Reconstruction of full-length LINE-1 progenitors from ancestral genomes.

Sequences derived from the Long INterspersed Element-1 (L1) family of retrotransposons occupy at least 17% of the human genome, with 67 distinct subfamilies representing successive waves of expansion and extinction in mammalian lineages. L1s contribute extensively to gene regulation, but their molecular history is difficult to trace, because most are present only as truncated and highly mutated fossils. Consequently, L1 entries in current databases of repeat sequences are composed mainly of short diagnostic subsequences, rather than full functional progenitor sequences for each subfamily.

Fundamental immune-oncogenicity trade-offs define driver mutation fitness.

Missense driver mutations in cancer are concentrated in a few hotspots. Various mechanisms have been proposed to explain this skew, including biased mutational processes, phenotypic differences and immunoediting of neoantigens; however, to our knowledge, no existing model weighs the relative contribution of these features to tumour evolution. We propose a unified theoretical 'free fitness' framework that parsimoniously integrates multimodal genomic, epigenetic, transcriptomic and proteomic data into a biophysical model of the rate-limiting processes underlying the fitness advantage conferred on cancer cells by driver gene mutations.

The Human Transcription Factors.

Transcription factors (TFs) recognize specific DNA sequences to control chromatin and transcription, forming a complex system that guides expression of the genome. Despite keen interest in understanding how TFs control gene expression, it remains challenging to determine how the precise genomic binding sites of TFs are specified and how TF binding ultimately relates to regulation of transcription. This review considers how TFs are identified and functionally characterized, principally through the lens of a catalog of over 1,600 likely human TFs and binding motifs for two-thirds of them.

Multiparameter functional diversity of human C2H2 zinc finger proteins.

C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined.

Matrix M H5N1 Vaccine Induces Cross-H5 Clade Humoral Immune Responses in a Randomized Clinical Trial and Provides Protection from Highly Pathogenic Influenza Challenge in Ferrets.

Background And Methods: Highly pathogenic avian influenza (HPAI) viruses constitute a pandemic threat and the development of effective vaccines is a global priority. Sixty adults were recruited into a randomized clinical trial and were intramuscularly immunized with two virosomal vaccine H5N1 (NIBRG-14) doses (21 days apart) of 30 μg HA alone or 1.5, 7.

Evaluation of a virosomal H5N1 vaccine formulated with Matrix M™ adjuvant in a phase I clinical trial.

The avian influenza H5 virus epizootic continues to cause zoonosis with human fatalities, highlighting the continued need for pandemic preparedness against this subtype. This study evaluated the tolerability and immunogenicity of a Matrix M™ adjuvanted virosomal H5N1 vaccine in a phase I clinical trial. Sixty healthy adults were vaccinated intramuscularly with two doses of influenza H5N1 (NIBRG-14) virosomal vaccine alone (30 μg haemagglutinin (HA)) or 1.

Human monoclonal antibodies in single chain fragment variable format with potent neutralization activity against influenza virus H5N1.

Effective diagnostic and therapeutic strategies are needed to control and combat the highly pathogenic avian influenza virus (AIV) subtype H5N1. To this end, we developed human monoclonal antibodies (mAbs) in single chain fragment variable (scFv) format towards the H5N1 avian influenza virus to gain new insights for the development of immunotherapy against human cases of H5N1. Using a biopanning based approach a large array of scFvs against H5N1 virus were isolated from the human semi-synthetic ETH-2 phage antibody library.

Identification of the novel KI Polyomavirus in paranasal and lung tissues.

KI is a novel polyomavirus identified in the respiratory secretions of children with acute respiratory symptoms. Whether this reflects a causal role of the virus in the human respiratory disease remains to be established. To investigate the presence of KIV in the respiratory tissue, we examined 20 fresh lung cancer specimens and surrounding normal tissue along with one paranasal and one lung biopsy from two transplanted children.

Molecular analysis of avian H7 influenza viruses circulating in Eurasia in 1999-2005: detection of multiple reassortant virus genotypes.

Avian influenza infections by high and low pathogenicity H7 influenza viruses have caused several outbreaks in European poultry in recent years, also resulting in human infections. Although in some cases the source of H7 strains from domestic poultry was shown to be the viruses circulating in the wild bird reservoir, a thorough characterization of the entire genome of H7 viruses from both wild and domestic Eurasian birds, and their evolutionary relationships, has not been conducted. In our study, we have analysed low pathogenicity H7 influenza strains isolated from wild and domestic ducks in Italy and southern China and compared them with those from reared terrestrial poultry such as chicken and turkey.

Characterization of human H1N1 influenza virus variants selected in vitro with zanamivir in the presence of sialic acid-containing molecules.

Understanding the molecular mechanisms of influenza virus resistance to neuraminidase inhibitors is a main concern for their clinical use. In an attempt to reproduce in vivo selective conditions where influenza virus resistance to neuraminidase inhibitors can occur the zanamivir selection of an A/H1N1 influenza virus strain was carried out in Madin-Darby canine kidney cells performed in the presence or absence of sialic acid-containing inhibitor analogues that act as virus decoy receptors. The zanamivir-selected variants passaged in the presence of sialic acid-containing molecules resembling the human-like virus receptor lost the ability to bind red blood cells.

Generation of candidate human influenza vaccine strains in cell culture - rehearsing the European response to an H7N1 pandemic threat.

Background: Although H5N1 avian influenza viruses pose the most obvious imminent pandemic threat, there have been several recent zoonotic incidents involving transmission of H7 viruses to humans. Vaccines are the primary public health defense against pandemics, but reliance on embryonated chickens eggs to propagate vaccine and logistic problems posed by the use of new technology may slow our ability to respond rapidly in a pandemic situation.

Objectives: We sought to generate an H7 candidate vaccine virus suitable for administration to humans whose generation and amplification avoided the use of eggs.

Characterization of low-pathogenic H5 subtype influenza viruses from Eurasia: implications for the origin of highly pathogenic H5N1 viruses.

Highly pathogenic avian influenza (HPAI) H5N1 viruses are now endemic in many Asian countries, resulting in repeated outbreaks in poultry and increased cases of human infection. The immediate precursor of these HPAI viruses is believed to be A/goose/Guangdong/1/96 (Gs/GD)-like H5N1 HPAI viruses first detected in Guangdong, China, in 1996. From 2000 onwards, many novel reassortant H5N1 influenza viruses or genotypes have emerged in southern China.

Evolutionary analysis of HA and NS1 genes of H5N1 influenza viruses in 2004-2005 epidemics.

H5N1 avian influenza viruses circulating in early 2004 in eastern Asia appeared to be under strong purifying selection, except for the hemagglutinin (HA) and nonstructural 1 (NS1) genes, where few amino acid positions were found under positive selection pressure. To evaluate whether the widespread circulation of the H5N1 viruses in the following years was accompanied by a change in the evolution of the HA and NS1, phylogenetic and positive selection analyses were performed on 89 HA and 57 NS1 sequences. Results showed that the number of HA positively selected sites decreased compared to 2004; no selection pressure for NS1 was found.

Different pH requirements are associated with divergent inhibitory effects of chloroquine on human and avian influenza A viruses.

Chloroquine is a 4-aminoquinoline previously used in malaria therapy and now becoming an emerging investigational antiviral drug due to its broad spectrum of antiviral activities. To explore whether the low pH-dependency of influenza A viruses might affect the antiviral effects of chloroquine at clinically achievable concentrations, we tested the antiviral effects of this drug on selected human and avian viruses belonging to different subtypes and displaying different pH requirements. Results showed a correlation between the responses to chloroquine and NH4Cl, a lysosomotropic agent known to increase the pH of intracellular vesicles.

Antigenic and genetic evolution of swine influenza A (H3N2) viruses in Europe.

In the early 1970s, a human influenza A/Port Chalmers/1/73 (H3N2)-like virus colonized the European swine population. Analyses of swine influenza A (H3N2) viruses isolated in The Netherlands and Belgium revealed that in the early 1990s, antigenic drift had occurred, away from A/Port Chalmers/1/73, the strain commonly used in influenza vaccines for pigs. Here we show that Italian swine influenza A (H3N2) viruses displayed antigenic and genetic changes similar to those observed in Northern European viruses in the same period.

A sensitive one-step real-time PCR for detection of avian influenza viruses using a MGB probe and an internal positive control.

Background: Avian influenza viruses (AIVs) are endemic in wild birds and their introduction and conversion to highly pathogenic avian influenza virus in domestic poultry is a cause of serious economic losses as well as a risk for potential transmission to humans. The ability to rapidly recognise AIVs in biological specimens is critical for limiting further spread of the disease in poultry. The advent of molecular methods such as real time polymerase chain reaction has allowed improvement of detection methods currently used in laboratories, although not all of these methods include an Internal Positive Control (IPC) to monitor for false negative results.

Influenza virus circulation in wild aquatic birds in Italy during H5N2 and H7N1 poultry epidemic periods (1998 to 2000).

Two epidemics of avian influenza due to H5 and H7 highly pathogenic viruses occurred in poultry in Italy in 1997/98 and 1999/2000, respectively. The circulation of these serotypes in wild aquatic birds was investigated examining 638 cloacal swabs and 621 sera collected from 150 gulls, 162 coots, and 326 ducks trapped in Italian wetlands from 1998 to 2000. Seroprevalences against influenza A viruses, detected by a double-antibody sandwich-blocking enzyme-linked immunosorbent assay (ELISA), were 11% in gulls, 16% in coots, and 45% in ducks.

H5N1 influenza virus evolution: a comparison of different epidemics in birds and humans (1997-2004).

The selection pressure acting along the entire genome sequence of H5N1 avian influenza viruses isolated from several bird species and humans infected in the 1997 and 2004 outbreaks, and on the HA1 genes from H5N1 viruses isolated during the entire study period, in eastern Asia was evaluated. According to maximum-likelihood analysis, viral genes appeared to be, in both epidemics, under strong purifying selection, with only the PB2, HA and NS1 genes under positive selection. Specific codons under positive selection were detected by using codon-based substitution models.

Influenza vaccine administration in patients with systemic lupus erythematosus and rheumatoid arthritis. Safety and immunogenicity.

Objective: To evaluate immunological safety and immunogenicity of influenza vaccine administration in patients with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA).

Patients And Methods: Twenty-four patients with low and/or stable disease activity 14 with SLE (mean age 43.42+/-12.

Comparison of in vitro replication features of H7N3 influenza viruses from wild ducks and turkeys: potential implications for interspecies transmission.

In previous work, it was shown that turkey H7N3 influenza viruses, presumably derived 'in toto' from interspecies transmission of duck viruses in Northern Italy, had only 2 aa differences in haemagglutinin and a few amino acid differences as well as a 23 aa deletion in neuraminidase compared with duck viruses. Here, the replication of these duck and turkey viruses in Madin-Darby canine kidney cells was investigated with respect to virus-cell fusion and viral elution from red blood cells. Duck viruses showed similar receptor-binding properties to turkey viruses but possessed a higher pH of fusion activation than the turkey viruses.

Changes in the hemagglutinins and neuraminidases of human influenza B viruses isolated in Italy during the 2001-02, 2002-03, and 2003-04 seasons.

Throughout most of the last decade, B/Yamagata/16/88-lineage influenza viruses were predominant among the B isolates circulating worldwide, whereas B/Victoria/2/87-lineage viruses were isolated infrequently and restricted geographically to eastern Asia. During the 2001-02 influenza season, B/Victoria/2/87-lineage viruses re-emerged in North America and Europe and spread worldwide. Virological surveillance in Italy during that season showed wide circulation of influenza B viruses, of which most were antigenically related to the B/Sichuan/379/99 (Yamagata-lineage) vaccine strain, together with a smaller number of B viruses antigenically similar to B/HongKong/330/01, a recent B/Victoria/2/87-lineage antigenic variant.