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PubMed1999

Real-time observation of acrosomal dispersal from mouse sperm using GFP as a marker protein.

We produced transgenic mouse lines that accumulate mutated green fluorescent protein (EGFP) in sperm acrosome, a membrane limited organelle overlying the nucleus. The sperm showed normal fertilizing ability and the integrity of their acrosome was easily examined in a non-invasive manner by tracing the GFP in individual 'live' sperm with fluorescent microscopy. The time required for the dispersal of acrosomal contents was demonstrated to be approximately 3 s after the onset of acrosome reaction.

Acrosome↗
PubMed1992

Macroevolution of plasmids: a model for plasmid speciation.

A new evolutionary model for diversification in plasmid incompatibility groups (plasmid speciation) is suggested. The model is based on the formation of plasmid cointegrates from two compatible plasmids. The existence of plasmid cointegrates is well known, however, their potential key role in plasmid macroevolution has not yet been recognized. In a hypothesis presented here, one of the rep genes is supposed to be relaxed from selection in plasmid cointegrates and thus becomes free to accumulate mutations. These mutations can lead to a change in incompatibility specificity. Evidence supporting this hypothesis comes from the common occurrence of multi-replicon plasmids in nature as well as from experimental studies on plasmid cointegrate formation. A more speculative extension of this model hypothesizes an evolutionary scenario for origin of the eubacterial single-replicon genome and the eukaryotic multi-replicon genome, as well as the place of plasmids and viruses in this picture.

Bacteria↗
PubMed2006

Antigen presentation and the ubiquitin-proteasome system in host-pathogen interactions.

Relatively small genomes and high replication rates allow viruses and bacteria to accumulate mutations. This continuously presents the host immune system with new challenges. On the other side of the trenches, an increasingly well-adjusted host immune response, shaped by coevolutionary history, makes a pathogen's life a rather complicated endeavor. It is, therefore, no surprise that pathogens either escape detection or modulate the host immune response, often by redirecting normal cellular pathways to their advantage. For the purpose of this chapter, we focus mainly on the manipulation of the class I and class II major histocompatibility complex (MHC) antigen presentation pathways and the ubiquitin (Ub)-proteasome system by both viral and bacterial pathogens. First, we describe the general features of antigen presentation pathways and the Ub-proteasome system and then address how they are manipulated by pathogens. We discuss the many human cytomegalovirus (HCMV)-encoded immunomodulatory genes that interfere with antigen presentation (immunoevasins) and focus on the HCMV immunoevasins US2 and US11, which induce the degradation of class I MHC heavy chains by the proteasome by catalyzing their export from the endoplasmic reticulum (ER)-membrane into the cytosol, a process termed ER dislocation. US2- and US11-mediated subversion of ER dislocation ensures proteasomal degradation of class I MHC molecules and presumably allows HCMV to avoid recognition by cytotoxic T cells, whilst providing insight into general aspects of ER-associated degradation (ERAD) which is used by eukaryotic cells to purge their ER of defective proteins. We discuss the similarities and differences between the distinct pathways co-opted by US2 and US11 for dislocation and degradation of human class I MHC molecules and also a putatively distinct pathway utilized by the murine herpes virus (MHV)-68 mK3 immunoevasin for ER dislocation of murine class I MHC. We speculate on the implications of the three pathogen-exploited dislocation pathways to cellular ER quality control. Moreover, we discuss the ubiquitin (Ub)-proteasome system and its position at the core of antigen presentation as proteolysis and intracellular trafficking rely heavily on Ub-dependent processes. We add a few examples of manipulation of the Ub-proteasome system by pathogens in the context of the immune system and such diverse aspects of the host-pathogen relationship as virus budding, bacterial chromosome integration, and programmed cell death, to name a few. Finally, we speculate on newly found pathogen-encoded deubiquitinating enzymes (DUBs) and their putative roles in modulation of host-pathogen interactions.

Animals↗
PubMed2001

PD0084430: a non-nucleoside inhibitor of human cytomegalovirus replication in vitro.

Human cytomegalovirus (HCMV) is a major opportunistic pathogen in immunocompromised individuals. Current therapies target viral DNA replication and accumulate mutations that yield cross-resistance among the approved drugs. A novel, non-nucleoside inhibitor of HCMV replication, PD0084430, was identified in a screening assay using the HCMV beta-galactosidase recombinant RC256. The EC(50) for PD0084430 by inhibition of beta-galactosidase production is 1+/-0.7 microM. This antiviral activity was confirmed by yield reduction and plaque reduction assays using HCMV strain AD169. The TC(50) of PD0084430 as measured by (4C)thymidine incorporation is approximately 30 microM and by XTT is approximately 90 microM. The TC(50) for inhibition of cellular proliferation is approximately 20 microM. Time of addition experiments displayed a similar drop in efficacy for both PD0084430 and GCV when added after the onset of viral DNA replication. The transcomplementation assay for viral DNA replication, using a transfected ori(Lyt) containing plasmid, confirmed that viral DNA synthesis was inhibited at the same concentrations that showed antiviral activity. Western blots showed no apparent block of immediate early or early gene expression. Two ganciclovir (GCV) resistant isolates of HCMV tested showed no cross-resistance to PD0084430. These data suggested a potentially promising novel compound that inhibited HCMV at or before viral DNA replication. However, in vivo testing in mice dosed either orally or intraperitoneally showed rapid glucuronidation on the -OH group. SAR studies on this backbone showed that the -OH group was essential for the antiviral activity in vitro.

Animals↗
PubMed2000

Molecular markers for the identification and global tracking of whitefly vector-Begomovirus complexes.

Recent unprecedented upsurges in populations of the whitefly Bemisia tabaci (Genn.) have drawn much attention to its worldwide importance as an insect pest and as the vector of emergent begomoviruses (Family: Geminiviridae; Genus: Begomovirus). Several begomoviruses that are considered 'new' and others previously regarded as minor pathogens have been linked to recent epidemics. Recent studies have revealed much variation in begomoviruses, despite the view that DNA-containing viruses do not rapidly accumulate mutations. Also, certain B. tabaci 'variants' are known that more effectively or selectively transmit certain begomoviruses and exhibit biotic differences that may influence their spread. Patterns of distribution and dissemination of begomoviruses transmitted by B. tabaci are poorly understood because standardized molecular-based tracking methods have not been available. Understanding virus/whitefly vector/host plant interrelationships in the context of emerging problems can be achieved only by linking predicted evolutionary histories with epidemiology using molecular phylogenetic approaches. Identification and validation of informative molecular sequences are essential initial steps in this process. Genus-wide degenerate polymerase chain reaction (PCR) primers have been developed to amplify and sequence the 'core' region of the coat protein open reading frame (ORF) (V1), permitting 'universal' detection and provisional virus identification by comparisons with described viral genotypes. In subsequent studies reported here, several potentially informative viral ORFs and a non-coding region are explored. Of particular use for expanding diversity studies are group- or virus-specific sequences that can be targeted by utilizing newly available core CP sequences, or additional conserved regions around which broad spectrum primers can be designed to target variable sequences in key ORFs or non-coding regions. Prospective markers under exploration were selected with a basis in the most highly conserved viral ORFs, CP (V1) and a portion of replication-associated protein (REP) (L1/C1), and a key non-coding sequence that contain sufficient variability and/or virus-specific sequences, and are consequently of potential epidemiological relevance. Because B. tabaci occurs as a cryptic species, or species complex, that exhibits biotic polymorphism, yet morphological invariance, traditional morphologically based identification is impossible. An overriding complication to establishing molecular markers for identifying whitefly vector variants is that whitefly sequences in general, have not been available. However, recent work has shown that a partial mitochondria cytochrome oxidase I (mt COI) sequence separates vector variants with a basis in geographical origin, suggesting it is useful for further exploring variability and the phylogenetic history of whiteflies on a large scale. Here, the utility of whitefly mt COI nucleotides (nt) sequences is illustrated for inferring relationships between B. tabaci collected from major world regions. Used collectively, these approaches permit investigations of the patterns of distribution and dissemination of begomovirus-whitefly vector complexes for the first time. Ultimately, more immediate recognition of exotic viruses and whitefly vectors and early detection of upsurges in vector populations and of emerging viruses will be possible.

Amino Acid Sequence↗
PubMed2003

Genetic alterations detected on chromosomes 13 and 14 in Chinese non-small cell lung carcinomas.

Genetic alterations in 28 non-small cell lung carcinoma patients were detected on chromosomes 13q and 14q with microsatellite markers by polymerase chain reaction techniques. Loss of heterozygosity of up to 50% was detected with chromosome 13 markers and of up to 37% for chromosome 14. Microsatellite instability was as high as 30% on chromosome 13 and up to 19% on chromosome 14. Accumulated mutation frequencies of up to 94 and 93% were observed for chromosomes 13 and 14, respectively. Of eight tumors displaying high mutation frequencies, 1 also carried a K-ras mutation and 4 had p53 mutations. A significant association was observed between p53 mutations and genetic instability.

Adult↗
PubMed1998

The evolution of aging: a new approach to an old problem of biology.

Most gerontologists believe aging did not evolve, is accidental, and is unrelated to development. The opposite viewpoint is most likely correct. Genetic drift occurs in finite populations and leads to homozygosity in multiple-alleled traits. Episodic selection events will alter random drift towards homozygosity in alleles that increase fitness with respect to the selection event. Aging increases population turnover, which accelerates the benefit of genetic drift. This advantage of aging led to the evolution of aging systems (ASs). Periodic predation was the most prevalent episodic selection pressure in evolution. Effective defenses to predation that allow exceptionally long lifespans to evolve are shells, extreme intelligence, isolation, and flight. Without episodic predation, aging provides no advantage and aging systems will be deactivated to increase reproductive potential in unrestricted environments. The periodic advantage of aging led to the periodic evolution of aging systems. Newer aging systems co-opted and added to prior aging systems. Aging organisms should have one dominant, aging system that co-opts vestiges of earlier-evolved systems as well as vestiges of prior systems. In human evolution, aging systems chronologically emerged as follows: telomere shortening, mitochondrial aging, mutation accumulation, senescent gene expression (AS#4), targeted somatic tissue apoptotic-atrophy (AS#5), and female reproductive tissue apoptotic-atrophy (AS#6). During famine or drought, to avoid extinction, reproduction is curtailed and aging is slowed or somewhat reversed to postpone or reverse reproductive senescence. AS#4-AS#6 are gradual and reversible aging systems. The life-extending/rejuvenating effects of caloric restriction support the idea of aging reversibility. Development and aging are timed by the gradual loss of cytosine methylation in the genome. Methylated cytosines (5mC) inhibit gene transcription, and deoxyribonucleic acid (DNA) cleavage by restriction enzymes. Cleavage inhibition prevents apoptosis, which requires DNA fragmentation. Free radicals catalyze the demethylation of 5mC while antioxidants catalyze the remethylation of cytosine by altering the activity of DNA methyltransferases. Hormones act as either surrogate free radicals by stimulating the cyclic adenosine monophosphate (cAMP) pathway or as surrogate antioxidants through cyclic guanosine monophosphate (cGMP) pathway stimulation. Access to DNA containing 5mC inhibited developmental and aging genes and restriction sites is allowed by DNA helicase strand separation. Tightly wound DNA does not allow this access. The DNA helicase generates free radicals during strand separation; hormones either amplify or counteract this effect. Caloric restriction slows or reverses the aging process by increasing melatonin levels, which suppresses reproductive and free radical hormones, while increasing antioxidant hormone levels. Cell apoptosis during CR leads to somatic wasting and a release of DNA, which increases bioavailable cGMP. The rapid aging diseases of progeria, the three diseases: (xeroderma pigmentosum (XP), Cockayne syndrome(CS), and ataxia telangiectasia (AT)), and Werner's syndrome are related to or caused by defects in three separate DNA helicases. The rapid aging diseases caused by mitochondrial malfunctions mirror those seen in XP, CS, and AT. Comparing these diseases allows for assignment of the different symptoms of aging to their respective aging systems. Follicle-stimulating hormone (FSH) demethylates the genes of AS#4, luteinizing hormone (LH) of AS#5, and estrogen of AS#6 while cortisol may act cooperatively with FSH and LH, and 5-alpha dihydrotestosterone (DHT) with FSH in these role. The Werner's DNA helicase links timing of the age of puberty, menopause, and maximum lifespan in one mechanism. Telomerase is under hormonal control. Most cancers likely result from malfunctions in the programmed apoptosis of AS#5 and AS#6. The Hayflick limit is reached primarily through loss of cytosine methylation of genes that inhibit replication. Men suffer the diseases of AS#4 at a higher rate than women who suffer from AS#5 more often. Adult mammal cloning suggests aging-related cellular demethylation, and thus aging, is reversible. This theory suggests that the protective effect of smoking and ibuprofen for Alzheimer's disease is caused through LH suppression.

Aging↗
PubMed2000

Pandemic influenza is a zoonosis, as it requires introduction of avian-like gene segments in the human population.

Human influenza viruses manage to cause epidemics almost every year. The circulating viruses change their surface glycoproteins by accumulating mutations (antigenic drift) which results in variant viruses of the same subtype that are able to evade the immune pressure in the population. Every now and then, a completely new subtype of influenza A virus is introduced in the human population, which can result in an influenza pandemic. Pandemic human influenza viruses have been emerging for many centuries. Based on the genetic information of influenza viruses that have been isolated in this century, introduction of genes of the avian influenza virus reservoir obviously is required. Interspecies transmission, via another mammalian host and reassortment of avian and human influenza viruses are potential mechanisms for such an introduction. A summary of the cases in which influenza viruses containing avian-like gene segments were introduced into the human population is presented. In three cases, such infections resulted in conjunctivitis. Influenza-like illness and even pneumonia was reported in some other infections. Finally, a mortality rate of 33% was observed in the avian influenza A (H5N1) viruses that infected 18 people in Hong Kong in 1997. Although some of these viruses fulfilled some criteria of pandemic influenza viruses, they lacked the ability to rapidly spread through the human population.

Animals↗
PubMed1997

Origin, evolution, and excision of internal elimination segments in germline genes of ciliates.

Three hypothesis on the evolutionary/molecular origin of internal eliminated segments (IESs) in the germline of hypotrichous ciliates are discussed in the context of the high rate of mutation accumulation in IESs, shifting of IESs during speciation, and evolutionary scrambling of segments within some hypotrich germline genes. Developmental excision of IESs from the germline in Paramecium suggests that the parental macronucleus may provide nucleic acid sequence information to guide excision of IESs and splicing of macronuclear-destined sequences. In ciliates of the oxytrichid/stylonychid group, such a mechanism could explain the precision of excision of IESs and gene unscrambling. Recently initiated molecular/genetic studies may eventually clarify the role of the parental macronucleus in IES excision and gene unscrambling as well as the molecular mechanisms of these events.

Animals↗
PubMed2002

Hepatitis B and hepatitis C.

Hepatitis B and C are worldwide infectious hepatitides which are distinct in terms of epidemiology and molecular biology, but which may be quite similar in terms of clinical manifestations and histopathology, in both the acute and chronic stages. Hepatitis B virus (HBV), the human prototype of the Hepadnaviridae family of viruses is not directly cytopathic and viral hepatitis is caused by the cellular immune response to HBV. Patients infected with HBV may also have hepatitis D (delta) virus (HDV) infection, either as co-infection or a superinfection. Hepatitis D virus does not infect independently. Better control of HBV has also led to a decline in the incidence of HDV. Hepatitis C virus (HCV) is on of the Flaviviridae family of viruses, and is quite heterogeneous, with six major genotypes and more than 100 subtypes. Hepatitis C virus circulates as quasispecies that result from mutations accumulated over time, which probably enable HCV to replicate efficiently or resist immune mechanisms. Quasispecies have complicated vaccine development. Both HBV and HCV will recur in the transplanted liver. The risk of developing hepatocellular carcinoma is significantly greater in both HBV- and HCV-infected individuals.

Biopsy↗
PubMed2001

Rates of movement and distribution of transposable elements in Drosophila melanogaster: in situ hybridization vs Southern blotting data.

Genomic copy numbers and the rates of movement of nine families of transposable elements (TEs) of Drosophila melanogaster were estimated in two sets of mutation accumulation lines: Beltsville and Madrid. Southern blotting was used to screen a large number of samples from both genetic backgrounds for TEs. The Madrid lines were also screened by in situ hybridization of TEs to polytene chromosomes, in order to obtain more detailed information about the behaviour of TEs in the euchromatin. Southern blotting data provided evidence of insertions and excision events in both genetic backgrounds, occurring at rates of approximately 10(-5) and 10(-6) per element copy per generation, respectively. In contrast, in situ data from the Madrid background presented a completely different picture, with no evidence for excisions, and a significantly higher rate of transposition (1.01 x 10(-4)). Direct comparison of the two data sets suggests that the Southern blotting technique had serious deficiencies: (i) it underestimated element abundance; (ii) it revealed less than 30% of the new insertions detected by in situ hybridization; and (iii) changes in the size of restriction fragments from any source were spuriously identified as simultaneous insertion-excision events. Our in situ data are consistent with previous studies, and suggest that selection is the main force controlling element spread by transposition.

Animals↗
PubMed2006

The genetic outcomes of sex and recombination in long-term functionally parthenogenetic lineages of Australian Sitobion aphids.

The typical life cycle of an aphid is cyclical parthenogenesis which involves the alternation of sexual and asexual reproduction. However, aphid life cycles, even within a species, can encompass everything on a continuum from obligate sexuality, through facultative sexuality to obligate asexuality. Loss of the sexual cycle in aphids is frequently associated with the introduction of a new pest and can occur for a number of environmental and genetic reasons. Here we investigate loss of sexual function in Sitobion aphids in Australia. Specifically, we aimed to determine whether an absence of sexual reproduction in Australian Sitobion results from genetic loss of sexual function or environmental constraints in the introduced range. We addressed our aims by performing a series of breeding experiments. We found that some lineages have genetically lost sexual function while others retain sexual function and appear environmentally constrained to asexuality. Further, in our crosses, using autosomal and X-linked microsatellite markers, we identified processes deviating from normal Mendelian segregation. We observed strong deviations in X chromosome transmission through the sexual cycle. Additionally, when progeny genotypes were examined across multiple loci simultaneously we found that some multilocus genotypes are significantly over-represented in the sample and that levels of heterozygosity were much higher than expected at almost all loci. This study demonstrates that strong biases in the transmission of X chromosomes through the sexual cycle are likely to be widespread in aphids. The mechanisms underlying these patterns are not clear. We discuss several possible alternatives, including mutation accumulation during periods of functional asexuality and genetic imprinting.

Animals↗
PubMed2001

Trematode infection and the distribution and dynamics of parthenogenetic snail populations.

According to the Red Queen hypothesis for sex, cross-fertilization should be positively associated with the probability of exposure (risk) to virulent parasites. Unfortunately, risk is difficult to measure in the wild, and prevalence of infection is often substituted for risk. Here I suggest that prevalence of infection may not generally suffice as a surrogate for risk, since the Red Queen model can make opposite predictions depending on the distribution of risk in the wild. Specifically, the results of a matching-alleles model suggest that asexual populations should be more infected than sexual populations, when (1) the variance in risk among populations is small, and (2) the mean risk of exposure to parasites is near the point where selection switches to favouring sex over asex. If, however, the variance in risk among populations is large, sexual reproduction should be positively associated with the prevalence of infection. In addition, the coefficient of variation for reproductive mode should increase sharply at the switch point. In light of these results, I re-evaluated data from two studies on the distribution of males in 95 populations of a freshwater snail (Potamopyrgus antipodarum). Populations of these snails are often mixtures of sexual and asexual individuals, and the frequency of males is correlated with the frequency of sexual females in the population. The results show a large, highly skewed variance among populations for prevalence of infection by larval trematodes. The results also show a positive, significant relationship between prevalence of infection and the frequency of males, with a sharp increase in the coefficient of variation at intermediate prevalence. In addition, experimental studies suggest that some of the necessary conditions of the Red Queen hypothesis are also met in this system. Specifically, the most common trematode infecting these snails is (1) adapted to infecting local host populations of the snail, and is (2) more infective to clones that were common in the recent past. It is too early to knoxv if the parasite theory is sufficient to explain the widespread distribution of sex. I suggest that the theory is not sufficient, but that parasites in combination with mutation accumulation in clonal lines may explain the maintenance of sex in species that occasionally produce apomictic mutants.

Animals↗
PubMed1999

Structural instability of 297 element in Drosophila melanogaster.

297 element Southern pattern modifications previously detected in mutation accumulation lines of Drosophila melanogaster were further investigated by in situ hybridisation, Southern blotting with different combinations of genomic digest-probe, and PCR. Only one out of the nine pattern modifications studied could be interpreted as an excision and was detectable by in situ hybridisation to polytene chromosomes. Results were consistent with most pattern modifications being small rearrangements within the body of the element. In agreement with the existence of spontaneous rearrangements of this kind is the observation that many genomic copies of element 297 are defective and these are not limited to heterochromatin. These findings have important implications for the models of transposable element (TE) number regulation as well as for the study of genome evolution.

Animals↗
PubMed2004

Molecular characterization of nosRZDFYLX genes coding for denitrifying nitrous oxide reductase of Bradyrhizobium japonicum.

The nosRZDFYLX gene cluster for the respiratory nitrous oxide reductase from Bradyrhizobium japonicum strain USDA110 has been cloned and sequenced. Seven protein coding regions corresponding to nosR, nosZ, the structural gene, nosD, nosF, nosY, nosL, and nosX were detected. The deduced amino acid sequence exhibited a high degree of similarity to other nitrous oxide reductases from various sources. The NosZ protein included a signal peptide for protein export. Mutant strains carrying either a nosZ or a nosR mutation accumulated nitrous oxide when cultured microaerobically in the presence of nitrate. Maximal expression of a P nosZ-lacZ fusion in strain USDA110 required simultaneously both low level oxygen conditions and the presence of nitrate. Microaerobic activation of the fusion required FixLJ and FixK(2).

Amino Acid Sequence↗
PubMed1980

Efficiency of the adaptive response of Escherichia coli to alkylating agents.

When cultures of Escherichia coli are exposed to a low level of the alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) they accumulate mutations for about 20 min and then become resistant to further mutagenesis by that level of MNNG. This 'adaptive response, has been shown to be due, at least in part, to induction of the rapid repair of O6-alkylguanine which appears to be the main mutagenic and carcinogenic lesion produced by simple alkylating agents. A similar kind of repair has been demonstrated in the livers of rats exposed to nitrosamines, and this presumably helps to protect animals against carcinogenesis by the various alkylating agents thjat are widespread in our environment. It seemed important, therefore, to find out just how effectively such adaptive responses can control mutations rates.

Adaptation, Physiological↗
PubMedDate not supplied

Nucleotide sequence evidence for rapid genotypic shifts in the bovine mitochondrial DNA D-loop.

Mitochondrial DNA (mtDNA) is unusual in its rapid rate of evolution and high level of intraspecies sequence variation. The latter is thought to be related to the strict maternal inheritance of mtDNA, which effectively isolates within a species mitochondrial gene pools that accumulate mutations and vary independently. A fundamental and as yet unexplained aspect of this process is how, in the face of somatic and germ-line mtDNA ploidy of 10(3) to 10(5) (refs 4, 5), individual variant mtDNA molecules resulting from mutational events can come to dominate the large intracellular mtDNA population so rapidly. To help answer this question, we have determined here the nucleotide sequence of all or part of the D-loop region in 14 maternally related Holstein cows. Four different D-loop sequences can be distinguished in the mtDNA of these animals. One explanation is that multiple mitochondrial genotypes existed in the maternal germ line and that expansion or segregation of one of these genotypes during oogenesis or early development led to the rapid genotypic shifts observed.

Animals↗
PubMed2003

RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity.

Helicases are molecular motors that move along and unwind double-stranded nucleic acids. RecBCD enzyme is a complex helicase and nuclease, essential for the major pathway of homologous recombination and DNA repair in Escherichia coli. It has sets of helicase motifs in both RecB and RecD, two of its three subunits. This rapid, highly processive enzyme unwinds DNA in an unusual manner: the 5'-ended strand forms a long single-stranded tail, whereas the 3'-ended strand forms an ever-growing single-stranded loop and short single-stranded tail. Here we show by electron microscopy of individual molecules that RecD is a fast helicase acting on the 5'-ended strand and RecB is a slow helicase acting on the 3'-ended strand on which the single-stranded loop accumulates. Mutational inactivation of the helicase domain in RecB or in RecD, or removal of the RecD subunit, altered the rates of unwinding or the types of structure produced, or both. This dual-helicase mechanism explains how the looped recombination intermediates are generated and may serve as a general model for highly processive travelling machines with two active motors, such as other helicases and kinesins.

DNA↗