Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER

Structure predictions have matched the accuracy of experimental structures from close homologues, providing suitable models for molecular replacement phasing. Even in predictions that present large differences due to the relative movement of domains or poorly predicted areas, very accurate regions tend to be present. These are suitable for successful fragment-based phasing as implemented in ARCIMBOLDO. The particularities of predicted models are inherently addressed in the new predicted_model mode, rendering preliminary treatment superfluous but also harmless. B-value conversion from predicted LDDT or error estimates, the removal of unstructured polypeptide, hierarchical decomposition of structural units from domains to local folds and systematically probing the model against the experimental data will ensure the optimal use of the model in phasing. Concomitantly, the exhaustive use of models and stereochemistry in phasing, refinement and validation raises the concern of crystallographic model bias and the need to critically establish the information contributed by the experiment. Therefore, in its predicted_model mode ARCIMBOLDO_SHREDDER will first determine whether the input model already constitutes a solution or provides a straightforward solution with Phaser. If not, extracted fragments will be located. If the landscape of solutions reveals numerous, clearly discriminated and consistent probes or if the input model already constitutes a solution, model-free verification will be activated. Expansions with SHELXE will omit the partial solution seeding phases and all traces outside their respective masks will be combined in ALIXE, as far as consistent. This procedure completely eliminates the molecular replacement search model in favour of the inferences derived from this model. In the case of fragments, an incorrect starting hypothesis impedes expansion. The predicted_model mode has been tested in different scenarios.

Serial macromolecular crystallography at ALBA Synchrotron Light Source. Erratum

A revised version of Table 2 of Martin-Garcia et al. [J. Synchrotron Rad. (2022). 29, 896-907] is provided.

Serial macromolecular crystallography at ALBA Synchrotron Light Source

The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In this work, we report the first SSX experiments with viscous jets conducted at ALBA beamline BL13-XALOC. Small crystals (15-30 µm) of five soluble proteins (lysozyme, proteinase K, phycocyanin, insulin and α-spectrin-SH3 domain) were suspended in lipidic cubic phase (LCP) and delivered to the X-ray beam with a high-viscosity injector developed at Arizona State University. Complete data sets were collected from all proteins and their high-resolution structures determined. The high quality of the diffraction data collected from all five samples, and the lack of specific radiation damage in the structures obtained in this study, confirm that the current capabilities at the beamline enables atomic resolution determination of protein structures from microcrystals as small as 15 µm using viscous jets at room temperature. Thus, BL13-XALOC can provide a feasible alternative to X-ray free-electron lasers when determining snapshots of macromolecular structures.

Structural and biochemical evidence that ATP inhibits the cancer biomarker human aldehyde dehydrogenase 1A3

Human aldehyde dehydrogenase (ALDH) participates in the oxidative stress response and retinoid metabolism, being involved in several diseases, including cancer, diabetes and obesity. The ALDH1A3 isoform has recently elicited wide interest because of its potential use as a cancer stem cell biomarker and drug target. We report high-resolution three-dimensional ALDH1A3 structures for the apo-enzyme, the NAD⁺ complex and a binary complex with ATP. Each subunit of the ALDH1A3-ATP complex contains one ATP molecule bound to the adenosine-binding pocket of the cofactor-binding site. The ATP complex also shows a molecule, putatively identified as a polyethylene glycol aldehyde, covalently bound to the active-site cysteine. This mimics the thioacyl-enzyme catalytic intermediate, which is trapped in a dead enzyme lacking an active cofactor. At physiological concentrations, ATP inhibits the dehydrogenase activity of ALDH1A3 and other isoforms, with a K_i value of 0.48 mM for ALDH1A3, showing a mixed inhibition type against NAD⁺. ATP also inhibits esterase activity in a concentration-dependent manner. The current ALDH1A3 structures at higher resolution will facilitate the rational design of potent and selective inhibitors. ATP binding to ALDH1A3 enables activity modulation by the energy status of the cell and metabolic reprogramming, which may be relevant in several disease conditions.

Three X-ray structures are presented of human aldehyde dehydrogenase family 1 member A3 (ALDH1A3), a potential cancer stem cell biomarker (alone, with NAD+ and with ATP) and structure determination performed using molecular replacement.

Improving data quality and expanding BioSAXS experiments to low-molecular-weight and low-concentration protein samples

The addition of compounds to scavenge the radical species produced during biological small-angle X-ray scattering (BioSAXS) experiments is a common strategy to reduce the effects of radiation damage and produce better quality data. As almost half of the experiments leading to structures deposited in the SASBDB database used scavengers, finding potent scavengers would be advantageous for many experiments. Here, four compounds, three nucleosides and one nitrogenous base, are presented which can act as very effective radical-scavenging additives and increase the critical dose by up to 20 times without altering the stability or reducing the contrast of the tested protein solutions. The efficacy of these scavengers is higher than those commonly used in the field to date, as verified for lysozyme solutions at various concentrations from 7.0 to 0.5 mg ml^-1. The compounds are also very efficient at mitigating radiation damage to four proteins with molecular weights ranging from 7 to 240 kDa and pH values from 3 to 8, with the extreme case being catalase at 6.7 mg ml^-1, with a scavenging factor exceeding 100. These scavengers can therefore be instrumental in expanding BioSAXS to low-molecular-weight and low-concentration protein samples that were previously inaccessible owing to poor data quality. It is also demonstrated that an increase in the critical dose in standard BioSAXS experiments leads to an increment in the retrieved information, in particular at higher angles, and thus to higher resolution of the model.

[Laparoscopy in chronic abdominal pain in children]

The recurrent chronic abdominal pain (RAP) is one of the most usual pathologies in pediatrics. It may appear in the form of periodical or continuous sharp crisis. In order to be accepted as chronic, the presence of this pain must last at least 3 months. In many of the reference publications, only between 5 and 1% of the cases are considered to have an organic ethiology and the rest are labelled as functional processes of psychological origin. The reason for our communication is to show our experience on 304 RAP patients from 1995 to 2001. We also want to highlight the usefulness of laparoscopy in order to diagnose and treat 14.45% (44) of cases of this group of patients.

MATERIAL AND METHODOLOGY

304 patients between 5 and 14 years old were studied from 1995 to 2001. We followed a protocol of: medical and personal medical record, specific anamnesis for RAP, detailed description of the diet and intestinal habits, physical exploration. Laboratory: 1) blood analysis, hepatic profile, glucose, cholesterol, creatinine, amylase, 2) urine sediment and may be urine culture, 3) faeces analysis and 4) vaginal flow analysis. Image diagnosis is: simple abdomen radiography, ultrasonography and intestinal Rx. Guided and specific determinations: spired urea test, gastric chemism, lactose test, gastroscopy and biopsy, colonoscopy and biopsy, laparoscopy.

RESULTS

In short, we can say: 74 patients (23.4%) come with inappropiate feeding diets, 31 (10.1%) with helicobacter pilori, 20 (6.5%) with adenoids, pharynx and pharyngeal processes, the same figure from gynaecologic origin, 18 (5.9%) from psychological origin, and in 44 cases (14.45%) laparoscopy was indicated.

CONCLUSIONS

The anatomopathological study in the cases in which we carried out laparoscopic appendicectomy does not allow us to accept the symptoms of chronic appendicitis. The exploratory laparoscopy and the appendectomy have meant benefits for the solution to this pathology in 14.45% of patients. It is essential to carry out a long-term follow-up, at least 12 months, to be sure RAP is cured. We must carry on looking for aetiological cause of RAP.

[Surgical treatment of a pheocromocytoma bilateral in a 5 year old patient with the von Hippel-Lindau disease]

INTRODUCTION

The disease of Von Hippel Lindau (VHL) is hereditary and causes a predisposition to the development of tumours. Organs such as the cerebellum, the pancreas, the kidney, the suprarenal glands and the retina are more usually affected by this disease.

CLINICAL CASE

We present the case of a 5-year-old patient who suffers from asiymptomatic high blood pressure. In the family antecedents, it is relevant the case of the father, with pheocromocytoma bilateral, which led us to carry out a genetic study of his two sons. Our patient, the younger; presented a mutation of the VHL gene in the short arm of the chromosome 3. In one of the periodic controls, it could be detected high blood pressure of 160/100 mm. Hg, clinically asymptomatic. The other child did not present a genetic mutation and has no disease. The presence of high catecholamines, the detection of a 3 cm left suprarenal mass through the ecography, the TAC that did not show a right suprarenal pathology and the MBIG scintigraphy confirmed the diagnostic of pheocromocytoma. The RNM showed another 0.8-cm mass which confirmed a pheocromocytoma bilateral. We started the treatment against high blood pressure with fenoxibenzamine and diltiazem, and we controlled this problem. We also prepared the pre-and-post operation anesthetic strategy, which is so important for the surgical success. The operation started by a laparoscopic, we made left adrenalectomy and we had to reconvert to laparotomy to make partial right adrenalectomy. Six months after the operation, the patient is free from symptomatology and follows a treatment with glucocorticoides with smaller and smaller doses.

COMMENTS

The case is exceptional because it embodies the following characteristics: early diagnostic age, family affectation and discovery of asymptomatic high blood pressure. It needed an appropriate preanesthetic and anesthetic preparation, which gave way to an operation without complications. The postoperation was also stable and presented no complications.

[Intestinal myopathy in Steinert's disease]

The myothonic dystrophy or Steinert's disease is a congenital, autosomal, dominant disorder which seriously affects the striated muscle and also to a certain extent, several organs and systems and on rare occasions, the intestinal smooth muscle. In the case, we treated a four years old girl in whom Steinert's disease was diagnosed when she was born and who developed the characteristics of severe constipation after a few months of life. The ano-rectal manometry showed a paradoxical reaction of external Sphincter with a normal inhibitory reflex. The rectal biopsy revelated a miophathy which affected the muscularis propia with the normal neuronal innervation. The X-ray studies showed that motility disorder was stopped in the distal area of the left colon. A colostomy in the healthy zone worked extremely well. Six months later, the normal colon was brought down retro-rectal. Only a partial incontinence remained in the external sphincter caused by Steinert's disease. The interest of this case lies in the pathological association, striade muscle and smooth muscle, in such an early age of life. It is a new contribution to the complex chapter of the intestinal pseudo-obstruction.

Usefulness of urinary antigen detection by an immunochromatographic test for diagnosis of pneumococcal pneumonia in children

We evaluated an immunochromatographic assay detecting pneumococcal antigen in urine samples from children diagnosed with pneumococcal pneumonia. The sensitivity and specificity of the immunochromatographic test with nonconcentrated urine (NCU) were 86.7 and 62.9%, respectively; with concentrated urine (CU), they were 100 and 11.7%, respectively. Pneumococcal antigen was also detected in 42.5% of NCU and 87.1% of CU samples from nasopharyngeal carriers. This is a nonspecific test for the diagnosis of pneumococcal pneumonia in children, particularly the very young.

[Usefulness of transrectal ultrasonography in the diagnosis of anomalies of intersexual conditions]

INTRODUCTION

Between the external genital exploration and the internal genital direct vision, through laparoscopia, there is a black point which is the pelvic floor; we have to know whether there is a vagina or not, what it is like and where it arrives at. The reason for this research is to present our experience with the transrectal ecography, which allows us a very good exploration of the pelvic floor.

MATERIAL AND METHODS

We present 6 patients, the youngest is 16 months old and the oldest is 19 years old, who have a diagnostic of 3 congenital adrenal hyperplasia (HSC), 2 gonadal dysgenesis and 1 vaginal agenesis (S. Rokitanski). Under sedation, we carried out a transrectal ecography with Aloka SSD650 ecograph and 7.5 MHz vaginal scanner. Ultrasone.

RESULTS

In case of HSC (16 months old), the transrectal ecography showed the vaginal arrival at the urethra and we were able to measure the distance from the external sphincter. In the other two HSC, which had been surgically corrected, the transrectal ecography clearly showed the vagina (length and calibre). In the two gonadal dysgenesis (two 11-and-19-year-old sisters, the first of whom had undergone vulvo-vaginoplasty, we appreciated the length of the vagina and, in the case of the sister with a relatively normal vagina, we confirmed the presence of the vagina connected to the uterus. In the vaginal agenesis, in which a neovagina with amnion membrane had been carried out, which, in its turn, ended in a situation of hematometra due to a stenosis, the transrectal ecography was really helpful to obtain vaginal dilatations.

CONCLUSIONS

Ecography is an easily available technique and provides both through and detailed information of the genital structures going through the pelvic floor, a zone which is otherwise difficult to explore. It was done under sedation for the patient's age and idiosyncrasy. The experience has just started but we are sure that in the future it will replace the genitograma.

[Radio-guided surgery with MIBG in a case of abdominal neuroblastoma]

Radio-guided surgery is a new technique which can provide benefits for pediatric oncology, as in our patient with neuroblastoma in stage IV, that after a chemotherapy, surgical, radiotherapy and autologous bone marrow transplant treatment kept showing, at 2 years, residual tumoral fragments and increase of catecholamines. Radio-guided surgery allowed an easy and exact location. This technique decreases surgery time and let us find residual tumoral tissue no matter how small. With radio-guided surgery we can obtain higher survival and even cure the patient.

Apolipoprotein(B) identifies dyslipidemic phenotypes associated with cardiovascular risk in normocholesterolemic type 2 diabetic patients

OBJECTIVE

Apolipoprotein(B) [apo(B)] reflects the total mass of atherogenic particles (VLDL, IDL, and LDL), and its increase is associated with cardiovascular disease independently of LDL cholesterol (LDLc) levels. Apo(B) determination has been recently standardized, but attention to regional reference limits is advisable. Our aim was to analyze the frequency of dyslipidemic phenotypes, including those dependent on increased apo(B) in normocholesterolemic type 2 diabetic patients.

RESEARCH DESIGN AND METHODS

A total of 100 consecutively seen type 2 diabetic patients (63 men, 37 women; aged 59 +/- 11 years) were included, after excluding those on lipid-lowering therapy. Apo(B) cutoff (1.1 g/l) was obtained from a group of normolipidemic (47 men, 21 women) control subjects, and LDLc, triglycerides, and HDL cholesterol (HDLc) cutoff points were those from the National Cholesterol Education Program guidelines. LDLc levels were obtained by ultracentrifugation if triglyceride levels were > 3.45 mmol/l; otherwise, they were calculated (Friedwald). Apo(B) levels were measured by immunoturbidimetry.

RESULTS

Normocholesterolemia (LDLc < 4.13 mmol/l) appeared in 75 of the 100 patients, of whom 55 were normo- and 20 hypertriglyceridemic. Hyperapolipoprotein(B) [hyperapo(B)] was the most frequent lipid disorder, present in 34 (45%) of the normocholesterolemic patients (22 normo- and 12 hypertriglyceridemic). Low HDLc levels were more prevalent (53%) in patients with hyperapo(B) than in the rest (24%).

CONCLUSIONS

Hyperapo(B) was found in almost half of the normocholesterolemic type 2 diabetic patients and was frequently associated with low HDLc levels and hypertriglyceridemia. Thus, given its independent association with cardiovascular disease and that it identifies high-risk phenotypes in normocholesterolemic diabetic patients apo(B) should be used to evaluate the lipidic pattern of these patients.

Plasma lipoprotein(a) levels are not influenced by glycemic control in type 1 diabetes

OBJECTIVE

To determine the influence of glycemic control improvement with intensive therapy on lipoprotein(a) [Lp(a)] concentrations in type 1 diabetic patients.

RESEARCH DESIGN AND METHODS

A total of 105 poorly controlled type 1 diabetic patients (60 men, 45 women) without diabetic complications participated in a longitudinal study performed in a tertiary referral center, to compare lipid, lipoprotein, and Lp(a) levels before and after 3 months of intensive therapy with multiple insulin doses. Lp(a) levels were measured by the Terumo method. Differences between the two periods were assessed by the paired t test and Wilcoxon's test.

RESULTS

After 3 months of intensive therapy, all patients exhibited improved glycemic control. HbA1c decreased from 8.9 +/- 2.4 to 6.5 +/- 1.6% (P < 0.0001), being < or =6% in 47% of patients. However, although a more favorable lipoprotein profile was obtained, no changes in Lp(a) concentrations were observed in the whole group of patients (16.7 +/- 17.3 vs. 17.2 +/- 17.7 mg/dl) or in patients with baseline Lp(a) levels above 30 mg/dl (47.1 +/- 14.8 vs. 47.4 +/- 18.9 mg/dl) or below 30 mg/dl (9.6 +/- 7.3 vs. 10.2 +/- 6.7 mg/dl). In addition, patients reaching HbA1c < or =6 or >6% presented similar Lp(a) levels (19.7 +/- 18.0 vs. 15.0 +/- 17.4 mg/dl), and changes in Lp(a) did not correlate with those observed in HbA1c.

CONCLUSIONS

These data demonstrate that the improvement of glycemic control does not influence plasma Lp(a) concentrations in type 1 diabetic patients independently of baseline Lp(a) levels and the degree of glycemic control.

Lack of change of lipoprotein(a) levels by the optimization of glycemic control with insulin therapy in NIDDM patients

OBJECTIVE

To evaluate the effect of glycemic control improvement with insulin therapy on lipoprotein(a) [Lp(a)] levels in patients with NIDDM.

RESEARCH DESIGN AND METHODS

We performed a longitudinal study in a tertiary referral center to compare lipid and Lp(a) levels before and after 3 months of insulin therapy in 60 poorly controlled NIDDM patients (32 men, 28 women). Patients previously treated with oral hypoglycemic agents (n = 50) received one to two insulin doses, and those previously treated with insulin (n = 10) received multiple insulin doses. Lp(a) levels were measured by the Terumo method. Differences between the two periods were assessed by the paired t test and Wilcoxon's test.

RESULTS

After 3 months of insulin therapy, HbA1c decreased from 9.6 +/- 1.9 to 6.0 +/- 1.4% (P < 0.0005) in all patients and from 9.1 +/- 2.1 to 6.1 +/- 2.9% (P < 0.05) in patients under multiple insulin doses, being < or = 6.0% in 59% of patients. Total triglyceride and VLDL cholesterol levels decreased (P < 0.01) and HDL cholesterol increased significantly (P < 0.0005). However, no changes in Lp(a) levels were observed in all patients (25.3 +/- 25.0 vs 25.7 +/- 27.2% mg/dl) and in patients with baseline Lp(a) levels above (63.5 +/- 15.5 vs. 65.1 +/- 23.1 mg/dl) or below 30 mg/dl (11.5 +/- 7.5 vs. 11.5 +/- 7.3 mg/dl). In addition, patients reaching HbA1c levels < or = 6.0% or > 6.0% presented similar Lp(a) levels (26.0 +/- 29.1 vs 25.3 +/- 25.0 mg/dl). Moreover, no correlations were observed between changes in Lp(a) levels and in the glycemic control parameters.

CONCLUSIONS

This study shows that the improvement of glycemic control by insulin therapy does not influence plasma Lp(a) levels, measured by the Terumo method, in NIDDM patients, independently of baseline values and the degree of glycemic control reached.

[The mixed gonadal dysgenesis. Diagnostic criteria and surgical treatment]

The Mixed Gonadal Dysgenesis represents the 7.6% of all our patients with intersexual states. We report 14 patients who present Mixed Gonadal Dysgenesis. We have studied: diagnosis age; external genitalia description; sex assigned in birth and if has changed; the karyotype; sex chromatine; hormonal study; genitography; internal genitalia and internal Mullerians ducts structures; gonadal histologycal study; surgical treatment and hormonal treatment. The results show that 50% of the cases presents a 46XY karyotype and the other 50% mosaicisme 45XO/46XY. The histological study is very distinctive. A vulvovagynoplasty and clitoroplasty was made in all the cases. Four patients must follow an hormonal treatment after reaching puberal age. Summing up, with patients having ambiguous genitalia we can suspect it consists of a Mixed Gonadal Dysgenesis. The diagnosis must be precocious. And this diagnosis will be based in an ambiguous genitalia, with a karyotype 46XY or 45XO/46XY, the persistence of the internal Müllerian duct structures, and the histological study with a dysgenetic testis. These patients should be raised as females because they can obtain a good morphological and functional development like a normal female.

[Androgen insensitivity syndrome. Diagnosis and therapy]

Ten patients with complete or incomplete androgens insensitivity syndrome (A.I.S.) is reported. Diagnosis of A.I.S. is presented on the basis: clinical, phenotype, studies of sexual steroids specially androgens, gonadotropins, 5-alpha-reductase activity and possible abnormality of androgen target cells from the genital skin. Histology of the testes is shown. Surgical treatment of these patients is reported, depending of the abnormality of the genitalia.

[Appendicular peritonitis: antibiotics and complications (author's transl)]

A retrospective study of the complications and bacteriologic findings in a group of 500 appendectomies in children under seven years is reported. A prospective trial on 64 appendiceal peritonitis revealed that there were no significant differences between two antibiotic policies (clindamycin plus gentamycin vs. cefoxitine alone) in regard to postoperative septic complications. Nevertheless, both policies significantly decreased the number of intraabdominal abscesses as compared with the treatments applied during the years of the retrospective study. No improvement was observed in the number of wound infections.

[Thoracic and abdominal trauma in children: study of 122 cases (author's transl)]

Authors present a review of patients under 7 years of age affected with thoracic and/or abdominal trauma not due to birth injuries, observed in the period 1966-1979. In these 122 patients, they observed 154 injuries, including 63 abdominal, 58 renal, 28 thoracic and 5 vertebral. Automobile accidents, falls and penetrating injuries, in this order are the etiological factors. Six patients died due to brain injuries (66%) and the rest of septic and hemorrhagic shock. Authors observed a high incidence of multiple injuries involving thehead, skeleton, abdomen and chest and the importance of recognizing these coexisting injuries to improve the prognosis. Finally, they point out that the pediatric surgeon's function is not only to treat the patient but to prevent the injuries through interdisciplinary meetings.