mebipred: identifying metal-binding potential in protein sequence.

MOTIVATION: metal-binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal-binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal-binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability. RESULTS: we developed a novel machine learning-based method, mebipred, for identifying metal-binding proteins from sequence-derived features. This method is over 80% accurate in recognizing proteins that bind metal ion-containing ligands; the specific identity of 11 ubiquitously present metal ions can also be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and is thus faster than alignment-based methods; it is also more accurate than other sequence-based prediction methods. Additionally, mebipred can identify protein metal-binding capabilities from short sequence stretches, e.g. translated sequencing reads, and, thus, may be useful for the annotation of metal requirements of metagenomic samples. We performed an analysis of available microbiome data and found that ocean, hot spring sediments and soil microbiomes use a more diverse set of metals than human host-related ones. For human microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal-binding proteins. These results highlight mebipred's utility in analyzing microbiome metal requirements. AVAILABILITY AND IMPLEMENTATION: mebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Chinaberry tree (Melia azedarach) poisoning in dog: a case report.

This article describes a case of Chinaberry tree poisoning diagnosed in a dog. The initial clinical signs were variable and included tremors (muscular seizures) and a moderate limp in the dog's back leg, which evolved to a more severe condition in the following hours. Abdominal radiographic evaluation was requested, and abundant small, foreign, radio-dense bodies were detected, which were associated with Chinaberry tree fruits after surgical extraction. Adequate treatment was established, and the patient recovered completely. In addition, we compare clinical and gross postmortem findings in other similar cases reported in the literature. There is a general lack of information of such poisoning in pets.

[Spinal cord infarction and recurrent venous thrombosis in association with estrogens and the 20210A allele of the prothrombin gene]. / Mielopatía aguda isquémica y trombosis venosa recurrente asociada a estrógenos y alelo 20210A del gen de la protrombina.

The acute spinal cord infarction is a rare cause of acute-onset paraplegia. Furthermore, it is specially uncommon that the infarction occurs in patients with apparent low predisposition to vascular disease. The 20210A allele of the prothrombin gene (causing a threefold-increased risk in venous thromboembolism) was recently associated with unexplained spinal cord infarction in young women under treatment with estrogens (contraceptive pill). We report a case of anterior spinal artery syndrome resulting from an ischaemic infarction at the anterior aspect of the spinal cord in a healthy 50-year-old woman, carrying this mutation, being the first published case under treatment with transdermal estradiol. She referred the typical sudden-onset back pain associated to clinical anterior spinal artery syndrome with sphincter dysfunction and nontraumatic paraplegia. A possible multiple sclerosis was ruled out and the steroids or immunoglobulin therapy induced no clinical improvement. Cerebrospinal fluid and other investigations were all negative. Sequential MRI scans revealed development of spinal cord infarction from T10 to T11, with increased signal in T2-weighted image (T2). Because she referred a previous thrombophlebitis and suffered a deep-vein thrombosis one month after paraplegia, a complete coagulation study was performed. Antithrombin, proteins C and S, homocysteine, factor V Leiden, lupus anticoagulant and anticardiolipin antibodies were all normal or negatives. In opposite, the 20210A variation was positive (heterozygous) and the factor VIIIc level was very high (280 U/dl eight months later). We argue the relative importance of both findings. The patient had no a substantial recovery over a period of 20 months.Certainly, the prothrombin 20210A seems to be associated with unexplained ischemic myelopathy among the young women with estrogens.

Mielopatía aguda isquémica y trombosis venosa recurrente asociada a estrógenos y alelo 20210a del gen de la protrombina / Spinal cord infarction and recurrent venous thrombosis in association with estrogens and the 20210A allele of the prothrombin gene

El infarto de médula espinal es una causa infrecuente de paraplejía de instauración brusca. Su presentación en sujetos con bajo riesgo vascular resulta especialmente inexplicable. El alelo 20210A del gen de la protrombina (que triplica el riesgo de tromboembolismo venoso) fue asociado recientemente con infarto medular en mujeres jóvenes expuestas a estrógenos (píldora anticonceptiva).Referimos un caso de síndrome de arteria espinal anterior con infarto que afecta a los cordones anteriores en una mujer sana de 50 años portadora de esta variante genética, el primero publicado bajo tratamiento con estradiol transdérmico. La paciente refería la típica dorsalgia de comienzo súbito asociada a paraplejia atraumática y disfunción de esfínteres. Se descartó esclerosis múltiple, resultando ineficaces los corticoides y las inmunoglobulinas. El examen del LCR fue negativo. La imagen de resonancia magnética fue compatible con infarto (de astas anteriores) desde D10 a D11, con señal hiperintensa en T2.Por sus antecedentes de tromboflebitis y la aparición de una trombosis venosa profunda un mes después se le practicó estudio completo de trombofilia. La determinación de antitrombina, proteínas C y S, homocisteína, factor V Leiden, anticoagulante lúpico y anticuerpos anticardiolipina fue normal o negativa. Sin embargo, la paciente expresaba la variante 20210A del gen de la protrombina en estado heterozigoto y valores persistentemente elevados de factor VIIIc (8 meses después, 280 U/dl). Se discute la posible implicación de ambos hallazgos. La paciente no experimentó recuperación tras un período de 20 meses. Concluimos que la protrombina 20210A parece asociada a mielopatía isquémica escasamente explicada en mujeres jóvenes que reciben estrógenos (AU)

Distinctive cognate sequence discrimination, bound DNA conformation, and binding modes in the E2 C-terminal domains from prototype human and bovine papillomaviruses.

The C-terminal DNA binding domain of the E2 protein is involved in transcriptional regulation and DNA replication in papillomaviruses. At low ionic strength, the domain has a tendency to form aggregates, a process readily reversible by the addition of salt. While fluorescence anisotropy measurements show a 1:1 stoichiometry at pH 5.5, we observed that a second HPV-16 E2 C-terminal dimer can bind per DNA site at pH 7.0. This was confirmed by displacement of bis-ANS binding, tryptophan fluorescence, native electrophoresis, and circular dichroism. The two binding events are nonequivalent, with a high-affinity binding involving one E2C dimer per DNA molecule with a K(D) of 0.18 +/- 0.02 nM and a lower affinity binding mode of 2.0 +/- 0.2 nM. The bovine (BPV-1) E2 C-terminal domain binds to an HPV-16 E2 site with 350-fold lower affinity than the human cognate domain and binds 7-fold less tightly even to a bovine-derived DNA site. The ability to discriminate between cognate and noncognate sequences is 50-fold higher for the human domain, and the latter is 180-fold better than the bovine at discriminating specific from nonspecific DNA. A substantial conformational change in bound DNA is observed by near-UV circular dichroism. The bovine domain imposes a different DNA conformation than that caused by the human counterpart, which could be explained by a more pronounced bent. Structure-function differences and biochemical properties of the complexes depend on the protein domain rather than on the DNA, in line with crystallographic evidence. Despite the strong sequence homology and overall folding topology, the differences observed may explain the distinctive transcriptional regulation in bovine and human viruses.

Expression and biochemical characterisation of recombinant AceA, a bacterial alpha-mannosyltransferase.

Biosynthesis of repeat-unit polysaccharides and N-linked glycans proceeds by sequential transfer of sugars from the appropriate sugar donor to an activated lipid carrier. The transfer of each sugar is catalysed by a specific glycosyltransferase. The molecular basis of the specificity of sugar addition is not yet well understood, mainly because of the difficulty of isolating these proteins. In this study, the aceA gene product expressed by Acetobacter xylinum, which is involved in the biosynthesis of the exopolysaccharide acetan, was overproduced in Escherichia coli and its function was characterised. The aceA ORF was subcloned into the expression vector pET29 in frame with the S.tag epitope. The recombinant protein was identified, and culture conditions were optimised for production of the soluble protein. The results of test reactions showed that AceA is able to transfer one alpha-mannose residue from GDP-mannose to cellobiose-P-P-lipid to produce alpha-mannose-cellobiose-P-P-lipid. AceA was not able to use free cellobiose as a substrate, indicating that the pyrophosphate-lipid moiety is needed for enzymatic activity.

[Haemophilus influenzae type B meningitis: typical and atypical presentation]. / Meningitis por Haemophilus influenzae tipo B: presentación típica y atípica.

We present 2 cases of Haemophilus influenzae meningitis. The first is a patient with atypical simptomatology: abdominal pain, fever and two days later pain in the back of his legs. Abdominal pathology was not found. The cerebrospinal fluid (CSF) showed polymorphonuclear cells, hyperproteinorachia and lowered glucose. CSF culture revealed Haemophilus influenzae, blood culture was sterile. The second had suffered surgery at maxilar and ethmoid sinuses four years before, and unknown germ meningitis 6 months before. Haemophilus influenzae was isolated from CSF cultures and CSF rhinorrhea was detected by isotopic cisternography.

Xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence.

Xanthan is an industrially important exopolysaccharide produced by the phytopathogenic, gram-negative bacterium Xanthomonas campestris pv. campestris. It is composed of polymerized pentasaccharide repeating units which are assembled by the sequential addition of glucose-1-phosphate, glucose, mannose, glucuronic acid, and mannose on a polyprenol phosphate carrier (L. Ielpi, R. O. Couso, and M. A. Dankert, J. Bacteriol. 175:2490-2500, 1993). A cluster of 12 genes in a region designated xpsI or gum has been suggested to encode proteins involved in the synthesis and polymerization of the lipid intermediate. However, no experimental evidence supporting this suggestion has been published. In this work, from the biochemical analysis of a defined set of X. campestris gum mutants, we report experimental data for assigning functions to the products of the gum genes. We also show that the first step in the assembly of the lipid-linked intermediate is severely affected by the combination of certain gum and non-gum mutations. In addition, we provide evidence that the C-terminal domain of the gumD gene product is sufficient for its glucosyl-1-phosphate transferase activity. Finally, we found that alterations in the later stages of xanthan biosynthesis reduce the aggressiveness of X. campestris against the plant.