Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum

A method is presented to computationally identify core promoters in the Plasmodium falciparum genome using only DNA physicochemical properties

Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction

<p>Abstract</p> <p>Background</p> <p>Subtelomeric <it>RIFIN </it>genes constitute the most abundant multigene family in <it>Plasmodium falciparum</it>. <it>RIFIN </it>products are targets for the human immune response and contribute to the antigenic variability of the parasite. They are transmembrane proteins grouped into two sub-families (RIF_A and RIF_B). Although recent data show that RIF_A and RIF_B have different sub-cellular localisations and possibly different functions, the same structural organisation has been proposed for members of the two sub-families. Despite recent advances, our knowledge of the regulation of <it>RIFIN </it>gene expression is still poor and the biological role of the protein products remain obscure.</p> <p>Results</p> <p>Comparative studies on <it>RIFINs </it>in three clones of <it>P. falciparum </it>(3D7, HB3 and Dd2) by Multidimensional scaling (MDS) showed that gene sequences evolve differently in the 5'upstream, coding, and 3'downstream regions, and suggested a possible role of highly conserved 3' downstream sequences. Despite the expected polymorphism, we found that the overall structure of <it>RIFIN </it>repertoires is conserved among clones suggesting a balance between genetic drift and homogenisation mechanisms which guarantees emergence of novel variants but preserves the functionality of genes. Protein sequences from a <it>bona fide </it>set of 3D7 RIFINs were submitted to predictors of secondary structure elements. In contrast with the previously proposed structural organisation, no signal peptide and only one transmembrane helix were predicted for the majority of RIF_As. Finally, we developed a strategy to obtain a reliable 3D-model for RIF_As. We generated 265 possible structures from 53 non-redundant sequences, from which clustering and quality assessments selected two models as the most representative for putative RIFIN protein structures.</p> <p>Conclusion</p> <p>First, comparative analyses of <it>RIFIN </it>repertoires in different clones of <it>P. falciparum </it>provide insights on evolutionary mechanisms shaping the multigene family. Secondly, we found that members of the two sub-families RIF_As and RIF_Bs have different structural organization in accordance with recent experimental results. Finally, representative models for RIF_As have an "Armadillo-like" fold which is known to promote protein-protein interactions in diverse contexts.</p

Deoxygenation of non-edible vegetable oil to produce hydrocarbons over Mg-Al mixed oxides

none7noopenRomero, Max; Pizzi, Andrea; Toscano, Giuseppe; Casazza, Alessandro Alberto; Busca, Guido; Bosio, Barbara; Arato, ElisabettaRomero, Max; Pizzi, Andrea; Toscano, Giuseppe; Casazza, Alessandro Alberto; Busca, Guido; Bosio, Barbara; Arato, Elisabett

A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum

<p>Abstract</p> <p>Background</p> <p><it>Plasmodium </it>parasites are causative agents of malaria which affects >500 million people and claims ~2 million lives annually. The completion of <it>Plasmodium </it>genome sequencing and availability of PlasmoDB database has provided a platform for systematic study of parasite genome. Aminoacyl-tRNA synthetases (<it>aaRS</it>s) are pivotal enzymes for protein translation and other vital cellular processes. We report an extensive analysis of the <it>Plasmodium falciparum </it>genome to identify and classify <it>aaRSs </it>in this organism.</p> <p>Results</p> <p>Using various computational and bioinformatics tools, we have identified 37 <it>aaRS</it>s in <it>P. falciparum</it>. Our key observations are: (i) fraction of proteome dedicated to <it>aaRS</it>s in <it>P. falciparum </it>is very high compared to many other organisms; (ii) 23 out of 37 <it>Pf-aaRS </it>sequences contain signal peptides possibly directing them to different cellular organelles; (iii) expression profiles of <it>Pf-aaRSs </it>vary considerably at various life cycle stages of the parasite; (iv) several <it>PfaaRSs </it>posses very unusual domain architectures; (v) phylogenetic analyses reveal evolutionary relatedness of several parasite <it>aaRS</it>s to bacterial and plants <it>aaRSs</it>; (vi) three dimensional structural modelling has provided insights which could be exploited in inhibitor discovery against parasite <it>aaRSs</it>.</p> <p>Conclusion</p> <p>We have identified 37 <it>Pf-aaRSs </it>based on our bioinformatics analysis. Our data reveal several unique attributes in this protein family. We have annotated all 37 <it>Pf-aaRSs </it>based on predicted localization, phylogenetics, domain architectures and their overall protein expression profiles. The sets of distinct features elaborated in this work will provide a platform for experimental dissection of this family of enzymes, possibly for the discovery of novel drugs against malaria.</p

A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins

<p>Abstract</p> <p>Background</p> <p>The most common substitution matrices currently used (BLOSUM and PAM) are based on protein sequences with average amino acid distributions, thus they do not represent a fully accurate substitution model for proteins characterized by a biased amino acid composition. This problem has been addressed recently by adjusting existing matrices, however, to date, no empirical approach has been taken to build matrices which offer a substitution model for comparing proteins sharing an amino acid compositional bias. Here, we present a novel procedure to construct series of symmetrical substitution matrices to align proteins from similarly biased <it>Plasmodium </it>proteomes.</p> <p>Results</p> <p>We generated substitution matrices by selecting from the BLOCKS database those multiple alignments with a compositional bias similar to that of <it>P. falciparum </it>and <it>P. yoelii </it>proteins. A novel 'fuzzy' clustering method was adopted to group sequences within these alignments, showing that this method retains more complete information on the amino acid substitutions when compared to hierarchical clustering. We assessed the performance against the BLOSUM62 series and showed that the usage of our matrices results in an improvement in the performance of BLAST database searches, greatly reducing the number of false positive hits. We then demonstrated applications of the use of novel matrices to improve the annotation of homologs between the two <it>Plasmodium </it>species and to classify members of the <it>P. falciparum </it>RIFIN/STEVOR family.</p> <p>Conclusion</p> <p>We confirmed that in the case of compositionally biased proteins, standard BLOSUM matrices are not suited for optimal alignments, and specific substitution matrices are required. In addition, we showed that the usage of these matrices leads to a reduction of false positive hits, facilitating the automatic annotation process.</p

Mucinous and Signet-Ring Cell Colonic Adenocarcinoma in Inflammatory Bowel Disease: A Case-Control Study

Simple Summary Chronic active inflammation is a known risk factor for colorectal cancer (CRC) in inflammatory bowel disease (IBD), while the adenoma-carcinoma sequence appears to be associated with sporadic CRC. In the general population, mucinous and signet-ring cell adenocarcinomas are characterized by a worse prognosis. In IBD, a higher frequency of these CRC histotypes has been reported. In the present study, we investigated the frequency and characteristics of mucinous and signet-ring cell adenocarcinomas in patients with IBD versus age-matched non-IBD Controls. CRC was more frequently represented by mucinous/signet-ring cell adenocarcinoma in IBD than in Controls. In rectal CRC, there was a higher proportion of mucinous/signet-ring cell adenocarcinoma vs. standard adenocarcinoma in IBD but not in non-IBD Controls. No risk factors for these two CRC histotypes were identified in IBD. Present findings support that the frequency of mucinous/signet-ring cell colorectal adenocarcinoma is higher in IBD, being associated with rectal involvement of CRC. A higher frequency of mucinous and signet-ring cell colonic adenocarcinoma has been reported in inflammatory bowel disease (IBD). The primary aim was to investigate the frequency of mucinous and signet-ring cell colorectal adenocarcinoma in patients with IBD (Cases) versus age-matched non-IBD Controls. The secondary aims were to compare the characteristics of these two histotypes of colorectal cancer (CRC) in IBD patients vs. Controls and to search for specific risk factors in IBD. In a case-control study, all IBD patients with CRC diagnosed from 2000 to 2022 were enrolled and matched for age (1:2) with non-IBD Controls with CRC. The study population included 120 CRC patients (40 IBD, 80 Controls). In IBD, CRC included standard adenocarcinoma in 23 (57.5%) patients mucinous/signet-ring cell adenocarcinoma in 17 (42.5%) patients. The proportion of mucinous/signet-ring cell adenocarcinoma was higher in IBD than in Controls (17 [42.5%] vs. 18 [22.5%]; p = 0.03). In rectal CRC, the proportion of mucinous/signet-ring cell adenocarcinoma was higher than standard adenocarcinoma in IBD (8 [47.1%] vs. 4 [17.4%]; p = 0.04) but not in Controls (4 [22.2%] vs. 20 [32.2%]; p = 0.59). In rectal CRC, the proportion of these two histotypes was higher in Cases than in Controls (8/12 [66.6%] vs. 4/24 [16.6%]; p = 0.008), with no risk factors identified in IBD. CRC was more frequently represented by mucinous/signet-ring cell adenocarcinoma in IBD than in age-matched non-IBD Controls. In IBD, these two CRC histotypes were more frequent in the rectum

Plasma Cystatin C correlates with plasma NfL levels and predicts disease progression in Parkinson's disease

INTRODUCTION: Previous studies reported increased plasma levels of Cystatin C (Cys-C) in Parkinson's disease (PD) and claimed for a possible association with disease severity and progression. The aim of this study was to evaluate plasma Cys-C in PD and healthy controls (HC) and test its association with markers of peripheral inflammation, neurodegeneration and clinical progression in a longitudinal study. METHODS: Plasma Cys-C, high-sensitive C-reactive protein (hsCRP), interleukin 6 (IL-6) and Neurofilament Light Chain (NfL) were assessed at the baseline in 71 consecutive non-demented PD and 69 HC. PD patients underwent an extensive motor and cognitive assessment at baseline and after 2 years of follow-up. The association of Cys-C with disease severity was evaluated in a multilinear model adjusted for the effect of age, sex, disease duration and peripheral inflammation. RESULTS: Cys-C levels appeared to be higher in PD compared to controls and correlated with the plasma neuronal marker NfL (r = 0.204, p = 0.046). In longitudinal analyses, PD patients with higher Cys-C levels exhibited faster motor progression at two years of follow-up independently from the peripheral inflammatory profile. CONCLUSIONS: Cys-C was associated with higher NfL levels and a remarkably faster motor progression in PD independently from peripheral inflammation. Further studies are needed in order to understand the mechanisms underpinning the association of Cys-C with higher neuronal damage markers in neurodegenerative diseases

Serum NFL as a predictor of disease progression in dementia with Lewy bodies

AbstractBackgroundCSF and plasma neurofilament light chain (NfL) levels have been consistently proposed as reliable markers of neurodegeneration able to discriminate between Parkinson's disease (PD) and atypical parkinsonisms. Increased Serum NfL might predict worse motor and cognitive progression in PD patients at single subject level.Methodplasma NfL was assessed in a longitudinal study including 93 patients with Parkinson's disease and 27 patients with DLB who underwent an extensive motor and cognitive assessment and after 2 years of follow‐up. The study evaluated the correlation between NfL plasma levels and motor, non‐motor symptoms, cognitive and behavioral abnormalities in the two cohorts, as well as benignant/malignant phenotypes and motor/cognitive progression in PD after 2 years of follow‐up.ResultSerum NfL correlated with age and age at onset in the cohort. In DLB, NfL correlated with disease duration, hyposmia and neuropsychiatric symptoms, but not with motor function assessed by UPDRS‐III. We found no significant associations between NfL and disease progression in DLB patients. In PD, higher NfL levels correlated with hyposmia (p=0.01), total UPDRS‐II and UPDRS‐III scores (0.001), gait speed (0.04) and several disability milestones, including mild cognitive impairment (0.001), symptomatic dysautonomia (0.001), loss of independency in activities of daily living (p=0.01) and instrumental daily living (p=0.001). At two years of follow‐up, NfL was the best marker in multivariate regression analyses for both motor and cognitive progression beyond malignant/benignant phenotypes.ConclusionElevated serum NfL levels are associated with fast progression in PD patients and could thus represent target of interventions in specific subpopulation of patients

Acidic microenvironment plays a key role in human melanoma progression through a sustained exosome mediated transfer of clinically relevant metastatic molecules

Background: Microenvironment cues involved in melanoma progression are largely unknown. Melanoma is highly influenced in its aggressive phenotype by the changes it determinates in its microenvironment, such as pH decrease, in turn influencing cancer cell invasiveness, progression and tissue remodelling through an abundant secretion of exosomes, dictating cancer strategy to the whole host. A role of exosomes in driving melanoma progression under microenvironmental acidity was never described. Methods: We studied four differently staged human melanoma lines, reflecting melanoma progression, under microenvironmental acidic pHs pressure ranging between pH 6.0-6.7. To estimate exosome secretion as a function of tumor stage and environmental pH, we applied a technique to generate native fluorescent exosomes characterized by vesicles integrity, size, density, markers expression, and quantifiable by direct FACS analysis. Functional roles of exosomes were tested in migration and invasion tests. Then we performed a comparative proteomic analysis of acid versus control exosomes to elucidate a specific signature involved in melanoma progression. Results: We found that metastatic melanoma secretes a higher exosome amount than primary melanoma, and that acidic pH increases exosome secretion when melanoma is in an intermediate stage, i.e. metastatic non-invasive. We were thus able to show that acidic pH influences the intercellular cross-talk mediated by exosomes. In fact when exposed to exosomes produced in an acidic medium, pH naïve melanoma cells acquire migratory and invasive capacities likely due to transfer of metastatic exosomal proteins, favoring cell motility and angiogenesis. A Prognoscan-based meta-analysis study of proteins enriched in acidic exosomes, identified 11 genes (HRAS, GANAB, CFL2, HSP90B1, HSP90AB1, GSN, HSPA1L, NRAS, HSPA5, TIMP3, HYOU1), significantly correlating with poor prognosis, whose high expression was in part confirmed in bioptic samples of lymph node metastases. Conclusions: A crucial step of melanoma progression does occur at melanoma intermediate -stage, when extracellular acidic pH induces an abundant release and intra-tumoral uptake of exosomes. Such exosomes are endowed with pro-invasive molecules of clinical relevance, which may provide a signature of melanoma advancement