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PubMed1995

Host factors and pneumonia in hospitalised children.

Acute respiratory infections (ARI) account for 20-24% of childhood deaths in India. The present study investigated the host related risk factors in the outcome of pneumonia in 127 hospitalised children between the ages of 2 months and 5 years. The case fatality rate in the study was 11.8%. Presence of malnutrition is a significantly important factor for both increased duration of pneumonia and fatal outcome. Other factors for increased pneumonia mortality include the presence of associated illness and the severity of the pneumonia.

Age Factors↗

PubMed1995

Intracellular cleavage and ligation of hepatitis delta virus genomic RNA: regulation of ribozyme activity by cis-acting sequences and host factors.

During replication, a ribozyme within the genomic RNA of hepatitis delta virus cleaves multimeric precursors to release a unit-length linear intermediate. Intramolecular ligation of this intermediate produces the circular genomic RNA. Although one copy of the ribozyme is reconstituted by such ligation, it does not subsequently cleave and destroy the circular conformation. We have identified cis-acting attenuator sequences that prevent self-cleavage of the circular product by base pairing with and inactivating the ribozyme. Furthermore, we have shown that during the initial processing of the multimeric precursor RNA, host-specific factors activate the ribozyme by preventing its association with the attenuator sequences. Thus, we demonstrate a novel switching mechanism that regulates ribozyme activity inside the cell.

Base Sequence↗

PubMed2003

Inequalities in survival from colorectal cancer: a comparison of the impact of deprivation, treatment, and host factors on observed and cause specific survival.

OBJECTIVE: To investigate whether socioeconomic deprivation is associated with cause specific and all cause survival for colorectal cancer and to what extent this is independent of significant prognostic factors. DESIGN: Prospective cohort. SETTING: The former Wessex Health Region, South West England. PARTICIPANTS: All patients resident in Wessex registered with a diagnosis of colorectal cancer over three years (n=5176). Survival analysis was carried out on those patients with compete data for all factors and a positive survival time (n=4419). OUTCOMES: Death from colorectal cancer and all cause over five year follow up from initial diagnosis. MAIN RESULTS: Deprivation was significantly associated with survival for both outcomes in univariate analysis; the unadjusted hazard ratio for dying from colorectal cancer (most deprived compared with most affluent) was 1.12 (95% CI 1.00 to 1.25) and for all cause was 1.18 (1.07 to 1.30). Significant prognostic factors for both outcomes were age, specialisation of surgeon, Dukes's stage, and emergency compared with elective surgery. Comorbidity and gender were only associated with all cause survival. After adjustment for prognostic factors, the effect of deprivation on both cause specific and all cause mortality was reduced, and it was non-significant for colorectal cancer. However, the most deprived group had consistently worse survival than the most affluent. CONCLUSIONS: Factors associated with survival with colorectal cancer depend on the outcome measure. Socioeconomic deprivation is adversely associated with survival in patients with colorectal cancer. This is strongest for non-colorectal cancer death, partly reflecting higher comorbidity, but it is there for colorectal cancer though not statistically significant. Conclusive evidence of the inequalities by socioeconomic status and underlying reasons needs to come from studies using individual based measures of socioeconomic status and more detail on treatment and host related factors.

Adult↗

PubMed1982

Escherichia coli host factor required specifically for the phi X174 stage III reaction: in vitro identification and partial purification.

A cell-free extract prepared from phi X174-infected Escherichia coli cells sustained in vitro synthesis of viral DNA (stage III reaction) when supplemented with fraction II from uninfected cells. The reaction was dependent upon deoxyribonucleoside triphosphate, ATP, added phi X174 replicative form I DNA template, and the fraction II from uninfected cells. This reaction differed from the stage II reaction (semiconservative replication of duplex replicative form DNA) by the production of stable viral protein-DNA complexes sensitive to anti-phi X174 antiserum. Three types of protein-DNA complexes were identified, 50S, 92S, and a 114S complex that cobanded in CsCl and cosedimented in neutral sucrose gradients with a phi X174 phage marker. The sensitivity of these complexes to anti-phi X174 antiserum and Staphylococcus aureus provided a relatively rapid biochemical assay for direct measurement of the amount of DNA synthesized by the stage III reaction. With this assay, an E. coli factor (SIII) required specifically for the synthesis of viral protein-DNA complexes was identified and purified 200-fold from uninfected E. coli cells. The partially purified SIII factor was required for the synthesis of DNA and viral protein-DNA complexes in the phi X174-infected cell extracts and could not be replaced by rep protein, single-strand binding protein, or DNA polymerase III holoenzyme.

Bacteriophage phi X 174↗

PubMed1988

Binding of integration host factor (IHF) to the ilvGp1 promoter of the ilvGMEDA operon of Escherichia coli K12.

Crude extracts of Escherichia coli K-12 were found to bind DNA restriction fragments containing ilvGp1. Our analysis using a series of restriction fragments and a BamHI linker mutation indicate that a factor binds to ilvGp1 or adjacent to it. Analysis with mutant strains of E. coli K-12 and purified IHF indicate that IHF binds to ilvGp1. Furthermore, both analysis in vivo and in vitro indicate that IHF precludes transcription from ilvGp1.

Bacterial Proteins↗

PubMed1995

Glucose starvation stimulon of Escherichia coli: role of integration host factor in starvation survival and growth phase-dependent protein synthesis.

The DNA-binding protein IHF was found to be required for starvation survival and for the induction of 14 proteins of the glucose starvation stimulon. Many of these proteins have been shown previously to be general responders to diverse stress conditions. Overexpression of IHF during balanced growth was not sufficient to induce these proteins, but it resulted in an increased synthesis of rpoH-dependent heat shock proteins.

Bacterial Proteins↗

PubMed2004

Host factors affecting the outcome of treatment of hepatitis C.

The development of peginterferon and ribavirin combination therapy has significantly improved the sustained virologic response (SVR) rates in patients with chronic hepatitis C. However, poor patient adherence to therapy negatively influences drug levels and drug exposure, often preventing the development of an inhibitory drug level. To optimize patient adherence, the clinician must recognize factors predicting low adherence and negotiate a treatment plan that the patient understands and to which he or she commits. If adverse effects become intolerable, continuing patients on a reduced dose rather than withdrawing treatment seems to confer considerable advantage in preserving the chance for attaining an SVR. Results of a head-to-head comparison have demonstrated the possibility that, in cases of dose reduction, levels of peginterferon alfa-2a could remain above the limit of detection, whereas those of peginterferon alfa-2b might not.

Antiviral Agents↗

PubMed1995

Babesia bigemina: host factors affecting the invasion of erythrocytes.

Babesia bigemina merozoites enter their host's erythrocytes by an unknown mechanism that likely involves parasite surface components. Identification of the parasite ligands involved in invasion is hampered by a lack of basic information about the invasion characteristics of Babesia bigemina. Therefore, restrictions on the species of red blood cells (RBC) that are susceptible to invasion were examined as well as the roles of erythrocyte ligands. An invasion assay and a proliferation assay were developed for this study. Unlike some other species of Babesia that infect cattle, B. bigemina failed to enter RBC from most animals that are not natural hosts, suggesting that a species restricted receptor mechanism mediates invasion. Two carbohydrates which are prominent on the surface of bovine erythrocytes, N-acetylglucosamine and N-acetylgalactosamine, when added to cultures, reduced the ability of B. bigemina merozoites to invade erythrocytes. Neuraminidase or trypsin treatment of bovine erythrocytes significantly decreased their susceptibility to invasion whereas chymotrypsin had little effect. These data imply that proteinaceous erythrocyte ligands and carbohydrate residues may be involved in the invasion process. Identification of a species-specific pattern of invasion and RBC treatments that render cells refractory to invasion may provide the basis for the characterization of B. bigemina erythrocyte binding molecules based on their differential binding to invasion competent and refractory cells.

Acetylgalactosamine↗

PubMed1992

Supercoiling, integration host factor, and a dual promoter system, participate in the control of the bacteriophage lambda pL promoter.

The high level of efficiency of the bacteriophage lambda pL promoter is dependent upon the topological state of the promoter DNA and the binding of a DNA-bending protein, IHF, to a site centered -86 base-pairs upstream from the pL transcription start site. Abortive initiation assays indicate that DNA supercoiling stimulates open complex formation, whereas IHF enhances promoter recognition. IHF stimulates promoter recognition to the same extent on linear and supercoiled templates. We found that the pL region contains a second promoter, pL2, that initiates transcription 42 base-pairs upstream from pL. Although competitive with pL and inhibited by IHF, mutations in pL2 do not affect the regulation of pL. Stimulation by IHF is helix-face-dependent. IHF inhibits pL when the IHF binding site is displaced a helical half-turn upstream. The pL sequences protected against DNase I digestion by bound IHF and RNA polymerase do not overlap. However, DNase I-hypersensitive sites appear in the region between the two bound proteins. In addition, IHF enhances RNA polymerase binding to pL. These data suggest that stimulation of pL by IHF involves the interaction of IHF and RNA polymerase to form a loop or otherwise distort the DNA between their binding sites.

Bacterial Proteins↗

PubMed1993

Integration host factor (IHF) applied for partial digestion by restriction endonucleases in large DNA molecules (IARC procedure).

The IHF protein of Escherichia coli was successfully used in IHF-mediated Achilles' Heel Cleavage (IHF-AC) technique (Koob et al., 1988; Kur et al., 1992), and leads to the generation of very rare restriction sites in large DNA molecules. The first step of this procedure is methylation of DNA in the presence of IHF, when the overlapping ihf/restriction sites are protected from methylation, and in the second step the DNA is cut by the cognate restriction enzyme. The aim of the present study is to develop a very exact and reproducible procedure to obtain only a few well-defined cuts with the IHF-pre-treated DNA, depending on the variety of all parameters. This technique (IARC, i.e., IHF-assisted rare cutters) employs the restriction enzyme and only one auxiliary protein (IHF). The advantage of the IARC procedure is that no methylation is required (as opposed to the IHF-AC method). Using the IARC approach, the effects of various IHF concentrations were evaluated on cleaving the activity of the DraI, PacI, PmeI, and SwaI enzymes using DNA of phage lambda or the entire genomic 4.7-Mb DNA of E. coli. At low IHF concentrations only a few cut sites were eliminated by IHF binding, but at high IHF concentration, enzymes were able to cut in only one or several specific sites.

Amino Acid Sequence↗

PubMed2002

Integration host factor is essential for the optimal expression of the styABCD operon in Pseudomonas fluorescens ST.

The StyS/StyR two-component regulatory system of Pseudomonas fluorescens ST controls the expression of the styABCD operon coding for the styrene degradation upper pathway. In a previous work we showed that the promoter of the catabolic operon (PstyA) is induced by styrene and repressed to differing extents by organic acids or carbohydrates. In order to study the mechanisms controlling the expression of this operon, we performed a functional analysis on 5' deletions of PstyA by the use of a promoter-probe system. These studies demonstrated that a palindromic region (sty box), located from nucleotides -52 to -37 with respect to the transcriptional start point is essential for PstyA activity. Moreover, additional regulatory regions involved in the modulation of PstyA activity were found along the promoter sequence. In particular, deletion of a putative StyR binding site, homologous to the 3' half of the sty box and located upstream of this box, resulted in 65% reduction of the induction level of the reporter gene. Additionally, we performed bandshift assays with a DNA probe corresponding to PstyA and protein crude extracts from P. fluorescens ST, using specific DNA fragments as competitors. In these experiments we demonstrated that IHF binds an AT-rich region located upstream of the sty box. On the basis of this finding, coupled with the results obtained with PstyA functional analysis, we suggest that the role of the IHF-mediated DNA bend is to bring closer, in an overlapping position, the upstream StyR putative binding site and the downstream sty box, and that the formed complex enhances transcription.

Bacterial Proteins↗

PubMed1997

Role of upstream activation sequences and integration host factor in transcriptional activation by the constitutively active prokaryotic enhancer-binding protein PspF.

PspF, the transcriptional activator of the pspA operon of Escherichia coli, which belongs to the enhancer binding protein (EBP) family of sigma54 activator proteins, is constitutively active in an in vitro transcription assay. PspF protein, together with RNA polymerase holoenzyme containing sigma54, is required for in vitro transcription from the pspA promoter. EBP proteins are typically subject to regulation either by post-translational modification or interaction of a specific ligand with an N-terminal regulatory domain. However, unlike other members of the EBP family, PspF lacks this domain. pspA is positively regulated by IHF in vitro, and this regulation is dependent on the topology of the DNA; a linear template is much more dependent on IHF than a supercoiled template. EBP binding to upstream activating sequences (UAS) in their target promoters is mediated by the C-terminal domain which contains a helix-turn-helix DNA-binding motif. A mutant PspF protein lacking the C-terminal DNA-binding domain is active in vitro, although at much higher concentrations than the wild-type protein. In vitro transcription from pspA templates missing one or both of the UAS sites is reduced relative to wild-type templates, but is still appreciable; however, IHF acts as a negative regulator of pspA transcription on these mutant templates. Thus, PspF bound to non-specific sequences upstream of the pspA promoter can activate pspA transcription, but this activation is inhibited by IHF. These data, taken together, support the model that a precise promoter geometry is necessary for IHF to positively regulate transcription and that IHF may act to prevent activation from inappropriately spaced upstream sites.

Bacterial Proteins↗

PubMed2005

Promotion of hyphal growth and underlying chemical changes in Antrodia camphorata by host factors from Cinnamomum camphora.

The aim of this research was to investigate the hyphal growth-promoting factors (HGFs) of Antrodia camphorata from the host-related species, Cinnamomum camphora (CC) and the underlying chemical produced. The HGF was identified in the polysaccharide fraction of CC at levels ranging from 80 to 320 mg L(-1), and it maximally stimulated growth to 5.50 g L(-1) during a 14-day culture period compared to that of the control of 2.88 g L(-1). We also investigated the nature and chemical composition of the CC polysaccharide. Herein, size-exclusion column chromatography followed by high-performance anion-exchange chromatography after complete hydrolysis of the CC polysaccharide was performed to derive its molecular weight and sugar composition. The Mw values of the CC polysaccharide were determined to be 728.2, 187.5, 28.7, 7.5, and 1.9 kDa. Compositional analysis of the CC polysaccharide showed that galactosamine, mannose, and glucose were the major monosaccharides. Time-course studies of mycelial extracts of cultures revealed that prolonged incubation with the water-soluble extracts of CC resulted in an increase in the relative amounts of two lanostane-type compounds, i.e., dehydrosulphurenic acid and 15alpha-acetyl-dehydrosulphurenic acid, which are found in the fruiting bodies of A. camphorata. This finding offers the possibility of the reliable production of this medicinal fungus under laboratory conditions compared to its limited slow growth in nature.

Cell Extracts↗

PubMed1999

The Brucella abortus host factor I (HF-I) protein contributes to stress resistance during stationary phase and is a major determinant of virulence in mice.

Brucella abortus is a facultative intracellular pathogen that causes abortion and infertility in domestic animals and a severe debilitating febrile illness in humans. The mechanisms that this highly successful intracellular pathogen uses to adapt to, and survive within, the harsh intracellular environment of the host macrophage are presently unknown. Maintenance of the stationary phase growth state has been proposed to be critical for the virulence of several mammalian pathogens, but analysis of this relationship for the brucellae has not been undertaken. In order to evaluate this relationship, we examined the in vitro and in vivo characteristics of an isogenic hfq mutant constructed from virulent Brucella abortus 2308. In Escherichia coli, the hfq gene product is an RNA-binding protein that participates in the regulation of stationary phase stress resistance, at least partly by enhancing translation of the stationary phase-specific sigma factor RpoS. As expected, the Brucella abortus hfq mutant, designated Hfq3, showed increased sensitivity to H2O2, and decreased survival under acidic conditions (pH 4.0), during stationary phase growth compared with 2308. Hfq3 was also less able to withstand prolonged starvation than 2308. The Brucella abortus hfq mutant, unlike its parental strain 2308, fails to replicate in cultured murine macrophages, and is rapidly cleared from the spleens and livers of experimentally infected BALB/c mice. These findings suggest that the Brucella abortus hfq gene product makes an essential contribution to pathogenesis in mice, probably by allowing the brucellae to adapt appropriately to the harsh environmental conditions encountered within the host macrophage.

Animals↗

PubMed1972

Deoxyribonucleic acid repair in bacteriophage T4: observations on the roles of the x and v genes and of host factors.

Studies were carried out to determine the effect of mutation in the host pol I gene on survival of ultraviolet (UV)-irradiated bacteriophage T4. Whereas a slightly reduced survival was observed in Escherichia coli strain P-3478 (pol A(1)) compared to strain W-3110 (pol A(+)), no such difference was observed in two strains isogenic except for the pol A gene. It was also shown that, whereas bacteriophage T4x is sensitive to UV irradiation, X irradiation, and treatment with methyl-methanesulfonate (MMS), phage T4v(1) is sensitive only to UV irradiation. The survival of damaged phage T4x is neither affected by the presence of the rec A, rec B, or pol A mutations in the host, nor is there evidence that phage T4 effects repair of rec A or pol A mutants previously treated with either UV or MMS.

Alkanesulfonates↗

PubMed1993

Host factors in the pathogenesis of arthritis triggered by infectious organisms. Overview.

Individual variability in host immune responses to infectious agents is likely influenced by differences in the repertoires of antigenic peptides bound by self-major histocompatibility complex molecules (MHC) and in the repertoires of T-cell receptors expressed in each individual. Moreover, genes regulating the processing of foreign MHC antigens (for example, peptide pump genes and proteosome constituent genes) may also be important in this regard. Infectious organisms may subvert host immune responses through expression of constituents sharing structure homology with host molecules. Such structural mimicry may serve to either promote induction of potentially harmful cross-reactive autoimmune responses or impede effective host responses, thereby favoring persistence of the organism.

Arthritis, Infectious↗

PubMed1998

Genetic and immunological host factors associated with susceptibility to HIV-1 infection.

The probability of HIV transmission depends on the interplay of many different factors related to infectiousness of the HIV-infected partner, susceptibility of the HIV-uninfected partner, and biological characteristics of HIV strains. Here, we review recent studies of host immunological and genetic factors which may affect susceptibility to HIV-1 infection. These factors are summarized in Table 1. We propose how to explore biological correlates of susceptibility to HIV-1 infection in epidemiological studies, discuss the strengths and limitations of this research, and address the implications for public health.

Disease Susceptibility↗

PubMed2006

Modelling cytomegalovirus replication patterns in the human host: factors important for pathogenesis.

Human cytomegalovirus can cause a diverse range of diseases in different immunocompromised hosts. The pathogenic mechanisms underlying these diseases have not been fully elucidated, though the maximal viral load during infection is strongly correlated with the disease. However, concentrating on single viral load measures during infection ignores valuable information contained during the entire replication history up to the onset of disease. We use a statistical model that allows all viral load data sampled during infection to be analysed, and have applied it to four immunocompromised groups exhibiting five distinct cytomegalovirus-related diseases. The results show that for all diseases, peaks in viral load contribute less to disease progression than phases of low virus load with equal amount of viral turnover. The model accurately predicted the time of disease onset for fever, gastrointestinal disease and pneumonitis but not for hepatitis and retinitis, implying that other factors may be involved in the pathology of these diseases.

Cytomegalovirus↗