bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geminivirus C3 Protein: Replication Enhancement and Protein Interactions
Authors: Settlage Sharon B. , See Renee G. , Hanley-Bowdoin Linda 
Published: July 2005

ABSTRACT

Most dicot-infecting geminiviruses encode a replication enhancer protein (C3, AL3, or REn) that is required for optimal replication of their small, single-stranded DNA genomes. C3 interacts with C1, the essential viral replication protein that initiates rolling circle replication. C3 also homo-oligomerizes and interacts with at least two host-encoded proteins, proliferating cell nuclear antigen (PCNA) and the retinoblastoma-related protein (pRBR). It has been proposed that protein interactions contribute to C3 function. Using the C3 protein of
Tomato yellow leaf curl virus
, we examined the impact of mutations to amino acids that are conserved across the C3 protein family on replication enhancement and protein interactions. Surprisingly, many of the mutations did not affect replication enhancement activity of C3 in tobacco protoplasts. Other mutations either enhanced or were detrimental to C3 replication activity. Analysis of mutated proteins in yeast two-hybrid assays indicated that mutations that inactivate C3 replication enhancement activity also reduce or inactivate C3 oligomerization and interaction with C1 and PCNA. In contrast, mutated C3 proteins impaired for pRBR binding are fully functional in replication assays. Hydrophobic residues in the middle of the C3 protein were implicated in C3 interaction with itself, C1, and PCNA, while polar resides at both the N and C termini of the protein are important for C3-pRBR interaction. These experiments established the importance of C3-C3, C3-C1, and C3-PCNA interactions in geminivirus replication. While C3-pRBR interaction is not required for viral replication in cycling cells, it may play a role during infection of differentiated cells in intact plants.
Viral Diversity in Hot Springs of Pozzuoli, Italy, and Characterization of a Unique Archaeal Virus,
Acidianus
Bottle-Shaped Virus, from a New Family, the
Ampullaviridae
Authors: Häring Monika , Rachel Reinhard , Peng Xu , Garrett Roger A. , Prangishvili David 
Published: July 2005

ABSTRACT

Virus-like particles with five different morphotypes were observed in an enriched environmental sample from a hot, acidic spring (87 to 93°C, pH 1.5) in Pozzuoli, Italy. The morphotypes included rigid rods, flexible filaments, and novel, exceptional forms. Particles of each type were isolated, and they were shown to represent viable virions of five novel viruses which infect members of the hyperthermophilic archaeal genus
Acidianus
. One of these, named the
Acidianus
bottle-shaped virus, ABV, exhibits a previously unreported morphotype. The bottle-shaped virion carries an envelope which encases a funnel-shaped core. The pointed end of the virion is likely to be involved in adsorption and channeling of viral DNA into host cells. The broad end exhibits 20 (± 2) thin filaments which appear to be inserted into a disk, or ring, and are interconnected at their bases. These filaments are apparently not involved in adsorption. ABV virions contain six proteins in the size range 15 to 80 kDa and a 23.9-kb linear, double-stranded DNA genome. Virus replication does not cause lysis of host cells. On the basis of its unique morphotype and structure, we propose to assign ABV to a new viral family, the
Ampullaviridae
.
Characterization of a Human H5N1 Influenza A Virus Isolated in 2003
Authors: Shinya Kyoko , Hatta Masato , Yamada Shinya , Takada Ayato , Watanabe Shinji , Halfmann Peter , Horimoto Taisuke , Neumann Gabriele , Kim Jin Hyun , Lim Wilina , Guan Yi , Peiris Malik , Kiso Makoto , Suzuki Takashi , Suzuki Yasuo , Kawaoka Yoshihiro 
Published: July 2005

ABSTRACT
In 2003, H5N1 avian influenza virus infections were diagnosed in two Hong Kong residents who had visited the Fujian province in mainland China, affording us the opportunity to characterize one of the viral isolates, A/Hong Kong/213/03 (HK213; H5N1). In contrast to H5N1 viruses isolated from humans during the 1997 outbreak in Hong Kong, HK213 retained several features of aquatic bird viruses, including the lack of a deletion in the neuraminidase stalk and the absence of additional oligosaccharide chains at the globular head of the hemagglutinin molecule. It demonstrated weak pathogenicity in mice and ferrets but caused lethal infection in chickens. The original isolate failed to produce disease in ducks but became more pathogenic after five passages. Taken together, these findings portray the HK213 isolate as an aquatic avian influenza A virus without the molecular changes associated with the replication of H5N1 avian viruses in land-based poultry such as chickens. This case challenges the view that adaptation to land-based poultry is a prerequisite for the replication of aquatic avian influenza A viruses in humans.
Chlorella Virus-Encoded Deoxyuridine Triphosphatases Exhibit Different Temperature Optima
Authors: Zhang Yuanzheng , Moriyama Hideaki , Homma Kohei , Van Etten James L. 
Published: July 2005

ABSTRACT

A putative deoxyuridine triphosphatase (dUTPase) gene from chlorella virus PBCV-1 was cloned, and the recombinant protein was expressed in
Escherichia coli
. The recombinant protein has dUTPase activity and requires Mg
2+
for optimal activity, while it retains some activity in the presence of other divalent cations. Kinetic studies of the enzyme revealed a

K
m

of 11.7 μM, a turnover
k
cat
of 6.8 s
−1
, and a catalytic efficiency of
k
cat
/

K
m

= 5.8 × 10
5
M
−1
s
−1
. dUTPase genes were cloned and expressed from two other chlorella viruses IL-3A and SH-6A. The two dUTPases have similar properties to PBCV-1 dUTPase except that IL-3A dUTPase has a lower temperature optimum (37°C) than PBCV-1 dUTPase (50°C). The IL-3A dUTPase differs from the PBCV-1 enzyme by nine amino acids, including two amino acid substitutions, Glu81→Ser81 and Thr84→Arg84, in the highly conserved motif III of the proteins. To investigate the difference in temperature optima between the two enzymes, homology modeling and docking simulations were conducted. The results of the simulation and comparisons of amino acid sequence suggest that adjacent amino acids are important in the temperature optima. To confirm this suggestion, three site-directed amino acid substitutions were made in the IL-3A enzyme: Thr84→Arg84, Glu81→Ser81, and Glu81→Ser81 plus Thr84→Arg84. The single substitutions affected the optimal temperature for enzyme activity. The temperature optimum increased from 37 to 55°C for the enzyme containing the two amino acid substitutions. We postulate that the change in temperature optimum is due to reduction in charge and balkiness in the active cavity that allows more movement of the ligand and protein before the enzyme and substrate complex is formed.
Soluble Mimetics of Human Immunodeficiency Virus Type 1 Viral Spikes Produced by Replacement of the Native Trimerization Domain with aHeterologous Trimerization Motif: Characterization and Ligand Binding Analysis
Authors: Pancera Marie , Lebowitz Jacob , Schön Arne , Zhu Ping , Freire Ernesto , Kwong Peter D. , Roux Kenneth H. , Sodroski Joseph , Wyatt Richard 
Published: July 2005

ABSTRACTThe human immunodeficiency virus type 1 (HIV-1) exterior envelope glycoprotein, gp120, mediates binding to the viral receptors and, along with the transmembrane glycoprotein gp41, is a major target for neutralizing antibodies. We asked whether replacing the gp41 fusion/trimerization domain with a stable trimerization motif might lead to a more stable gp120 trimer that would be amenable to structural and immunologic analysis. To obtain stable gp120 trimers, a heterologous trimerization motif, GCN4, was appended to the C terminus of YU2gp120. Biochemical analysis indicated that the gp120-GCN4 trimers were superior to gp140 molecules in their initial homogeneity, and trilobed structures were observable by electron microscopy. Biophysical analysis of gp120-GCN4 trimers by isothermal titration calorimetry (ITC) and ultracentrifugation analyses indicated that most likely two molecules of soluble CD4 could bind to one gp120-GCN4 trimer. To further examine restricted CD4 stoichiometric binding to the gp120-GCN4 trimers, we generated a low-affinity CD4 binding trimer by introducing a D457V change in the CD4 binding site of each gp120 monomeric subunit. The mutant trimers could definitively bind only one soluble CD4 molecule, as determined by ITC and sedimentation equilibrium centrifugation. These data indicate that there are weak interactions between the gp120 monomeric subunits of the GCN4-stabilized trimers that can be detected by low-affinity ligand sensing. By similar analysis, we also determined that removal of the variable loops V1, V2, and V3 in the context of the gp120-GCN4 proteins allowed the binding of three CD4 molecules per trimer. Interestingly, both the gp120-GCN4 variants displayed a restricted stoichiometry for the CD4-induced antibody 17b of one antibody molecule binding per trimer. This restriction was not evident upon removal of the variable loops V1 and V2 loops, consistent with conformational constraints in the wild-type gp120 trimers and similar to those inherent in the functional Env spike. Thus, the gp120-GCN4 trimers demonstrate several properties that are consistent with some of those anticipated for gp120 in the context of the viral spike.
Herpes Simplex Virus Type 1 Strain HSV1716 Grown in Baby Hamster Kidney Cells Has Altered Tropism for Nonpermissive Chinese Hamster Ovary Cells Compared to HSV1716 Grown in Vero Cells
Authors: Conner Joe , Rixon Frazer J. , Brown S. Moira 
Published: July 2005

ABSTRACT
Chinese hamster ovary (CHO) cells are traditionally regarded as nonpermissive cells for herpes simplex virus type 1 (HSV-1) infection as they lack the specific entry receptors, and modified CHO cells have been instrumental in the identification of HSV-1 receptors in numerous studies. In this report we demonstrate that the HSV-1 strain 17+ variant HSV1716 is able to infect unmodified CHO cells but only if the virus is propagated in baby hamster kidney (BHK) cells. Infection of CHO cells by BHK-propagated HSV1716 results in expression of immediate-early, early, and late viral genes, and infectious progeny virions are produced. In normally cultured CHO cells, up to a maximum of 50% of cells were permissive for BHK-propagated HSV1716 infection, with 24 h of serum starvation increasing this to 100% of CHO cells, suggesting that the mechanism used by BHK-propagated virus to infect CHO cells was cell cycle dependent. The altered tropism of HSV1716 was also evident in another nonpermissive mouse melanoma cell line and is an exclusive property resulting from propagation of the virus using BHK cells, as viruses propagated on Vero, C8161 (a human melanoma cell line), or indeed, CHO cells were completely unable to infect either CHO or mouse melanoma cells.
Molecular Basis for Mitochondrial Localization of Viral Particles during
Beet Necrotic Yellow Vein Virus
Infection
Authors: Valentin Clarisse , Dunoyer Patrice , Vetter Guillaume , Schalk Catherine , Dietrich André , Bouzoubaa Salah 
Published: July 2005

ABSTRACT

During infection,
Beet necrotic yellow vein virus
(BNYVV) particles localize transiently to the cytosolic surfaces of mitochondria. To understand the molecular basis and significance of this localization, we analyzed the targeting and membrane insertion properties of the viral proteins. ORF1 of BNYVV RNA-2 encodes the 21-kDa major coat protein, while ORF2 codes for a 75-kDa minor coat protein (P75) by readthrough of the ORF1 stop codon. Bioinformatic analysis highlighted a putative mitochondrial targeting sequence (MTS) as well as a major (TM1) and two minor (TM3 and TM4) transmembrane regions in the N-terminal part of the P75 readthrough domain. Deletion and gain-of-function analyses based on the localization of green fluorescent protein (GFP) fusions showed that the MTS was able to direct a reporter protein to mitochondria but that the protein was not persistently anchored to the organelles. GFP fused either to MTS and TM1 or to MTS and TM3-TM4 efficiently and specifically associated with mitochondria in vivo. The actual role of the individual domains in the interaction with the mitochondria seemed to be determined by the folding of P75. Anchoring assays to the outer membranes of isolated mitochondria, together with in vivo data, suggest that the TM3-TM4 domain is the membrane anchor in the context of full-length P75. All of the domains involved in mitochondrial targeting and anchoring were also indispensable for encapsidation, suggesting that the assembly of BNYVV particles occurs on mitochondria. Further data show that virions are subsequently released from mitochondria and accumulate in the cytosol.
Marx's ‘Truly Social’ Labour Theory of Value: Part II, How Is Labour that Is Under the Sway of Capital Actually Abstract?
Authors: Murray Patrick 
Published: July 2005

AbstractIn the first part of this two-part article, I argued that, unlike the asocial classical (Ricardian) labour theory of value, Marx's labour theory of value is a ‘truly social’ one. In fact, it is a purely social one. Marx's theory of value is nothing but his theory of the social forms distinctive of the capitalist mode of production. Thus, we may speak of those forms as value-forms, the (generalised) commodity, money (in its several forms), capital, wage-labour, surplus-value and its forms of appearance (profit, interest, and rent), and more. The labour that produces value, then, is labour of a peculiar social sort. This thought is entirely foreign to the classical labour theory of value, and, likewise, to Marxist accounts of value theory that mistake it for a radical version of Ricardian value theory. The gulf between the classical and the Marxian labour theories of value is wide.
Debating Mobilisation, Class Struggle and the Left: A Response to a Reply
Authors: Gail Gregor 
Published: July 2005

AbstractJohn Kelly has replied to my assessment of his Rethinking Industrial Relations published earlier in this journal in a fraternal and constructive manner. Here, I wish to undertake two tasks. The first is to assess the response of other academics and writers to his book, in terms of reviews and the use of his work by others. The second is to engage with the points he makes to take the debate further forward.
Festschriften in Public International Law: An Annotated Bibliographical Compilation of Titles, 1930–2000/2001
Authors:   Schwietzke,   Macalister-Smith
Published: July 2005

AbstractThe authors survey the Festschriften within the literature of public international law. The recipients of the works are identified and the details of the volumes are presented in a comprehensive bibliography. A country synopsis and an index of names supply further information about this category of scholarly publications. The survey covers 325 relevant works that could be located from all countries around the world.
The Right to Strike, Labor Market Liberalization and the New Labor Code in Pre-Accession Lithuania
Authors:   Woolfson,   Beck
Published: July 2005

AbstractThis article examines legal inhibitions on the right to strike which have emerged in the new market economy of Lithuania. It illustrates how legal impediments impact on the right to strike by analyzing a specific episode of industrial conflict. Further to this, the complaint by the employees' trade union to the International Labor Organization is examined together with the legislative responses of Lithuanian authorities to concerns arising from this dispute. The paper suggests that a broader political imperative of labor market liberalization may be compromising the spirit, if not the letter, of both major ILO conventions on Freedom of Association and Collective Bargaining which are endorsed in the new Lithuanian Labor Code, and also the European Union Charter of Fundamental Rights to which Lithuania has subscribed.
A Comparative Study of the Protection of Civil Rights: The Civil Codes of CIS Countries
Authors:   Korableva
Published: July 2005

AbstractThis article is devoted to an examination of the civil law means for protecting subjective civil rights. The subject matter of this study are the provisions of the several civil codes that have been promulgated in the countries of the CIS in the post-Soviet period. The effort to harmonize private law in the region has given rise inter alia to several pieces of model legislation, perhaps the most notable of which is the CIS Model Civil Code.The use of the comparative method allows the author to trace the progressive development of the civil codes—and the model code—of countries in the CIS; this also enables the author to consider whether there are any gaps or codification hiatuses in the Civil Code of the Russian Federation. In doing so, the author points to those issues that, in her view, are relevant for court practice. As part of her consideration of this subject, the author has compiled a comparative table of relevant provisions of most of the civil codes in CIS countries.
International Organizations and Foreign States: Participants in Civil Law Relations in Russia
Authors: Kanachevskii Vladimir 
Published: July 2005

AbstractThe author examines the legal status of international organizations and foreign states in trade and commerce in the Russian Federation. The specifi c issues which are touched upon by the author include general problems of the participation of public entities—such as international organizations as legal persons and the immunity of foreign states and international organizations—in civil law relations. The author concludes that domestic legislation should not be considered to be the only source of law for regulating private international relations involving states; practice illustrates that international treaties are also a source of such rules and regulations. Special attention in this article is devoted to characteristic features of the legal personality of international organizations, the sources of law regulating relations in which international organizations participate, the role of domestic law and internal rules of international organization itself, the various aspects of the legal capacity of international organizations as subjects of Russian civil law including agreements involving international organizations, the legal status of their separate divisions, issues relating to the property rights of international organization, and the civil law status of representatives of foreign states attached to international organizations (and their civil servants). The legal base for this research is formed by international treaties, the charters and internal rules of international organizations, and rules of Russian civil legislation as well as decisions of Russian and international judicial bodies. By way of conclusion, the author postulates that it is wise for domestic (and foreign) natural and legal persons, which enter into relations with the international organizations and foreign states, to take into consideration the specifi c nature of the above-mentioned subjects. In practice, this may result in dismissal of a plaintiff 's claim in a RF court where the defendant is an international organization or foreign state. It may thereby be impossible to hold such an organization or state civilly liable (without its consent) for breaching a contractual undertaking.
Migration matters: regulatory T-cell compartmentalization determines suppressive activity in vivo
Authors: Siegmund Kerstin , Feuerer Markus , Siewert Christiane , Ghani Saeed , Haubold Uta , Dankof Anja , Krenn Veit , Schön Michael P. , Scheffold Alexander , Lowe John B. , Hamann Alf , Syrbe Uta , Huehn Jochen 
Published: July 2005

AbstractRegulatory T cells (Tregs) play a fundamental role in the suppression of different immune responses; however, compartments at which they exert suppressive functions in vivo are unknown. Although many groups have described the presence of Tregs within inflammatory sites, it has not been shown that inflamed tissues are, indeed, the sites of active suppression of ongoing immune reactions. Here, by using αE+ effector/memory-like Tregs from fucosyltransferase VII-deficient animals, which lack E/P-selectin ligands and fail to migrate into inflamed sites, we analyzed the functional importance of appropriate Treg localization for in vivo suppressive capacity in an inflammation model. Lack of suppression by Tregs deficient in E/P-selectin ligands demonstrates that immigration into inflamed sites is a prerequisite for the resolution of inflammatory reactions in vivo because these selectin ligands merely regulate entry into inflamed tissues. In contrast, control of proliferation of naive CD4+ T cells during the induction phase of the immune response is more efficiently exerted by the naive-like αE–CD25+ Treg subset preferentially recirculating through lymph nodes when compared with its inflammation-seeking counterpart. Together, these findings provide the first conclusive evidence that appropriate localization is crucial for in vivo activity of Tregs and might have significant implications for anti-inflammatory therapies targeting recruitment mechanisms.
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
Authors: Kosinski Jan , Feder Marcin , Bujnicki Janusz M 
Published: July 2005

Abstract
Background
The PD-(D/E)XK nuclease superfamily, initially identified in type II restriction endonucleases and later in many enzymes involved in DNA recombination and repair, is one of the most challenging targets for protein sequence analysis and structure prediction. Typically, the sequence similarity between these proteins is so low, that most of the relationships between known members of the PD-(D/E)XK superfamily were identified only after the corresponding structures were determined experimentally. Thus, it is tempting to speculate that among the uncharacterized protein families, there are potential nucleases that remain to be discovered, but their identification requires more sensitive tools than traditional PSI-BLAST searches.

Results
The low degree of amino acid conservation hampers the possibility of identification of new members of the PD-(D/E)XK superfamily based solely on sequence comparisons to known members. Therefore, we used a recently developed method HHsearch for sensitive detection of remote similarities between protein families represented as profile Hidden Markov Models enhanced by secondary structure. We carried out a comparison of known families of PD-(D/E)XK nucleases to the database comprising the COG and PFAM profiles corresponding to both functionally characterized as well as uncharacterized protein families to detect significant similarities. The initial candidates for new nucleases were subsequently verified by sequence-structure threading, comparative modeling, and identification of potential active site residues.

Conclusion
In this article, we report identification of the PD-(D/E)XK nuclease domain in numerous proteins implicated in interactions with DNA but with unknown structure and mechanism of action (such as putative recombinase RmuC, DNA competence factor CoiA, a DNA-binding protein SfsA, a large human protein predicted to be a DNA repair enzyme, predicted archaeal transcription regulators, and the head completion protein of phage T4) and in proteins for which no function was assigned to date (such as YhcG, various phage proteins, novel candidates for restriction enzymes). Our results contributes to the reduction of "white spaces" on the sequence-structure-function map of the protein universe and will help to jump-start the experimental characterization of new nucleases, of which many may be of importance for the complete understanding of mechanisms that govern the evolution and stability of the genome.