surface of cells.
Identification of basal and cyclic AMP regulatory elements in the promoter of the phosphoenolpyruvate carboxykinase gene.
Authors: Quinn P G , Wong T W , Magnuson M A , Shabb J B , Granner D K
Published: September 2015

Promoter elements important for basal and cyclic AMP (cAMP)-regulated expression of the phosphoenolpyruvate carboxykinase (PEPCK) gene have been identified by analysis of a series of PEPCK promoter mutations in transfection experiments. Fusion genes containing wild-type and mutated PEPCK promoter sequences from -600 to +69 base pairs (bp) fused to the coding sequence for chloramphenicol acetyltransferase were studied. Internal deletion mutations that replaced specific bases with a 10-bp linker within the region from -129 bp to -18 bp of the PEPCK promoter were examined. In addition, wild-type and mutated DNA templates were used as probes in DNase I protection experiments to determine sites of protein-DNA interaction. The PEPCK promoter contains a binding site for nuclear factor 1-CAAT. Deletion of the 5' end of this binding site reduced the size of the DNase I footprint in this region but had no effect on promoter activity. In contrast, deletion or disruption of the 3' end of this binding site completely eliminated protein binding and reduced promoter activity by 50%. Deletion of core sequences of the cAMP regulatory element (CRE) resulted in loss of cAMP responsiveness and an 85% decrease in basal promoter activity, indicating that the CRE also functions as a basal stimulatory element. Mutation of the core sequence of the CRE resulted in loss of the DNase I footprint over the CRE. Internal deletions flanking the CRE showed no loss of induction by cAMP but did have reduced promoter activity. This delimits the CRE to an 18-bp region between nucleotides -100 and -82. Analysis of mutations that disrupted bases between the CRE and the initiation site identified a basal inhibitory element adjacent to a basal stimulatory element, both located just 3' of the CRE, as well as a basal stimulatory element coincident with the TATA consensus sequence centered at -27. These data demonstrate that several cis-acting elements are located within 130 nucleotides of the initiation site of the PEPCK gene and that the CRE is essential for both basal promoter activity and cAMP-regulated expression of this gene.
The NF-kappa B-binding site mediates phorbol ester-inducible transcription in nonlymphoid cells.
Authors: Nelsen B , Hellman L , Sen R
Published: September 2015

The mouse immunoglobulin kappa light-chain enhancer can interact with at least three independent nuclear proteins. One of these proteins, NF-kappa B, is constitutively present only in nuclear extracts derived from B cells and plasma cells. A DNA-binding protein with the same sequence specificity (and therefore presumed to be NF-kappa B itself) can be induced in pre-B cells, T cells, and nonlymphoid cells by phorbol 12-acetate-13-myristate (PMA); however, it is not clear whether the induced factor can activate transcription in nonlymphoid cells as NF-kappa B does in B cells. In this paper we show that multimerization of a fragment of the mouse kappa enhancer that carried only the binding site for NF-kappa B behaved like a B-cell-specific regulatory element. Furthermore, this unit served to activate transcription in nonlymphoid cells after treatment with PMA (but not with cyclic AMP derivatives), and the kinetics of transcription activation correlated well with the kinetics of factor induction. Thus, the induced DNA-binding activity appeared to be functionally indistinguishable from that of NF-kappa B.
Induction of neuronal differentiation in PC12 cells by B-cell stimulatory factor 2/interleukin 6.
Authors: Satoh T , Nakamura S , Taga T , Matsuda T , Hirano T , Kishimoto T , Kaziro Y
Published: September 2015

B-cell stimulatory factor 2 (BSF-2) is a lymphokine which induces the final maturation of B cells. BSF-2 acts on a variety of cells other than B cells, and moreover, expression of BSF-2 mRNA is detected in interleukin-1 beta-stimulated glioblastoma and astrocytoma cell lines. Here, we studied the function of BSF-2 on pheochromocytoma PC12 cells, a model system for induction of neuronal differentiation. PC12 cells possess specific receptors for BSF-2. The BSF-2-stimulated PC12 cells expressed the c-fos proto-oncogene transiently, and they began to change morphologically to neurite-extending cells after several days. The number of voltage-dependent Na+ channels was also increased.
The carboxy-terminal sequence of p56lck can regulate p60c-src.
Authors: MacAuley A , Cooper J A
Published: September 2015

A chimera containing the coding region for residues 1 to 516 of p60c-src and residues 495 to 509 (the carboxy terminus) of p56lck was constructed and expressed in mouse fibroblasts. The chimeric protein appeared to be phosphorylated and regulated in the same fashion as p60c-src.
RAD1, an excision repair gene of Saccharomyces cerevisiae, is also involved in recombination.
Authors: Schiestl R H , Prakash S
Published: September 2015

The RAD1 gene of Saccharomyces cerevisiae is required for the incision step of excision repair of damaged DNA. In this paper, we report our observations on the effect of the RAD1 gene on genetic recombination. Mitotic intrachromosomal and interchromosomal recombination in RAD+, rad1, rad52, and other rad mutant strains was examined. The rad1 deletion mutation and some rad1 point mutations reduced the frequency of intrachromosomal recombination of a his3 duplication, in which one his3 allele is deleted at the 3' end while the other his3 allele is deleted at the 5' end. Mutations in the other excision repair genes, RAD2, RAD3, and RAD4, did not lower recombination frequencies in the his3 duplication. As expected, recombination between the his3 deletion alleles in the duplication was reduced in the rad52 mutant. The frequency of HIS3+ recombinants fell synergistically in the rad1 rad52 double mutant, indicating that the RAD1 and RAD52 genes affect this recombination via different pathways. In contrast to the effect of mutations in the RAD52 gene, mutations in the RAD1 gene did not lower intrachromosomal and interchromosomal recombination between heteroalleles that carry point mutations rather than partial deletions; however, the rad1 delta mutation did lower the frequency of integration of linear plasmids and DNA fragments into homologous genomic sequences. We suggest that RAD1 plays a role in recombination after the formation of the recombinogenic substrate.
Promoter sequences required for transcription of Xenopus laevis histone genes in injected frog oocyte nuclei.
Authors: Heindl L M , Weil T S , Perry M
Published: September 2015

Amphibian oogenesis is accompanied by the accumulation of histone mRNA and proteins in the absence of ongoing DNA replication. To begin an analysis of the mechanisms by which histone gene expression is regulated during frog oogenesis and embryogenesis, we used oocyte injection to examine the upstream sequences required for transcription of genes encoding each of the five histone classes. We found that sequences necessary for maximal levels of transcription are located 100 to 200 base pairs upstream of the corresponding start sites. In this region, each promoter examined contains conserved sequence elements, several of which seem to be histone gene class specific, in addition to other, more common sequence elements believed to be used by general transcription factors.
Adenovirus transcriptional regulatory regions are conserved in mammalian cells and Saccharomyces cerevisiae.
Authors: Kornuc M , Altman R , Harrich D , Garcia J , Chao J , Kayne P , Gaynor R
Published: September 2015

The adenovirus early region 3 (E3) promoter is an early viral promoter which is strongly induced by the adenovirus transactivator protein E1A. DNase I footprinting with HeLa cell extracts has identified four factor-binding domains which appear to be involved in basal and E1A-induced transcriptional regulation. These binding domains may bind TATA region-binding factors (site I), the CREB/ATF protein (site II), the AP-1 protein (site III), and nuclear factor I/CTF (site IV). Recently, it has been shown that the DNA-binding domain of transcription factor AP-1 has homology with the yeast transcription factor GCN4 and that the yeast transactivator protein GAL4 is able to stimulate transcription in HeLa cells from promoters containing GAL4-binding sites. These results suggest an evolutionary conservation of both transcription factors and the mechanisms responsible for transcriptional activation in Saccharomyces cerevisiae and higher eucaryotic organisms. To determine whether similar patterns of transcriptional regulation were seen with the E3 promoter in HeLa and yeast cells, the E3 promoter fused to the chloramphenicol acetyltransferase (cat) gene was cloned into a high-copy-number plasmid and stably introduced into yeast cells. S1 analysis revealed that similar E3 promoter mRNA start sites were found in yeast and HeLa cells. DNase I footprinting with partially purified yeast extracts revealed that four regions of the E3 promoter were protected. Several of these regions were similar to binding sites determined by using HeLa cell extracts. Oligonucleotide mutagenesis of these binding domains indicated their importance in the transcriptional regulation of the E3 promoter in yeast cells. These results suggest that similar cellular transcription factor-binding sites may be involved in the regulation of promoters in both yeast and mammalian cells.
Evolution, expression, and chromosomal location of a novel receptor tyrosine kinase gene, eph.
Authors: Maru Y , Hirai H , Yoshida M C , Takaku F
Published: September 2015

Partial sequence analysis of the genomic eph locus revealed that the splicing points of kinase domain-encoding exons were completely distinct from those of the other protein tyrosine kinase members reported, suggesting that this is the earliest evolutionary split within this family. In Northern (RNA) blot analysis, the eph gene was expressed in liver, lung, kidney, and testis of rat, and screening of 25 human cancers of various cell types showed preferential expression in cells of epithelial origin. Overexpression of eph mRNA was found in a hepatoma and a lung cancer without gene amplification. Comparison of cDNA sequences derived from a normal liver and a hepatoma that overproduces eph mRNA demonstrated that two of them were completely identical throughout the transmembrane to the carboxy-terminal portions. Southern blot analysis of DNAs from human-mouse hybrid clones with an eph probe showed that this gene was present on human chromosome 7.
Holliday intermediates and reaction by-products in FLP protein-promoted site-specific recombination.
Authors: Meyer-Leon L , Huang L C , Umlauf S W , Cox M M , Inman R B
Published: September 2015

Holliday structures are formed and resolved by FLP protein during site-specific recombination. These structures have been isolated and are visualized in both native and partially denatured states by electron microscopy. No single-strand breaks are found within the junction, indicating that the structure results from a reciprocal exchange of strands. These structures have properties consistent with being reaction intermediates. Double-strand cleavage products and "Y structures" are also detected and appear to be by-products of the reaction. The Y structures are three-armed branched molecules with a covalently closed junction located at the FLP recombination target site. Models are discussed, suggesting that both of these novel structures are made by aberrant cleavages during formation and resolution of the Holliday intermediate.
Structural and functional conservation between yeast and human 3-hydroxy-3-methylglutaryl coenzyme A reductases, the rate-limiting enzyme of sterol biosynthesis.
Authors: Basson M E , Thorsness M , Finer-Moore J , Stroud R M , Rine J
Published: September 2015

The pathway of sterol biosynthesis is highly conserved in all eucaryotic cells. We demonstrated structural and functional conservation of the rate-limiting enzyme of the mammalian pathway, 3-hydroxy-3-methyl-glutaryl coenzyme A reductase (HMG-CoA reductase), between the yeast Saccharomyces cerevisiae and humans. The amino acid sequence of the two yeast HMG-CoA reductase isozymes was deduced from DNA sequence analysis of the HMG1 and HMG2 genes. Extensive sequence similarity existed between the region of the mammalian enzyme encoding the active site and the corresponding region of the two yeast isozymes. Moreover, each of the yeast isozymes, like the mammalian enzyme, contained seven potential membrane-spanning domains in the NH2-terminal region of the protein. Expression of cDNA clones encoding either hamster or human HMG-CoA reductase rescued the viability of hmg1 hmg2 yeast cells lacking this enzyme. Thus, mammalian HMG-CoA reductase can provide sufficient catalytic function to replace both yeast isozymes in vivo. The availability of yeast cells whose growth depends on human HMG-CoA reductase may provide a microbial screen to identify new drugs that can modulate cholesterol biosynthesis.
Isolation and structural characterization of the human 4F2 heavy-chain gene, an inducible gene involved in T-lymphocyte activation.
Authors: Gottesdiener K M , Karpinski B A , Lindsten T , Strominger J L , Jones N H , Thompson C B , Leiden J M
Published: September 2015

The human 4F2 cell surface antigen is a 120-kilodalton (kDa) disulfide-linked heterodimer which is composed of an 80- to 90-kDa glycosylated heavy chain (4F2HC) and a 35- to 40-kDa nonglycosylated light chain (4F2LC). 4F2 belongs to a family of inducible cell surface molecules which are involved in T-lymphocyte activation and growth. To better understand the molecular mechanism(s) that controls 4F2HC gene expression in both resting and activated T cells, a 4F2HC human genomic clone was isolated and structurally characterized. The 4F2HC gene spans 8 kilobases of chromosome 11 and is composed of nine exons. The 5' upstream region of the gene displays several properties which are characteristic of housekeeping genes. It is G+C rich and hypomethylated in peripheral blood lymphocyte DNA and contains multiple binding sites for the Sp1 transcription factor while lacking TATA or CCAAT sequences. This region of the gene also displays sequence homologies with several other inducible T-cell genes, including the interleukin-2, interleukin-2 receptor alpha chain, dihydrofolate reductase, thymidine kinase, and transferrin receptor genes. A 255-base-pair fragment of the 4F2HC gene which contains 154 base pairs of the 5' flanking sequence was able to efficiently promote expression of the bacterial chloramphenicol acetyltransferase gene in human Jurkat T cells, indicating that it contains promoter or enhancer (or both) sequences. Analyses of chromatin structure in resting and lectin-activated T cells revealed the presence of stable DNase I-hypersensitive sites within both the 5' flanking and intron 1 regions of the 4F2HC gene. Although the 4F2HC gene displayed many of the structural features characteristic of a constitutively expressed gene, lectin-mediated activation of resting peripheral blood T lymphocytes resulted in a dramatic increase in steady-state levels of 4F2HC mRNA.
Polycistronic transcripts in trypanosomes and their accumulation during heat shock: evidence for a precursor role in mRNA synthesis.
Authors: Muhich M L , Boothroyd J C
Published: September 2015

Maturation of mRNA precursors in trypanosomes involves an apparent trans splicing event in which a 39-nucleotide miniexon sequence, common to all trypanosome mRNAs, is joined to the 5' end of a protein-coding exon. We demonstrate that the processing machinery responsible for the maturation of tubulin mRNA precursors in Trypanosoma brucei can be disrupted by heat shock. This results in an accumulation of polycistronic RNA species and a decrease in the abundance of branched splicing intermediates. At normal temperatures, tubulin polycistronic transcripts were also detected and were shown in pulse-chase experiments to be abundantly synthesized and very rapidly turned over. These results, combined with results of the heat shock experiments, suggest that these polycistronic transcripts are the precursors of the (monocistronic) tubulin mRNAs of trypanosomes.
Transcriptional unit of the murine Thy-1 gene: different distribution of transcription initiation sites in brain.
Authors: Spanopoulou E , Giguere V , Grosveld F
Published: September 2015

Structural analysis of the mouse Thy-1.2 gene has shown that the major promoter of the gene is characterized by a tissue-specific DNase I-hypersensitive site and is located within a methylation-free island. The gene is regulated at the transcriptional level, and steady-state mRNA analysis reveals that the previously reported exon Ib contributes at most 5% of the total mRNA. The major promoter uses several transcription initiation sites within a region of 100 base pairs. The frequency of usage of these sites in brain is markedly different from that in other tissues.
Glucocorticoid and developmental regulation of amylase mRNAs in mouse liver cells.
Authors: Samuelson L C , Keller P R , Darlington G J , Meisler M H
Published: September 2015

We characterized alpha-amylase expression in the hepatoma cell line Hepa 1-6 and in normal mouse liver. Both Amy-1 and Amy-2 were expressed in Hepa 1-6 and were regulated by glucocorticoids. Transcription in the hepatoma cells was initiated at the same start sites as in mouse tissues. Glucocorticoid treatment increased the abundance of Amy-1 and Amy-2 transcripts by 10 to 20-fold. This increase was detected within 4 h and was maximal by 24 h. The pattern of amylase expression in this hepatoma cell line accurately reflects amylase expression in the liver in vivo. During liver development, we observed a large increase in the abundance of Amy-1 transcripts just before birth, at a time when circulating glucocorticoids are also elevated. Adult mouse liver expressed Amy-1 and Amy-2 at levels comparable to those of fully induced hepatoma cells. Liver is thus a likely source of both amylase isozymes in mouse serum. These studies demonstrate that Amy-2 expression is not limited to the pancreas but also occurs at a low level in liver cells.
The amino-terminal region of the adenovirus serotype 5 E1a protein performs two separate functions when expressed in primary baby rat kidney cells.
Authors: Smith D H , Ziff E B
Published: September 2015

Adenovirus serotype 5 E1a proteins immortalize primary cells and in cooperation with products of a second oncogene, such as adenovirus serotype 5 E1b or EJ ras, produce full transformation. E1a also activates transcription of specific viral and cellular promoters, represses enhancer-dependent genes, and induces cellular DNA synthesis in quiescent cells. Comparison of different adenovirus serotypes has identified three conserved regions in the E1a protein sequence. We have analyzed E1a mutants with deletions-linker insertions in or preceding the first conserved region, region 1 (amino acids 40 through 77 of adenovirus serotype 5 E1a). E1a mutants which have in-frame deletions-substitutions in region 1 or pre-region 1 sequences were reconstructed into adenovirus to yield a total of 14 mutant viruses. All the mutant viruses showed wild-type growth in HeLa cells, confirming that region 1 is nonessential in these cells. However, we show that region 1 provides two distinct functions in infected primary rodent cells. One function is essential for induction of cell DNA synthesis, and the other is essential for focus formation. In addition, our results are consistent with a requirement for the DNA induction function in focus formation.
Efficient repair of HO-induced chromosomal breaks in Saccharomyces cerevisiae by recombination between flanking homologous sequences.
Authors: Rudin N , Haber J E
Published: September 2015

Novel recombinational repair of a site-specific double-strand break (DSB) in a yeast chromosome was investigated. When the recognition site for the HO endonuclease enzyme is embedded in nonyeast sequences and placed between two regions of homology, expression of HO endonuclease stimulates recombination between the homologous flanking regions to yield a deletion, the apparent product of an intrachromosomal exchange between direct repeats. This deletion-repair event is very efficient, thus preventing essentially all the potential lethality due to the persistence of a DSB. Interestingly, unlike previous studies involving spontaneous recombination between chromosomal repeats, the recombination events stimulated by HO-induced DSBs are accompanied by loss of the sequences separating the homologous regions greater than 99.5% of the time. Repair is dependent on the RAD52 gene. The deletion-repair event provides an in vivo assay for the sensitivity of any particular recognition site to HO cleavage. By taking advantage of a galactose-inducible HO gene, it has been possible to follow the kinetics of this event at the DNA level and to search for intermediates in this reaction. Deletion-repair requires approximately 45 min and is inhibited when cycloheximide is added after HO endonuclease cleavage.
Expression of the c-myb and c-myc genes is regulated independently in differentiating mouse erythroleukemia cells by common processes of premature transcription arrest and increased mRNA turnover.
Authors: Watson R J
Published: September 2015

The mechanisms that modulate c-myb mRNA levels in mouse erythroleukemia cells induced toward erythroid differentiation were compared with those that act on c-myc. Both genes exhibited regulation at the levels of premature transcription arrest and RNA turnover. However, these common processes allowed temporally distinct control of gene expression.
Mapping of cellular protein-binding sites on the products of early-region 1A of human adenovirus type 5.
Authors: Egan C , Jelsma T N , Howe J A , Bayley S T , Ferguson B , Branton P E
Published: September 2015

The binding sites for the 300-, 107-, and 105-kilodalton cellular proteins which associate with human adenovirus type 5 E1A products were studied with E1A deletion mutants. All appeared to bind to the amino-terminal half of E1A products in regions necessary for oncogenic transformation. These results suggest that these cellular species may be important for the biological activity of E1A products.
The six amino-terminal amino acids of p60src are sufficient to cause myristylation of p21v-ras.
Authors: Buss J E , Der C J , Solski P A
Published: September 2015

We have used oligonucleotide-directed mutagenesis to replace the N-terminal amino acids of p21v-ras with residues which mimic the amino terminus of p60v-src. p21v-ras protein possessing only the first five amino acids of p60src was not myristylated, while substitution of residue 6 (serine) produced a protein p21(GSSKS) which incorporated [3H]myristic acid that was stable to hydroxylamine, sensitive to inhibitors of protein synthesis, and found in both the normally nonacylated precursor and mature forms of p21(GSSKS). This defines the minimum framework of the p60v-src myristylation signal (glycine 2 and serine 6) and identifies serine 6 as a crucial part of that signal for myristylation of a protein in vivo.
Transscleral cyclophotocoagulation in refractory acute and chronic angle closure glaucoma
Authors: Yusuf Imran H , Shah Mital , Shaikh Asifa , James C Bruce
Published: September 2015

Angle closure glaucoma, both acute and chronic, is a major cause of blindness worldwide. Transscleral cyclophotocoagulation (TSCP) is conventionally undertaken non-urgently in patients with advanced glaucoma and poor visual potential with poor control of intraocular pressure (IOP). We describe a case of a patient with refractory acute angle closure glaucoma and severe pain in whom emergency TSCP was undertaken 12 h after presentation, reducing the IOP from 68 to 10 mm Hg. Further, a patient with chronic angle closure glaucoma underwent TSCP, reducing the IOP from 78 to 14 mm Hg. Both patients consequently underwent uneventful phacoemulsification cataract surgery with preservation of visual acuity and long-term IOP control. TSCP may achieve prompt IOP control and symptomatic relief in the acute setting in patients with acute and chronic forms of angle closure glaucoma refractory to medical therapy. TSCP may reduce the risk of definitive surgical intervention by temporising phacoemulsification or trabeculectomy surgery until the IOP is well controlled.
Lymphangiogenic factors are associated with the severity of hypersensitivity pneumonitis
Authors: Yamashita Masahiro , Mouri Takashi , Niisato Miyuki , Nitanai Hiroo , Kobayashi Hitoshi , Ogasawara Masahito , Endo Ryujin , Konishi Kazuki , Sugai Tamotsu , Sawai Takashi , Yamauchi Kohei
Published: September 2015

Background

Antigen presenting cells play a pivotal role in the adaptive immune response in hypersensitivity pneumonitis (HP). It was hypothesised that lymphangiogenesis is involved in the pathophysiology of HP via cell transport.

Objective

To determine the clinical significance of lymphangiogenic factors in HP.

Methods

Levels of vascular endothelial growth factors (VEGF)-A, VEGF-C, VEGF-D and CCL21 in the serum and bronchoalveolar lavage fluid (BALF) were measured in 29 healthy volunteers, 14 patients with idiopathic pulmonary fibrosis (IPF) and 26 patients with HP by ELISA. Additionally, immunohistochemical analyses were performed using lung specimens of patients with HP (n=8) and IPF (n=10).

Results

BALF VEGF-D levels were significantly elevated in patients with HP compared to the other groups. BALF VEGF–D levels in patients with HP correlated significantly with the BALF total cell and lymphocyte counts (r=0.485, p=0.014 and r=0.717, p<0.0001, respectively). BALF VEGF-C and CCL21 levels were increased in patients with HP compared to healthy volunteers, but not patients with IPF. BALF CCL21 levels were negatively correlated with the forced expiratory volume in 1 s percentage and diffuse capacity of the lung for carbon monoxide (r=−0.662, p=0.007 and r=−0.671, p=0.024, respectively). According to the immunohistochemical analyses, CCL21 was expressed in the lymphatic endothelium in both conditions and CCR7+cells were aggregated around lymphatics in patients with HP, but not in patients with IPF.

Conclusions

Lymphangiogenic factors might be associated with the inflammatory and functional severity of HP. The increased BALF VEGF-D levels were associated with lymphatic alveolitis intensity, and CCL21 with lung function impairment.
Conformational change in individual enzyme molecules
Authors: Crawford Jeremie J. , Itzkow Frannie , MacLean Joanna , Craig Douglas B.
Published: September 2015

Single β-galactosidase molecule assays were performed using a capillary electrophoresis based protocol, employing post-column laser-induced fluorescence detection. In a first set of experiments, the distribution of single β-galactosidase molecule catalytic rates and electrophoretic mobilities were determined from lysates of Escherichia coli strains containing deletions for different heat shock proteins and grown under normal and heat shock conditions. There was no clear observed pattern of effect of heat shock protein expression on these distributions. In a second set of experiments, individual enzyme molecule catalytic rates were determined at 21 °C before and after 2 sequential brief periods of incubation at 50, 28, and 10 °C. The brief incubations at 50 °C caused a change in the enzyme molecules resulting in a different catalytic rate. Any given molecule was just as likely to show an increase in rate as a decrease, resulting in no significant difference in the average rate of the population. The average change in individual molecule rate was dependent upon the temperature of the brief incubation period, with a lesser average change occurring at 28 °C and negligible change at 10 °C. A third set of experiments was similar to that of the second with the exception that it was electrophoretic mobility that was considered. This provided a similar result. Incubation at higher temperature resulted in a change in electrophoretic mobility. The probability of an individual molecules switching to a higher mobility was approximately equal to that of switching to a lower mobility, resulting in no net average change in the population. The magnitude of the changes in electrophoretic mobilities suggest that the associated conformational changes are subtle.
Candida antarctica lipase B-catalyzed regioselective deacylation of dihydroxybenzenes acylated at both phenolic hydroxy groups
Authors: Miyazawa Toshifumi , Hamada Manabu , Morimoto Ryohei
Published: September 2015

Candida antarctica lipase B proved to be highly active in the deacylation of substituted hydroquinones and resorcinols acylated at both phenolic hydroxy groups. The deacylation reactions were much faster than the corresponding direct acylations of these dihydroxybenzenes catalyzed by the same lipase. More importantly, they took place generally in a markedly regioselective manner: the acyloxy group remote from the substituent was preferentially cleaved. The main or exclusive products obtained were the regioisomers of those produced through the direct acylation of the dihydroxybenzenes. In the case of alkyl-substituted hydroquinone derivatives, the regioselectivity increased with an increase in the bulk of the substituent. In the case of 4-substituted diacylated resorcinols, the 3-O-monoacyl derivatives were obtained generally as the sole products. Quite interestingly, some secondary alcohols proved to act as better acyl acceptors than the corresponding primary alcohols in these enzymatic deacylations.
A field experiment informs expected patterns of conifer regeneration after disturbance under changing climate conditions
Authors: Rother Monica T. , Veblen Thomas T. , Furman Luke G.
Published: September 2015

Climate change may inhibit tree regeneration following disturbances such as wildfire, altering post-disturbance vegetation trajectories. We implemented a field experiment to examine the effects of manipulations of temperature and water on ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson) and Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) seedlings planted in a low-elevation, recently disturbed setting of the Colorado Front Range. We implemented four treatments: warmed only (Wm), watered only (Wt), warmed and watered (WmWt), and control (Co). We found that measures of growth and survival varied significantly by treatment type. Average growth and survival was highest in the Wt plots, followed by the Co, WmWt, and Wm plots, respectively. This general trend was observed for both conifer species, although average growth and survival was generally higher in ponderosa pine than in Douglas-fir. Our findings suggest that warming temperatures and associated drought are likely to inhibit post-disturbance regeneration of ponderosa pine and Douglas-fir in low-elevation forests of the Colorado Front Range and that future vegetation composition and structure may differ notably from historic patterns in some areas. Our findings are relevant to other forested ecosystems in which a warming climate may similarly inhibit regeneration by dominant tree species.
Proper flight technique for using a small rotary-winged drone aircraft to safely, quickly, and accurately survey raptor nests
Authors: Junda James , Greene Erick , Bird David M.
Published: September 2015

Small rotary-winged unmanned aerial vehicles or “drones” mounted with a small video camera were successful in surveying the nest contents of four species of raptor, including Osprey (Pandion haliaetus), Bald Eagle (Haliaeetus leucocephalus), Ferruginous Hawk (Buteo regalis), and Red-tailed Hawk (B. jamaicensis) in an accurate and safe manner when the proper flight technique was employed. A total of 110 surveys were completed in 2013 and 2014 with quality images of nest contents obtained in 106 or (96.4%) of flights. A successful and safe flight requires two personnel: the pilot who controls the aircraft and the spotter who monitors the behaviour of the adult birds defending the nest and keeps the pilot updated on all potentially dangerous interactions between aircraft and the birds. With the video camera recording, the aircraft is flown above the nest to a predetermined location that allows an unobscured camera shot of the nest. This technique can be readily adapted to a variety of habitat types and species. The accuracy of data obtained combined with the flexibility, low cost, and speed of this technique make it a useful technological alternative to the safety risks and obtrusiveness associated with traditional survey techniques.
Path integral for confined Dirac fermions in a constant magnetic field
Authors: Merdaci Abdeldjalil , Jellal Ahmed , Chetouani Lyazid
Published: September 2015

In this paper, we consider Dirac fermion confined in harmonic potential and submitted to a constant magnetic field. The corresponding solutions of the energy spectrum are obtained by using the path integral techniques. For this, we begin by establishing a symmetric global projection, which provides a symmetric form for the Green function. Based on this, we show that it is possible to end up with the propagator of the harmonic oscillator for one charged particle. After some transformations, we derive the normalized wave functions and the eigenvalues in terms of different physical parameters and quantum numbers. By interchanging quantum numbers, we show that our solutions have interesting properties. The density of current and the nonrelativistic limit are analyzed where different conclusions are obtained. Finally, the completeness of the Dirac oscillator eigenfunctions is proved by using the standard properties of the generalized Laguerre polynomials.
The RG flow of Nambu–Jona-Lasinio model at finite temperature and density
Authors: Aoki Ken-Ichi , Yamada Masatoshi
Published: September 2015

We study the Nambu–Jona-Lasinio model at finite temperature and finite density by using the functional renormalization group. The RG flows of the four-Fermi coupling constant in the NJL model are investigated. We obtain the chiral phase boundary in cases of the large-[Formula: see text] leading approximation and an improved approximation. The large-[Formula: see text] nonleading term at the vanishing temperature has a singularity at the Fermi surface. We show that the quantum corrections by the large-[Formula: see text] nonleading term largely influence the phase boundary at low temperature and high density region.
Key to enhance thermoelectric performance by controlling crystal size of strontium titanate
Authors: Wang Jun , Ye Xinxin , Yaer Xinba , Wu Yin , Zhang Boyu , Miao Lei
Published: September 2015

One-step molten salt synthesis process was introduced to fabricate nano to micrometer sized [Formula: see text] powders in which effects of synthesis temperature, oxide-to-flux ratios and raw materials on the generation of [Formula: see text] powders were examined. 100 nm or above sized pure [Formula: see text] particles were obtained at relatively lower temperature of 900[Formula: see text]C. Micro-sized rhombohedral crystals with a maximum size of approximately 12 [Formula: see text]m were obtained from [Formula: see text] or [Formula: see text] strontium source with 1:1 O/S ratio.

Controlled crystal size and morphology of Nb-doped [Formula: see text] particles are prepared by using this method to confirm the performance of thermoelectric properties. The Seebeck coefficient obtained is significantly high when compared with the reported data, and the high ratio of nano particles in the sample has a positive effect on the increase of Seebeck coefficient too, which is likely due to the energy filtering effect at large numbers of grain boundaries resulting from largely distributed structure.
Design of Grid Multiscroll Chaotic Attractors via Transformations
Authors: Ai Xingxing , Sun Kehui , He Shaobo , Wang Huihai
Published: September 2015

Three transformation approaches for generating grid multiscroll chaotic attractors are presented through theoretical analysis and numerical simulation. Three kinds of grid multiscroll chaotic attractors are generated based on one-dimensional multiscroll Chua system. The dynamics of the multiscroll chaotic attractors are analyzed by means of equilibrium points, eigenvalues, the largest Lyapunov exponent and complexity. As the experimental verification, we implemented the circular grid multiscroll attractor on DSP platform. The simulation and experimental results are consistent well with that of theoretical analysis, and it shows that the design approaches are effective.
Medium Amplitude Limit Cycles of Some Classes of Generalized Liénard Systems
Authors: Rebollo-Perdomo Salomón
Published: September 2015

We will consider two special families of polynomial perturbations of the linear center. For the resulting perturbed systems, which are generalized Liénard systems, we provide the exact upper bound for the number of limit cycles that bifurcate from the periodic orbits of the linear center.
Cannibalistic Predator–Prey Model with Disease in Predator — A Delay Model
Authors: Biswas Santosh , Samanta Sudip , Chattopadhyay Joydev
Published: September 2015

In this paper, we propose and analyze a cannibalistic predator–prey model with a transmissible disease in the predator population. The disease can be transmitted through contacts with infected individuals as well as the cannibalism of an infected predator. We also consider incubation delay in disease transmission, where the incubation period represents the time in which the infectious agent develops in the host. Local stability analysis of the system around the biologically feasible equilibria is studied. Bifurcation analysis of the system around interior equilibrium is also studied. Applying the normal form theory and central manifold theorem, the direction of Hopf bifurcation, the stability and the period of bifurcating periodic solutions are derived. Under appropriate conditions, the permanence of the system with time delay is proved. Our results suggest that incubation delay destabilizes the system and can produce chaos. We also observe that cannibalism can control disease and population oscillations. Extensive numerical simulations are performed to support our analytical results.
THE IMPORTANCE OF PROPER SEQUENCING IN ESTIMATING THE LENGTH AND FRACTAL DIMENSION OF TORTUOUS CURVES
Authors: IMRE ATTILA R. , BIDDER OWEN R.
Published: September 2015

There are several cases when tortuous continuous lines have to be discretized in order to measure length and other related quantities. In this methodological paper, we are going to demonstrate the importance of the proper sequencing (ranking) of the discrete points and call attention to some typical errors caused by improper sequencing. For demonstration, the fractal dimensions of an animal track with well-known original sequencing and for some mixed sequencing are estimated and the extent of errors is shown.
Rings in which every element is either a sum or a difference of a nilpotent and an idempotent
Authors: Breaz Simion , Danchev Peter , Zhou Yiqiang
Published: September 2015

Generalizing the notion of nil-cleanness from [A. J. Diesl, Nil clean rings, J. Algebra 383 (2013) 197–211], in parallel to [P. V. Danchev and W. Wm. McGovern, Commutative weakly nil clean unital rings, J. Algebra 425 (2015) 410–422], we define the concept of weak nil-cleanness for an arbitrary ring. Its comprehensive study in different ways is provided as well. A decomposition theorem of a weakly nil-clean ring is obtained. It is completely characterized when an abelian ring is weakly nil-clean. It is also completely determined when a matrix ring over a division ring is weakly nil-clean.
Theoretical study of the structure, spectroscopic properties and anti-cancer activity of tetrahydrochromeno[4,3-b]quinolines
Authors: Ardjani Ahmed Taki Eddine , Mekelleche Sidi Mohamed
Published: September 2015

In the present work, a theoretical study of the geometrical structures and spectroscopic (IR, 1H and [Formula: see text]C NMR, UV-visible) properties, and anti-cancer activity of cis-fused tetrahydrochromeno[4,3-b]quinolines have been performed. The equilibrium geometries have been optimized at the B3LYP/6-31G(d) computational level and the present study puts in evidence the stability preference of the cis stereoisomers in comparison with the trans ones as expected experimentally. The vibrational frequencies and IR spectra were calculated at the same level of theory and compared to experimental FT-IR spectra and the spectral peaks have been assigned on the basis of potential energy distribution results. UV-visible absorption bands were calculated using the TD-DFT/B3LYP/6-31G(d) method. The [Formula: see text]C nuclear magnetic resonance chemical shifts and the coupling constants were calculated at the B3LYP level using the gauge independent atomic orbital (GIAO) method in chloroform solvent. The 1H chemical shifts were calculated using the recently proposed WP04/6-31G(d) DFT functional. The visualization of the molecular electrostatic potential (MEP) surfaces and the docking simulation show that the absence of the methyl group at 2-position of tetrahydrochromeno[4,3-b]quinoline moiety is responsible of the potential anti-cancer activity of this compound.
Relation between the spin Hall conductivity and the spin Chern number for Dirac-like systems
Authors: Dayi Ömer F. , Yunt Elif
Published: September 2015

A semiclassical formulation of the spin Hall effect for physical systems satisfying Dirac-like equation is introduced. We demonstrate that the main contribution to the spin Hall conductivity is given by the spin Chern number whether the spin is conserved or not at the quantum level. We illustrated the formulation within the Kane–Mele model of graphene in the absence and in the presence of the Rashba spin-orbit coupling term.
The positive Q-matrix completion problem
Authors: Sarma Bhaba Kumar , Sinha Kalyan
Published: September 2015

A real [Formula: see text] matrix is a [Formula: see text]-matrix if for [Formula: see text] the sum of all [Formula: see text] principal minors is positive. A digraph [Formula: see text] is said to have positive [Formula: see text]-completion if every partial positive [Formula: see text]-matrix specifying [Formula: see text] can be completed to a positive [Formula: see text]-matrix. In this paper, necessary conditions for a digraph to have positive [Formula: see text]-completion are obtained and sufficient conditions for a digraph to have positive [Formula: see text]-completion are provided. The digraphs of order at most 4 that include all loops and have positive [Formula: see text]-completion are characterized. Tournaments whose complements have positive [Formula: see text]-completion are singled out. Further, some comparisons between the [Formula: see text]-matrix and positive [Formula: see text]-matrix completion problems have been made.
Molecular-Scale Tools for Studying Mechanotransduction
Authors: LaCroix Andrew S. , Rothenberg Katheryn E. , Hoffman Brenton D.
Published: September 2015

Mechanical stimuli are known to be potent regulators of the form and function of cells and organisms. Although biological regulation has classically been understood in terms of principles from solution biochemistry, advancements in many fields have led to the development of a suite of techniques that are able to reveal the interplay between mechanical loading and changes in the biochemical properties of proteins in systems ranging from single molecules to living organisms. Here, we review these techniques and highlight the emergence of a new molecular-scale understanding of the mechanisms mediating the detection and response of cells to mechanical stimuli, a process termed mechanotransduction. Specifically, we focus on the role of subcellular adhesion structures in sensing the stiffness of the surrounding environment because this process is pertinent to applications in tissue engineering as well the onset of several mechanosensitive disease states, including cancer.