Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13

Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3-9 and 13 of P. falciparum clone 3D7--these chromosomes account for approximately 55% of the total genome. We describe the methods used to map, sequence and annotate these chromosomes. By comparing our assemblies with the optical map, we indicate the completeness of the resulting sequence. During annotation, we assign Gene Ontology terms to the predicted gene products, and observe clustering of some malaria-specific terms to specific chromosomes. We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts.

Blood platelets of the African elephant

Platelet counts of 22 elephants varied between 229 x 10(9) and 622 x 10(9)/L. Light microscopy showed the platelets to be small, while electron microscopy revealed well preserved but activated platelets with some morphological differences from other mammalian platelets. Dense bodies, alpha-granules, glycogen and mitochondria were present in most sections. Microtubules and the surface connecting canalicular system appeared to be absent, but numerous filamentous structures and Golgi bodies were observed.

The genome sequence of Schizosaccharomyces pombe

We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.

Comparison of optokinetic scene effects on the somatogyral illusion

The objective of this study was to determine during rotation the relative importance of a scene in achieving "visual dominance" over non-visual vestibular orientation inputs, e.g., otolith and semicircular canals. Five visual scenes were presented, while rotating the subject (at three angular acceleration rates), to obtain the vestibular and optokinetic nystagmus and perception of rotation. The onset time and direction of rotation, as well as EOG and chair velocity were recorded. Adaptation times during rotation at constant angular velocity and during post-rotation were also recorded. Analysis of perceived times (onset, adaptation, and post-rotatory adaptation) with the EOG slow-phase velocity at respectively perceived times were analyzed using the SAS procedures Analysis of Variance (ANOVA) and General Linear Models (GLM). Basic hypotheses for the study were: "There are no differences in latencies for either onset time (L1), adaptation to rotation (L2), or adaptation to post rotatory motion (L4), between treatment conditions, or between Groups of subjects, or between acceleration rates, between constant rotation velocities, or between direction of rotation." From the results, it was concluded that pilots are highly visually dependent; additionally, if there is a sensory conflict, a larger percentage of individuals (pilots) will follow visual perceptions even if the demands of the aerial environment and our perception is incorrect. However, in sensory conflict conditions, with degraded visual scene individuals including pilots will revert to vestibular perception rather than visual perception (less visually coupled), approaching percentages as noted with a dark environment.

Smoking and mental illness

Patients with mental illness have a higher incidence of smoking than the general population and are the major consumers of tobacco products. This population includes subjects with schizophrenia, manic depression, depression, posttraumatic stress disorder (PTSD), attention-deficit disorder (ADD), and several other less common diseases. Smoking cessation treatment in this group of patients is difficult, often leading to profound depression. Several recent findings suggest that increased smoking in the mentally ill may have an underlying biological etiology. The mental illness schizophrenia has been most thoroughly studied in this regard. Nicotine administration normalizes several sensory-processing deficits seen in this disease. Animal models of sensory deficits have been used to identify specific nicotinic receptor subunits that are involved in these brain pathways, indicating that the alpha 7 nicotinic receptor subunit may play a role. Genetic linkage in schizophrenic families also supports a role for the alpha 7 subunit with linkage at the alpha 7 locus on chromosome 15. Bipolar disorder has some phenotypes in common with schizophrenia and also exhibits genetic linkage to the alpha 7 locus, suggesting that these two disorders may share a gene defect. The alpha 7 receptor is decreased in expression in schizophrenia. [(3)H]-Nicotine binding studies in postmortem brain indicate that high-affinity nicotinic receptors may also be affected in schizophrenia.

Blood lactic acid levels after artificial heart implantation

The aim of this study is to investigate blood lactic acid levels after the placement of the AbioCor implantable replacement heart to determine whether circulatory support with the AbioCor device results in adequate tissue perfusion. Tissue perfusion may not be adequate during cardiac surgery, especially with the use of cardiopulmonary bypass (CPB). Inadequate perfusion is usually associated with anaerobic metabolism, metabolic acidosis, and lactate accumulation. Ten calves had implantation of the AbioCor by means of a right thoracotomy. Standard cardiopulmonary bypass was performed during surgery. Lactic acid levels and blood gas analyses were measured. All animals were monitored for pressures in the aorta, pulmonary artery, and left and right atria. The output of the AbioCor was calculated based on beat rate and stroke volume. All animals were rapidly weaned off cardiopulmonary bypass to full AbioCor support and had normal hemodynamics with normal filling pressures. The lactic acid levels were elevated after surgery, peaked at 8 to 12 hours, and then gradually decreased to the normal range 24 hours after surgery. There was a positive relationship between lactate levels, oxygen consumption, and extraction rate, that is, the lactic acid levels were higher in the presence of increased oxygen consumption and increased oxygen extraction rate. There was a negative relationship between lactate levels and oxygen delivery, and arterial and venous oxygen content, that is, the lactic acid levels were higher when oxygen delivery and arterial and venous oxygen contents were low. The pathophysiology of lactic acidosis is uncertain, but is most likely due to inadequate perfusion during cardiopulmonary bypass, and lactate washout after adequate perfusion has been established. The return to aerobic metabolism with clearance of lactate demonstrates that the AbioCor is able to provide complete circulatory support with normal tissue perfusion.

Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18

Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual global burden of approximately 16 million cases, leading to 600,000 fatalities. Many S. enterica serovars actively invade the mucosal surface of the intestine but are normally contained in healthy individuals by the local immune defence mechanisms. However, S. typhi has evolved the ability to spread to the deeper tissues of humans, including liver, spleen and bone marrow. Here we have sequenced the 4,809,037-base pair (bp) genome of a S. typhi (CT18) that is resistant to multiple drugs, revealing the presence of hundreds of insertions and deletions compared with the Escherichia coli genome, ranging in size from single genes to large islands. Notably, the genome sequence identifies over two hundred pseudogenes, several corresponding to genes that are known to contribute to virulence in Salmonella typhimurium. This genetic degradation may contribute to the human-restricted host range for S. typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis.

Genome sequence of Yersinia pestis, the causative agent of plague

The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to nineteenth centuries) and modern plague (nineteenth century to the present day). The recent identification of strains resistant to multiple drugs and the potential use of Y. pestis as an agent of biological warfare mean that plague still poses a threat to human health. Here we report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is unusually rich in insertion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic recombination. Many genes seem to have been acquired from other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins). The genome contains around 150 pseudogenes, many of which are remnants of a redundant enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve.

Salmonella enterica serovar Typhi possesses a unique repertoire of fimbrial gene sequences

Salmonella enterica serotype Typhi differs from nontyphoidal Salmonella serotypes by its strict host adaptation to humans and higher primates. Since fimbriae have been implicated in host adaptation, we investigated whether the serotype Typhi genome contains fimbrial operons which are unique to this pathogen or restricted to typhoidal Salmonella serotypes. This study established for the first time the total number of fimbrial operons present in an individual Salmonella serotype. The serotype Typhi CT18 genome, which has been sequenced by the Typhi Sequencing Group at the Sanger Centre, contained a type IV fimbrial operon, an orthologue of the agf operon, and 12 putative fimbrial operons of the chaperone-usher assembly class. In addition to sef, fim, saf, and tcf, which had been described previously in serotype Typhi, we identified eight new putative chaperone-usher-dependent fimbrial operons, which were termed bcf, sta, stb, ste, std, stc, stg, and sth. Hybridization analysis performed with 16 strains of Salmonella reference collection C and 22 strains of Salmonella reference collection B showed that all eight putative fimbrial operons of serotype Typhi were also present in a number of nontyphoidal Salmonella serotypes. Thus, a simple correlation between host range and the presence of a single fimbrial operon seems at present unlikely. However, the serotype Typhi genome differed from that of all other Salmonella serotypes investigated in that it contained a unique combination of putative fimbrial operons.

The failure of different strains of Yersinia pestis to produce lipopolysaccharide O-antigen under different growth conditions is due to mutations in the O-antigen gene cluster

The lipopolysaccharide (LPS) from eight strains of Yersinia pestis which had been cultured at 28 degrees C appeared to be devoid of an O-antigen when analysed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. LPS isolated from three of these strains which had been cultured at 37 degrees C also appeared to be devoid of an O-antigen. When the LPS from Y. pestis strain CO92 was purified and analysed by matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry, the observed signals were in the mass range predicted for molecules containing lipid A plus the core oligosaccharide but lacking an O-antigen. The nucleotide sequence of Y. pestis strain CO92 revealed the presence of a putative O-antigen gene cluster. However, frame-shift mutations in the ddhB, gmd, fcl and ushA genes are likely to prevent expression of the O-antigen thus explaining the loss of phenotype.

Yersinia pestis pFra shows biovar-specific differences and recent common ancestry with a Salmonella enterica serovar Typhi plasmid

Population genetic studies suggest that Yersinia pestis, the cause of plague, is a clonal pathogen that has recently emerged from Yersinia pseudotuberculosis. Plasmid acquisition is likely to have been a key element in this evolutionary leap from an enteric to a flea-transmitted systemic pathogen. However, the origin of Y. pestis-specific plasmids remains obscure. We demonstrate specific plasmid rearrangements in different Y. pestis strains which distinguish Y. pestis bv. Orientalis strains from other biovars. We also present evidence for plasmid-associated DNA exchange between Y. pestis and the exclusively human pathogen Salmonella enterica serovar Typhi.

Role of stress responses in human cell survival following exposure to ultraviolet C radiation

PURPOSE

To investigate in human skin and other cells the role of tyrosine kinase and protein kinase-C (PKC) in eliciting cell-signalling responses to UV radiation (UVR) that affect the survival of irradiated cells.

MATERIALS AND METHODS

The survival of HeLa S3 cells, NCTC 2544 human keratinocytes and A431 human epidermal carcinoma cells was measured following incubation with various tyrosine kinase or PKC inhibitors and exposure to UVC (254nm) radiation. In addition, Western blotting measured PKC isozyme expression in human keratinocytes following UVC exposure.

RESULTS

It was confirmed that inhibition of tyrosine kinase activation reduces the survival of UV-irradiated HeLa S3 cells. However, no effect was seen on the survival of either NCTC 2544 human keratinocytes or A431 human epidermal carcinoma cells. In contrast, specific inhibition of PKC reduced the survival of UV-irradiated keratinocytes but had no effect on HeLa cells. Comparison of the effects of different inhibitors in keratinocytes suggested that this effect was mediated mostly through PKCmu and PKClambda/iota. In addition, keratinocyte exposure to UVC induced large and temporally distinct increases in PKCmu and PKClambda/iota.

CONCLUSIONS

The survival of NCTC 2544 keratinocytes, but not HeLa S3 cells, following UVC exposure is mediated by signalling through PKC, mostly PKCmu and PKClambda/iota. Further study is required to confirm these results in normal human keratinocytes.

Massive gene decay in the leprosy bacillus

Leprosy, a chronic human neurological disease, results from infection with the obligate intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus. Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted every effort at culture in the laboratory. Comparing the 3.27-megabase (Mb) genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium tuberculosis (4.41 Mb) provides clear explanations for these properties and reveals an extreme case of reductive evolution. Less than half of the genome contains functional genes but pseudogenes, with intact counterparts in M. tuberculosis, abound. Genome downsizing and the current mosaic arrangement appear to have resulted from extensive recombination events between dispersed repetitive sequences. Gene deletion and decay have eliminated many important metabolic activities including siderophore production, part of the oxidative and most of the microaerophilic and anaerobic respiratory chains, and numerous catabolic systems and their regulatory circuits.

Creating temperature-sensitive winged helix transcription factors. Amino acids that stabilize the DNA binding domain of HNF3

Winged helix transcription factors contain two polypeptide loops, or "wings," that make minor groove contacts with DNA from either side of a three-helix bundle that binds the DNA major groove. While wing 1 is stabilized by a beta-sheet, parameters that stabilize wing 2 are unknown. Herein we identify two bulky aromatic residues in wing 2 that stabilize the loop structure and, thereby, the entire protein's DNA binding and transcriptional stimulatory activity by interacting with other residues in the three-helix bundle. Mutations of these wing 2 residues create proteins that are temperature-sensitive for transcriptional activity. Aromatic and/or hydrophobic residues are highly conserved among the 150 known winged helix proteins, suggesting conserved function. We suggest that the winged helix structure evolved by the acquisition of aromatic and/or hydrophobic residues in distal polypeptide sequences that helped stabilize the association of a protein loop (wing 2) with the three-helix bundle, thereby enhancing DNA binding.

Initial experience with the AbioCor implantable replacement heart at the University of Louisville

Potential benefits of heart transplantation are limited by the severe donor organ shortage. The AbioCor implantable replacement heart has been developed as a potential alternative to heart transplantation. We report our initial experience with the AbioCor in a bovine model. A right thoracotomy was performed for access to the heart and great vessels. After initiation of cardiopulmonary bypass, excision of the native ventricles was followed by orthotopic placement of the IRH and complete implantation of the transcutaneous energy transfer coil, controller, and battery pack. Invasive monitoring of IVC, SVC, carotid artery, pulmonary artery, and left atrial (LA) pressures was performed in all animals. Twelve calves have undergone implantation of the AbioCor. There were three early deaths, one from bleeding, one from respiratory failure, and one from neurodysfunction from low flow during CPB. Nine animals have had a normal recovery and survived a mean of 24.5 days (range, 4-48 days). All the animals have demonstrated excellent hemodynamics with the maintenance of normal pressures in the LA, SVC, IVC, pulmonary artery, and aorta. Adjustment of the right-sided internal hydraulic fluid shunt has allowed for control of right-left balance and, thereby, manipulation of left and right side filling pressures. Late morbidity has consisted of neck wound infection and sepsis, pneumonia, and bleeding. Successful orthotopic implantation of all components of the AbioCor has been achieved in a bovine model. This device has demonstrated restoration of normal hemodynamics and excellent function of the atrial hydraulic shunt to achieve right-left balance.

Splice variants of the mouse Tec gene are differentially expressed in vivo

Tec is a cytoplasmic protein tyrosine kinase that participates in the signalling pathways of a broad range of cytokines. Up to five different Tec isoforms have been reported in the literature. We report here the genomic organisation of the mouse Tec gene and the tissue expression pattern of the two predominant transcripts, TecIII and TecIV. The mouse Tec gene consists of 18 exons, spans more than 86 kb, and is 2.6 kb 5' to the gene for Txk, a Tec family member. Comparison of mouse and human Btk, human TXK, and mouse Tec genomic structures shows a high level of conservation of exon/intron boundaries. Compared with TecIV, the TecIII transcript has a 66-bp deletion in the SH3 domain encoding region and is revealed here to arise by alternative splicing of exon 8. We show that both TecIII and TecIV are expressed as early as embryonic day 10.5 in mouse development, as well as in adult and embryonic organs. The ratio of TecIV to TecIII expression is markedly reduced in adult liver and kidney tissues and d16 embryonic limb.

Smoking and schizophrenia: abnormal nicotinic receptor expression

Biological and genetic evidence suggests a role for the neuronal nicotinic receptors in the neuropathophysiology of schizophrenia. Nicotine normalizes an auditory evoked potential deficit seen in subjects who suffer from the disease. Nicotinic receptors with both high and low affinity for nicotine are decreased in postmortem brain of schizophrenics compared to control subjects. The chromosomal locus of the human alpha-7 gene (15q14) is linked to the gating deficit with a lod of 5.3, and antagonists of the alpha-7 receptor (alpha-bungarotoxin and methyllycaconitine) induce a loss of gating in rodents. We have cloned the human alpha-7 gene and found it to be partially duplicated proximal to the full-length gene. The duplication is expressed in both the brain and in peripheral blood cells of normal subjects, but is missing in some schizophrenic subjects. The results of these studies suggest the presence of abnormal expression and function of the neuronal nicotinic receptor gene family in schizophrenia.

Immune activation in the early puerperium is related to postpartum anxiety and depressive symptoms

The pathophysiology of the postpartum blues, common transient mood disorders in the first week postpartum, has remained elusive. Recently, however, it has been shown that depression and anxiety disorders are accompanied by activation of the inflammatory response system (IRS). This study was developed to determine whether the postnatal blues is associated with IRS activation. Serum concentrations of interleukin-6 (IL-6), IL-6 receptor (IL-6R), gp130 (the IL-6 signaling protein), IL-1R antagonist (IL-1RA) and leukemia inhibitory factor receptor (LIFR) were assayed in 22 nonpregnant women and in 91 pregnant women before delivery and 1 and 3 days after delivery. On each occasion the parturient women completed the State version of the Spielberger State-Trait-Anxiety-Inventory (STAI) and the Zung Depression Rating Scale (ZDS). Serum IL-6, IL-1RA and LIFR were significantly higher in pregnant women at the end of term than in nonpregnant women.

Effects of pregnancy and delivery on serum prolyl endopeptidase (PEP) activity: alterations in serum PEP are related to increased anxiety in the early puerperium and to postpartum depression

BACKGROUND

There is now some evidence that anxiety or anxiety disorders are related to increased activity of serum prolyl endopeptidase (PEP) and that major depression is related to lower serum PEP. The aims of the present study were to examine (i) the effects of pregnancy and delivery on serum PEP and (ii) the relationships between serum PEP and postpartum depression, anxiety in the early puerperium and a past history of depression.

METHODS

Serum PEP activity was measured in 11 healthy nonpregnant and in 98 pregnant women 3 days before delivery and 1 and 3 days after delivery. On the same occasions, pregnant females completed the Spielberger State Anxiety Inventory (STAI) and were divided into high and low anxiety responders, as defined by changes in the STAI. The presence of a previous depression and postpartum depression within 3 months of delivery was assessed by means of DSM-IV criteria.

RESULTS

Serum PEP activity was significantly higher 1 and 3 days after delivery than before. Women with a past history of depression as well as anxiety responders had significantly increased serum PEP activity over nonpregnant women and puerperae with a negative history and anxiety nonresponders, respectively. Parturients who developed a postpartum major, but not minor, depression had significantly lower serum PEP than parturients without postpartum depression. The results were controlled for maternal and labor variables, such as type of analgesia and delivery, induction of labor, breast feeding, parity, and duration of pregnancy and labor.

CONCLUSIONS

Our results show that, in puerperae, increased serum PEP is related to increased state anxiety in the early puerperium and that lowered serum PEP is related to a subsequent postpartum major depression.

INTERPRETATION

The results suggest that increased serum PEP may be related to postpartum anxious blues and that lowered serum PEP may predispose toward postpartum major depression.

Genetic basis for lipopolysaccharide O-antigen biosynthesis in bordetellae

Bordetella bronchiseptica and Bordetella parapertussis express a surface polysaccharide, attached to a lipopolysaccharide, which has been called O antigen. This structure is absent from Bordetella pertussis. We report the identification of a large genetic locus in B. bronchiseptica and B. parapertussis that is required for O-antigen biosynthesis. The locus is replaced by an insertion sequence in B. pertussis, explaining the lack of O-antigen biosynthesis in this species. The DNA sequence of the B. bronchiseptica locus has been determined and the presence of 21 open reading frames has been revealed. We have ascribed putative functions to many of these open reading frames based on database searches. Mutations in the locus in B. bronchiseptica and B. parapertussis prevent O-antigen biosynthesis and provide tools for the study of the role of O antigen in infections caused by these bacteria.