Origin of fungal hybrids with pathogenic potential from warm seawater environments

Hybridisation is a common event in yeasts often leading to genomic variability and adaptation. The yeast Candida orthopsilosis is a human-associated opportunistic pathogen belonging to the Candida parapsilosis species complex. Most C. orthopsilosis clinical isolates are hybrids resulting from at least four independent crosses between two parental lineages, of which only one has been identified. The rare presence or total absence of parentals amongst clinical isolates is hypothesised to be a consequence of a reduced pathogenicity with respect to their hybrids. Here, we sequence and analyse the genomes of environmental C. orthopsilosis strains isolated from warm marine ecosystems. We find that a majority of environmental isolates are hybrids, phylogenetically closely related to hybrid clinical isolates. Furthermore, we identify the missing parental lineage, thus providing a more complete overview of the genomic evolution of this species. Additionally, we discover phenotypic differences between the two parental lineages, as well as between parents and hybrids, under conditions relevant for pathogenesis. Our results suggest a marine origin of C. orthopsilosis hybrids, with intrinsic pathogenic potential, and pave the way to identify pre-existing environmental adaptations that rendered hybrids more prone than parental lineages to colonise and infect the mammalian host.

Fungal Planet description sheets: 1478-1549

Novel species of fungi described in this study include those from various countries as follows: Australia, Aschersonia mackerrasiae on whitefly, Cladosporium corticola on bark of Melaleuca quinquenervia, Penicillium nudgee from soil under Melaleuca quinquenervia, Pseudocercospora blackwoodiae on leaf spot of Persoonia falcata, and Pseudocercospora dalyelliae on leaf spot of Senna alata. Bolivia, Aspicilia lutzoniana on fully submersed siliceous schist in high-mountain streams, and Niesslia parviseta on the lower part and apothecial discs of Erioderma barbellatum on a twig. Brazil, Cyathus bonsai on decaying wood, Geastrum albofibrosum from moist soil with leaf litter, Laetiporus pratigiensis on a trunk of a living unknown hardwood tree species, and Scytalidium synnematicum on dead twigs of unidentified plant. Bulgaria, Amanita abscondita on sandy soil in a plantation of Quercus suber. Canada, Penicillium acericola on dead bark of Acer saccharum, and Penicillium corticola on dead bark of Acer saccharum. China, Colletotrichum qingyuanense on fruit lesion of Capsicum annuum. Denmark, Helminthosphaeria leptospora on corticioid Neohypochnicium cremicolor. Ecuador (Galapagos), Phaeosphaeria scalesiae on Scalesia sp. Finland, Inocybe jacobssonii on calcareous soils in dry forests and park habitats. France, Cortinarius rufomyrrheus on sandy soil under Pinus pinaster, and Periconia neominutissima on leaves of Poaceae. India, Coprinopsis fragilis on decaying bark of logs, Filoboletus keralensis on unidentified woody substrate, Penicillium sankaranii from soil, Physisporinus tamilnaduensis on the trunk of Azadirachta indica, and Poronia nagaraholensis on elephant dung. Iran, Neosetophoma fici on infected leaves of Ficus elastica. Israel, Cnidariophoma eilatica (incl. Cnidariophoma gen. nov.) from Stylophora pistillata. Italy, Lyophyllum obscurum on acidic soil. Namibia, Aureobasidium faidherbiae on dead leaf of Faidherbia albida, and Aureobasidium welwitschiae on dead leaves of Welwitschia mirabilis. Netherlands, Gaeumannomycella caricigena on dead culms of Carex elongata, Houtenomyces caricicola (incl. Houtenomyces gen. nov.) on culms of Carex disticha, Neodacampia ulmea (incl. Neodacampia gen. nov.) on branch of Ulmus laevis, Niesslia phragmiticola on dead standing culms of Phragmites australis, Pseudopyricularia caricicola on culms of Carex disticha, and Rhodoveronaea nieuwwulvenica on dead bamboo sticks. Norway, Arrhenia similis half-buried and moss-covered pieces of rotting wood in grass-grown path. Pakistan, Mallocybe ahmadii on soil. Poland, Beskidomyces laricis (incl. Beskidomyces gen. nov.) from resin of Larix decidua ssp. polonica, Lapidomyces epipinicola from sooty mould community on Pinus nigra, and Leptographium granulatum from a gallery of Dendroctonus micans on Picea abies. Portugal, Geoglossum azoricum on mossy areas of laurel forest areas planted with Cryptomeria japonica, and Lunasporangiospora lusitanica from a biofilm covering a biodeteriorated limestone wall. Qatar, Alternaria halotolerans from hypersaline sea water, and Alternaria qatarensis from water sample collected from hypersaline lagoon. South Africa, Alfaria thamnochorti on culm of Thamnochortus fraternus, Knufia aloeicola on Aloe gariepensis, Muriseptatomyces restionacearum (incl. Muriseptatomyces gen. nov.) on culms of Restionaceae, Neocladosporium arctotis on nest of cases of bag worm moths (Lepidoptera, Psychidae) on Arctotis auriculata, Neodevriesia scadoxi on leaves of Scadoxus puniceus, Paraloratospora schoenoplecti on stems of Schoenoplectus lacustris, Tulasnella epidendrea from the roots of Epidendrum × obrienianum, and Xenoidriella cinnamomi (incl. Xenoidriella gen. nov.) on leaf of Cinnamomum camphora. South Korea, Lemonniera fraxinea on decaying leaves of Fraxinus sp. from pond. Spain, Atheniella lauri on the bark of fallen trees of Laurus nobilis, Halocryptovalsa endophytica from surface-sterilised, asymptomatic roots of Salicornia patula, Inocybe amygdaliolens on soil in mixed forest, Inocybe pityusarum on calcareous soil in mixed forest, Inocybe roseobulbipes on acidic soils, Neonectria borealis from roots of Vitis berlandieri × Vitis rupestris, Sympoventuria eucalyptorum on leaves of Eucalyptus sp., and Tuber conchae from soil. Sweden, Inocybe bidumensis on calcareous soil. Thailand, Cordyceps sandindaengensis on Lepidoptera pupa, buried in soil, Ophiocordyceps kuchinaraiensis on Coleoptera larva, buried in soil, and Samsoniella winandae on Lepidoptera pupa, buried in soil. Taiwan region (China), Neophaeosphaeria livistonae on dead leaf of Livistona rotundifolia. Türkiye, Melanogaster anatolicus on clay loamy soils. UK, Basingstokeomyces allii (incl. Basingstokeomyces gen. nov.) on leaves of Allium schoenoprasum. Ukraine, Xenosphaeropsis corni on recently dead stem of Cornus alba. USA, Nothotrichosporon aquaticum (incl. Nothotrichosporon gen. nov.) from water, and Periconia philadelphiana from swab of coil surface. Morphological and culture characteristics for these new taxa are supported by DNA barcodes. Citation: Crous PW, Osieck ER, Shivas RG, et al. 2023. Fungal Planet description sheets: 1478-1549. Persoonia 50: 158- 310. https://doi.org/10.3767/persoonia.2023.50.05.

Reclassification of Facklamia ignava, Facklamia sourekii and Facklamia tabacinasalis as Falseniella ignava gen. nov., comb. nov., Hutsoniella sourekii gen. nov., comb. nov., and Ruoffia tabacinasalis gen. nov., comb. nov., and description of Ruoffia halotolerans sp. nov., isolated from hypersaline Inland Sea of Qatar

A Gram-stain-positive, non-pigmented, coccus-shaped, facultatively anaerobic and α-hemolytic bacterium designated as INB8^T was isolated from a hypersaline marine water sample collected at the Inland Sea of Qatar. The isolate was able to grow at 25-40 °C (optimum, 30 °C), at pH 5-11 and with 2-8% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain INB8^T was placed within the family Aerococcaceae with the highest sequence similarity to Facklamia tabacinasalis CCUG 30090^T (99.5%), followed by Facklamia hominis CCUG 36813^T (93.9%), Facklamia sourekii Y17312^T (93.8%), Facklamia ignava CCUG 37419^T (93.6%), Facklamia miroungae CCUG 42728^T (93.5%), Suicoccus acidiformans ZY16052^T (93.5%), Facklamia languida CCUG 37842^T (93.2%), Ignavigranum ruoffiae (93.1%), and Dolosicoccus paucivorans DSM 15742^T (90.8%). Average nucleotide identity and digital DNA-DNA hybridization values between strain INB8^T and F. tabacinasalis CCUG 30090^T were determined to be 94.5% and 58.9% respectively, confirming strain INB8^T represents a novel species. The major fatty acids were C_14:0, C_16:0, C_18:0 and C_18:1 ω9c_. The G + C content of strain INB8^T determined from the genome was 36.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic information, it is proposed that Facklamia tabacinasalis should be reclassified as Ruoffia tabacinasalis, Facklamia ignava be reclassified as Falseniella ignava, and Facklamia sourekii be reclassified Hutsoniella sourekii. It is further proposed that strain INB8^T should be classified as a species of the genus Ruoffia for which the name Ruoffia halotolerans sp. nov. is proposed. The type strain is INB8^T (= LMG 30291^T = CCUG 70701^T = QCC/B60/17^T).

Draft Genome Sequences of Seven Vibrio cholerae Isolates from Adult Patients in Qatar

We report the draft genome sequences of seven Vibrio cholerae isolates from patients. Four isolates were profiled as multilocus sequence type 69, serogroup O1, a subset of seventh-pandemic El Tor clonal isolates. Presented here are genome assemblies and evidence for major pathogenicity islands, virulence factors, and antimicrobial resistance genes.

Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf

Strain B66^T was isolated from a marine water sample collected at Al Ruwais, located on the northern tip of Qatar. Cells were Gram-stain-negative, strictly aerobic and short- rod-shaped with a polar flagellum. The isolate was able to grow at 15-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 6.5-8) and with 0-6 % NaCl. 16S rRNA gene sequence analysis revealed that strain B66^T was affiliated with the family Alteromonadaceae, sharing the highest sequence similarities to the genera Alteromonas (93.7-95.4 %), Aestuariibacter (94.0-95.1 %), Agaribacter (93.3-93.7 %), Glaciecola (92.0-93.7 %), Marisendiminitalea (93.2-93.3 %) and Planctobacterium (92.9 %). In the phylogenetic trees, strain B66^T demonstrated the novel organism formed a distinct lineage closely associated with Aestuariibacter and Planctobacterium. Major fatty acids were C_16 : 0, summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c/iso-C_15 : 0 2-OH and iso-C_15 : 0 3-OH. The major respiratory quinone was ubiquinone-8 and the major polar lipids are phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content derived from the genome was 43.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain B66^T is considered to represent a novel species and genus for which the name Ningiella ruwaisensis gen. nov., sp. nov., is proposed. The type strain is B66^T (=QCC B003/17^T=LMG 30288 ^T=CCUG 70703^T).

Toxicocladosporium aquimarinum sp. nov. and Toxicocladosporium qatarense sp. nov., isolated from marine waters of the Arabian Gulf surrounding Qatar

The Arabian Gulf surrounding Qatar is distinct from other marine ecosystems due to its high salinity (35-75 PSU) and extreme water temperature fluctuations (11-40 °C). Furthermore, in the last decade, Qatar has been witnessing an industrial boom as well as extensive infrastructure construction activities. Marine micro-organisms, including fungi, remain largely unexplored in the Arabian Gulf. During a 3 year study, we investigated the diversity of marine fungi in coastal waters around Qatar. As a result, two new Toxicocladosporium species were isolated from the Qatari marine environment. Molecular and phylogenetic analyses of rRNA gene sequences of five loci, namely the internal transcribed spacer 1 and 2 regions and the D1/D2 domains of the large subunit rRNA, actin, RNA polymerase second largest subunit and beta-tubulin genes, were used to confirm the identity of the novel species for which we propose the names Toxicocladosporium aquimarinum sp. nov. and Toxicocladosporium qatarense sp. nov.

Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish (Tenualosa ilisha) marketed for human consumption in Bangladesh

AIMS

This study conducted bacterial community, virulence and antibiogram profiling inside the hindgut and skin of freshly caught hilsa fish and those sold at markets.

METHODS AND RESULTS

The results of 16S rRNA-based high-throughput sequencing showed a higher number of bacterial genera in marketed fish samples than in fresh fish samples. The total operational taxonomic units, genus counts and diversity index were significantly higher (P > 0·05) in marketed fish, which also had abundant pathogenic bacterial groups. Skin samples had a lower profusion of pathogenic bacteria than gut samples. A total of 52 bacterial isolates from nine species were identified in this study, of which 25 were from a Chittagong market and 22 were from a Dhaka market, whereas only five were from fresh hilsa. The polymerase chain reaction amplification of 12 species-specific virulence genes in the 52 isolates, namely, aer, hly, chxA, toxB, rtxC, sfa, uge, norB, trx, toxA, ipaH, sigA and coa, indicated a high number of positive samples containing Vibrio cholerae, Aeromonas spp., Klebsiella pneumoniae, Escherichia coli and Staphylococcus aureus. Antibiogram profiling of these bacteria against 10 commercial antibiotics showed high-resistance patterns of the isolates against sulfamethoxazole, kanamycin, neomycin, ampicillin and tetracycline.

CONCLUSION

The results reveal the spread of multidrug-resistant bacteria in hilsa fish marketed for human consumption in Bangladesh.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study highlights the risk of spreading environmentally and clinically pathogenic bacteria in fish sold for human consumption in Bangladesh. Such bacteria come from aquatic pollution and poor handling, storage and transportation practices that may predispose fish to major outbreaks of infectious and waterborne diseases.

Naganishia qatarensis sp. nov., a novel basidiomycetous yeast species from a hypersaline marine environment in Qatar

Two yeast strains (INY29 and INY13) representing a novel yeast species were isolated from the hypersaline marine environment of the Inland Sea, Qatar. Phylogenetic analysis based on the D1/D2 domains of the large subunit (LSU) regions and internal transcribed spacer (ITS1 and ITS2) regions showed that the two strains represent a single species in the genus Naganishia that is distinct from other species. These two strains were classified as members of the genus Naganishia and clustered in a strongly supported clade represented by Naganishia albidus in the Filobasidiales order in the phylogenetic tree drawn from ITS and D1/D2 sequences. The novel species was most closely related to the type strain of Naganishia cerealis but the two species differed by 1 % sequence divergence (four substitutions and one gap) in the D1/D2 domains and (five substitutions and one gap) in the ITS regions. In contrast to the closest relative, N. cerealis, the novel yeast species assimilated melibiose, glycerol, meso-erythritol, dl-lactate, methanol, propane 1-2-diol, butane 2-3-diol, and grew at 35 °C. The name Naganishia qatarensis sp. nov. is proposed to accommodate these strains, with INY29 as the holotype.

Description of the Halophile Euplotes qatarensis nov. spec. (Ciliophora, Spirotrichea, Euplotida) Isolated from the Hypersaline Khor Al-Adaid Lagoon in Qatar

The morphology, ontogenesis, and phylogenetic relationships of a halophile euplotid ciliates, Euplotes qatarensis nov. spec., isolated from the Khor Al-Adaid Lagoon in Qatar were investigated based on live observation as well as protargol- and silver nitrate-impregnated methods. The new species is characterised by a combination of features: the halophile habitat, a cell size of 50-65 × 33-40 μm, seven dorsal ridges, 10 commonly sized frontoventral cirri, two widely spaced marginal cirri, 10 dorsolateral kineties, and a double silverline pattern. The morphogenesis is similar to that of its congeners: (i) the oral primordium develops hypoapokinetally and the parental oral apparatus is retained; (ii) the frontoventral-transverse field of five streaks gives rise to the frontal, ventral, and transverse cirri, but not to the cirri I/1 and the marginal cirri; (iii) the dorsal somatic ciliature develops by intrakinetal proliferation of basal bodies in two anlagen per kinety that are just anterior and posterior to the future division furrow; (iv) the caudal cirri are formed by the two rightmost dorsolateral kineties. The SSU rDNA sequence of E. qatarensis branches with full support in the Euplotopsis elegans-Euplotes nobilii-Euplotopsis raikovi clade. The closest related publicly available SSU rDNA sequence is the one of E. nobilii, with which E. qatarensis has 93.4% sequence similarity. Euplotes parawoodruffi Song & Bradbury, 1997 is transferred to the genus Euplotoides based on the absence of frontoventral cirrus VI/3.

Isolation and screening of probiotic candidates from marron, Cherax cainii (Austin, 2002) gastrointestinal tract (GIT) and commercial probiotic products for the use in marron culture

Six strains of bacteria including Bacillus mycoides (A10) and Shewanella species (A12) isolated from healthy marron intestine, Bacillus species (PM1), Bacillus subtilis (PM3), Bacillus sp. (PM4) and Bacillus sp. (AQ) from commercial probiotic products were investigated for probiotic potential in marron culture. Antibiotic susceptibility tests indicated PM3 and PM4 were susceptible to all nine antibiotics evaluated. A10, A12 and AQ were resistant to class penicillins, whereas PM1 was resistant to class penicillin and macrolides. All strains were non-pathogenic for marron. Strong inhibition against Vibrio mimicus and Vibrio cholerae non-01 was exhibited by PM4 and PM3. A10 inhibited V. mimicus at 72 h of growth, but not V. cholerae non-01, whereas A12 inhibited V. cholerae non-01 but not V. mimicus, and AQ showed no inhibition activity. A wide range of enzymes were produced by A10 and AQ using the API ZYM test. Protease enzymes were produced by PM3, PM4, AQ and PM1. In order of effectiveness, the following bacteria have probiotic potential: B. subtilis (PM3), Bacillus sp. (PM4) and B. mycoides (A10). Further study is required to determine the bacterium or any combination that gives a multibeneficial effect on marron.

Discrepancy in MALDI-TOF MS identification of uncommon Gram-negative bacteria from lower respiratory secretions in patients with cystic fibrosis

INTRODUCTION

Early identification of microbial organisms from respiratory secretions of patients with cystic fibrosis (CF) is important to guide therapeutic decisions. The objective was to compare the accuracy of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) relative to the conventional phenotypic method in identifying common bacterial isolates, including nonfermenting Gram-negative bacteria, in a cohort of patients with CF.

METHODS

A total of 123 isolates from 50 patients with CF representing 14 bacterial species from respiratory specimens were identified using MALDI-TOF MS in parallel with conventional phenotypic methods. Discrepancies were confirmed by 16S ribosomal RNA (rRNA) gene sequencing in five Gram-negative isolates.

RESULTS

The MALDI-TOF MS managed to identify 122/123 (99.2%) bacterial isolates to the genus level and 118/123 (95.9%) were identified to the species level. The MALDI-TOF MS results were 100% consistent to the species level with conventional phenotypic identification for isolates of Staphylococcus aureus, Pseudomonas aeruginosa, Haemophilus influenzae, Streptococcus pyogenes, Achromobacter xylosoxidans, Stenotrophomonas maltophilia, and other uncommon organisms such as Chryseobacterium gleum and Enterobacter cloacae. The 5/123 (4.6%) isolates misidentified were all Gram-negative bacteria. The isolation of E. cloacae and Haemophilus paraphrohaemolyticus may extend the potentially pathogenic list of organisms isolated from patients with CF.

CONCLUSION

Although the technique provides an early identification and antimicrobial therapy approach in patients with CF, limitation in the diagnosis of uncommon Gram-negative bacteria may exist.

SP600125 suppresses Cdk1 and induces endoreplication directly from G2 phase, independent of JNK inhibition

Cell cycle controls ensure that DNA replication (S phase) follows mitosis resulting in two precise copies of the genome. A failure of the control mechanisms can result in multiple rounds of DNA replication without cell division. In endoreplication, cells with replicated genomes bypass mitosis, then replicate their DNA again, resulting in polyploidy. Endoreplication from G2 phase lacks all hallmarks of mitosis. Using synchronized cells, we show that the c-Jun N-terminal kinase (JNK) inhibitor, SP600125, prevents the entry of cells into mitosis and leads to endoreplication of DNA from G2 phase. We show that cells proceed from G2 phase to replicate their DNA in the absence of mitosis. This effect of SP600125 is independent of its suppression of JNK activity. Instead, the inhibitory effect of SP600125 on mitotic entry predominantly occurs upstream of Aurora A kinase and Polo-like kinase 1, resulting in a failure to remove the inhibitory phosphorylation of Cdk1. Importantly, our results directly show that the inhibition of Cdk1 activity and the persistence of Cdk2 activity in G2 cells induces endoreplication without mitosis. Furthermore, endoreplication from G2 phase is independent of p53 control.

Comparison of stool antigen detection kits to PCR for diagnosis of amebiasis

The present study was conducted to compare two stool antigen detection kits with PCR for the diagnosis of Entamoeba histolytica infections by using fecal specimens submitted to the Department of Microbiology at St. Vincent's Hospital, Sydney, and the Institute of Medical and Veterinary Science, Adelaide, Australia. A total of 279 stool samples containing the E complex (E. histolytica, Entamoeba dispar, and Entamoeba moshkovskii) were included in this study. The stool specimens were tested by using two commercially produced enzyme immunoassays (the Entamoeba CELISA PATH and TechLab E. histolytica II kits) to detect antigens of E. histolytica. DNA was extracted from all of the samples with a Qiagen DNA stool mini kit (Qiagen, Hilden, Germany), and a PCR targeting the small-subunit ribosomal DNA was performed on all of the samples. When PCR was used as a reference standard, the CELISA PATH kit showed 28% sensitivity and 100% specificity. The TechLab ELISA (enzyme-linked immunosorbent assay) kit did not prove to be useful in detecting E. histolytica, as it failed to identify any of the E. histolytica samples which were positive by PCR. With the TechLab kit, cross-reactivity was observed for three specimens, one of which was positive for both E. dispar and E. moshkovskii while the other two samples contained E. moshkovskii. Quantitative assessment of the PCR and ELISA results obtained showed that the ELISA kits were 1,000 to 10,000 times less sensitive, and our results show that the CELISA PATH kit and the TechLab ELISA are not useful for the detection of E. histolytica in stool samples from patients in geographical regions where this parasite is not endemic.

Laboratory diagnostic techniques for Entamoeba species

The genus Entamoeba contains many species, six of which (Entamoeba histolytica, Entamoeba dispar, Entamoeba moshkovskii, Entamoeba polecki, Entamoeba coli, and Entamoeba hartmanni) reside in the human intestinal lumen. Entamoeba histolytica is the causative agent of amebiasis and is considered a leading parasitic cause of death worldwide in humans. Although recent studies highlight the recovery of E. dispar and E. moshkovskii from patients with gastrointestinal symptoms, there is still no convincing evidence of a causal link between the presence of these two species and the symptoms of the host. New approaches to the identification of E. histolytica are based on detection of E. histolytica-specific antigen and DNA in stool and other clinical samples. Several molecular diagnostic tests, including conventional and real-time PCR, have been developed for the detection and differentiation of E. histolytica, E. dispar, and E. moshkovskii in clinical samples. The purpose of this review is to discuss different methods that exist for the identification of E. histolytica, E. dispar, and E. moshkovskii which are available to the clinical diagnostic laboratory. To address the need for a specific diagnostic test for amebiasis, a substantial amount of work has been carried out over the last decade in different parts of the world. The molecular diagnostic tests are increasingly being used for both clinical and research purposes. In order to minimize undue treatment of individuals infected with other species of Entamoeba such as E. dispar and E. moshkovskii, efforts have been made for specific diagnosis of E. histolytica infection and not to treat based simply on the microscopic examination of Entamoeba species in the stool. The incorporation of many new technologies into the diagnostic laboratory will lead to a better understanding of the public health problem and measures to control the disease.

Amoebiasis: current status in Australia

Entamoeba histolytica is one of the most common parasitic infections worldwide, infecting about 50 million people and resulting in 40,000-100,000 deaths a year. In Australia, people at risk of infection include immigrants, travellers returning from countries of high endemicity, Indigenous people, and men who have sex with men. Clinical manifestations range from asymptomatic carriage to invasive disease. Amoebic colitis and amoebic liver abscess are the most common invasive manifestations observed in Australia. Diagnosis depends on a high index of suspicion and laboratory investigations. Molecular methods (using the polymerase chain reaction) are the most sensitive for identifying and differentiating Entamoeba species. Treatment should always include a luminal agent to eradicate colonisation, prevent spread and/or reduce the risk of invasive disease. Medical therapy can successfully cure invasive disease, including amoebic liver abscesses.

Prevalence of enteric protozoa in human immunodeficiency virus (HIV)-positive and HIV-negative men who have sex with men from Sydney, Australia

A prospective, comparative study of the prevalence of enteric protozoa was determined among human immunodeficiency virus (HIV)- positive and HIV-negative men who have sex with men (MSM) in Sydney, Australia. A total of 1,868 patients submitted stool specimens; 1,246 were from MSM (628 HIV positive and 618 HIV positive) and 622 from non-MSM were examined over a 36-month period. A total of 651 (52.2%) stool specimens from MSM were positive for protozoa compared with 85 (13%) from non-MSM. There was a significant difference in the prevalence of Blastocystis hominis, Endolimax nana, Entamoeba histolytica/dispar complex, Entamoeba hartmanni, Iodamoeba butschlii, and Enteromonas hominis detected between MSM and non-MSM (P<0.001). The only notable difference between HIV-negative and HIV-positive MSM was that HIV-infected MSM were found to more likely have a Cryptosporidium parvum infection. Entamoeba histolytica was found in 3 patients, E. dispar in 25, and E. moshkovskii in 17, all of whom were MSM. When compared with a control group, MSM were significantly more likely to harbor intestinal protozoa and have multiple parasites present. The results of this study show high rates of enteric parasites persist in MSM and highlight the importance of testing for intestinal parasites in MSM. This is the first report of E. moshkovskii from MSM.

PCR detection of Entamoeba histolytica, Entamoeba dispar, and Entamoeba moshkovskii in stool samples from Sydney, Australia

This study investigated the presence of Entamoeba histolytica, Entamoeba dispar, and Entamoeba moshkovskii in stool samples from a patient population in Sydney, Australia. Stool samples were tested by microscopy and PCR. Five patients were found with E. histolytica infections, while E. dispar and E. moshkovskii were observed in 63 (70.8%) and 55 (61.8%) patients, respectively, by PCR. This is the first study in Australia using molecular techniques to determine the presence of E. histolytica, E. dispar, and E. moshkovskii.

Childhood illnesses and malnutrition in under five children in drought affected desert area of western Rajasthan, India

The study was undertaken to asses the impact of drought on childhood illnesses and nutrition in under five children of rural population using three stage sampling design. The study has been carried out in 24 villages belonging to 6 tehsils of Jodhpur district which was a drought affected desert district of Western Rajasthan in 2003. A total of 914 under five children (0-5 years) could be examined for their childhood illnesses, malnutrition, dietary intake and clinical signs of nutritional deficiency. Childhood illnesses observed at the time of drought were respiratory (7.5 %), gastroentrological (7.5%), and 5.6% fever (viral, malaria and jaundice), higher in males than females. Children suffered from recent and long term malnutrition were 39% and 26% respectively as per National Centre for Health Statistics (NCHS) standards. The extent of malnutrition was significantly higher in females than in males (p<0.01). Vitamin A & B complex deficiencies were 0.7% and 3/% respectively. The protein energy malnutrition (PEM) was observed in 44.4%. Overall mean calorie and protein intake deficit was observed to be very high (76.0 & 54.0 %). The comparison of present drought results with earlier studies in normal and drought conditions showed higher prevalence of PEM and deficiencies of calories & proteins in their diet. Respiratory, gastroentrological and fever were main childhood illnesses observed and were higher in males at the time of drought. PEM, vitamin A & B- complex deficiencies, anemia along with deficit in calories and proteins in their diet was observed higher in present study as compared to non desert areas, which may be due to the harsh environmental conditions in desert areas and paucity in the consumption of daily food intake. Due to inadequate consumption of daily food, the children were suffering from PEM resulting in several childhood illnesses. Effective measures making availability of adequate calories and proteins to all age groups especially to under five children through the ongoing nutrition programs needs to be ensured.

Comparison of phospholipase and proteinase activity in Candida albicans and C. dubliniensis

Although the production of virulence enzymes by Candida albicans has been extensively explored, little attention has been given to the virulence factors of C. dubliniensis. In the present study, an attempt was made to investigate phospholipase activity (Pz value) and secretory aspartyl proteinase production of C. dubliniensis and compare it with C. albicans. None of the 87 C. dubliniensis isolates tested, produced phosholipases whereas, in contrast all the 52 (100%) C. albicans isolates tested demonstrated varying degree of phospholipase activity (Pz value: 0.37-0.74), with 35 (67.3%) of them eliciting a higher phospholipase activity (Pz values between 0.37 and 0.50). Only 32% of the C. dubliniensis isolates exhibited moderate activity (score of 1+) of secretory aspartyl proteinase whereas a vast majority (68%) of them were non-proteolytic. On the contrary, a strong proteinase activity (score of 2+) was observed for 79% of C. albicans while the remaining 21% isolates showed moderate proteinase activity (score of 1+). As phospholipases and aspartyl proteinases of C. albicans are considered important virulence factors, the absence or lowered expression of these enzymes in C. dubliniensis may indicate the less virulent nature of this novel yeast species when compared with C. albicans.

Prevalence of Candida dubliniensis among germ tube-positive yeasts recovered from the respiratory specimens in HIV-negative patients. Der Anteil von Candida dubliniensis bei keimschlauchpositiven Hefen in Untersuchungsproben aus dem Respirationstrakt HIV-negativer Patienten

The present investigation was conducted to identify Candida dubliniensis, from respiratory specimens, recovered from HIV-negative patients. Over a 7-month period, 75 germ tube and chlamydospore-positive yeasts were screened for C. dubliniensis, using a variety of phenotypic characteristics. Their identification was based on sugar assimilation reactions using API 20 C Aux. A total of seven (9%) isolates recovered from sputum, bronchial lavage and nasopharyngeal aspirate were identified as C. dubliniensis. All the isolates were susceptible to amphotericin B. One isolate each showed resistance to fluconazole and ketoconazole, and two were resistant to itraconazole. A significantly high percentage (43%) of C. dubliniensis showed resistance to flucytosine.

Candida dubliniensis at a university hospital in Saudi Arabia

Candida dubliniensis is a newly described yeast species that is a close phylogenetic relative of C. albicans. Although it has been reported from different parts of the world, no detailed investigation of this species has been done in Saudi Arabia. The purpose of the present study was to identify C. dubliniensis isolates recovered from clinical specimens at a tertiary-care hospital in Riyadh, Saudi Arabia, and to determine the drug susceptibility profiles of those isolates. Over a period of 8 months, 823 germ tube- and chlamydospore-positive yeasts identified as C. albicans and recovered from different clinical specimens were screened for their ability to grow at 45 degrees C on Sabouraud dextrose agar. Isolates which failed to grow at 45 degrees C were presumptively identified as C. dubliniensis. The species identities were further confirmed by the production of pseudohyphae and chlamydospores on Staib agar and their inability to assimilate D-xylose and alpha-methyl-D-glucoside by using the API 20C AUX system. A total of 27 (3.3%) isolates were identified as C. dubliniensis. They were all recovered from 23 human immunodeficiency virus-negative patients. The prevalence of C. dublinensis in bronchoalveolar lavage (33.3%), oral (16.7%), and blood (16.7%) specimens was high. In addition, 33 isolates previously identified as C. albicans and preserved among our stock blood culture isolates were also recruited for the study. Of these, 5 isolates were found to be C. dubliniensis, thus making the total number of isolates identified as this species 32. Antifungal susceptibility testing of the C. dubliniensis isolates showed 100% sensitivity to amphotericin B, 97% sensitivity to each of fluconazole and ketoconazole, and 87.5% sensitivity to itraconazole. However, in contrast to other studies, the majority of the isolates (65.6%) showed high levels of resistance to flucytosine (MIC > 64 microg/ml). Further studies are warranted to investigate the cause of this unusually high rate of resistance to flucytosine of the C. dubliniensis isolates in this region.

Identification of chlamydospore-negative Candida albicans using CHROMagar Candida medium

This study was undertaken to evaluate the utility of CHROMagar Candida medium for the identification of chlamydospore-negative Candida albicans. A total of 60 isolates including 45 chlamydospore-negative C. albicans, 10 chlamydospore-positive C. albicans (positive controls) and five non-C. albicans (negative controls) were investigated. On the basis of germ tube test, assimilation of trehalose (Tre), glucosamine (GlcN), N-acetyl glucosamine (GlcNAc), secretory aspartyl production and serotyping, the 45 chlamydospore-negative C. albicans isolates were assigned to the reported three groups. Eighteen isolates showing positive germ tube test, negative for the assimilation of Tre, GlcN/GlcNAc, strong producers of proteinase (2+) and assigned to serotype B belonged to group I. Whereas, the isolates in group II and group III showed common characteristics including assimilation of Tre, GlcN/GlcNAc, moderate production of proteinase (1+) and were serotype A, except for the fact that group II isolates were germ tube positive and group III isolates were negative. Using CHROMagar Candida medium, all the 45 chlamydospore-negative and 10 positive control isolates were accurately identified on the basis of characteristic green color at 37 degrees C for 48 h of incubation. On the other hand at an optimum incubation temperature of 37 degrees C none of the non-C. albicans (negative controls) showed characteristic green color thus yielding a 100% sensitivity and specificity. Isolates in group-I showed a slow growth rate and no visible growth was observed at 24 h, whereas, groups II, III and the control isolates showed visible growth at 24 h. Besides differences in growth rates, these isolates also varied in their characteristic colony color which gradually changed over a period of time. The results of this study clearly suggest that CHROMagar Candida medium is not only a simple, reliable and cost effective method for the identification of chlamydospore-negative atypical C. albicans, but can also be used to differentiate various groups of chlamydospore-negative C. albicans.

Recovery and studies on chlamydospore-negative Candida albicans isolated from clinical specimens

During a period of 31 months, we isolated 3525 strains of Candida albicans from different patient specimens. Twenty-five of these (0.71%), obtained from female patients, displayed morphological and biochemical characteristics different from those seen in typical C. albicans. The failure to produce chlamydospores in cornmeal agar was the common denominator in this group. The strains were categorized into three groups: Group I contained 13 isolates that produced germ tubes but were unable to assimilate trehalose (TRE), glucosamine (GLN) and N-acetylglucosamine (NAG); Group II contained four isolates that were germ-tube positive and able to assimilate TRE, GLN and NAG; and Group III contained eight isolates that were germ-tube negative and able to assimilate TRE, GLN and NAG. These isolates were further studied to determine their biotypes, serotypes, extracellular proteinase production and antifungal susceptibility. Group I isolates were of serotype B, whereas Groups II and III were serotype A. All isolates produced high to moderate amounts of extracellular proteinase. Six group I isolates were resistant to 5-fluorocytosine, whereas all groups II and III isolates were susceptible to this drug. Five of the 12 isolates of group II and III were resistant to fluconazole, itraconazole and ketoconazole.

The large subunit of replication factor C promotes cell survival after DNA damage in an LxCxE motif- and Rb-dependent manner

Retinoblastoma (Rb) protein promotes cell survival after DNA damage. We show here that the LxCxE binding site in Rb mediates both cell survival and cell-cycle arrest after DNA damage. Replication factor C (RF-C) complex plays an important role in DNA replication. We describe a novel function of the large subunit of RF-C in promoting cell survival after DNA damage. RF-Cp145 contains an LxCxE motif, and mutation of this motif abolishes the protective effect of RF-Cp145. The inability of wild-type RF-Cp145 to promote cell survival in Rb-null cells is rescued by Rb but not by Rb mutants defective in binding LxCxE proteins. RF-C thus enhances cell survival after DNA damage in an Rb-dependent manner.

Vector potential of houseflies (Musca domestica) in the transmission of Vibrio cholerae in India

It is well known that diarrhoeal infections due to Vibrio cholerae are spread through fecal-oral route of transmission. In the present study an attempt was made to isolate and identify V. cholerae from houseflies, Musca domestica collected from a low socioeconomic area in Delhi, India, where an outbreak of cholera was encountered. Of the ten fly pools examined, six (60%) were positive for V. cholerae. Of these six pools, three (50%) showed V. cholerae Ogawa T2 El Tor and one (17.5%) V. cholerae non-O1. Two isolates could not be typed. During the outbreak period, V. cholerae Ogawa T2 El Tor was isolated from stools of patients suffering from diarrhoea. These findings suggest that houseflies act as mechanical vectors of V. cholerae biotype El Tor and may help in their dissemination. The present study highlights the recovery of V. cholerae El Tor from M. domestica which, to the authors knowledge, has not been reported previously.

The functions of the cdk-cyclin kinase inhibitor p21WAF1

p21WAF1 plays a critical role in regulating cell growth and the cell response to DNA damage. The primary targets of p21WAF1 (hereafter referred to as p21) are the cdk-cyclins which regulate the progression of eukaryotic cells through the cell cycle, and proliferating cell nuclear antigen (PCNA), an accessory protein of DNA polymerase delta. p21 forms complexes with a class of cdk-cyclins to inhibit their kinase activity and with PCNA to inhibit DNA synthesis. These distinct properties map to the N-terminal and the C-terminal regions of p21, respectively. Cell cycle arrest in G-1 (G-1 checkpoint) following DNA damage is mediated by p53 and is deficient in p21 null cells. p53 thus upregulates p21 expression in response to DNA damage, which in turn inhibits cdk2-associated kinase activity. Retinoblastoma protein is regulated by cdk-cyclin kinases, and acts as a downstream target of p21 in DNA damage-induced G-1 arrest. Furthermore, accumulating evidence indicates that p21 may play a role in maintaining G-2 arrest after DNA damage. Transcriptional control of p21 by factors other than p53 is critical for growth arrest and for cell differentiation in many instances.

Growth inhibition by CDK-cyclin and PCNA binding domains of p21 occurs by distinct mechanisms and is regulated by ubiquitin-proteasome pathway

The CDK inhibitor, p21WAF1/Cip1 blocks cell cycle progression. In vitro, the N-terminus of p21 binds and inhibits CDK-cyclin kinase activity, whereas the C-terminus binds and inhibits PCNA (proliferating cell nuclear antigen) function. PCNA is essential for processivity of both DNA polymerase delta and epsilon. We have performed a detailed analysis of growth inhibition by the N- and C-terminal regions of p21, and determined whether the N- and C-terminal regions mediate this effect by different mechanisms. Expression of either the N- or the C-terminal region of p21 inhibits DNA synthesis and cell growth, but not as efficiently as full length p21. The effectiveness of the two p21 domains is dependent on their stability which is determined by the ubiquitin-proteasome pathway. The stabilization of the N- and C-terminal region of p21 increases their effectiveness as inhibitors of DNA synthesis to levels comparable to full length p21. Inhibition of DNA synthesis by the N-terminal region of p21 involves suppression of E2F activity. In contrast, inhibition by the C-terminal region of p21 is not accompanied by suppression of E2F activity, but is mediated via PCNA binding. The C-terminal region of p21 therefore inhibits cell growth by a mechanism distinct from that of the N-terminal region containing the CDK-cyclin inhibitory domain.

Effect of p21waf1/cip1 transgene on radiation induced apoptosis in T cells

The cyclin kinase inhibitor p21WAF1/Cip1 is upregulated by the tumor suppressor p53. While p21 is central for the G-1 arrest mediated by p53, it is still unclear if p21 also functions as a downstream effector of p53 dependent apoptosis. Apoptosis induced by DNA damage but not dexamethasone is p53 dependent in thymocytes. To investigate the physiological role of p21 in apoptosis, we have generated transgenic mice in which the p21 transgene is targeted for restricted expression in the T cell lineage. Thymocytes from p21 transgenic mice were hypersensitive to cell death induced by DNA damaging agents such as ionizing radiation and UV, but not be dexamethasone. Irradiated p21 transgenic thymocytes had approximately twofold more apoptotic cells as compared to irradiated age matched littermate control mice. Radiation induced death is comparable in thymocytes from p21 + Bcl2 + double transgenic mice and age matched littermate controls, indicating that the Bcl2 transgene rescues the radiation hypersensitivity imposed by p21. However, thymocytes from p53-/- mice even when they expressed the p21 transgene, were resistant to death induced by radiation. Together these results show that thymocytes from p21 transgenic mice are hypersensitive to radiation induced programmed cell death and suggest that the radiation hypersensitivity of p21 transgenic thymocytes involves p53 dependent pathway and signals in addition to p21.

Growth inhibition by CDK-cyclin and PCNA binding domains of p21 occurs by distinct mechanisms and is regulated by ubiquitin-proteasome pathway

The CDK inhibitor, p21(WAF1/Cip1) blocks cell cycle progression. In vitro, the N-terminus of p21 binds and inhibits CDK-cyclin kinase activity, whereas the C-terminus binds and inhibits PCNA (proliferating cell nuclear antigen) function. PCNA is essential for processivity of both DNA polymerase delta and epsilon. We have performed a detailed analysis of growth inhibition by the N- and C-terminal regions of p21, and determined whether the N- and C-terminal regions mediate this effect by different mechanisms. Expression of either the N- or the C-terminal region of p21 inhibits DNA synthesis and cell growth, but not as efficiently as full length p21. The effectiveness of the two p21 domains is dependent on their stability which is determined by the ubiquitin-proteasome pathway. The stabilization of the N- and C-terminal region of p21 increases their effectiveness as inhibitors of DNA synthesis to levels comparable to full length p21. Inhibition of DNA synthesis by the N-terminal region of p21 involves suppression of E2F activity. In contrast, inhibition by the C-terminal region of p21 is not accompanied by suppression of E2F activity, but is mediated via PCNA binding. The C-terminal region of p21 therefore inhibits cell growth by a mechanism distinct from that of the N-terminal region containing the CDK-cyclin inhibitory domain.

Cellular response to DNA damage. Link between p53 and DNA-PK

Cells which lack DNA-activated protein kinase (DNA-PK) are very susceptible to ionizing radiation and display an inability to repair double strand DNA breaks. DNA-PK is a member of a protein kinase family that includes ATR and ATM which have strong homology in their carboxy-terminal kinase domain with PL-3 kinase. ATM has been proposed to act upstream of p53 in cellular response to ionizing radiation. DNA-PK may similarly interact with p53 in cellular growth control and in mediation of the response to ionizing radiation.

Stepwise reconstitution of interphase microtubule dynamics in permeabilized cells and comparison to dynamic mechanisms in intact cells

Microtubules in permeabilized cells are devoid of dynamic activity and are insensitive to depolymerizing drugs such as nocodazole. Using this model system we have established conditions for stepwise reconstitution of microtubule dynamics in permeabilized interphase cells when supplemented with various cell extracts. When permeabilized cells are supplemented with mammalian cell extracts in the presence of protein phosphatase inhibitors, microtubules become sensitive to nocodazole. Depolymerization induced by nocodazole proceeds from microtubule plus ends, whereas microtubule minus ends remain inactive. Such nocodazole-sensitive microtubules do not exhibit subunit turnover. By contrast, when permeabilized cells are supplemented with Xenopus egg extracts, microtubules actively turn over. This involves continuous creation of free microtubule minus ends through microtubule fragmentation. Newly created minus ends apparently serve as sites of microtubule depolymerization, while net microtubule polymerization occurs at microtubule plus ends. We provide evidence that similar microtubule fragmentation and minus end-directed disassembly occur at the whole-cell level in intact cells. These data suggest that microtubule dynamics resembling dynamics observed in vivo can be reconstituted in permeabilized cells. This model system should provide means for in vitro assays to identify molecules important in regulating microtubule dynamics. Furthermore, our data support recent work suggesting that microtubule treadmilling is an important mechanism of microtubule turnover.

Apoptosis and the cell cycle

Apoptosis is a genetically controlled response by which eukaryotic cells undergo programmed cell death. This phenomenon plays a major role in developmental pathways (1), provides a homeostatic balance of cell populations, and is deregulated in many diseases including cancer. Control of cell number is determined by an intricate balance of cell death and cell proliferation. Accumulation of cells through suppression of death can contribute to cancer and to persistent viral infections, while excessive death can result in impaired development and in degenerative diseases. Identification of genes that control cell death, and understanding of the impact of apoptosis in both development and disease has advanced our knowledge of apoptosis in the past few years. There appears to be a linkage between apoptosis and cell cycle control mechanisms. Elucidating the mechanisms that link cell cycle control with apoptosis will be of key importance in understanding tumour progression and designing new models of effective tumour therapy.

Cell cycle control of DNA replication

The cell cycle is driven by the sequential activation of a family of cyclin-dependent kinases (cdk), which phosphorylate and activate proteins that execute events critical to cell cycle progression. In mammalian cells cdk2-cyclin A has a role in S phase. Many replication proteins are potential substrates for this cdk kinase, suggesting that initiation, elongation and checkpoint control of replication could all be regulated by cdk2. The association of PCNA, a replication protein, with cdk-cyclins during G-1 to S phase transition and with cdk-cyclin inhibitors, adds an interesting complexity to regulation of DNA replication.

Proteolytic cleavage of retinoblastoma protein upon DNA damage and Fas-mediated apoptosis

Proteolytic cleavage of key cellular proteins by caspases (ICE, CPP32, and Ich-1/Nedd2) may be crucial to the apoptotic process. The retinoblastoma tumor suppressor gene is a negative regulator of cell growth and the retinoblastoma protein (pRb) exhibits anti-apoptotic function. We show that pRb is cleaved during apoptosis induced by either UV irradiation or anti-Fas antibody. Our studies implicate CPP32-like activity in the proteolytic cleavage of pRb. The kinetics of proteolytic cleavage of pRb during apoptosis differ from that observed for other cellular proteins, suggesting that the specific cleavage of pRb during apoptosis may be an important event.

Prevalence of Candida tropicalis in clinical specimens from patients with variable clinical syndromes over a 5-year period

In this study, we have examined our records for the isolation of Candida tropicalis from clinical specimens of patients with heterogeneous clinical presentations during the past 5 years. We have found that this species ranks third among all yeasts in frequency of isolation from clinical specimens and that the trend of recovery from the specimens is rising over the years. The isolation rate of C. tropicalis was highest from urine specimens (36%) followed by respiratory specimens (22%). The frequency of isolation of C. tropicalis from vaginal specimens was relatively high (14%), however the trend was declining over the years. In general, the high recovery of Candida tropicalis from clinical specimens of patients with variable disease supports the views of this organism being a major pathogen.

Association of cyclin A and cdk2 with SV40 DNA in replication initiation complexes is cell cycle dependent

The cell cycle is driven by the sequential activation of a family of cyclin-dependent kinases (CDK) in association with cyclins. In mammalian cells the timing of activation of cyclin A-associated kinase activity coincides with the onset of DNA synthesis in S-phase. Using in vitro replication of SV40 origin-containing DNA as a model system, we have analyzed the proteins associated with DNA during initiation of DNA replication in S-phase cell extracts. This analysis reveals that, in addition to replication initiation proteins, cyclin A and cdk2 are also specifically associated with DNA. The association of cyclin A and cdk2 with DNA during initiation is cell cycle regulated and occurs specifically in the presence of SV40 origin-containing plasmid and SV40 T antigen (the viral replication initiator protein). The interactions among proteins involved in initiation play an important role in DNA replication. We therefore investigated the ability of cyclin A and cdk2 to associate with replication initiation proteins. Under replication initiation conditions, cyclin A and cdk2 from S-phase extracts specifically associate with SV40 T antigen. Further, the interaction of cyclin A-cdk2 with SV40 T antigen is mediated via cyclin A, and purified recombinant cyclin A associates directly with SV40 T antigen. Taken together, our results suggest that cyclin A and cdk2 are components of the SV40 replication initiation complex, and that protein-protein interactions between cyclin A-cdk2 and T antigen may facilitate the association of cyclin A-cdk2 with the complex.

Role for cyclin A-dependent kinase in DNA replication in human S phase cell extracts

Cell cycle progression is regulated by cyclin-dependent kinases. Using in vitro replication of SV40 origin containing DNA as a model system, we have performed a detailed analysis of the dependence on cyclin-associated kinases of mammalian DNA replication. Complete immunodepletion of cyclin A from human S phase cell extracts decreases replication, and replication activity of cyclin A-depleted S phase extracts can subsequently be restored by the addition of purified CDK2-cyclin A kinase. Addition of cyclin A alone reconstitutes both kinase activity and DNA replication, whereas addition of cyclin E or cyclin B reconstitutes neither. We therefore conclude that reconstitution of DNA replication specifically correlates with an increase in kinase activity. By comparison, depletion of cyclin E from S phase cell extracts does not have any significant inhibitory effect on DNA replication. Moreover, specific p21(Waf1) mutants that bind to CDK2-cyclin and inhibit both cyclin A and cyclin E kinase activities, but do not bind to proliferating cell nuclear antigen, inhibit DNA replication to the same extent as cyclin A depletion. Together, these results show that the kinase activity associated with cyclin A, but not with cyclin E, is primarily responsible for activating SV40 plasmid replication in mammalian S phase cell extracts. Finally, we present evidence that the cyclin-dependent kinase does not influence the assembly of initiation complexes but acts at a stage prior to elongation.

A conserved domain of the large subunit of replication factor C binds PCNA and acts like a dominant negative inhibitor of DNA replication in mammalian cells

Replication factor C (RF-C), a complex of five polypeptides, is essential for cell-free SV40 origin-dependent DNA replication and viability in yeast. The cDNA encoding the large subunit of human RF-C (RF-Cp145) was cloned in a Southwestern screen. Using deletion mutants of RF-Cp145 we have mapped the DNA binding domain of RF-Cp145 to amino acid residues 369-480. This domain is conserved among both prokaryotic DNA ligases and eukaryotic poly(ADP-ribose) polymerases and is absent in other subunits of RF-C. The PCNA binding domain maps to amino acid residues 481-728 and is conserved in all five subunits of RF-C. The PCNA binding domain of RF-Cp145 inhibits several functions of RF-C, such as: (i) in vitro DNA replication of SV40 origin-containing DNA; (ii) RF-C-dependent loading of PCNA onto DNA; and (iii) RF-C-dependent DNA elongation. The PCNA binding domain of RF-Cp145 localizes to the nucleus and inhibits DNA synthesis in transfected mammalian cells. In contrast, the DNA binding domain of RF-Cp145 does not inhibit DNA synthesis in vitro or in vivo. We therefore conclude that amino acid residues 481-728 of human RF-Cp145 are critical and act as a dominant negative mutant of RF-C function in DNA replication in vivo.

p21 contains independent binding sites for cyclin and cdk2: both sites are required to inhibit cdk2 kinase activity

Cyclin dependent kinases regulate the progression of eukaryotic cells through the cell cycle. p21Cip1/Waf1/Sdi1 is an inhibitor of cdk-cyclin kinase activity, and has been shown to form complexes with cdk-cyclins and with PCNA, an accessory protein of DNA polymerase delta. The kinase inhibitory domain maps to the N-terminus (1-82) and contains the cdk2 binding site (28-82). We have generated a panel of deletion mutants of p21. A functional characterization of p21 mutants in the N-terminal domain reveals that cyclins bind to this domain independently of cdk2. Correlating with these results we find that p21 can associate with cyclin-cdk kinases in two functionally distinct forms, one in which the kinase activity is inhibited and the other in which the kinase is still active. The cdk2 and cyclin binding sites on p21 are both required to inhibit kinase activity. The second type of interaction, in which an active cyclin-cdk complex only interacts with p21 either via the cyclin or the cdk2 binding site but not through both, does not lead to inhibition of cyclin kinase activity. These results thus provide a basis for understanding the mechanism by which p21, and perhaps other cdk-cyclin kinase inhibitory proteins, suppress kinase activity.

Changing pattern of Candida species in a bone marrow transplant patient

A report on a patient with multiple myeloma, undergoing bone marrow transplant, who developed systemic fungal infection due to Candida krusei after bone marrow transplantation. The subsequent appearance of Ketoconazole resistant C. krusei is probably the first report of its kind from India. The significance of the findings is discussed.

Changes in the subcellular localization of replication initiation proteins and cell cycle proteins during G1- to S-phase transition in mammalian cells

DNA replication in eukaryotic cells is restricted to the S-phase of the cell cycle. In a cell-free replication model system, using SV40 origin-containing DNA, extracts from G1 cells are inefficient in supporting DNA replication. We have undertaken a detailed analysis of the subcellular localization of replication proteins and cell cycle regulators to determine when these proteins are present in the nucleus and therefore available for DNA replication. Cyclin A and cdk2 have been implicated in regulating DNA replication, and may be responsible for activating components of the DNA replication initiation complex on entry into S-phase. G1 cell extracts used for in vitro replication contain the replication proteins RPA (the eukaryotic single-stranded DNA binding protein) and DNA polymerase alpha as well as cdk2, but lack cyclin A. On localizing these components in G1 cells we find that both RPA and DNA polymerase alpha are present as nuclear proteins, while cdk2 is primarily cytoplasmic and there is no detectable cyclin A. An apparent change in the distribution of these proteins occurs as the cell enters S-phase. Cyclin A becomes abundant and both cyclin A and cdk2 become localized to the nucleus in S-phase. In contrast, the RPA-34 and RPA-70 subunits of RPA, which are already nuclear, undergo a transition from the uniform nuclear distribution observed during G1, and now display a distinct punctate nuclear pattern. The initiation of DNA replication therefore most likely occurs by modification and activation of these replication initiation proteins rather than by their recruitment to the nuclear compartment.