bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile
Authors: Hanada Kousuke , Vallejo Veronica , Nobuta Kan , Slotkin R. Keith , Lisch Damon , Meyers Blake C. , Shiu Shin-Han , Jiang Ning 
Published: January 2009

AbstractGene duplication is an important mechanism for evolution of new genes. In plants, a special group of transposable elements, called Pack-MULEs or transduplicates, is able to duplicate and amplify genes or gene fragments on a large scale. Despite the abundance of Pack-MULEs, the functionality of these duplicates is not clear. Here, we present a comprehensive analysis of expression and purifying selection on 2809 Pack-MULEs in rice (Oryza sativa), which are derived from 1501 parental genes. At least 22% of the Pack-MULEs are transcribed, and 28 Pack-MULEs have direct evidence of translation. Chimeric Pack-MULEs, which contain gene fragments from multiple genes, are much more frequently expressed than those derived only from a single gene. In addition, Pack-MULEs are frequently associated with small RNAs. The presence of these small RNAs is associated with a reduction in expression of both the Pack-MULEs and their parental genes. Furthermore, an assessment of the selection pressure on the Pack-MULEs using the ratio of nonsynonymous (Ka) and synonymous (Ks) substitution rates indicates that a considerable number of Pack-MULEs likely have been under selective constraint. The Ka/Ks values of Pack-MULE and parental gene pairs are lower among Pack-MULEs that are expressed in sense orientations. Taken together, our analysis suggests that a significant number of Pack-MULEs are expressed and subjected to purifying selection, and some are associated with small RNAs. Therefore, at least a subset of Pack-MULEs are likely functional and have great potential in regulating gene expression as well as providing novel coding capacities.
The Plastidial 2-C-Methyl-d-Erythritol 4-Phosphate Pathway Provides the Isoprenyl Moiety for Protein Geranylgeranylation in Tobacco BY-2 Cells
Authors: Gerber Esther , Hemmerlin Andréa , Hartmann Michael , Heintz Dimitri , Hartmann Marie-Andrée , Mutterer Jérôme , Rodríguez-Concepción Manuel , Boronat Albert , Van Dorsselaer Alain , Rohmer Michel , Crowell Dring N. , Bach Thomas J. 
Published: January 2009

AbstractProtein farnesylation and geranylgeranylation are important posttranslational modifications in eukaryotic cells. We visualized in transformed Nicotiana tabacum Bright Yellow-2 (BY-2) cells the geranylgeranylation and plasma membrane localization of GFP-BD-CVIL, which consists of green fluorescent protein (GFP) fused to the C-terminal polybasic domain (BD) and CVIL isoprenylation motif from the Oryza sativa calmodulin, CaM61. Treatment with fosmidomycin (Fos) or oxoclomazone (OC), inhibitors of the plastidial 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway, caused mislocalization of the protein to the nucleus, whereas treatment with mevinolin, an inhibitor of the cytosolic mevalonate pathway, did not. The nuclear localization of GFP-BD-CVIL in the presence of MEP pathway inhibitors was completely reversed by all-trans-geranylgeraniol (GGol). Furthermore, 1-deoxy-d-xylulose (DX) reversed the effects of OC, but not Fos, consistent with the hypothesis that OC blocks 1-deoxy-d-xylulose 5-phosphate synthesis, whereas Fos inhibits its conversion to 2-C-methyl-d-erythritol 4-phosphate. By contrast, GGol and DX did not rescue the nuclear mislocalization of GFP-BD-CVIL in the presence of a protein geranylgeranyltransferase type 1 inhibitor. Thus, the MEP pathway has an essential role in geranylgeranyl diphosphate (GGPP) biosynthesis and protein geranylgeranylation in BY-2 cells. GFP-BD-CVIL is a versatile tool for identifying pharmaceuticals and herbicides that interfere either with GGPP biosynthesis or with protein geranylgeranylation.
TheArabidopsisMYB5 Transcription Factor Regulates Mucilage Synthesis, Seed Coat Development, and Trichome Morphogenesis
Authors: Li Song Feng , Milliken Olga Nicolaou , Pham Hanh , Seyit Reg , Napoli Ross , Preston Jeremy , Koltunow Anna M. , Parish Roger W. 
Published: January 2009

AbstractThe Arabidopsis thaliana MYB5 gene is expressed in trichomes and seeds, including the seed coat. Constitutive expression of MYB5 resulted in the formation of more small trichomes and ectopic trichomes and a reduction in total leaf trichome numbers and branching. A myb5 mutant displayed minimal changes in trichome morphology, while a myb23 mutant produced increased numbers of small trichomes and two-branched trichomes. A myb5 myb23 double mutant developed more small rosette trichomes and two-branched trichomes than the single mutants. These results indicate that MYB5 and MYB23 regulate trichome extension and branching. The seed coat epidermal cells of myb5 and myb5 myb23 were irregular in shape, developed flattened columellae, and produced less mucilage than those of the wild type. Among the downregulated genes identified in the myb5 seeds using microarray analysis were ABE1 and ABE4 (α/β fold hydrolase/esterase genes), MYBL2, and GLABRA2. The same genes were also downregulated in transparent testa glabra1 (ttg1) seeds, suggesting that MYB5 collaborates with TTG1 in seed coat development. These genes were upregulated in leaves and roots by ectopically expressed MYB5. The MYBL2, ABE1, and ABE4 promoters were active in seeds, including seed coats, and the latter two also in trichomes. Models of the MYB5 regulatory networks involved in seed coat and trichome development are presented.
Who profits from neoadjuvant radiochemotherapy for locally advanced esophageal carcinoma?
Authors: Kersting Stephan , Konopke Ralf , Dittert Dag , Distler Marius , Rückert Felix , Gastmeier Jörg , Baretton Gustavo B , Saeger Hans D 
Published: January 2009

AbstractBackground:  Patients suffering from locally advanced esophageal carcinoma are generally treated using multimodal therapies. This prospective, non‐randomized trial was performed to evaluate the survival benefit of neoadjuvant radiochemotherapy prior to surgery in comparison with surgery only.Patients & Methods:  Histopathological outcomes and survival were compared between 61 patients who underwent neoadjuvant radiochemotherapy and 64 comparable control patients who had been under‐staged. After neoadjuvant therapy, tumor regression was assessed using the method described by Mandard in 1994. Survival curves for the two groups were estimated using the Kaplan‐Meier method, and compared with the log‐rank test.Results:  Median and 3‐year recurrence‐free survival for the entire group were 26 months and 39.7%, respectively. The median and 3‐year overall survival reached 34 months and 48.1%. Patients who showed complete response to neoadjuvant therapy had significantly improved survival (35 months) compared to patients with residual tumor cells (28 months), patients with tumors unresponsive to radiochemotherapy (22 months), or patients who received surgery only (control group, 29 months). Patients with nodal‐negative carcinomas showed significantly longer survival after surgery only and after neoadjuvant therapy compared to patients with lymph node‐positive cancers.Conclusions:  Complete response after neoadjuvant radiochemotherapy is associated with significantly improved survival. Negative nodal status is a major determinant of outcomes following primary operation or neoadjuvant treatment.
ULCER OF THE UTERINE CERVIX IN THE JAPANESE FEMALE WITH REFERENCE TO THE HIGH MORTALITY FROM CERVICAL CANCER*
Authors: Imai Tamaki , Wada Takato 
Published: January 2009

Sixty‐three uteri, extirpated for lesions other than uterine cancer, from Japanese females whose clinical records contained no histories of preoperative biopsy, and 66 uteri obtained from autopsies of Japanese females who died of various causes other than uterine diseases, were examined histologically.In 57.1% of the surgical and 65.2% of the autopsy cases, there were fresh or chronic ulcers which occurred in the squamocolumnar junction of the cervix. The posterior and the anterior lips were among the predilection sites. The possibility of statistical correlation between cervical ulcer and cancer was speculated for the reason that the mortality from cervical cancer was fairly high in Japan, and that; in addition, there was a conformity between both lesions, with regard to the topographic distribution. Final conclusion was reserved for geographical‐pathologic studies to be carried out in the future, comparing the data among different populations, one with low and the other with high cervical cancer mortality. ACTA PATH. JAP. 18: 161–170, 1968.
AN AUTOPSY CASE OF RELAPSING POLYCHONDRITIS
Authors: Shinoda Yoshio , Kitamura Shiro , Okazaki Etsuo 
Published: January 2009

The first autopsy case of relapsing polychondritis in Japan in a 25‐year‐ old woman was presented. The disease began first in the nasal septum, and gradually involved both external ears and the respiratory tract.The pathological changes were exclusively confined to the cartilaginous tissues. The extent and severity of the lesions were apparently different from cartilage to cartilage. The changes consisted essentially of alterations and disappearance of cartilaginous tissues with acute chondritis and perichondritis accompanied by various inflammatory cell infiltrations. Leucocytic reactions in these lesions seemed to be more intensive than those in cases reported before. The initial change was supposed to be loss of basophilia in the matrix, later developing to chondrocyte alterations and marginal erosion of the cartilage. ACTA PATH. JAP. 18: 185–195, 1968.
PATHOLOGY OF ACUTE ISCHEMIC MYOCARDIUM SPECIAL REFERENCES TO (I) EVALUATION OF MORPHOLOGICAL METHODS FOR DETECTION OF EARLY MYOCARDIAL INFARCTS, AND (II) LIPID METABOLISM IN INFARCTED MYOCARDIUM
Authors: Sakurai Isamu 
Published: January 2009

Morphological changes of early myocardial infarction within 24 hours after the onset of the acute attack were described together with a review of the literatures. For the practical purpose in detecting very early infarcts, enzymatic histochemistry is the most reliable method. Other methods previously reported such as wavy pattern of the muscle fibers and fuchsinophilia are still controversial.Lipid metabolism in the infarcted myocardium of dogs was studied both morphologically and biochemically. Up to 3 hours, after the coronary ligation, the tissue lipids accumulated in the necrotic areas with a rise of triglyceride, but later than 6 hours the lipids decreased and were lost from the necrotic tissue, while the surrounding living cells were accumulated with neutral lipids. Serum free fatty acids were elevated in the coronary sinus blood in 6 hours after the ligation. Linolic acids were contained in high proportion in both coronary venous blood after 6 hours, and normal myocardial phospholipid. These results may lead to another possible factor in addition to catecholamine activity to elevate serum FFA in acute myocardial infarction that fatty acids may be released partly from tissue phospholipid and once ever accumulated triglyceride. ACTA PATH. JAP. 27: 587˜603, 1977.
Critical consumer issues in St. Lucia: an examination of consumer challenges and related learning among rural adults according to income levels
Authors: Clement Peter 
Published: January 2009

AbstractConsumer education is a relatively new and growing interest in St. Lucia. Neither the government nor the National Consumer Association has established a consumer education programme to address the growing consumer concerns in the country. The purpose of this study was to examine critical consumer issues, related learning challenges and strategies among rural adults in St. Lucia according to income levels. Rural adult consumers are most disadvantaged in terms of levels of education, income and access to resources, which may help to prevent and mediate consumer concerns. The specific research questions examined were: (1) What is the nature of problems experienced by rural St. Lucian adult consumers in the marketplace? (2) How do rural St. Lucian adult consumers solve the challenges they encounter in the marketplace? (3) What is it like for rural St. Lucian adult consumers as they go about trying to learn to solve the consumer issues they face? and (4) What do rural St. Lucian adult consumers perceive to be the requisites for effective decision making in the marketplace? Data were collected using a questionnaire comprising of 29 questions divided into four sections (problems, strategies, solving consumer problems and making effective decisions) and two biographical questions. A total of 500 rural adult consumers were surveyed verbally through door‐to‐door contact. The findings of this study revealed that middle‐income rural adult consumers experience more problems in the marketplace than those with each lower or higher level of income. Middle‐income rural adult St. Lucian consumers in particular seek more information and are comfortable with using more strategies than the lower‐ and higher‐income rural adult consumers. This research gives us a better understanding of the problems faced by rural adult consumers based on their income. Research results will be useful to the government of St. Lucia and the National Consumer Association when they decide to establish an adult consumer education programme for St. Lucia.
The G-Alpha Protein GNA3 of
Hypocrea jecorina
(Anamorph
Trichoderma reesei
) Regulates Cellulase Gene Expression in the Presence of Light
Authors: Schmoll Monika , Schuster André , Silva Roberto do Nascimento , Kubicek Christian P. 
Published: January 2009

ABSTRACT

Although the enzymes enabling
Hypocrea jecorina
(anamorph
Trichoderma reesei
) to degrade the insoluble substrate cellulose have been investigated in some detail, little is still known about the mechanism by which cellulose signals its presence to the fungus. In order to investigate the possible role of a G-protein/cyclic AMP signaling pathway, the gene encoding GNA3, which belongs to the adenylate cyclase-activating class III of G-alpha subunits, was cloned.
gna3
is clustered in tandem with the mitogen-activated protein kinase gene
tmk3
and the glycogen phosphorylase gene
gph1
. The
gna3
transcript is upregulated in the presence of light and is almost absent in the dark. A strain bearing a constitutively activated version of GNA3 (
gna3
QL) exhibits strongly increased cellulase transcription in the presence of the inducer cellulose and in the presence of light, whereas a
gna3
antisense strain showed delayed cellulase transcription under this condition. However, the
gna3
QL mutant strain was unable to form cellulases in the absence of cellulose. The necessity of light for stimulation of cellulase transcription by GNA3 could not be overcome in a mutant which expressed
gna3
under control of the constitutive
gpd1
promoter also in darkness. We conclude that the previously reported stimulation of cellulase gene transcription by light, but not the direct transmission of the cellulose signal, involves the function and activation of GNA3. The upregulation of
gna3
by light is influenced by the light modulator ENVOY, but GNA3 itself has no effect on transcription of the light regulator genes
blr1
,
blr2
, and
env1
. Our data for the first time imply an involvement of a G-alpha subunit in a light-dependent signaling event in fungi.
Heterologous Expression of Mycobacterial Proteins in
Saccharomyces cerevisiae
Reveals Two Physiologically Functional 3-Hydroxyacyl-Thioester Dehydratases, HtdX and HtdY, in Addition to HadABC and HtdZ
Authors: Gurvitz Aner , Hiltunen J. Kalervo , Kastaniotis Alexander J. 
Published: January 2009

ABSTRACT

We report on
Mycobacterium tuberculosis
Rv0241c and Rv3389c, representing two physiologically functional 3-hydroxyacyl-thioester dehydratases (Htd). These enzymes are potentially entrained in type 2 fatty acid synthase (FASII). Mycobacterial FASII is involved in the synthesis of mycolic acids, which are the major constituents of the protective layer around the pathogen, shielding it from noxious chemicals and the host's immune system. Mycolic acids are additionally associated with the virulence and resilience of
M. tuberculosis
. Here, Rv0241c and Rv3389c, which are distinct from the previously identified heterodimers Rv0635-Rv0636 (HadAB) and Rv0636-Rv0637 (HadBC) but also the homodimer Rv0130 (HtdZ), were identified by expressing the corresponding candidate open reading frames in
Saccharomyces cerevisiae htd2
Δ cells lacking mitochondrial 3-hydroxyacyl-acyl carrier protein dehydratase activity, followed by scoring for phenotype rescue. The
htd2
Δ mutant fails to produce sufficient levels of lipoic acid and does not respire or grow on nonfermentable carbon sources. Soluble protein extracts made from mutant
htd2
Δ cells expressing mitochondrially targeted Rv0241c or Rv3389c contained 3-hydroxyacyl-thioester hydratase activity. Moreover, mutant yeast cells expressing Rv0241c or Rv3389c were able to recover their respiratory growth on glycerol medium and efficiently reduce 2,3,5-triphenyltetrazolium chloride. Additionally, expression of mitochondrial Rv0241c or Rv3389c in
htd2
Δ cells also restored de novo lipoic acid synthesis to 92 and 40% of the level in the wild-type strain, respectively. We propose naming Rv0241c and Rv3389c as HtdX and HtdY, respectively, and discuss the implications of our finding with reference to Rv0098, a candidate mycobacterial FabZ homologue with intrinsic thioesterase and hydratase activities that lacks the eukaryotic-like hydratase-2 motif.
Autogenous Regulation ofEscherichia coliPolynucleotide Phosphorylase Expression Revisited
Authors: Carzaniga Thomas , Briani Federica , Zangrossi Sandro , Merlino Giuseppe , Marchi Paolo , Dehò Gianni 
Published: January 2009

ABSTRACTTheEscherichia colipolynucleotide phosphorylase (PNPase; encoded bypnp), a phosphorolytic exoribonuclease, posttranscriptionally regulates its own expression at the level of mRNA stability and translation. Its primary transcript is very efficiently processed by RNase III, an endonuclease that makes a staggered double-strand cleavage about in the middle of a long stem-loop in the 5′-untranslated region. The processedpnpmRNA is then rapidly degraded in a PNPase-dependent manner. Two non-mutually exclusive models have been proposed to explain PNPase autogenous regulation. The earlier one suggested that PNPase impedes translation of the RNase III-processedpnpmRNA, thus exposing the transcript to degradative pathways. More recently, this has been replaced by the current model, which maintains that PNPase would simply degrade the promoter proximal small RNA generated by the RNase III endonucleolytic cleavage, thus destroying the double-stranded structure at the 5′ end that otherwise stabilizes thepnpmRNA. In our opinion, however, the first model was not completely ruled out. Moreover, the RNA decay pathway acting upon thepnpmRNA after disruption of the 5′ double-stranded structure remained to be determined. Here we provide additional support to the current model and show that the RNase III-processedpnpmRNA devoid of the double-stranded structure at its 5′ end is not translatable and is degraded by RNase E in a PNPase-independent manner. Thus, the role of PNPase in autoregulation is simply to remove, in concert with RNase III, the 5′ fragment of the cleaved structure that both allows translation and prevents the RNase E-mediated PNPase-independent degradation of thepnptranscript.
Analysis by Mutagenesis of a Chromosomal Integron Integrase from
Shewanella amazonensis
SB2BT
Authors: Larouche André , Roy Paul H. 
Published: January 2009

ABSTRACT

Integrons are mobile genetic elements that can integrate and disseminate genes as cassettes by a site-specific recombination mechanism. Integrons contain an integrase gene (
intI
) that carries out recombination by interacting with two different target sites; the
attI
site in
cis
with the integrase and the palindromic
attC
site of a cassette. The plasmid-specified IntI1 excises a greater variety of cassettes (principally antibiotic resistance genes), and has greater activity, than chromosomal integrases. The aim of this study was to analyze the capacity of the chromosomal integron integrase SamIntIA of the environmental bacterium
Shewanella amazonensis
SB2BT to excise various cassettes and to compare the properties of the wild type with those of mutants that substitute consensus residues of active integron integrases. We show that the SamIntIA integrase is very weakly active in the excision of various cassettes but that the V206R, V206K, and V206H substitutions increase its efficiency for the excision of cassettes. Our results also suggest that the cysteine residue in the β-5 strand is essential to the activity of
Shewanella
-type integrases, while the cysteine in the β-4 strand is less important for the excision activity.
The Rcs Two-Component System Regulates Expression of Lysozyme Inhibitors and Is Induced by Exposure to Lysozyme
Authors: Callewaert Lien , Vanoirbeek Kristof G. A. , Lurquin Ine , Michiels Chris W. , Aertsen Abram 
Published: January 2009

ABSTRACT

The
Escherichia coli
Rcs regulon is triggered by antibiotic-mediated peptidoglycan stress and encodes two lysozyme inhibitors, Ivy and MliC. We report activation of this pathway by lysozyme and increased lysozyme sensitivity when Rcs induction is genetically blocked. This lysozyme sensitivity could be alleviated by complementation with Ivy and MliC.
Involvement of the Cra Global Regulatory Protein in the Expression of the
iscRSUA
Operon, Revealed during Studies of Tricarballylate Catabolism in
Salmonella enterica
Authors: Lewis Jeffrey A. , Boyd Jeffrey M. , Downs Diana M. , Escalante-Semerena Jorge C. 
Published: January 2009

ABSTRACT

In
Salmonella enterica
, tricarballylate (Tcb) catabolism requires function of TcuB, a membrane-bound protein that contains [4Fe-4S] clusters and heme. TcuB transfers electrons from reduced flavin adenine dinucleotide in the Tcb dehydrogenase (TcuA) to electron acceptors in the membrane. We recently showed that functions needed to assemble [Fe-S] clusters (i.e., the
iscRSUA-hscBA-fdx
operon) compensate for the lack of ApbC during growth of an
apbC
strain on Tcb. ApbC had been linked to [Fe-S] cluster metabolism, and we showed that an
apbC
strain had decreased TcuB activity. Here we report findings that expand our understanding of the regulation of expression of the
iscRSUA
genes in
Salmonella enterica
. We investigated why low levels of glucose or other saccharides restored growth of an
apbC
strain on Tcb. Here we report the following findings. (i) A ≤1 mM concentration of glucose, fructose, ribose, or glycerol restores growth of an
apbC
strain on Tcb. (ii) The saccharide effect results in increased levels of TcuB activity. (iii) The saccharide effect depends on the global regulatory protein Cra. (iv) Putative Cra binding sites are present in the regulatory region of the
iscRSUA
operon. (v) Cra protein binds to all three sites in the
iscRSUA
promoter region in a concentration-dependent fashion. To our knowledge, this is the first report of the involvement of Cra in [Fe-S] cluster assembly.