Molecular approaches to malaria: MAM 2004 and beyond

This special issue of Trends in Parasitology comprises a collection of timely reviews arising from the 2nd Molecular Approaches to Malaria meeting held 1-5 February 2004 in Lorne, Australia, four years after the successful inaugural meeting. As the name suggests, Molecular Approaches to Malaria focused on the latest molecular developments in malaria research, and their biological and clinical implications. By no means is this special issue intended to represent a comprehensive recapitulation of all of the presentations at the meeting. Rather, the articles address, in more general terms, recent advances on broader themes that were prominent at Molecular Approaches to Malaria meeting 2004.     

Cellular aggregate size as the critical factor for flavonoid production by suspension cultures of <Emphasis Type="Italic">Saussurea medusa</Emphasis>

Three previously established cell lines (yellow, red and white) of Saussurea medusa were investigated for jaceosidin and hispidulin production. Maximum yields of the jaceosidin and hispidulin were obtained in the red cell line at 75 ± 0.41 and 6.4 ± 0.31 mg l^-1. Production of jaceosidin and hispidulin correlated with the sizes of compact callus aggregates (CCA) and cellular viability. In the red cell line, the sizes of CCA were predominantly of 2–4mm diameter and accounted for 64% biomass. This line had a sustained cell viability over 10 successive sub-cultures.Revisions requested 3 September 2004/27 October 2004; Revisions received 22 October 2004/18 November 2004     

Changes in the rates of antimicrobial resistance among clinical isolates of Pseudomonas aeruginosa between 2002 and 2004 in a tertiary-care teaching hospital in Turkey

Pseudomonas aeruginosa is an important opportunistic pathogen usually resistant to most antimicrobials. We present changes in the resistance pattern of P. aeruginosa to amikacin (AK) and ciprofloxacin (CIP) between January 2002 and June 2004. The physicians of each unit were given information on antibiotic resistance rates of P. aeruginosa isolated from ward patients at regular intervals. The antibiotic resistance of 161 P. aeruginosa isolates isolated from intensive care units (ICUs) and non-ICUs were tested by disk diffusion method, and the results were interpreted according to the guidelines of National Committee for Clinical Laboratory Standards. Thirty-five percent of all the P. aeruginosa isolates were resistant to AK in 2002, 18% in 2003, and 20% in 2004. The CIP resistance rates were 4% in 2002, 26% in 2003, and 20% in 2004. In that period, resistance to AK decreased, whereas resistance to CIP increased. The usage rate of AK in 2002 was 32%, which fell to 26% in 2003 (p < 0.05). This rate increased to 27% in 2004 (p < 0.05). The usage rate of CIP was very low in 2002 (3%). Subsequently, it increased to 8% in 2003 and 2004 (p < 0.05). The changes in resistance rates may have been due to alteration in drug usage policy in our hospital. It is important to provide physicians with information on antibiotic resistance rates at regular intervals to guide therapy for critical P. aeruginosa infections.     

Plasmodium post-genomics: an update

The concept behind the first Molecular Approaches to Malaria meeting, held 1-5 February 2000 in Lorne, Australia, was ahead of its time; to convene a meeting of malaria researchers, database developers and genomics scientists, and to discuss how genomic sciences and their relevant disciplines could be applied to solve important problems in malaria research. The success of the second Molecular Approaches to Malaria meeting, held 1-5 February 2004 in the same place, together with the influence of genomics on malaria research, is testament to the vision that the organizers had at the first meeting. This review attempts to capture some of the current efforts in the post-genomics era of malaria research and highlights the approaches discussed at the Molecular Approaches to Malaria 2004 meeting.     

Molecular epidemiology of human coronavirus OC43 reveals evolution of different genotypes over time and recent emergence of a novel genotype due to natural recombination

Although human coronavirus OC43-OC43 (HCoV-OC43) is the coronavirus most commonly associated with human infections, little is known about its molecular epidemiology and evolution. We conducted a molecular epidemiology study to investigate different genotypes and potential recombination in HCoV-OC43. Twenty-nine HCoV-OC43 strains from nasopharyngeal aspirates, collected from 2004 to 2011, were subjected to RNA-dependent RNA polymerase (RdRp), spike, and nucleocapsid gene analysis. Phylogenetic analysis showed at least three distinct clusters of HCoV-OC43, although 10 unusual strains displayed incongruent phylogenetic positions between RdRp and spike genes. This suggested the presence of four HCoV-OC43 genotypes (A to D), with genotype D most likely arising from recombination. The complete genome sequencing of two genotype C and D strains and bootscan analysis showed recombination events between genotypes B and C in the generation of genotype D. Of the 29 strains, none belonged to the more ancient genotype A, 5 from 2004 belonged to genotype B, 15 from 2004 to 2006 belonged to genotype C, and 1 from 2004 and all 8 from 2008 to 2011 belonged to the recombinant genotype D. Molecular clock analysis using spike and nucleocapsid genes dated the most recent common ancestor of all genotypes to the 1950s, genotype B and C to the 1980s, genotype B to the 1990s, and genotype C to the late 1990s to early 2000s, while the recombinant genotype D strains were detected as early as 2004. This represents the first study to describe natural recombination in HCoV-OC43 and the evolution of different genotypes over time, leading to the emergence of novel genotype D, which is associated with pneumonia in our elderly population.     

Leucistic southern elephant seal at Marion Island?

An extraordinary light coloured, young southern elephant seal Mirounga leonina was seen at Marion Island during the 2004 austral spring. This is the second record of an extraordinary white colour morph for the species here. It was not unequivocally established that the animal was leucistic.     

苏北滨海湿地麋鹿恢复种群的研究

1986年至2004年,在苏北滨海湿地开展恢复麋鹿野生种群的研究。从每年的2月份开始,在麋鹿的产仔期按照每旬记录产仔数,直至产仔结束。逐年统计半散养和野生麋鹿种群结构。选择不同年龄阶段和不同性别的麋鹿进行称重,分析个体的身体发育程度。半散养麋鹿种群由1986年引进的39 头,发展到2004年的706 头,年均出生率21.7%,鹿群年均增长率为17.5%,现已繁殖了子四代;野生放养麋鹿由31 头增加到2004年的41头,年均出生率16.3%,年均增长率为9.0% ,且于2003年、2004年各产1 头完全属野生的子二代。产仔季节相由引进时的紊乱已调整至目前的规律性产仔。研究表明大丰麋鹿种群繁殖很成功,其寿命、行为、生理发育、繁殖周期等都较引进时发生了显著的变化,已完全适应了黄海湿地生态环境。人类活动干扰仍是影响麋鹿种群恢复的一个重要因素。     

浙江省森林生物量动态

以浙江省1976至2004年森林资源连续清查资料为数据源,采用基于生物量与蓄积之间关系的生物量转换因子连续函数法,对全省林分生物量和包括林分在内的森林生物量动态进行估计。森林生物量为包括林分、疏林、灌木林、竹林、经济林和四旁树在内的所有林木生物量之和。结果表明,浙江省1976至2004年间森林生物量从1.00828&#215;10^8Mg上升到2.44426&#215;10^8Mg;其中,林分生物量由0.5712&#215;10^8Mg上升到1.51128&#215;10^8Mg。森林生物量和林分生物量的年平均增长速度分别为5.1%和9.1%。在1999至2004年间,森林生物量和林分生物量增长速度均明显加快,分别达到8.6%和10.1%。在1976至2004年间,全省森林面积年均增长速度为1.0%,森林平均生物量从16.50Mg&#183;hm^-2上升到36.59Mg&#183;hm^-2。但是,在森林资源总量不断增加的同时,全省林分质量仍维持较低水平。2004年全省林分单位面积生物量为38.40Mg&#183;hm^-2,远低于全国平均水平（77.40Mg&#183;hm^-2）。研究还表明,利用森林资源连续清查数据和基于单株测树因子的森林生物量模型能够估计大尺度范围内的森林生物量及其动态,但亟待在统一标准下建立和完善覆盖所有树种的生物量模型。     

Papillomatosis in a European bison

Five European bison (Bison bonasus) from three European zoos were shipped to the Bukovské Vrchy Hills (Slovakia) in June 2004 and kept together in an acclimatization enclosure. The European bison were released into the wild in December 2004. At that time, papillomas were found at the medial canthus of the left eye of a 12-yr-old female bison. Cutaneous papillomatosis was confirmed histologically. Negative stain transmission electron microscopic examination revealed papillomavirus in the papillomas, and papillomavirus DNA also was detected using the polymerase chain reaction with FAP59 and FAP64 primers. The amplified 413 bp DNA sequence was identical to that of BAPV2 bovine papillomavirus. This paper is the first report of papillomatosis in European bison.     

Marine biological community baselines in unimpacted tropical ecosystems: spatial and temporal analysis of reefs at Howland and Baker Islands

Howland and Baker Islands are two small, isolated reef and sand islets located near the equator in the central Pacific Ocean that are situated approximately 60 km apart. In 2004 and 2006, species-level monitoring at multiple sites, coupled with towed-diver surveys in 2002, 2004, and 2006 on both of these federally protected islands, revealed diverse fish, coral, macroinvertebrate, and algal assemblages. This study examines inter- and intra-island spatial and temporal differences in community composition among sites and presents baseline biological community parameters for two of the least impacted reef systems in the world. Despite similarities in species composition, permutational multivariate analysis of variance (PERMANOVA) and multidimensional scaling ordinations (nMDS) suggest biological communities at the two islands are distinct with Baker Island containing a greater percent cover of branched Acroporid corals and turf algae and Howland Island containing a greater percent cover of crustose coralline red algae and small, compact genera of coral. Both islands also contained considerable cover of non-invasive macroalgae. PERMANOVA further revealed benthic and fish species composition to differ between forereef and reef shelf sites from different sides of each island. When islands were considered as a whole, temporal changes were not noted between 2004 and 2006; however, temporal changes at select sites did occur, with coral cover decreasing significantly along the west side of Baker Island from 2004 to 2006.     

Chromosomal aberration frequencies determined by conventional methods: Parallel increases over time in the region of a petrochemical industry and throughout the Czech Republic

The rationale for cytogenetic monitoring to determine if safe maximum allowable concentrations (MAC) of genotoxic chemicals are being maintained in a workplace is that exposure levels that do not increase chromosomal aberration frequencies are without harmful effects. Such monitoring, widely used in occupational health programs in the Czech Republic (CR), includes workers exposed to 1,3-butadiene (BD) or other chemicals. Studies of BD exposed workers in the years 1992, 1993, 1994, 1998, and 2004 compared mean frequencies of cells carrying chromosomal aberrations (frequency of aberrant cells=%AB.C.) in exposed workers with those in non-exposed matched controls in the same plant or in other individuals living in the region of the same petrochemical industry. Workers potentially exposed to acrylonitrile at this site were also evaluated in 2000, along with another unexposed matched control group. The %AB.C. values of exposed workers and their controls were also compared with reference values determined for normal individuals (ages 20-59 years) throughout the CR. Substantial discrepancies were noted between subjects in the region of the petrochemical industry (exposed workers and controls) for the years 2000 and 2004 and the reference CR-wide normal values that had been determined during an earlier time period. The matched non-exposed controls at the petrochemical industry site showed a mean %AB.C. value of 1.56+/-1.23% (N=25) in 1998; this rose to a mean of 2.65+/-2.29% (N=33) in 2000. In 2004, values for non-exposed matched controls at the industry site were 2.64+/-1.75% for males (N=25) and 2.38+/-1.74% (N=26) for females. However, the earlier determined CR-wide %AB.C. mean reference values for normal individuals were 1.77+/-1.16% (N=1305) for the interval 1977-1988 and 1.45+/-1.17% (N=2140) for the interval 1991-1999. As both reference values are substantially lower than those determined in 2000 and 2004 for the non-exposed matched controls at the petrochemical industry site, an analysis of the CR-wide mean normal individual reference values for this same 2000-2004 period was conducted. Unexpectedly, it was found that this reference value too had risen to 1.95+/-1.36% (N=1045) and was comparable to the concurrent matched control values at the petrochemical industry site where the monitoring studies were conducted. This substantial increase in %AB.C. values in 2000 and 2004, therefore, has occurred throughout the CR and is probably unrelated to chemicals uniquely present at the petrochemical industry site.     

Characterization of Photosynthetic Apparatus of Pea Chlorophyll Mutants and their Heterotic F1 Hybrids with Standard Genotype (cv. Torsdag)

In comparison to cv. Torsdag, in leaves of low-productive Pisum sativum L. chlorophyll mutants the decrease in chlorophyll content was caused by the decrease in cell number per unit volume. Qualitative changes in activities of photosystem (PS) 1 in mutant M2004, and quantitative changes of PS1 and PS2 in mutants M2004 and M2014 and in hybrids were also found. However, the activity of ribulose-1,5-bisphosphate carboxylase (RuBPC) in M2014, and those of RuBPC and glyceraldehyde phosphate dehydrogenase in M2004 and hybrids were higher than in cv. Torsdag. The hybrids inherited the normal structure of photosynthetic apparatus of standard genotype in parallel with the compensatory gene complex of M2004, which was expressed at many levels of organization. This may be the basis of hybrid vigour in this case.     

INCREASING THE IMPACT OF BIOINFORMATICS

The year 2004 has been very successful for Bioinformatics. Thejournal's latest impact factor from the Institute for ScientificInformation has increased from 4.615 to 6.701. This is quitean exceptional increase reflecting the increasing standard ofwork in the journal as well as the increasing stature of thefield. Early in 2004, we implemented     

Peritoneal Dialysis in Acute Kidney Injury: Trends in the Outcome across Time Periods

Peritoneal dialysis (PD) should be considered a suitable method of renal replacement therapy in acute kidney injury (AKI) patients. This study is the largest cohort providing patient characteristics, clinical practice, patterns and their relationship to outcomes in a developing country. Its objective was to describe the main determinants of patient and technique survival, including trends over time of PD treatment in AKI patients. This was a Brazilian prospective cohort study in which all adult AKI patients on PD were studied from January/2004 to January/2014. For comparison purposes, patients were divided into 2 groups according to the year of treatment: 2004-2008 and 2009-2014. Patient survival and technique failure (TF) were analyzed using the competing risk model of Fine and Gray. A total of 301 patients were included, 51 were transferred to hemodialysis (16.9%) during the study period. The main cause of TF was mechanical complication (47%) followed by peritonitis (41.2%). There was change in TF during the study period: compared to 2004-2008, patients treated at 2009-2014 had relative risk (RR) reduction of 0.86 (95% CI 0.77 – 0.96) and three independent risk factors were identified: period of treatment at 2009 and 2014, sepsis and age> 65 years. There were 180 deaths (59.8%) during the study. Death was the leading cause of dropout (77.9% of all cases) mainly by sepsis (58.3%), followed cardiovascular disease (36.1%). The overall patient survival was 41% at 30 days. Patient survival improved along study periods: compared to 2004-2008, patients treated at 2009-2014 had a RR reduction of 0.87 (95% CI 0.79 – 0.98). The independent risk factors for mortality were sepsis, age >70 years, ATN-ISS > 0.65 and positive fluid balance. As conclusion, we observed an improvement in patient survival and TF along the years even after correction for several confounders and using a competing risk approach.     

Naturally acquired anthrax antibodies in a cheetah (Acinonyx jubatus) in Botswana

An outbreak of anthrax in the Jwana Game Reserve in Jwaneng, Botswana, was first observed when three cheetahs (Acinonyx jubatus) died of the disease in November 2004. In the aftermath of this event, banked serum samples collected from 23 wild-caught cheetahs were examined, by the inhibition enzyme-linked immunoassay (ELISA), for antibodies to the protective antigen (PA) of Bacillus anthracis. Of the 23 cheetahs, 16 regularly accessed the reserve. Antibodies to PA were detected in one cheetah collected in May 2004, indicating the disease was occurring well before it was first noticed. This appears to be the first demonstration of naturally acquired anthrax antibodies in cheetahs. The finding of one antibody-positive animal amongst at least 16 potentially exposed individuals is consistent with existing reports that it is uncommon for cheetahs to develop natural immunity to anthrax.     

Population Decline of Loggerhead Turtles: Two Potential Scenarios for Fethiye Beach,Turkey

Based on nesting data over a 12-year period (1993–2004), this study points to a negative population trend of the loggerhead turtle population at Fethiye beach, Turkey. The number of nests fluctuated from a maximum of 186 in 1995 to a minimum of 58 in 2004. Successively smaller peaks at 3-year intervals were followed by successively smaller troughs. Two analyses—one representing a dampened oscillation, the other retaining the period and the amplitudes of the nesting cycles—predict that nest number will drop to about 40–50 by 2015, i.e. to about 22–27% of its highest value. This drop at Fethiye does not correspond with a visible increase at neighboring beaches, leading to the interpretation that the number of nesting turtles here is declining. Moreover, the carapace size of emerging adult females is apparently decreasing, as are clutch sizes. Such a potential negative trend at a key Turkish nesting beach is cause for concern, an incentive for continued study, and a call for more coordinated and effective conservation programs in this region of the Mediterranean.     

Thermodynamics of the Corn-Ethanol Biofuel Cycle

This article defines sustainability and sustainable cyclic processes, and quantifies the degree of non-renewability of a major biofuel: ethanol produced from industrially grown corn. It demonstrates that more fossil energy is used to produce ethanol from corn than the ethanol's calorific value. Analysis of the carbon cycle shows that all leftovers from ethanol production must be returned back to the fields to limit the irreversible mining of soil humus. Thus, production of ethanol from whole plants is unsustainable. In 2004, ethanol production from corn will generate 8 million tons of incremental CO₂, over and above the amount of CO₂ generated by burning gasoline with 115% of the calorific value of this ethanol. It next calculates the cumulative exergy (available free energy) consumed in corn farming and ethanol production, and estimates the minimum amount of work necessary to restore the key non-renewable resources consumed by the industrial corn-ethanol cycle. This amount of work is compared with the maximum useful work obtained from the industrial corn-ethanol cycle. It appears that if the corn-ethanol exergy is used to power a car engine, the minimum restoration work is about 6 times the maximum useful work from the cycle. This ratio drops down to 2 if an ideal fuel cell is used to process the ethanol. The article estimates the U.S. taxpayer subsidies of the industrial corn-ethanol cycle at $3.8 billion in 2004. The parallel subsidies by the environment are estimated at $1.8 billion in 2004. The latter estimate will increase manifold when the restoration costs of aquifers, streams, and rivers, and the Gulf of Mexico are also included. Finally, the article estimates that (per year and unit area) the inefficient solar cells produce ～ 100 times more electricity than corn ethanol. There is a need for more reliance on sunlight, the only source of renewable energy on the earth.     

Ageing and the immune system in vivo: commentary on the 16th session of British Society for Immunology Annual Congress,Harrogate, December 2004

The problems associated with the ageing immune system coupled with possible solutions were discussed recently at the British Society for Immunology Annual Congress in Harrogate in December 2004. The session "Ageing and the Immune System in vivo" dealt in details with the immune risk phenotype and the potential methods of reversing the problems of an ageing immune system. This is a commentary on that session.     

Soldier caste with morphological and reproductive division in the aphid tribe Nipponaphidini

Summary. We investigated demographic, morphological and histological aspects of Distylaphis foliorum, a gall-forming nipponaphidine aphid from Java, Indonesia, whose first instar nymphs had been reported to have enlarged forelegs and attack other insects. The gall inhabitants of D. foliorum consisted of two discrete populations; one developing normally and the other remaining at the first instar. Morphometric analysis identified two types of first instar nymphs; nymphs with relatively long forelegs and slender abdomen, and nymphs with relatively short forelegs and fat abdomen. The former nymphs were found from both young galls and mature galls, while the latter nymphs were from young galls only. Histological analysis strongly suggested a reproductive division in the first instar. In the former nymphs from mature galls, ovaries and mycetomes were degenerate and replaced by well-developed fat body cells. These results indicated that D. foliorum has a morphologically differentiated sterile soldier caste in the first instar. This study is the first report of a soldier caste with morphological and reproductive division in the aphid tribe Nipponaphidini, and suggests that highly specialized soldier castes have evolved at least four times in aphids.Received 25 June 2004; revised 24 September 2004; accepted 11 October 2004.     

Individual and combined effects of dosages of azoxystrobin and epoxiconazole in wheat

The effects of single fungicide applications on Mycosphaerella graminicola (septoria leaf blotch) control and winter wheat yield were evaluated in field trials conducted in central Belgium between 2000 and 2004. Individual applications of 25, 50, 75 and 100% of the manufacturer's recommended dose rates of azoxystrobin and epoxiconazole, and all the combinations of these treatments, were made at GS 39 in 2001 to 2004 and at GS 59 in 2000. Disease assessments were made at growth stage 75, some 7-8 weeks after the last applications. Between 2000 and 2003, no significant difference was observed for disease control between the products when applied alone. With regard to the dose responses, the differences between the recommended dose rates and the 50% reduced dosages were not important. In 2004, azoxystrobin was less effective than epoxiconazole. This was probably the result of strobilurin-resistant isolates of M. graminicola reaching an occurrence of 32% before fungicide application. The combination of different dosages of azoxystrobin and epoxiconazole revealed that there was very little synergy between these products when applied in a single application. The combinations of these products were better than individual applications only when high dosages of both compounds were used.