Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli.

The rpsO mRNA, encoding ribosomal protein S15, is only partly stabilized when the three ribonucleases implicated in its degradation--RNase E, polynucleotide phosphorylase, and RNase II--are inactivated. In the strain deficient for RNase E and 3'-to-5' exoribonucleases, degradation of this mRNA is correlated with the appearance of posttranscriptionally elongated molecules. We report that these elongated mRNAs harbor poly(A) tails, most of which are fused downstream of the 3'-terminal hairpin at the site where transcription terminates. Poly(A) tails are shorter in strains containing 3'-to-5' exoribonucleases. Inactivation of poly(A) polymerase I (pcnB) prevents polyadenylylation and stabilizes the rpsO mRNA if RNase E is inactive. In contrast polyadenylylation does not significantly modify the stability of rpsO mRNA undergoing RNase E-mediated degradation.

Lichtheimia Infection in a Lymphoma Patient: Case Report and a Brief Review of the Available Diagnostic Tools

We describe the case of a patient with a T-lymphoblastic lymphoma whose disseminated mucormycosis was diagnosed with delay, and we address the diagnostic and therapeutic decision-making process and review the diagnostic workup of patients with potential IFD. The diagnosis was delayed despite a suggestive radiological presentation of the patient's pulmonary lesion. The uncommon risk profile (T-lymphoblastic lymphoma, short neutropenic phases) wrongly led to a low level of suspicion. The diagnosis was also hampered by the lack of indirect markers for infections caused by Mucorales, the low sensitivity of both fungal culture and panfungal PCR, and the limited availability of species-specific PCR. A high level of suspicion of IFD is needed, and aggressive diagnostic procedures should be promptly initiated even in apparently low-risk patients with uncommon presentations. The extent of the analytical workup should be decided on a case-by-case base. Diagnostic tests such as the galactomannan and β-D-glucan test and/or PCR on biological material followed by sequencing should be chosen according to their availability and after evaluation of their specificity and sensitivity. In high-risk patients, preemptive therapy with a broad-spectrum mould-active antifungal agent should be started before definitive diagnostic findings become available.

Substrate specifity of protein kinases and computational prediction of substrates

To ensure signalling fidelity, kinases must act only on a defined subset of cellular targets. Appreciating the basis for this substrate specificity is essential for understanding the role of an individual protein kinase in a particular cellular process. The specificity in the cell is determined by a combination of peptide specificity of the kinase (the molecular recognition of the sequence surrounding the phosphorylation site), substrate recruitment and phosphatase activity. Peptide specificity plays a crucial role and depends on the complementarity between the kinase and the substrate and therefore on their three-dimensional structures. Methods for experimental identification of kinase substrates and characterization of specificity are expensive and laborious, therefore, computational approaches are being developed to reduce the amount of experimental work required in substrate identification. We discuss the structural basis of substrate specificity of protein kinases and review the experimental and computational methods used to obtain specificity information. (c) 2005 Elsevier B.V. All rights reserved.

The mode of action of the plant antimicrobial peptide MiAMP1 differs from that of its structural homologue, the yeast killer toxin WmKT

The plant antimicrobial peptide MiAMP1 from Macadamia integrifolia and the yeast killer toxin peptide WmKT from Williopsis mrakii are structural homologues. Comparative studies of yeast mutants were performed to test their sensitivity to these two antimicrobial peptides. No differences in susceptibility to MiAMP1 were detected between wild-type and several WmKT-resistant mutant yeast strains. A yeast mutant MT1, resistant to MiAMP1 but unaffected in its susceptibility to plant defensins and hydrogen peroxide, also did not show enhanced tolerance towards WmKT. It is therefore probable that the Greek key beta-barrel structure shared by MiAMP1 and WmKT provides a robust structural framework ensuring stability for the two proteins but that the specific action of the peptides depends on other motifs. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

Recognition and inactivation of LPS by lipophorin particles

Lipophorin is the major lipid carrier in insects, but various observations indicate that lipophorin is also involved in immune reactions. To examine a possible role of lipophorin in defence reactions, we mixed hemolymph plasma from Galleria mellonella with LPS and noticed that lipophorin forms detergent-insoluble aggregates, while most other plasma proteins are not affected. Lipophorin particles isolated by low-density gradient centrifugation retained LPS-induced aggregation properties, which suggested to us that these immune-reactive particles are able to recognise LPS and respond by forming insoluble aggregates. Antibodies against LPS-binding proteins, such as immulectin-2 and beta-1,3-glucan binding protein, cross-reacted with proteins associated with purified lipophorin particles. To examine whether LPS-mediated aggregates inactivate LPS, we added LPS-lipophorin mixtures to purified lipophorin particles and monitored aggregate formation. Under these conditions lipophorin did not form insoluble aggregates, which indicates that lipophorin particles sequester LPS into non-toxic aggregates. (c) 2005 Elsevier Ltd. All rights reserved.

Three classes of starch granule swelling: Influence of surface proteins and lipids

The role of non-carbohydrate surface components of granular starch in determining gelatinisation behaviour has been tested by treatment of native starches with a range of extractants. Resulting washed starches were analysed for (bio)chemical, calorimetric and theological properties. Sodium dodecyl sulphate (SDS) was the most efficient extractant tested, and resulted in major changes to the subsequent theological properties of wheat and maize starches but not other starches. Three classes of starch granule swelling behaviour are identified: (i) rapid swelling (e.g. waxy maize, potato), (ii) slow swelling that can be converted to rapid swelling by extraction of surface proteins and lipids (e.g. wheat, maize), and (iii) limited swelling not affected by protein/lipid extraction (e.g. high amylose maize/potato). Comparison of a range of extractants suggests that all of protein, lipid and amylose are involved in restriction of swelling for wheat or maize starches. Treatment of starches with SDS leads to a residue at comparable (low) levels of SDS for all starches. C-13 NMR analysis shows that this SDS is present as a glucan inclusion complex, even for waxy maize starch. We infer that under the conditions used, glucan inclusion complexation of SDS is equally likely with amylopectin as with amylose. (c) 2006 Elsevier Ltd. All rights reserved.

Detection and quantification of protein oxidation in sarcopenic models:a mass spectrometry study

Oxidised biomolecules in aged tissue could potentially be used as biomarkers for age-related diseases; however, it is still unclear whether they causatively contribute to ageing or are consequences of the ageing process. To assess the potential of using protein oxidation as markers of ageing, mass spectrometry (MS) was employed for the identification and quantification of oxidative modifications in obese (ob/ob) mice. Lean muscle mass and strength is reduced in obesity, representing a sarcopenic model in which the levels of oxidation can be evaluated for different muscular systems including calcium homeostasis, metabolism and contractility. Several oxidised residues were identified by tandem MS (MS/MS) in both muscle homogenate and isolated sarcoplasmic reticulum (SR), an organelle that regulates intracellular calcium levels in muscle. These modifications include oxidation of methionine, cysteine, tyrosine, and tryptophan in several proteins such as sarcoplasmic reticulum calcium ATPase (SERCA), glycogen phosphorylase, and myosin. Once modifications had been identified, multiple reaction monitoring MS (MRM) was used to quantify the percentage modification of oxidised residues within the samples. Preliminary data suggests proteins in ob/ob mice are more oxidised than the controls. For example SERCA, which constitutes 60-70% of the SR, had approximately a 2-fold increase in cysteine trioxidation of Cys561 in the obese model when compared to the control. Other obese muscle proteins have also shown a similar increase in oxidation for various residues. Further analysis with complex protein mixtures will determine the potential diagnostic use of MRM experiments for analysing protein oxidation in small biological samples such as muscle needle biopsies.

Dextranas e seus derivados fosforilados: obtenção e avaliação do potencial antioxidante, imunomodulatório e anticoagulante

Glucans are polysaccharides with different pharmacological and biological activities described. However, there are some reports about the activities of the glucan type α (alpha). In this context, a group of α-D-glucans called dextrans extracted from Leuconostoc mesenteroides bacteria, with molecular weights of 10 (D10), 40 (D40) and 147 (D147) kDa and their phosphorylated derivatives P10, P40 and P147, were evaluated as for their antioxidant, anticoagulant and immunomodulatory potential for the first time, in order to elucidate compounds with potent activities and low toxicity. Infrared spectroscopy analysis, monosaccharide composition and chemical dosages showed that these dextrans are the same polysaccharide, but with different molecular weights, besides confirming the success of phosphorylation. None presented with anticoagulant features. The reducing power test showed that D147 was twice as potent as other dextrans. On the other hand, all six samples showed similar activity (50%) when it came to scavenging the OH radical. To the superoxide ion scavenging, only D10 had a pronounced activity (50%). D40 was the single native dextran that presented with immunomodulatory features since it double stimulated the proliferation of murine macrophages (RAW 264.7) and double the release of nitric oxide by the cells, both in the absence and presence of lipopolysaccharides (LPS). In addition, D40 showed a greater scavenging activity (50%) for the hydrogen peroxide, which caused it to also be the more potent dextran when it came to inhibiting lipid peroxidation (70%). On other hand, P147 showed the highest iron and copper ion chelation activity (~85%). P10 proved be the most effective compound to macrophage proliferation. The results point toward dextrans with a 40 kDa weight as being ideal for antioxidant and immunomodulatory use, could be supplemented with phosphorylated derivatives. However, future studies with the D40 and other similarly dextrans are to confirm this hypothesis.

Proteção pela glucana em modelo experimental de sepse

OBJETIVO: Neste trabalho avaliou-se a ação da glucana ? ? 1-3 insolúvel, um polissacarídeo extraído da parede celular interna do fungo Saccharomyces cerevisae, como agente imunoestimulante inespecífico em camundongos submetidos a modelo de sepse experimental. MÉTODOS: Foram utilizados 73 camundongos Swiss, os quais receberam glucana em diferentes doses pelas vias intraperitoneal (i.p.). Sepse difusa foi induzida através da técnica de ligadura e punção do ceco, transfixado e drenado com fio multifilamentar. RESULTADOS: Os animais tratados com glucana apresentaram um aumento significante no número de leucócitos no lavado peritoneal, diminuição no número de unidades formadoras de colônias bacterianas. Observou-se um aumento significante na sobrevida dos animais tratados com glucana insolúvel, a qual proporcionou um maior controle da infecção bacteriana por aumentar o número de células de defesa. CONCLUSÃO: A glucana insolúvel, quando usada em camundongos por via intraperitoneal, em modelo de sepse abdominal, contribuiu para melhorar a sobrevida, induziu proteção contra a formação de colônias bacterianas no líquido peritoneal e aumentou a migração leucocitária

Secretome analysis of Trichoderma atroviride T17 biocontrol of Guignardia citricarpa

The fungal species Guignardia citricarpa is an important pathogen in citriculture. Members of the fungal genus Trichoderma are recognized as biocontrol agents but studies on the interactions between both fungi are scarce. This study aimed to identify extracellular proteins secreted by Trichoderma atroviride T17 that are related to the control of G. citricarpa. Two-dimensional gel electrophoresis (2D) was used to study the patterns of proteins secreted by T. atroviride T17 in medium containing glucose (control) and in medium containing G. citricarpa GC3 inactivated mycelium. We identified 59 of the 116 spots differentially expressed (50.86%) by LC–MS/MS. Of these, we highlight the presence of glycoside hydrolases (CAZy families 3, 43, 54, 76 and 93), chitinase, mutanase, a-1,3-glucanase, a-1,2-mannosidase, carboxylic hydrolase ester, carbohydrate-binding module family 13, glucan 1,3-b-glucosidase, a-galactosidase and Neutral protease 2. These proteins are related to mycoparasitism processes, stimuli and therefore to the biological control of pathogens. The results obtained are in agreement with reports describing an increase in the secretion of proteins related to mycoparasitism and biological control and a reduction in the secretion of proteins related to the metabolism of Trichoderma species grown in the presence of the pathogen. Moreover, these results are pioneer in understanding T. atroviride interaction with G. citricarpa. For the first time, we identified potential candidate proteins that may have a role in the antagonism mechanism of G. citricarpa by T. atroviride T17. Thus our results shed a light into the molecular mechanisms that T. atroviride use to control G. citricarpa.

Domestication and the storage starch biosynthesis pathway: Signatures of selection from a whole sorghum genome sequencing strategy

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either ‘Landraces’ or ‘Wild and Weedy’ genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

Proteção pela glucana em modelo experimental de sepse

OBJETIVO: Neste trabalho avaliou-se a ação da glucana ? ? 1-3 insolúvel, um polissacarídeo extraído da parede celular interna do fungo Saccharomyces cerevisae, como agente imunoestimulante inespecífico em camundongos submetidos a modelo de sepse experimental. MÉTODOS: Foram utilizados 73 camundongos Swiss, os quais receberam glucana em diferentes doses pelas vias intraperitoneal (i.p.). Sepse difusa foi induzida através da técnica de ligadura e punção do ceco, transfixado e drenado com fio multifilamentar. RESULTADOS: Os animais tratados com glucana apresentaram um aumento significante no número de leucócitos no lavado peritoneal, diminuição no número de unidades formadoras de colônias bacterianas. Observou-se um aumento significante na sobrevida dos animais tratados com glucana insolúvel, a qual proporcionou um maior controle da infecção bacteriana por aumentar o número de células de defesa. CONCLUSÃO: A glucana insolúvel, quando usada em camundongos por via intraperitoneal, em modelo de sepse abdominal, contribuiu para melhorar a sobrevida, induziu proteção contra a formação de colônias bacterianas no líquido peritoneal e aumentou a migração leucocitária

Acetilação do exopolissacarídeo (1→6)-β-D-glucana (lasiodiplodana): derivatização química e caracterização

Lasiodiplodan is an exocellular β-glucan with biological functionalities such as antioxidant, antiproliferative, hypocholesterolemic, protective activity against DNA damage induced by doxorubicin and hypoglycemic activity. Chemical derivatization of polysaccharide macromolecules has been considered as a potentiating mechanism for bioactivity. In this context, this work proposes the derivatization of lasiodiplodan by acetylation. Acetic anhydride was used as derivatizing agent and pyridine as catalyst and reaction medium. The derivatives obtained were evaluated by its water solubility, degree of substitution (DS), antioxidant potential, and characterized by infrared spectroscopy (FT-IR), thermal analysis, differential scanning calorimetry, X-ray diffraction and scanning electron microscopy. Acetylated derivatives with different degrees of substitution (1.26; 1.03; 0.66 and 0.48) were obtained, and there was correlation between the concentration of derivatizing agent and DS. FT-IR spectroscopy analysis confirmed the insertion of acetyl groups into derivatized macromolecules (LAS-AC) through of specific bands concerning to carbonyl group (C = O) and increase in C-O vibration. SEM analysis indicated that native lasiodiplodan presents morphological structure in the form of thin films with translucent appearance and folds along its length. Derivatization led to morphological changes in the polymer, including aspects thickness, translucency and agglomeration. Thermal analysis indicated the native sample and derivative with DS 0.48 presented three weight loss stages. The first stage occurred until 125 ° C (loss of water) and there were two consecutive events of weight loss (200 ° C - 400 ° C) attributed to molecule degradation. Samples with DS 1.26; 1.03 and 0.66 demonstrated four weight loss stages. The first stage occurred until 130 ° C (loss of water), following by two consecutive events of weight loss (200 ° C - 392 ° C) attributed to degradation of the biopolymer. The fourth stage was between 381 ° C and 532 ° C (final decomposition) with exothermic peaks between 472 ° C and 491 ° C. X-ray diffraction patterns showed that native and acetylated lasiodiplodan have amorphous structure with semicrystalline regions. Derivatization did not contribute to increased solubility of the macromolecule, but potentiated its antioxidant capacity. Acetylation of lasiodiplodan allowed to obtaining a new macromolecule with higher antioxidant potential than the native molecule and with technological properties applicable in various industrial sectors.