bluuebunny/crossref_metadata_2025_split huggingface dataset:
Helix-Destabilizing, β-Branched, and Polar Residues in the Baboon Reovirus p15 Transmembrane Domain Influence the Modularity of FAST Proteins
Authors: Clancy Eileen K. , Duncan Roy 
Published: March 2011

ABSTRACT
The fusogenic reoviruses induce syncytium formation using the fusion-associated small transmembrane (FAST) proteins. A recent study indicated the p14 FAST protein transmembrane domain (TMD) can be functionally replaced by the TMDs of the other FAST proteins but not by heterologous TMDs, suggesting that the FAST protein TMDs are modular fusion units. We now show that the p15 FAST protein is also a modular fusogen, as indicated by the functional replacement of the p15 ectodomain with the corresponding domain from the p14 FAST protein. Paradoxically, the p15 TMD is not interchangeable with the TMDs of the other FAST proteins, implying that unique attributes of the p15 TMD are required when this fusion module is functioning in the context of the p15 ecto- and/or endodomain. A series of point substitutions, truncations, and reextensions were created in the p15 TMD to define features that are specific to the functioning of the p15 TMD. Removal of only one or two residues from the N terminus or four residues from the C terminus of the p15 TMD eliminated membrane fusion activity, and there was a direct correlation between the fusion-promoting function of the p15 TMD and the presence of N-terminal, hydrophobic β-branched residues. Substitution of the glycine residues and triserine motif present in the p15 TMD also impaired or eliminated the fusion-promoting activity of the p15 TMD. The ability of the p15 TMD to function in an ecto- and endodomain-specific context is therefore influenced by stringent sequence requirements that reflect the importance of TMD polar residues and helix-destabilizing residues.
The Human Cytomegalovirus Gene UL79 Is Required for the Accumulation of Late Viral Transcripts
Authors: Perng Yi-Chieh , Qian Zhikang , Fehr Anthony R. , Xuan Baoqin , Yu Dong 
Published: March 2011

ABSTRACT

In this study, we adopted a conditional protein genetic approach to characterize the role of the human cytomegalovirus (HCMV) gene UL79 during virus infection. We constructed AD
dd
UL79, a recombinant HCMV in which the annotated UL79 open reading frame (ORF) was tagged with the destabilization domain of a highly unstable variant of the human FKBP12 protein (
dd
FKBP). The
dd
FKBP domain targets the tagged protein for rapid proteasomal degradation, but the synthetic ligand Shield-1 can stabilize
dd
FKBP, allowing accumulation of the tagged protein. AD
dd
UL79 failed to replicate without Shield-1, but it grew at wild-type levels with Shield-1 or in human foreskin fibroblasts overexpressing hemagglutinin (HA)-tagged UL79 (HF-UL79HA cells), indicating an essential role of UL79 and the effectiveness of this approach. Without Shield-1, representative immediate-early and early viral proteins as well as viral DNA accumulated normally, but late transcripts and proteins were markedly reduced. UL79 was transcribed with early-late kinetics, which was also regulated via a positive-feedback loop. Using HF-UL79HA cells, we found that the UL79 protein localized to viral replication compartments during HCMV infection. Finally, we created a second UL79 mutant virus (AD
in
UL79

stop

) in which the UL79 ORF was disrupted by a stop codon mutation and found that AD
in
UL79

stop

phenocopied AD
dd
UL79 under the destabilizing condition. Taking these results together, we conclude that UL79 acts after viral DNA replication to promote the accumulation of late viral transcripts. Importantly, the comparative analysis of AD
dd
UL79 and AD
in
UL79

stop

viruses provide additional proof for the power of the protein stability-based conditional approach to dissect the role of viral factors in HCMV biology.
Sequential Deletion of the Integrase (Gag-Pol) Carboxyl Terminus Reveals Distinct Phenotypic Classes of Defective HIV-1
Authors: Mohammed Kevin D. , Topper Michael B. , Muesing Mark A. 
Published: March 2011

ABSTRACT
A requisite step in the life cycle of human immunodeficiency virus type 1 (HIV-1) is the insertion of the viral genome into that of the host cell, a process catalyzed by the 288-amino-acid (32-kDa) viral integrase (IN). IN recognizes and cleaves the ends of reverse-transcribed viral DNA and directs its insertion into the chromosomal DNA of the target cell. IN function, however, is not limited to integration, as the protein is required for other aspects of viral replication, including assembly, virion maturation, and reverse transcription. Previous studies demonstrated that IN is comprised of three domains: the N-terminal domain (NTD), catalytic core domain (CCD), and C-terminal domain (CTD). Whereas the CCD is mainly responsible for providing the structural framework for catalysis, the roles of the other two domains remain enigmatic. This study aimed to elucidate the primary and subsidiary roles that the CTD has in protein function. To this end, we generated and tested a nested set of IN C-terminal deletion mutants in measurable assays of virologic function. We discovered that removal of up to 15 residues (IN 273) resulted in incremental diminution of enzymatic function and infectivity and that removal of the next three residues resulted in a loss of infectivity. However, replication competency was surprisingly reestablished with one further truncation, corresponding to IN 269 and coinciding with partial restoration of integration activity, but it was lost permanently for all truncations extending N terminal to this position. Our analyses of these replication-competent and -incompetent truncation mutants suggest potential roles for the IN CTD in precursor protein processing, reverse transcription, integration, and IN multimerization.
Structural Characterization of an Early Fusion Intermediate of Influenza Virus Hemagglutinin
Authors: Xu Rui , Wilson Ian A. 
Published: March 2011

ABSTRACT
The hemagglutinin (HA) envelope protein of influenza virus mediates viral entry through membrane fusion in the acidic environment of the endosome. Crystal structures of HA in pre- and postfusion states have laid the foundation for proposals for a general fusion mechanism for viral envelope proteins. The large-scale conformational rearrangement of HA at low pH is triggered by a loop-to-helix transition of an interhelical loop (B loop) within the fusion domain and is often referred to as the “spring-loaded” mechanism. Although the receptor-binding HA1 subunit is believed to act as a “clamp” to keep the B loop in its metastable prefusion state at neutral pH, the “pH sensors” that are responsible for the clamp release and the ensuing structural transitions have remained elusive. Here we identify a mutation in the HA2 fusion domain from the influenza virus H2 subtype that stabilizes the HA trimer in a prefusion-like state at and below fusogenic pH. Crystal structures of this putative early intermediate state reveal reorganization of ionic interactions at the HA1-HA2 interface at acidic pH and deformation of the HA1 membrane-distal domain. Along with neutralization of glutamate residues on the B loop, these changes cause a rotation of the B loop and solvent exposure of conserved phenylalanines, which are key residues at the trimer interface of the postfusion structure. Thus, our study reveals the possible initial structural event that leads to release of the B loop from its prefusion conformation, which is aided by unexpected structural changes within the membrane-distal HA1 domain at low pH.
Structure of a Packaging-Defective Mutant of Minute Virus of Mice Indicates that the Genome Is Packaged via a Pore at a 5-Fold Axis
Authors: Plevka Pavel , Hafenstein Susan , Li Lei , D'Abrgamo Anthony , Cotmore Susan F. , Rossmann Michael G. , Tattersall Peter 
Published: March 2011

ABSTRACT
The parvovirus minute virus of mice (MVM) packages a single copy of its linear single-stranded DNA genome into preformed capsids, in a process that is probably driven by a virus-encoded helicase. Parvoviruses have a roughly cylindrically shaped pore that surrounds each of the 12 5-fold vertices. The pore, which penetrates the virion shell, is created by the juxtaposition of 10 antiparallel β-strands, two from each of the 5-fold-related capsid proteins. There is a bottleneck in the channel formed by the symmetry-related side chains of the leucines at position 172. We report here the X-ray crystal structure of the particles produced by a leucine-to-tryptophan mutation at position 172 and the analysis of its biochemical properties. The mutant capsid had its 5-fold channel blocked, and the particles were unable to package DNA, strongly suggesting that the 5-fold pore is the packaging portal for genome entry.
Structure of Bombyx mori Densovirus 1, a Silkworm Pathogen
Authors: Kaufmann Bärbel , El-Far Mohamed , Plevka Pavel , Bowman Valorie D. , Li Yi , Tijssen Peter , Rossmann Michael G. 
Published: March 2011

ABSTRACT

Bombyx mori
densovirus 1 (BmDNV-1), a major pathogen of silkworms, causes significant losses to the silk industry. The structure of the recombinant BmDNV-1 virus-like particle has been determined at 3.1-Å resolution using X-ray crystallography. It is the first near-atomic-resolution structure of a virus-like particle within the genus
Iteravirus
. The particles consist of 60 copies of the 55-kDa VP3 coat protein. The capsid protein has a β-barrel “jelly roll” fold similar to that found in many diverse icosahedral viruses, including archaeal, bacterial, plant, and animal viruses, as well as other parvoviruses. Most of the surface loops have little structural resemblance to other known parvovirus capsid proteins. In contrast to vertebrate parvoviruses, the N-terminal β-strand of BmDNV-1 VP3 is positioned relative to the neighboring 2-fold related subunit in a “domain-swapped” conformation, similar to findings for other invertebrate parvoviruses, suggesting domain swapping is an evolutionarily conserved structural feature of the
Densovirinae
.
Reconciliation of Rotavirus Temperature-Sensitive Mutant Collections and Assignment of Reassortment Groups D, J, and K to Genome Segments
Authors: Criglar Jeanette , Greenberg Harry B. , Estes Mary K. , Ramig Robert F. 
Published: March 2011

ABSTRACT

Four rotavirus SA11 temperature-sensitive (
ts
) mutants and seven rotavirus RRV
ts
mutants, isolated at the National Institutes of Health (NIH) and not genetically characterized, were assigned to reassortment groups by pairwise crosses with the SA11 mutant group prototypes isolated and characterized at Baylor College of Medicine (BCM). Among the NIH mutants, three of the RRV mutants and all four SA11 mutants contained mutations in single reassortment groups, and four RRV mutants contained mutations in multiple groups. One NIH mutant [RRV
ts
K(2)] identified the previously undefined 11th reassortment group (K) expected for rotavirus. Three NIH single mutant RRV viruses, RRV
ts
D(7), RRV
ts
J(5), and RRV
ts
K(2), were in reassortment groups not previously mapped to genome segments. These mutants were mapped using classical genetic methods, including backcrosses to demonstrate reversion or suppression in reassortants with incongruent genotype and temperature phenotype. Once located to specific genome segments by genetic means, the mutations responsible for the
ts
phenotype were identified by sequencing. The reassortment group K mutant RRV
ts
K(2) maps to genome segment 9 and has a Thr280Ileu mutation in the capsid surface glycoprotein VP7. The group D mutant RRV
ts
D(7) maps to segment 5 and has a Leu140Val mutation in the nonstructural interferon (IFN) antagonist protein NSP1. The group J mutant RRV
ts
J(5) maps to segment 11 and has an Ala182Gly mutation affecting only the NSP5 open reading frame. Rotavirus
ts
mutation groups are now mapped to 9 of the 11 rotavirus genome segments. Possible segment locations of the two remaining unmapped
ts
mutant groups are discussed.
Keratinocytes Are Cell Targets of West Nile Virus
In Vivo
Authors: Lim Pei-Yin , Behr Melissa J. , Chadwick Chrystal M. , Shi Pei-Yong , Bernard Kristen A. 
Published: March 2011

ABSTRACT

West Nile virus (WNV) replicates in the skin; however, cell targets in the skin have not been identified. In the current studies, WNV infected the epidermis and adnexal glands of mouse skin, and the epidermal cells were identified as keratinocytes by double labeling for WNV antigen and keratin 10. Inoculation of mice with WNV replicon particles resulted in high levels of replication in the skin, suggesting that keratinocytes are an initial target of WNV. In addition, primary keratinocytes produced infectious virus
in vitro
. In conclusion, keratinocytes are cell targets of WNV
in vivo
and may play an important role in pathogenesis.
A Guide to the Natural History of Freshwater Lake Bacteria
Authors: Newton Ryan J. , Jones Stuart E. , Eiler Alexander , McMahon Katherine D. , Bertilsson Stefan 
Published: March 2011

SUMMARY
Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.
Activation and Function of the MAPKs and Their Substrates, the MAPK-Activated Protein Kinases
Authors: Cargnello Marie , Roux Philippe P. 
Published: March 2011

SUMMARYThe mitogen-activated protein kinases (MAPKs) regulate diverse cellular programs by relaying extracellular signals to intracellular responses. In mammals, there are more than a dozen MAPK enzymes that coordinately regulate cell proliferation, differentiation, motility, and survival. The best known are the conventional MAPKs, which include the extracellular signal-regulated kinases 1 and 2 (ERK1/2), c-Jun amino-terminal kinases 1 to 3 (JNK1 to -3), p38 (α, β, γ, and δ), and ERK5 families. There are additional, atypical MAPK enzymes, including ERK3/4, ERK7/8, and Nemo-like kinase (NLK), which have distinct regulation and functions. Together, the MAPKs regulate a large number of substrates, including members of a family of protein Ser/Thr kinases termed MAPK-activated protein kinases (MAPKAPKs). The MAPKAPKs are related enzymes that respond to extracellular stimulation through direct MAPK-dependent activation loop phosphorylation and kinase activation. There are five MAPKAPK subfamilies: the p90 ribosomal S6 kinase (RSK), the mitogen- and stress-activated kinase (MSK), the MAPK-interacting kinase (MNK), the MAPK-activated protein kinase 2/3 (MK2/3), and MK5 (also known as p38-regulated/activated protein kinase [PRAK]). These enzymes have diverse biological functions, including regulation of nucleosome and gene expression, mRNA stability and translation, and cell proliferation and survival. Here we review the mechanisms of MAPKAPK activation by the different MAPKs and discuss their physiological roles based on established substrates and recent discoveries.
Road traffic injuries in I.R. Iran: the role of interventions implemented by traffic police
Authors: Soori H , Royanian M , Ainy E , Movahedinejad A , Movahedi M , Mahfouzpour S , Hatamabadi H R , Vafaee R , Massoudinejad M R 
Published: March 2011

IntroductionThere is 65 deaths per day from road traffic injuries (RTIs). In Iran. Despite some interventions having been implemented, the impacts of these interventions on mortality and morbidity rates have not been evaluated.ObjectiveTo ascertain the pattern of RTIs in Iran for the years 2004–2007 and to compare the epidemiological trends of RTIs, before and 2 years after four road safety programs were put into place.MethodsA 4-year database from two sources, the traffic police and medico-legal data were employed. The four interventions concurrently/simultaneously put into place in 2005 were as follows: enforcement of laws on the mandatory fastening of seat belts, enforcement of the laws on use of motorcycle helmets, enforcement of general traffic laws and mass media educational campaigns on national radio and television.ResultsThere was a significant decrease in RTIs-related-death and morbidity rates in Iran, after the intervention programs (p<0.001). The death rate decreased from 38.2 per 100 000 in 2004 to 31.8 in 2007 (OR 0.83, 95% CI 0.82 to 0.85). The death rate per 10 000 vehicles also showed a significant decline from 24.2 to 13.4 (OR 0.56, 95% CI 0.55 to 0.57). Similar reductions were seen among non-fatal RTIs.ConclusionThese findings demonstrate the role of traffic police interventions, initiated simultaneously on a national level, in RTI prevention. They do highlight the importance of the contribution made by law enforcement and mass education campaigns.
Evaluation of school sports injury problem at school level among children of Dhaka City: “Development of sport injury surveillance system at large urban environment”
Authors: Ali S M Idris , Khatun M , Rahman A K M Fazlur 
Published: March 2011

Injury is an emerging public health problem in both developed and developing countries, including Bangladesh. A total of 5122 diseased patients were attended in the Health clinic out of which 586 (11.4%) were injury related in 1-year time. On an average, 48 injury-related patients attended per month. Peak incidence of injury was found in the month of June, July and September. On injury category trauma and abrasion were found as frequent injuries. Among the injuries trauma amounting the highest incidence 64.5%. The next common injury was abrasion/laceration (17.1%). Injury trauma includes simple trauma, traumatic haematoma and fractures. The fractures were diagnosed from referral Hospital.Sports injury has been found as a major cause of illness among the school children. So prevention of sports injuries should be included in ongoing school health programme.
Parents perceptions of barriers to and facilitators for injury prevention: a qualitative study
Authors: Stewart J , Kendrick D , Towner E , Pitchforth E , Sealey P , Goodenough T , Deave T 
Published: March 2011

ObjectivesTo explore parents perceptions of barriers and facilitators to injury prevention.BackgroundEven if we develop interventions that are effective and cost-effective in preventing falls, poisoning and scalds among young children at home, we often do not know whether parents will use these interventions. Unless we understand barriers to and facilitators for parents using injury prevention interventions in the home it is unlikely we will be able to develop interventions that parents can and do use and are effective.MethodsWe will recruit parents participating in a multi-centre case–control study of fall, scald and poisoning injuries in children under 5 years. We will undertake semi-structured interviews with parents of children with and without injuries a range of injuries and varied socioeconomic backgrounds. Framework analysis will be used.ResultsReporting results from 64 interviews we will describe commonalities and differences according to a child's age, gender, socioeconomic status, injury type and whether they have experienced an injury. We will describe barriers and facilitators to injury prevention in the home, whether and how these vary according the age and gender of the child and the socioeconomic status of the family.ConclusionThe findings will show how parents perceptions of barriers to and facilitators for injury prevention can vary and how these need to be taken into account to develop interventions likely to be implemented by parents. This work can therefore contribute to the development of evidence based interventions.
YOURS: challenging researchers and professionals to get more involved in road safety
Authors: Lieshout F 
Published: March 2011

Road traffic crashes take young lives indiscriminately. Every day, over 1000 young people are killed on the world's roads. This issue is a global health concern and is recognised by the World Health Organization as the leading cause of death among 10–24 year olds. The vast majority of these deaths and injuries occur in low- and middle-income countries.Environmental factors, developmental factors and gender-related factors come together to put young people at high risk for road traffic injuries. Often, road infrastructures do not accommodate the needs of non-motorised road users and even force them to share the road with motorised traffic. Children face developmental limitations whereas young people actively seek out risk, while they are still inexperienced and dealing with peer influences and social pressures. Finally, several gender specific factors put young males at more risk of being involved in road traffic crashes.Recognising these risks, young people have mobilised to address global road safety and have pledged to become part of the solution. Youth representatives from around the world have united to form YOURS – Youth for Road Safety, the first global youth non-governmental organisation for road safety. YOURS acts to keep young people safe on the world's roads by: advocating for young people on a global level, inspiring, connecting and uniting young people worldwide; and building the capacity of young advocates.YOURS would like to challenge researchers and professionals to get more involved in road safety. Together we can explore ways how knowledge, generated through research, can be translated into action. More specifically how it can be presented to young people and policy makers around the world and stimulate youth involvement in road safety, especially in interventions aiming to decrease youth deaths and injuries.
Risk factors and seatbelt use in Argentina
Authors: Vacchino M 
Published: March 2011

Few studies examined the use of seatbelt and risk factors in lower- or middle-income countries. We investigated the associations between no seatbelt use and age, gender, education, obesity, excessive ingestion of alcohol in the past 30 days and region in Argentina.In 2005 National Survey of Risk Factors, seatbelt use was asked “How often do you use seatbelts when you drive or ride in a car? Responses were coded dichotomously (always = 0 vs less than always = 1).Multivariable logistic regression was used to calculate ODs and 95% CIs for not using seatbelt and sex, age and education level. Because interaction effects were evident for sex, obesity, alcohol intake and region, we performed a stratified analysis by sex using as covariables age, education level, obesity, alcohol intake and region. Adjusted ODs for no seatbelt use were 1.23 (1.11 to 1.36) for women, 3.44 (2.83 to 4.17) for education level less than primary school) and 2.61 (2.20 to 3.10) for 18–24 age group, among others. Stratified analysis by sex showed strong associations between increased BMI and no seatbelt use in extremely obese women, OR=2.50(1.30 to 4.81), and Northwest, OR=6.10 (5.08 to 7.33). In men, significant associations with alcohol abuse OR=1.58 (1.28 to 1.97). Effective preventive interventions are needed to promote seatbelt use among women, young and less educated people and to control the alcohol intake, especially in certain country's regions.