A practical methodology for reproducible experimentation: an application to the Double-row Facility Layout Problem.

Reproducibility of experiments is a complex task in stochastic methods such as evolutionary algorithms or metaheuristics in general. Many works from the literature give general guidelines to favor reproducibility. However, none of them provide both a practical set of steps and also software tools to help on this process. In this paper, we propose a practical methodology to favor reproducibility in optimization problems tackled with stochastic methods. This methodology is divided into three main steps, where the researcher is assisted by software tools which implement state-of-theart techniques related to this process. The methodology has been applied to study the Double Row Facility Layout Problem, where we propose a new algorithm able to obtain better results than the state-of-the-art methods. To this aim, we have also replicated the previous methods in order to complete the study with a new set of larger instances. All the produced artifacts related to the methodology and the study of the target problem are available in Zenodo.

Investigating the effect of 28 BRCA1 and BRCA2 mutations on their related transcribed mRNA.

Germline inactivating mutations in the BRCA1 and BRCA2 genes are responsible for hereditary breast and ovarian cancer syndrome (HBOCS). Genetic testing of these genes identifies a significant proportion of variants of uncertain significance (VUS). Elucidation of the clinical impact of these variants is an important challenge in genetic diagnostics and counseling. In this study, we assess the RNA effect of 28 BRCA1 and BRCA2 VUS identified in our set of HBOCS families with the aim of gaining insight into their clinical relevance. mRNA was extracted from VUS carriers and controls lymphocytes cultured for 5-6 days and treated with puromycin. RNA was reverse transcribed to perform transcriptional analysis for the study of splicing aberrations. In silico prediction tools were used to select those variants most likely to affect the RNA splicing process. Six out of the 28 variants analyzed showed an aberrant splicing pattern and could therefore be classified as probably pathogenic mutations. Reclassification of VUS improves the genetic counseling and clinical surveillance of carriers of these mutations and highlights the importance of RNA studies in routine diagnostic laboratories.

Identification of two novel KIF5A mutations in hereditary spastic paraplegia associated with mild peripheral neuropathy.

Spastic paraplegia type 10 (SPG10) is a rare form of autosomal dominant hereditary spastic paraplegia (AD-HSP) due to mutations in KIF5A, a gene encoding the neuronal kinesin heavy-chain involved in axonal transport. KIF5A mutations have been associated with a wide clinical spectrum, ranging from pure HSP to isolated peripheral nerve involvement or complicated HSP phenotypes. Most KIF5A mutations are clustered in the motor domain of the protein that is necessary for microtubule interaction. Here we describe two Spanish families with an adult onset complicated AD-HSP in which neurological studies revealed a mild sensory neuropathy. Intention tremor was also present in both families. Molecular genetic analysis identified two novel mutations c.773 C>T and c.833 C>T in the KIF5A gene resulting in the P258L and P278L substitutions respectively. Both were located in the highly conserved kinesin motor domain of the protein which has previously been identified as a hot spot for KIF5A mutations. This study adds to the evidence associating the known occurrence of mild peripheral neuropathy in the adult onset SPG10 type of AD-HSP.

The transmembrane activator TACI triggers immunoglobulin class switching by activating B cells through the adaptor MyD88.

BAFF and APRIL are innate immune mediators that trigger immunoglobulin G (IgG) and IgA class-switch recombination (CSR) in B cells by engaging the receptor TACI. The mechanism that underlies CSR signaling by TACI remains unknown. Here we found that the cytoplasmic domain of TACI encompasses a conserved motif that bound MyD88, an adaptor that activates transcription factor NF-kappaB signaling pathways via a Toll-interleukin 1 (IL-1) receptor (TIR) domain. TACI lacks a TIR domain, yet triggered CSR via the DNA-editing enzyme AID by activating NF-kappaB through a Toll-like receptor (TLR)-like MyD88-IRAK1-IRAK4-TRAF6-TAK1 pathway. TACI-induced CSR was impaired in mice and humans lacking MyD88 or the kinase IRAK4, which indicates that MyD88 controls a B cell-intrinsic, TIR-independent, TACI-dependent pathway for immunoglobulin diversification.

Laparoscopic duodenal-jejunal exclusion in the treatment of type 2 diabetes mellitus in patients with BMI<30 kg/m2 (LBMI).

BACKGROUND: The association between medical and dietetic-behavioral treatments of type 2 diabetes mellitus (T2DM) has demonstrated to have variable results. The surgical treatment of T2DM is justifiable after the observation of a successful glycemic control in patients submitted to Roux-en-Y gastric bypass and biliopancreatic diversion. Experiments have shown an important role of the proximal intestine in glycemia decrease and diabetes control. METHODS: Twenty diabetic patients underwent laparoscopic duodenal-jejunal exclusion. The variables studied were body mass index (BMI), fasting glycemia, glycosylated hemoglobin (HbA1c), and C-peptide, in the preoperative period and after 3 and 6 months. RESULTS: There was a BMI decrease up to the third month and a weight stabilization between the third and sixth months. There was a significant reduction in fasting glycemia (43.8%) and HbA1c (22.8%) up to the sixth month (p<0.001). C-peptide did not show any significant alteration until the third month, although there was a considerable increase (25%) between the third and the sixth months (p<0.001). Only two patients were on oral medication after the sixth month. CONCLUSIONS: Preliminary results have shown an important effect of the laparoscopic duodenal-jejunal exclusion in the treatment of T2DM. Studies with longer follow-up and a larger number of patients are necessary to better define the role of this new and promising procedure.

SR proteins and the nonsense-mediated decay mechanism are involved in human GLB1 gene alternative splicing.

BACKGROUND: The human GLB1 gene is known to give rise to two alternatively spliced mRNAs, which encode two different proteins: lysosomal beta-galactosidase (beta-gal) and elastin-binding protein (EBP). The beta-gal transcript includes the 16 exons of the GLB1 gene. In the EBP transcript, exons 3, 4 and 6 are skipped, while exon 5 has a different reading frame. However, little is known on how this alternative splicing is regulated. FINDINGS: Cycloheximide treatment of HeLa cells and human fibroblasts revealed the presence of new transcripts that are otherwise degraded by nonsense-mediated decay (NMD). A minigene carrying the exons involved in the alternative splicing of GLB1 was constructed. Improving the acceptor-site scores of exons 3 or 4 increased the relative inclusion of these exons, but did not stop them being skipped in some transcripts. Overexpression of different SR proteins altered the relative proportion of the different transcripts produced by the minigene, indicating a possible mechanism for the regulation of the alternative splicing of GLB1. Finally, a comparison of this gene among different species was performed. CONCLUSION: In the processing of the GLB1 RNA several transcripts are generated, but only those with a correct reading frame are not degraded. The differential inclusion/exclusion of exons could be partially explained by the relatively weak splice sites in the exons involved. Different SR proteins have an effect on the process of skipping of these exons, at least in the minigene conditions, indicating a possible mechanism for the regulation of the alternative splicing of the GLB1 gene.

Haplotype analysis suggests a single Balkan origin for the Gaucher disease [D409H;H255Q] double mutant allele.

Gaucher disease is an autosomal recessive lysosomal storage disease that is mainly due to mutations in the GBA gene. Most of the mutant alleles described so far bear a single mutation. However, there are a few alleles bearing two or more DNA changes. It has been reported that patients homozygous for the [D409H;H255Q] double mutant allele (HGVS-approved nomenclature, p.[D448H;H294Q]) present a more severe phenotype than patients homozygous for the relatively common D409H mutation. In this study, we confirmed the detrimental cumulative effect of these two mutations at the enzymatic activity level by the heterologous expression of the single and double mutant alleles. Additionally, we found a high frequency of the [D409H;H255Q] allele in patients from the Balkans and the Adriatic area of Italy. This prompted us to perform a haplotype analysis, using five microsatellite polymorphisms close to the GBA gene, to determine the origin of this allele. The results of the 37 chromosomes analysed showed that most of them share a common haplotype and are consistent with a single origin in the Balkans and the Adriatic area of Italy for the [D409H;H255Q] allele.

Serial magnetic resonance imaging and neurophysiological studies in multiple sulphatase deficiency.

We present serial clinical, magnetic resonance imaging (MRI) and neurophysiological findings of a patient with multiple sulphatase deficiency (MSD), who was first admitted at the age of 9 months, because of psychomotor retardation. MRI demonstrated extensive diffuse symmetrical high signal in the deep white matter of both cerebral hemispheres, as well as of the subcortical white matter and the brainstem, while there was additional enlargement of sulci and subdural spaces and mild atrophy. Assay of arylsulphatase A activity in white blood cell homogenates at the age of 29 months disclosed a marked deficiency of the enzyme, compatible with the diagnosis of early-infantile metachromatic leukodystrophy. During the course of a later admission, the presence of ichthyosis pointed out to the possible diagnosis of MSD; further assays of sulphatases in plasma, leukocytes as well as in cultured fibroblasts, combined with an abnormal excretion of mucopolysaccharides and sulphatides in urine confirmed the diagnosis. Molecular analysis identified a homozygous disease-causing mutation (R349W) of the SUMF1 gene. Serial neurophysiological and MRI studies demonstrated the progressive nature of the disorder (regarding both central and peripheral nervous system), correlating with the clinical deterioration (spastic quadriplegia, optic atrophy and epilepsy) with subsequent death at the age of 4 years.

Expression and characterization of 14 GLB1 mutant alleles found in GM1-gangliosidosis and Morquio B patients.

GM1-gangliosidosis and Morquio B disease are lysosomal storage disorders caused by beta-galactosidase deficiency attributable to mutations in the GLB1 gene. On reaching the endosomal-lysosomal compartment, the beta-galactosidase protein associates with the protective protein/cathepsin A (PPCA) and neuraminidase proteins to form the lysosomal multienzyme complex (LMC). The correct interaction of these proteins in the complex is essential for their activity. More than 100 mutations have been described in GM1-gangliosidosis and Morquio B patients, but few have been further characterized. We expressed 12 mutations suspected to be pathogenic, one known polymorphic change (p.S532G), and a variant described as either a pathogenic or a polymorphic change (p.R521C). Ten of them had not been expressed before. The expression analysis confirmed the pathogenicity of the 12 mutations, whereas the relatively high activity of p.S532G is consistent with its definition as a polymorphism. The results for p.R521C suggest that this change is a low-penetrant disease-causing allele. Furthermore, the effect of these beta-galactosidase changes on the LMC was also studied by coimmunoprecipitations and Western blotting. The alteration of neuraminidase and PPCA patterns in several of the Western blotting analyses performed on patient protein extracts indicated that the LMC is affected in at least some GM1-gangliosidosis and Morquio B patients.

Twenty-one novel mutations in the GLB1 gene identified in a large group of GM1-gangliosidosis and Morquio B patients: possible common origin for the prevalent p.R59H mutation among gypsies.

GM1-gangliosidosis and Morquio B disease are rare lysosomal storage disorders caused by beta-galactosidase deficiency due to mutations in the GLB1 gene. Three major clinical forms of GM1-gangliosidosis have been established on the basis of age of onset and severity of symptoms: infantile, late infantile/juvenile, and adult. We performed mutation analysis on 30 GM1-gangliosidosis and five Morquio B patients, mainly of Spanish origin, and all the causative mutations were identified. Thirty different mutations were found, 21 of which were novel. With the exception of two adults and one juvenile patient, all the GM1-gangliosidosis patients were affected by the infantile form. Clinical findings are presented for all patients. We report the association of the novel mutations p.T420K and p.L264S with the adult form and the juvenile form, respectively. In addition, the novel mutation p.Y83C was associated with Morquio B disease. Among the 30 GM1-gangliosidosis patients, 6 were of Gypsy origin (Roma). Moreover, those six Gypsy patients shared not only the same mutation (p.R59H) but also a common haplotype. This observation indicates a possible founder effect in this group and suggests that screening of the p.R59H mutation may be appropriate in GM1-gangliosidosis patients of Gypsy origin. This is the first exhaustive mutational analysis performed in a large group of Iberian GM1-gangliosidosis and Morquio B patients.

Homozygosity for the double D409H+H255Q allele in type II Gaucher disease.

Homozygosity for D409H has been associated with a unique type III subtype of the disease with a phenotype dominated by severe cardiovascular involvement, whereas neurological findings, if present, are restricted to oculomotor apraxia and features such as visceromegaly are either minimal or absent. Using PCR amplification followed by restriction enzyme analysis, 3 patients (1 Greek, 2 Albanians) were IDentified with the D409H/D409H genotype. All shared a very severe early-onset neurological phenotype that classified them as type II. Amplification and sequencing of the full coding region of the GBA gene revealed that all three patients were homozygous not only for D409H but also for H255Q. Both mutations were present on the same allele, as shown by analysis of the parental DNA. The double D409H+H255Q allele was found in heterozygosity in Greek, Bulgarian and Argentinian patients but was not IDentified in any Spanish patients carrying the D409H mutation.

Clinical and mutational characterization of three patients with multiple sulfatase deficiency: report of a new splicing mutation.

Multiple sulfatase deficiency (MSD) is a rare autosomal recessive lysosomal storage disease characterized by impaired activity of all known sulfatases. The gene SUMF1, recently identified, encodes the enzyme responsible for post-translational modification of a cysteine residue, which is essential for the activity of sulfatases. Fewer than 30 MSD patients have been reported to date and 23 different mutations in the SUMF1 gene have been identified. Here, we present the characterization of the mutant alleles of two Spanish and one Argentinean MSD patients. While the two Spanish patients were homozygous for the previously described mutations, c.463T>C (p.S155P) and c.1033C>T (p.R345C), the Argentinean patient was homozygous for the new mutation IVS7+5 G>T. A minigene approach was used to analyze the effect of the splice site mutation identified, due to the lack of sample from the patient. This experiment showed that this change altered the normal splicing of the RNA, which strongly suggests that this is the molecular cause of the disease in this patient.

Perinatal lethal phenotype with generalized ichthyosis in a type 2 Gaucher disease patient with the [L444P;E326K]/P182L genotype: effect of the E326K change in neonatal and classic forms of the disease.

Gaucher disease, the most common lysosomal storage disorder, encompasses a wide spectrum of clinical symptoms. The perinatal lethal form is very rare and is considered a distinct form of classic type 2 Gaucher disease. Prominent features of the severe perinatal form are hepatosplenomegaly variable, associated with hydrops fetalis and ichthyosis. Here, we describe a child who presented generalized ichthyosis and died at 25 days of age. Genotype analysis revealed compound heterozygosity for the complex allele [L444P;E326K] and mutation P182L, described for the first time in this patient. Mutations E326K and L444P were on the same chromosome. Expression studies of mutant glucocerebrosidases showed that the double mutant allele had lower activity, 8.5% of wild type, in contrast to the activity of individual E326K and L444P mutant enzymes, 42.7% and 14.1%, respectively. The P182L mutant enzyme showed no glucocerebrosidase activity. A revision of the genotypes identified in a series of Spanish patients with type 2 Gaucher disease showed that the complex allele [L444P;E326K] accounted for 19.2% of patient alleles and that homozygosity for this allele or its heterozygosity with mutation L444P, or another severe mutation such as P182L, was associated with the perinatal lethal presentation of the disease. In contrast, the [L444P;E326K] allele was not detected in patients with classic type 2 diagnosed when several months old. The high frequency of the E326K substitution observed in patients with type 2 as compared to the general population (0.5%) suggests that this change may have a modulating negative effect on the clinical condition of these Gaucher disease patients when present in combination with mutation L444P. The relatively high prevalence of the double mutant allele in Spanish patients prompted us to perform a haplotype analysis, using four polymorphic markers, which suggest a common origin for this allele. During the mutational analysis of the series of type 2 patients, a novel mutation, I260T (c.896T>C), was identified.

A mutation within the saposin D domain in a Gaucher disease patient with normal glucocerebrosidase activity.

Only two Gaucher disease (GD) patients bearing mutations in the prosaposin gene (PSAP), and not in the glucocerebrosidase gene (GBA), have been reported. In both cases, one mutant allele remained unidentified. We report here the identification of the second mutation in one of these patients, being the first complete genotype described so far in a SAP-C-deficient GD patient. This mutation, p.Q430X, is the first one reported in the saposin D domain and probably produces a null allele by nonsense mediated mRNA decay.

Compostado de la cascara del girasol: una experiencia piloto

Una experiencia piloto sobre el compostado de la cascara del girasol se ha llevado a cabo en el Depto de Agronomia , de la Universidad del Sur de la ciudad de Bahia Blanca, con el fin de darle una alternativa diferente a la disposicion final de este residuo y un valor agregado al mismo, de manera que se convierta en un recurso agricola para ser utilizado en el suelo como enmineda organica. En el presente trabajo se demuestra que a traves de un proceso sencillo como el compostado, es posible transformar a la cascara del girasol de residuo a subproducto

Compostado de la cascara del girasol: una experiencia piloto

Una experiencia piloto sobre el compostado de la cascara del girasol se ha llevado a cabo en el Depto de Agronomia , de la Universidad del Sur de la ciudad de Bahia Blanca, con el fin de darle una alternativa diferente a la disposicion final de este residuo y un valor agregado al mismo, de manera que se convierta en un recurso agricola para ser utilizado en el suelo como enmineda organica. En el presente trabajo se demuestra que a traves de un proceso sencillo como el compostado, es posible transformar a la cascara del girasol de residuo a subproducto