Genome-wide metabolic (re-) annotation of Kluyveromyces lactis

Background: Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic analysis. Nevertheless, until now, no complete metabolic functional annotation has been performed to the proteins encoded in the Kluyveromyces lactis genome. Results: In this work, a new metabolic genome-wide functional re-annotation of the proteins encoded in the Kluyveromyces lactis genome was performed, resulting in the annotation of 1759 genes with metabolic functions, and the development of a methodology supported by merlin (software developed in-house). The new annotation includes novelties, such as the assignment of transporter superfamily numbers to genes identified as transporter proteins. Thus, the genes annotated with metabolic functions could be exclusively enzymatic (1410 genes), transporter proteins encoding genes (301 genes) or have both metabolic activities (48 genes). The new annotation produced by this work largely surpassed the Kluyveromyces lactis currently available annotations. A comparison with KEGG’s annotation revealed a match with 844 (~90%) of the genes annotated by KEGG, while adding 850 new gene annotations. Moreover, there are 32 genes with annotations different from KEGG. Conclusions: The methodology developed throughout this work can be used to re-annotate any yeast or, with a little tweak of the reference organism, the proteins encoded in any sequenced genome. The new annotation provided by this study offers basic knowledge which might be useful for the scientific community working on this model yeast, because new functions have been identified for the so-called metabolic genes. Furthermore, it served as the basis for the reconstruction of a compartmentalized, genome-scale metabolic model of Kluyveromyces lactis, which is currently being finished.

Forma breve e fotografia: una narrativa del Mozambico

La relazione interdisciplinare tra letteratura e fotografia, nella rilettura della storia recente del Mozambico, è l’oggetto di studio della presente tesi. Il presupposto coincide in primo luogo con la disamina interna della dialettica esistente tra archivio coloniale e oralità, modalità narrativa in parte transitata nella estória, declinazione lusofona della forma breve che permette di recuperare l’eredità popolare del racconto tradizionale. Il dialogo tra verbale e visuale consente a sua volta di stabilire nuovi paradigmi interpretativi nel dibattito postcoloniale tra memoria, trauma e rappresentazione. L’analisi comparativa tra la narrativa di João Paulo Borges Coelho e la fotografia di Ricardo Rangel rivela sguardi diversi sul mondo circostante, ma anche convergenze contemplative che si completano nell’incorporazione reciproca delle “omologie strutturali” comuni alle due modalità espressive. La fotografia colma delle lacune fornendoci delle visioni del passato, ma, in quanto “rappresentazione”, ci mostra il mondo per come appare e non per come funziona. Il testo letterario, grazie al suo approccio dialogico-narrativo, consente la rielaborazione museologica della complessa pletora di interferenze semantiche e culturali racchiuse nelle immagini, in altre parole fornisce degli “indizi di verità” da cui (ri)partire per l’elaborazione di nuovi archetipi narrativi tra l’evento rappresentato e la Storia di cui fa parte. Il punto di tangenza tra i due linguaggi è la cornice, espediente fotografico e narrativo che permette di tracciare i confini tra l’indicibile e l’invisibile, ma anche tra ciò che si narra e ciò che sta fuori dalla narrazione, ovvero fuori dalla storia. La tensione dialettica che si instaura tra questi due universi è seminale per stabilire le ragioni della specificità letteraria mozambicana perché, come afferma Luandino Vieira, “nel contesto postcoloniale gli scrittori sono dei satelliti che ruotano intorno ai «buchi neri della storia» la cui forza di attrazione permette la riorganizzazione dell’intero universo letterario.

Blood glucose and prognosis in children with presumed severe malaria: is there a threshold for 'hypoglycaemia'?

OBJECTIVES: Hypoglycaemia (glucose <2.2 mmol/l) is a defining feature of severe malaria, but the significance of other levels of blood glucose has not previously been studied in children with severe malaria. METHODS: A prospective study of 437 consecutive children with presumed severe malaria was conducted in Mali. We defined hypoglycaemia as <2.2 mmol/l, low glycaemia as 2.2-4.4 mmol/l and hyperglycaemia as >8.3 mmol/l. Associations between glycaemia and case fatality were analysed for 418 children using logistic regression models and a receiver operator curve (ROC). RESULTS: There was a significant difference between blood glucose levels in children who died (median 4.6 mmol/l) and survivors (median 7.6 mmol/l, P < 0.001). Case fatality declined from 61.5% of the hypoglycaemic children to 46.2% of those with low glycaemia, 13.4% of those with normal glycaemia and 7.6% of those with hyperglycaemia (P < 0.001). Logistic regression showed an adjusted odds ratio (AOR) of 0.75 (0.64-0.88) for case fatality per 1 mmol/l increase in baseline blood glucose. Compared to a normal blood glucose, hypoglycaemia and low glycaemia both significantly increased the odds of death (AOR 11.87, 2.10-67.00; and 5.21, 1.86-14.63, respectively), whereas hyperglycaemia reduced the odds of death (AOR 0.34, 0.13-0.91). The ROC [area under the curve at 0.753 (95% CI 0.684-0.820)] indicated that glycaemia had a moderate predictive value for death and identified an optimal threshold at glycaemia <6.1 mmol/l, (sensitivity 64.5% and specificity 75.1%). CONCLUSIONS: If there is a threshold of blood glucose which defines a worse prognosis, it is at a higher level than the current definition of 2.2 mmol/l.

Argemone mexicana decoction for the treatment of uncomplicated falciparum malaria

A prospective, dose-escalating, quasi-experimental clinical trial was conducted with a traditional healer using a decoction of Argemone mexicana for the treatment of malaria in Mali. The remedy was prescribed in three regimens: once daily for 3 days (Group A; n=23); twice daily for 7 days (Group B; n=40); and four times daily for the first 4 days followed by twice daily for 3 days (Group C; n=17). Thus, 80 patients were included, of whom 80% were aged<5 years and 25% were aged<1 year. All presented to the traditional healer with symptoms of malaria and had a Plasmodium falciparum parasitaemia>2000/microl but no signs of severe malaria. The proportions of adequate clinical response (ACR) at Day 14 were 35%, 73% and 65% in Groups A, B and C, respectively (P=0.011). At Day 14, overall proportions of ACR were lower in children aged<1 year (45%) and higher in patients aged>5 years (81%) (P=0.027). Very few patients had complete parasite clearance, but at Day 14, 67% of patients with ACR had a parasitaemia<2000/microl. No patient needed referral for severe disease. Only minor side effects were observed. Further research should determine whether this local resource could represent a first-aid home treatment in remote areas.

Modulation of Immune Response in Lambs

Experiments using different types of antigen-adjuvant preparations were conducted in outbred sheep to compare effects of adjuvants on immune responses. Trinitrophenyl-ovalbumin (TNP-ovalbumin) incorporated in a preparation with nonionic block copolymers elicited high antibody titers to both ovalbumin and TNP. Different humoral immune responses were observed when Pasteurella haemolytica lipopolysaccharide (LPS) was added to the preparations. Responses to ovalbumin and TNP were reduced when Pasteurella haemolytica LPS was added to copolymer L121. The antibody titers to ovalbumin or TNP were not affected by the addition of LPS to the preparation containing copolymer L180.5. Lymphocyte proliferation assays demonstrated high stimulation indices at day 17 to ovalbumin by lymphocytes from lambs receiving preparations containing copolymers without Pasteurella haemolytica LPS.

Type I Hypersensitivity in Lambs With Coughing Syndrome

Lambs from two flocks with a chronic respiratory disease characterized by paroxysmal cough and rectal prolapses were tested for their skin reactivity to Mycoplasma ovipneumoniae (MO) and M. arginini (MA) antigens (Ags). There was a marked, immediate skin reaction to intradermal injection of MO Ag in many of the tested lambs. Some of these positive lambs also reacted to MA Ag. Phosphate buffered saline (PBS) used as a negative control gave no skin reaction in any of the tested animals. In addition, simultaneous serological tests revealed low antibody levels against MO and MA. However, both agents could be routinely isolated from nasal swabs of the affected lambs. There is reason to suspect that an immediate type hypersensitivity to MO Ag and perhaps to other allergens that develops in association with the mycoplasmal infection contributes to this coughing syndrome.

Immune Response in Lambs Naturally Infected With Mycoplasma Species

During the past several years, an ovine coughing syndrome characterized by paroxysmal cough leading to rectal prolapses has been observed in Iowa and neighboring states. Preliminary studies conducted by Kaeberle and Eness (1) several years ago indicated the presence of relatively high levels of M. ovipneumoniae (MO) antibody in lambs from affected flocks. In the present study, serum samples obtained from six flocks around the state of Iowa, at various stages of the clinical disease, were compared by ELISA for antibody to MO and M. arginini (MA). Results indicated low antibody levels to MO in flocks sampled at the early stages of infection whereas increased levels of antibody were evident in lambs from flocks that had apparently recovered from the disease. On the other hand, antibody levels to MA were more likely to increase earlier in the disease process. Our results suggest that the chronic nature of this disease may result from the failure of the immune system to produce antibodies that are protective against MO infection. At such a time that appreciable levels of specific antibodies appear in the serum (several weeks following infection) lambs seem to recover from the clinical disease. In addition, this lack of circulating antibody levels against MO would not be inconsistent with a predominant IgE response during early stages of the clinical disease as we have suggested in another entry in this issue of Sheep Research Reports.

Pasteurella Vaccination of Ewes

Pasteurella haemolytica is a major contributor to neonatal pneumonia in lambs; which continues to be a major problem. Experimentation was conducted to determine the efficacy of vaccinating pregnant ewes to reduce the incidence of pneumonia in newborn lambs. Vaccines utilized in this experimentation included three different commercial Pasteurella haemolytica vaccines intended for use in cattle and an experimental vaccine prepared in our laboratory. Only one of the commercial vaccines increased levels of anti-Pasteurella antibodies in serum of the ewes at time of lambing, but lambs from all three groups of vaccinated ewes had higher levels of antibodies than control lambs. Some lambs in all groups developed pneumonia during the neonatal period. Ewes administered the experimental vaccine had significantly higher levels of serum antibodies at lambing time. This increase was reflected in increased levels in serum of lambs from the vaccinated ewes. However, the antibodies appeared not to be protective, since as many lambs in the treatment group developed pneumonia as did in the control group.

Antibody Response to Inactivated Viral Vaccines Administered to Calves at Weaning

Respiratory disease in beef calves has been associated with the stress of weaning. Management practices commonly delay vaccination of calves to this time, and weaning stress could potentially suppress the immune response. To reduce this stress we have been experimenting with a procedure termed “pasture weaning” in which the dams are removed and the calves remain on pasture. Observation suggests that calves weaned with this approach adapt to the weaned state much better than those held in drylot. Consequently, one would expect less stress-mediated effects including those on the immune system. Calves were weaned and assigned to groups that were pasture or drylot weaned, and calves within the groups were vaccinated with one of two inactivated virus vaccines by either the intramuscular or subcutaneous route. Weaning placement did not affect antibody responses to the viruses included in the vaccines. The route of administration did not influence responses with subcutaneous injection inducing responses equivalent to the intramuscular site. Utilization of this route for vaccination could be advantageous because it precludes the tissue damage and hidden abscessation that sometimes results from intramuscular injections. A distinct difference was noted in the immunogenicity of the vaccines with the Vira Shield product yielding significantly better responses to all viral entities.

Antibody Responses of Vaccinated and Nonvaccinated Calves to Haemophilus somnus

Respiratory disease resulting from infection of calves with Haemophilus somnus (H. somnus) is an annual occurrence in fall calves at the McNay Farm. Previous observations of skin test reactivity to H. somnus antigens suggested a role for this phenomenon in the pathogenesis of the disease. Groups of calves, about 90 days of age, were vaccinated with four different commercial H. somnus vaccines, and serum levels of H. somnus antibodies were determined. Antibodies of the IgG and IgE classes were detected with ELISA procedures conducted on sera collected before and after vaccination. Most of the calves had detectable H. somnus IgE class antibodies at the start of the experimentation but IgG class antibodies were minimal. Antibodies of both classes increased in nonvaccinated and vaccinated calves during the 30 day period of experimentation. However, the level of IgE class antibodies in vaccinates was lower than in controls suggesting that vaccination may limit the IgE response.

Bovine Respiratory Syncytial Virus Infection in McNay Farm Calves

Clinical respiratory disease occurs almost every year in fall calves in the McNay Farm herd. Diagnostic procedures have implicated Haemophilus somnus (H. somnus) and bovine respiratory syncyial virus (BRSV) as the infectious agents primarily associated with this disease. Therefore, the 1995 calves were closely monitored after weaning and during the course of a respiratory disease. Serologic evidence indicated the involvement of the same two agents in the pathogenesis of the disease. Also, experimental evidence suggested a role for a preexisting immediate hypersensitivity to H. somnus and the development of this type of response to BRSV. We theorize that the pathogenesis of the clinical disease involved infection with H. somnus, establishment of immediate hypersensitivity in the lungs, viral infection with associated pathologic lesions, and viral exacerbation of the immediate hypersensitivity reaction with resultant clinical signs and tissue damage.

Prebreeding Immunization of Beef Cows

A number of infectious agents are potential threats to the fetus of a pregnant cow and may result in abortion. These agents include Leptospira sp., Campylobacter fetus and viruses such as infectious bovine rhinotracheitis (IBR) and bovine virus diarrhea (BVD). Maintenance in the cow of a high level of immunity to these agents during pregnancy can insure protection of the fetus. In particular, vaccines against BVD and IBR viruses can establish protective immunity throughout gestation. An appropriate vaccination regimen prior to breeding is required to establish this protective immunity. This can be achieved with a single dose of certain modified live virus vaccines, but those vaccines must be administered at least 30 days prior to breeding to avoid interference with conception. We have evaluated an oil-adjuvanted inactivated virus vaccine in cattle with differing immunological histories. Two doses of the vaccine administered 30 days apart to serologically negative animals induced appreciable levels of BVD and IBR anti-viral antibodies with persisting titers throughout gestation. In other experiments a single dose of the vaccine was administered to: (1) animals given two doses of the vaccine several months earlier, (2) animals previously vaccinated with other inactivated virus vaccines, or (3) animals previously vaccinated with modified live virus vaccine. The vaccine consistently induced marked anamnestic responses in these animals. Not only did mean titers rise, but a vast majority of individual animals responded. This contrasts with efforts to boost titers with modified live virus vaccines where the effect may be erratic among animals. The safety and efficacy of selected inactivated viral vaccines argues for their use in prebreeding immunization of beef cows.

Infectious Bovine Rhinotracheitis Virus Antibody Responses to Vaccines Used in Combination

The objective of this experimentation was to determine if circulating antibody titers to parainfluenza type-3 (PI-3) and infectious bovine rhinotracheitis (IBR) viruses could be enhanced by a combination of vaccines. The vaccines utilized were a modified live virus vaccine administered by the intranasal route and an inactivated virus vaccine injected intramuscularly. Virus neutralization tests were conducted on sera obtained at intervals before and following vaccination. Unfortunately, the calves were apparently exposed naturally to PI-3 virus, and the responses to that virus were inconclusive. However, antibody responses to IBR virus were dramatically enhanced by the combination of the two vaccines.

Antibody Responses of Young Calves to Inactivated Viral Vaccines

Three commercial inactivated virus vaccines were evaluated for immunogenicity in young calves with residual maternal antibodies. Groups of 30 calves were administered each of the vaccines at the start of the experimentation and were administered a second dose 32 days later. Serum was obtained from these calves and 30 calves in a nonvaccinated control group prior to vaccination and at 32, 61, 99 and 125 days thereafter. Antibody responses to viruses in two of the vaccines were extremely limited. The third vaccine overcame suppression by maternal antibodies and elicited responses clearly differentiated from antibody levels in the control group of calves.

Pasture Weaning at the McNay Memorial Research and Demonstration Farm: A Progress Report

In September 1995, 225 spring-born calves were weaned on pasture at the McNay Memorial Research and Demonstration Farm to explore procedures necessary to conduct a successful pasture-weaning program. In the two to three week post-weaning period, average daily gains (ADG) for the two groups weaned that year were 1.06 and 3.06 pounds; there were no health problems. In 1996, a research trial utilizing 242 spring-born calves was conducted to compare pastureweaned and feedlot-weaned calves. Half of the calves were weaned on pasture for three weeks and then placed in a feedlot for three more weeks. The other half of the calves were weaned directly into the feedlot for the six week post-weaning period. ADGs during the three week post-weaning period were 1.24 and 2.42 for the pastureweaned and feedlot-weaned calves. For the entire six week trial, ADGs were 1.83 and 2.40 for the pastureweaned and feedlot-weaned calves. There was no sickness in either weaning treatment during the six week trial. Initial experience indicates pasture-weaning is a feasible method of getting calves through a stressful procedure.