bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolution of oligotrophy: implications for the breeding of crop plants for low input agricultural systems
Authors: RAVEN J A , ANDREWS M , QUIGG A 
Published: May 2005

SummaryOligotrophy, the obligate or facultative capacity to live in low‐nutrient habitats, has played a major role in the evolution of photosynthetic organisms.

Energy/carbon deficiency: evolution of photosynthesis about 3.5 Gyr (billion years) ago, then use of H2O as electron donor, and accumulation of O2 from about 2.3 Gyr ago.
Deficiency in combined N: evolution of biological N2 fixation about 2.0‐2.3 Gyr ago.
Deficiency in soluble relative to particulate organic C: evolution of phagotrophy in eukaryotes, opening the way to endosymbiotic origin of photosynthesis in eukaryotes.
Deficiency of P and Fe resulting from oxygenation: evolution of mechanisms increasing access to P and Fe.
Deficiency of H2O for land plants gaining C from the atmosphere: evolution of homoiohydry following origin of significant land flora from 0.5 Gyr ago.
Deficiency of CO2 resulting from increased weathering by land plants: evolution of large leaves.
Increased competition for resources among land plants: evolution of mechanisms economizing in use of soil‐derived resources, and increasing ability to acquire resources.

Economising on resource use in photosynthetic organisms is subject to a number of constraints. There are very limited possibilities for reducing the use of N in proteins with a given catalytic function, but greater possibilities using substitution of an analogous protein with that function. The same applies to Fe. Possibilities for economising on the use of P are very limited if the growth rate is to be maintained: the marine cyanobacterium Prochlorococcus is a good example of restricted P requirement. H2O use can be constrained by C4 and, especially, CAM photosynthesis.A possible role of the study of oligotrophy in the context of sustainable, low‐input agriculture includes modified agricultural practice to minimise losses of resources. Information on oligotrophy and its evolution can also be used to inform the alteration of crop plants by genetic modification related to resource acquisition (e.g. associative, or nodule‐based, symbiotic diazotrophy) and the economy of resource use (e.g. partial or complete conversion of a C3 crop to a C4 crop which could economise in the use of N and/or H2O). The attempts to convert C3 to C4 plants have not thus far been fully successful, and the advantages of conversion to C4 are being increasingly offset by the effect of increasing atmospheric CO2 on C3 plants. However, more success has been achieved with selection of the most appropriate diazotrophic symbionts for crop plants in particular environments.
Amplified fragment length polymorphism among Rhynchosporium secalis isolates collected from a single barley field in Syria
Authors: KIROS‐MELES A , UDUPA S , ABANG M M , ABU‐BLAN H , BAUM M , CECCARELLI S , YAHYAOUI A H 
Published: May 2005

SummaryAFLP markers were used to measure the amount and distribution of genetic variation among Rhynchosporium secalis isolates on a microgeographical scale in Syria. Forty isolates hierarchically sampled from a single barley field were assayed for AFLP variation using primer combinations not previously tested in populations of the pathogen from Syria. In contrast to a previous study, which showed high clonality within field populations of R. secalis in Syria, the present study revealed a much higher level of genetic diversity, stressing the important roles that sampling strategies and the choice of primers/primer combinations play in the evaluation of genetic variation in R. secalis populations at a microgeographical scale. A high level of genetic variation was found to occur on a fine scale throughout the pathogen population examined, with 40 different haplotypes being identified among the 40 isolates sampled. Data were consistent with the hypothesis that the primary inoculum originated from a genetically diverse founding population, which may have consisted of ascospores of an as yet undescribed teleomorph and/or asexual spores of a highly mutable local population.
Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription
Authors: Lewinski M. K. , Bisgrove D. , Shinn P. , Chen H. , Hoffmann C. , Hannenhalli S. , Verdin E. , Berry C. C. , Ecker J. R. , Bushman F. D. 
Published: May 2005

ABSTRACTWe have investigated regulatory sequences in noncoding human DNA that are associated with repression of an integrated human immunodeficiency virus type 1 (HIV-1) promoter. HIV-1 integration results in the formation of precise and homogeneous junctions between viral and host DNA, but integration takes place at many locations. Thus, the variation in HIV-1 gene expression at different integration sites reports the activity of regulatory sequences at nearby chromosomal positions. Negative regulation of HIV transcription is of particular interest because of its association with maintaining HIV in a latent state in cells from infected patients. To identify chromosomal regulators of HIV transcription, we infected Jurkat T cells with an HIV-based vector transducing green fluorescent protein (GFP) and separated cells into populations containing well-expressed (GFP-positive) or poorly expressed (GFP-negative) proviruses. We then determined the chromosomal locations of the two classes by sequencing 971 junctions between viral and cellular DNA. Possible effects of endogenous cellular transcription were characterized by transcriptional profiling. Low-level GFP expression correlated with integration in (i) gene deserts, (ii) centromeric heterochromatin, and (iii) very highly expressed cellular genes. These data provide a genome-wide picture of chromosomal features that repress transcription and suggest models for transcriptional latency in cells from HIV-infected patients.
Selective Replication of Coronavirus Genomes That Express Nucleocapsid Protein
Authors: Schelle Barbara , Karl Nadja , Ludewig Burkhard , Siddell Stuart G. , Thiel Volker 
Published: May 2005

ABSTRACT
The coronavirus nucleocapsid (N) protein is a structural protein that forms a ribonucleoprotein complex with genomic RNA. In addition to its structural role, it has been described as an RNA-binding protein that might be involved in coronavirus RNA synthesis. Here, we report a reverse genetic approach to elucidate the role of N in coronavirus replication and transcription. We found that human coronavirus 229E (HCoV-229E) vector RNAs that lack the N gene were greatly impaired in their ability to replicate, whereas the transcription of subgenomic mRNA from these vectors was easily detectable. In contrast, vector RNAs encoding a functional N protein were able to carry out both replication and transcription. Furthermore, modification of the transcription signal required for the synthesis of N protein mRNAs in the HCoV-229E genome resulted in the selective replication of genomes that are able to express the N protein. This genetic evidence leads us to conclude that at least one coronavirus structural protein, the N protein, is involved in coronavirus replication.
Long-Range RNA-RNA Interactions Circularize the Dengue Virus Genome
Authors: Alvarez Diego E. , Lodeiro María F. , Ludueña Silvio J. , Pietrasanta Lía I. , Gamarnik Andrea V. 
Published: May 2005

ABSTRACT
Secondary and tertiary RNA structures present in viral RNA genomes play essential regulatory roles during translation, RNA replication, and assembly of new viral particles. In the case of flaviviruses, RNA-RNA interactions between the 5′ and 3′ ends of the genome have been proposed to be required for RNA replication. We found that two RNA elements present at the ends of the dengue virus genome interact in vitro with high affinity. Visualization of individual molecules by atomic force microscopy reveled that physical interaction between these RNA elements results in cyclization of the viral RNA. Using RNA binding assays, we found that the putative cyclization sequences, known as 5′ and 3′ CS, present in all mosquito-borne flaviviruses, were necessary but not sufficient for RNA-RNA interaction. Additional sequences present at the 5′ and 3′ untranslated regions of the viral RNA were also required for RNA-RNA complex formation. We named these sequences 5′ and 3′ UAR (upstream AUG region). In order to investigate the functional role of 5′-3′ UAR complementarity, these sequences were mutated either separately, to destroy base pairing, or simultaneously, to restore complementarity in the context of full-length dengue virus RNA. Nonviable viruses were recovered after transfection of dengue virus RNA carrying mutations either at the 5′ or 3′ UAR, while the RNA containing the compensatory mutations was able to replicate. Since sequence complementarity between the ends of the genome is required for dengue virus viability, we propose that cyclization of the RNA is a required conformation for viral replication.
The Open Reading Frame 3 Gene of Hepatitis E Virus Contains a
cis
-Reactive Element and Encodes a Protein Required for Infection of Macaques
Authors: Graff Judith , Nguyen Hanh , Yu Claro , Elkins William R. , St. Claire Marisa , Purcell Robert H. , Emerson Suzanne U. 
Published: May 2005

ABSTRACT

An infectious cDNA clone of hepatitis E virus was mutated in order to prevent synthesis of either open reading frame 2 (ORF2) protein or ORF3 protein. HuH-7 cells transfected with an ORF2-null mutant produced ORF3, and those transfected with an ORF3-null mutant produced ORF2. Silent mutations introduced into a highly conserved nucleotide sequence in the ORF3 coding region eliminated the synthesis of both ORF2 and ORF3 proteins, suggesting that it comprised a
cis
-reactive element. A mutant that was not able to produce ORF3 protein did not produce a detectable infection in rhesus macaques. However, a mutant that encoded an ORF3 protein lacking a phosphorylation site reported to be critical for function was able to replicate its genome in cell culture and to induce viremia and seroconversion in rhesus monkeys, suggesting that phosphorylation of ORF3 protein was not necessary for genome replication or for production of infectious virions.
Interaction with CD4 and Antibodies to CD4-Induced Epitopes of the Envelope gp120 from a Microglial Cell-Adapted Human Immunodeficiency Virus Type 1 Isolate
Authors: Martín-García Julio , Cocklin Simon , Chaiken Irwin M. , González-Scarano Francisco 
Published: May 2005

ABSTRACTWe previously showed that the envelope glycoprotein from an in vitro microglia-adapted human immunodeficiency virus type 1 isolate (HIV-1Bori-15) is able to use lower levels of CD4 for infection and demonstrates greater exposure of the CD4-induced epitope recognized by the 17b monoclonal antibody than the envelope of its parental, peripheral isolate (HIV-1Bori). We investigated whether these phenotypic changes were related to a different interaction of their soluble monomeric gp120 proteins with CD4 or 17b. Equilibrium binding analyses showed no difference between Bori and Bori-15 gp120s. However, kinetic analysis of surface plasmon resonance-based, real-time binding experiments showed that while both proteins have similar association rates, Bori-15 gp120 has a statistically significant, 3-fold-lower dissociation rate from immobilized CD4 than Bori and a statistically significant, 14-fold-lower dissociation rate from 17b than Bori in the absence of soluble CD4. In addition, using the sensitivity to inhibition by anti-CD4 antibodies as a surrogate for CD4:trimeric envelope interaction, we found that Bori-15 envelope-pseudotyped viruses were significantly less sensitive than Bori pseudotypes, with four- to sixfold-higher 50% inhibitory concentration values for the three anti-CD4 antibodies tested. These differences, though small, suggest that adaptation to microglia correlates with the generation of a gp120 that forms a more stable interaction with CD4. Nonetheless, the observation of limited binding changes leaves open the possibility that HIV-1 adaptation to microglia and HIV-associated dementia may be related not only to diminished CD4 dependence but also to changes in other molecular factors involved in the infection process.
Role of the E1
∧
E4 Protein in the Differentiation-Dependent Life Cycle of Human Papillomavirus Type 31
Authors: Wilson Regina , Fehrmann Frauke , Laimins Laimonis A. 
Published: May 2005

ABSTRACT

The most highly expressed protein in the productive life cycle of human papillomaviruses (HPVs) is E1
∧
E4, but its function is not well understood. To investigate the role of E1
∧
E4, we undertook a genetic analysis in the context of the complete HPV type 31 (HPV31) genome. A mutant HPV31 genome (E4M9) was constructed that contained a stop codon in the E4 open reading frame at amino acid 9 and was silent in the overlapping E2 coding sequence. Wild-type and mutant genomes were transfected into normal human foreskin keratinocytes (HFKs) and selected for drug resistance, and pooled cultures were examined for effects of E1
∧
E4 on viral functions. Southern blot analyses of transfected HFKs demonstrated that cells carrying the E4M9 mutant genomes were maintained as episomes at copy numbers similar to those in keratinocytes transfected with wild-type HPV31. Both sets of cells grew at similar rates, exhibited comparable extensions of life spans, and had equivalent levels of early transcripts. Following suspension of the cells in a semisolid medium, differentiation-dependent genome amplification and late gene expression were significantly decreased in cells maintaining the E4M9 mutant genome compared to those with wild-type HPV31. One explanation for these effects could be a reduction in the number of cells harboring mutant genomes that enter S phase upon differentiation. An analysis of cells containing E4M9 mutant genomes in organotypic raft cultures indicated a reduction in bromodeoxyuridine incorporation in differentiated suprabasal cells compared to that seen in wild-type rafts. Our results indicate that the HPV31 E1
∧
E4 protein plays a significant role in promoting HPV genome amplification and S phase maintenance during differentiation.
Papillomavirus Capsid Mutation To Escape Dendritic Cell-Dependent Innate Immunity in Cervical Cancer
Authors: Yang Rongcun , Wheeler Cosette M. , Chen Xiaojiang , Uematsu Satoshi , Takeda Kiyoshi , Akira Shizuo , Pastrana Diana V. , Viscidi Raphael P. , Roden Richard B. S. 
Published: May 2005

ABSTRACT
Infection with oncogenic human papillomaviruses (HPVs), typified by HPV type 16 (HPV16), is a necessary cause of cervical cancer. Prophylactic vaccination with HPV16 L1 virus-like particles (VLPs) provides immunity. HPV16 VLPs activate dendritic cells and a potent neutralizing immunoglobulin G (IgG) response, yet many cervical cancer patients fail to generate detectable VLP-specific IgG. Therefore, we examined the role of the innate recognition of HPV16 L1 in VLP-induced immune responses and its evasion during carcinogenesis. Nonconservative mutations within HPV16 L1 have been described in isolates from cervical cancer and its precursor, high-grade cervical intraepithelial neoplasia (CIN). We determined the effect of mutations in L1 upon in vitro self-assembly into VLPs and their influence upon the induction of innate and adaptive immune responses in mice. Several nonconservative mutations in HPV16 L1 isolated from high-grade CIN or cervical carcinoma prevent self-assembly of L1 VLPs. Intact VLPs, but not assembly-defective L1, activate dendritic cells to produce proinflammatory factors, such as alpha interferon, that play a critical role in inducing adaptive immunity. Indeed, effective induction of L1-specific IgG1 and IgG2a was dependent upon intact VLP structure. Dendritic cell activation and production of virus-specific neutralizing IgG by VLPs requires MyD88-dependent signaling, although the L1 structure that initiates MyD88-mediated signaling is distinct from the neutralizing epitopes. We conclude that innate recognition of the intact L1 VLP structure via MyD88 is critical in the induction of high-titer neutralizing IgG. Tumor progression is associated with genetic instability and L1 mutants. Selection for assembly-deficient L1 mutations suggests the evasion of MyD88-dependent immune control during cervical carcinogenesis.
The Carboxyl-Terminal Domain of RNA Polymerase II Is Phosphorylated by a Complex Containing cdk9 and Infected-Cell Protein 22 of Herpes Simplex Virus 1
Authors: Durand Lizette O. , Advani Sunil J. , Poon Alice P. W. , Roizman Bernard 
Published: May 2005

ABSTRACT

The infected-cell protein 22 (ICP22), a regulatory protein encoded by the α22 gene of herpes simplex virus 1, is required for the optimal expression of a set of late viral proteins that includes the products of the U
S
11, U
L
38, and U
L
41 genes. ICP22 has two activities. Thus, ICP22 and the U
L
13 protein kinase mediate the activation of cdc2 and degradation of its partners, cyclins A and B. cdc2 and its new partner, the DNA polymerase accessory factor (U
L
42), bind topoisomerase IIα in an ICP22-dependent manner. In addition, ICP22 and U
L
13 mediate an intermediate phosphorylation of the carboxyl terminus of RNA polymerase II (RNA POL II). Here we report another function of ICP22. Thus, ICP22 physically interacts with cdk9, a constitutively active cyclin-dependent kinase involved in transcriptional regulation. A protein complex containing ICP22 and cdk9 phosphorylates in vitro the carboxyl-terminal domain of RNA POL II in a viral U
S
3 protein kinase-dependent fashion. Finally, the carboxyl-terminal domain of RNA POL II fused to glutathione
S
-transferase is phosphorylated in reaction mixtures containing complexes pulled down with ICP22 or cdk9 immune precipitated from lysates of wild-type parent virus or ΔU
L
13 but not ΔU
S
3 mutant-infected cells. The experiments described here place ICP22 and cdk9 in a complex with the carboxyl-terminal domain of RNA POL II. At the same time we confirm the requirement of ICP22 and the U
L
13 protein kinase in the posttranslational modification of RNA POL II that alters its electrophoretic mobility, although U
S
3 kinase appears to play a role in a cell-type-dependent fashion.
Improvement of Influenza A/Fujian/411/02 (H3N2) Virus Growth in Embryonated Chicken Eggs by Balancing the Hemagglutinin and Neuraminidase Activities, Using Reverse Genetics
Authors: Lu Bin , Zhou Helen , Ye Dan , Kemble George , Jin Hong 
Published: May 2005

ABSTRACT
The H3N2 influenza A/Fujian/411/02-like virus strains that circulated during the 2003-2004 influenza season caused influenza epidemics. Most of the A/Fujian/411/02 virus lineages did not replicate well in embryonated chicken eggs and had to be isolated originally by cell culture. The molecular basis for the poor replication of A/Fujian/411/02 virus was examined in this study by the reverse genetics technology. Two antigenically related strains that replicated well in embryonated chicken eggs, A/Sendai-H/F4962/02 and A/Wyoming/03/03, were compared with the prototype A/Fujian/411/02 virus. A/Sendai differed from A/Fujian by three amino acids in the neuraminidase (NA), whereas A/Wyoming differed from A/Fujian by five amino acids in the hemagglutinin (HA). The HA and NA segments of these three viruses were reassorted with cold-adapted A/Ann Arbor/6/60, the master donor virus for the live attenuated type A influenza vaccines (FluMist). The HA and NA residues differed between these three H3N2 viruses evaluated for their impact on virus replication in MDCK cells and in embryonated chicken eggs. It was determined that replication of A/Fujian/411/02 in eggs could be improved by either changing minimum of two HA residues (G186V and V226I) to increase the HA receptor-binding ability or by changing a minimum of two NA residues (E119Q and Q136K) to lower the NA enzymatic activity. Alternatively, recombinant A/Fujian/411/02 virus could be adapted to grow in eggs by two amino acid substitutions in the HA molecule (H183L and V226A), which also resulted in the increased HA receptor-binding activity. Thus, the balance between the HA and NA activities is critical for influenza virus replication in a different host system. The HA or NA changes that increased A/Fujian/411/02 virus replication in embryonated chicken eggs were found to have no significant impact on antigenicity of these recombinant viruses. This study demonstrated that the reverse genetics technology could be used to improve the manufacture of the influenza vaccines.
Protein Kinase C θ Is Not Essential for T-Cell-Mediated Clearance of Murine Gammaherpesvirus 68
Authors: Giannoni Francesca , Lyon Ashley B. , Wareing Mark D. , Dias Peter B. , Sarawar Sally R. 
Published: May 2005

ABSTRACTMurine gammaherpesvirus 68 (MHV-68) is a naturally occurring rodent pathogen with significant homology to human pathogens Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus. T cells are essential for primary clearance of MHV-68 and survival of mice following intranasal infection. Previous reports have suggested that protein kinase C θ (PKCθ) is essential for T-cell activation and cytokine production in vitro. To determine the role of this molecule in vivo during the immune response to a viral infection, PKCθ−/−mice were infected with MHV-68. Despite the essential role of T cells in viral clearance, PKCθ−/−mice survived infection, cleared lytic virus, and maintained effective long-term control of latency. CD8 T-cell expansion, trafficking to the lung, and cytotoxic activity were similar in PKCθ+/+and PKCθ−/−mice, whereas antiviral antibody and T-helper cell cytokine production were significantly lower in PKCθ−/−mice than in PKCθ+/+mice. These studies demonstrate a differential requirement for PKCθ in the immune response to MHV-68 and show that PKCθ is not essential for the T-cell activation events leading to viral clearance.
Identification of Residues in the Hepatitis C Virus Core Protein That Are Critical for Capsid Assembly in a Cell-Free System
Authors: Klein Kevin C. , Dellos Sheri R. , Lingappa Jaisri R. 
Published: May 2005

ABSTRACT
Significant advances have been made in understanding hepatitis C virus (HCV) replication through development of replicon systems. However, neither replicon systems nor standard cell culture systems support significant assembly of HCV capsids, leaving a large gap in our knowledge of HCV virion formation. Recently, we established a cell-free system in which over 60% of full-length HCV core protein synthesized de novo in cell extracts assembles into HCV capsids by biochemical and morphological criteria. Here we used mutational analysis to identify residues in HCV core that are important for capsid assembly in this highly reproducible cell-free system. We found that basic residues present in two clusters within the N-terminal 68 amino acids of HCV core played a critical role, while the uncharged linker domain between them was not. Furthermore, the aspartate at position 111, the region spanning amino acids 82 to 102, and three serines that are thought to be sites of phosphorylation do not appear to be critical for HCV capsid formation in this system. Mutation of prolines important for targeting of core to lipid droplets also failed to alter HCV capsid assembly in the cell-free system. In addition, wild-type HCV core did not rescue assembly-defective mutants. These data constitute the first systematic and quantitative analysis of the roles of specific residues and domains of HCV core in capsid formation.