Interpretation of the LHCb P_{c}(4312)

We study the nature of the new signal reported by LHCb in the J/ψp spectrum. Based on the S-matrix principles, we perform a minimum-bias analysis of the underlying reaction amplitude, focusing on the analytic properties that can be related to the microscopic origin of the P_{c}(4312)^{+} peak. By exploring several amplitude parametrizations, we find evidence for the attractive effect of the Σ_{c}^{+}D[over ¯]^{0} channel, which is not strong enough, however, to form a bound state.

Analysis of 21 X-chromosome polymorphisms in urban and rural populations in Salta province (north-western Argentina).

Population genetic data for 21 X-chromosome markers (Alu insertions and STRs) are reported for two populations (rural and urban) in Salta province (north-western Argentina). New variants are described, confirming the complexity and variability of some markers in this set. Results reveal Salta populations harbor a high Native American component, despite their self-recognized European ancestry. Notwithstanding the high genetic similarity of both populations, the rural sample seems to have maintained a larger Amerindian legacy. Data further show these X-linked markers, especially STRs, are highly informative in Salta populations and, therefore, can contribute to the development of a local database for forensic purposes in north-western Argentina.

Accuracy of octa-polar bioelectrical impedance analysis for the assessment of total and appendicular body composition in children and adolescents with HIV: comparison with dual energy X-ray absorptiometry and air displacement plethysmography.

BACKGROUND: Body composition analysis has been used to investigate fat mass (FM) and bone mineral content (BMC) in children and adolescents diagnosed with HIV. Investigating the validity of bioelectrical impedance analysis (BIA) is interesting with respect to testing useful techniques for monitoring body composition in children and adolescents in clinical practice. The present study aimed to determine the validity of body composition analysis by BIA compared to dual-energy X-ray absorptiometry (DXA) and air displacement plethysmography (ADP) in children and adolescents an HIV diagnosis. METHODS: Sixty-four children and adolescents (35 females and 29 males) with a mean (SD) age of 12.22 (2.13) years and with an HIV diagnosis participated in the study. Fat-free mass (FFM), FM and body fat percentage (%BF) were obtained by BIA for comparison with DXA and ADP. Segmented FM (trunk, legs and arms), lean soft tissue mass (LSTM) (total and segmented) and BMC were obtained by BIA for comparison with DXA. RESULTS: BIA presented a clinically acceptable correlation with DXA and ADP for FFM. Values found by BIA were underestimated compared to ADP, and overestimated compared to DXA. BIA presented a clinically acceptable correlation with DXA for LSTM estimates (total and segmented parameters) in both sexes (underestimating FM and overestimating LSTM). For other components (%BF, FM and BMC), BIA had a clinically unacceptable correlation with the reference methods in both sexes. CONCLUSIONS: BIA was suitable for evaluating FFM and LSTM in children and adolescents with an HIV diagnosis. For FM, %BF and BMC, BIA was not suitable for performing an evaluation in both sexes.

Evolutionary history of Podarcis tiliguerta on Corsica and Sardinia.

BACKGROUND: Podarcis tiliguerta is a wall lizard endemic to the Mediterranean islands of Corsica and Sardinia. Previous findings of high mtDNA and morphological diversity have led to the suggestion that it may represent a species complex. Here, we analysed mitochondrial and nuclear markers (mtDNA, 3110 bp; 6 nDNA loci, 3961 bp) in P. tiliguerta sampled from thirty-two localities across Corsica and Sardinia. RESULTS: We find much greater intraspecific genetic divergence than between sister species of other Mediterranean island Podarcis, i.e., between P. lilfordi and P. pityusensis. We detected three mtDNA clusters in Corsica (North, South-East and South-West) and either two or three in Sardinia (North vs. South) depending on the clustering method. Only one or two nDNA groups were identified within each main island (again, depending on the method). A Bayesian time-calibrated multispecies coalescent tree was obtained from mtDNA and provided statistical support for a Miocene origin of the species (13.87 Ma, 95% HPD: 18.30-10.77 Ma). The posterior mean divergence time for the Corsican and Sardinian lineages was 12.75 Ma ago (95% HPD: 16.94-9.04 Ma). CONCLUSION: The results support the evolutionary distinctiveness of Corsican and Sardinian populations and also indicate a lack of post-divergence migration despite periods of contact being possible. Further to this, species delimitation analyses of Corsican and Sardinian lineages provided statistical support for their recognition as distinct (sister) taxa. Our results provide new insights into the biogeography of the Mediterranean biodiversity hotspot, and contribute important findings relevant to the systematics and evolution of this speciose lizard genus.

Risk factors for proximal neck complications after endovascular aneurysm repair using the endurant stentgraft.

OBJECTIVE: To assess the incidence and risk factors for proximal aneurysm neck related complications with a late generation device for endovascular abdominal aneurysm repair (EVAR). METHODS: Data were retrieved from a prospective registry (Endurant Stent Graft Natural Selection Global Postmarket Registry) involving 79 institutions worldwide. The risk factors tested were age, gender, surgical risk profile, proximal neck length (<10 mm), diameter (>30 mm), supra- and infrarenal angulation (>60° and 75°), mural thrombus/calcification (>50%) and taper (>10%), and AAA diameter (>65 mm). Two neck related composite endpoints were used, for intra-operative (type-1a endoleak, conversion, deployment/retrieval complication or unintentional renal coverage) and post-operative (type-1a endoleak or migration) adverse events. Independent risk factors were identified using multivariable backwards modeling. RESULTS: The study included 1263 patients (mean age 73, 10.3% female) from March 2009 to May 2011. Twenty three (1.8%) intra-operative adverse events occurred. Neck length <10 mm (OR 4.9, 95% CI 1.1-22.6) and neck thrombus/calcification >50% (OR 4.8, 95% CI 1.7-13.5) were risk factors for intra-operative events. The planned 1 year follow up visit was reached for the entire cohort, and the 2 year visit for 431 patients. During this time, 99 (7.8%) events occurred. Female gender (HR 1.9, 95% CI 1.1-3.2), aneurysm diameter >65 mm (HR 2.8, 95% CI 1.9-4.2), and neck length <10 mm (HR 2.8, 95% CI 1.1-6.9) were significant post-operative risk factors. Neck angulation, neck taper, large diameter neck, and presence of thrombus/calcification were not predictors of adverse outcome in this study. CONCLUSION: These results support the adequacy of this device in the face of adverse neck anatomy, and confirm neck length as the most relevant anatomical limitation for EVAR. Additionally, the study confirms the decline in early to mid-term intervention rates with a newer generation device in a large patient sample. Lastly, it suggests that neck related risk factors affect outcome and impact on prognosis in varying degrees.

Genetic analysis of 12 X-chromosome STRs in Western Mediterranean populations.

Haplotype and allele frequencies of 12 X-STRs included in the Investigator Argus X-12 kit are reported for 255 individuals, representing four Western Mediterranean populations: Valencia (eastern mainland Spain) and the Balearic Islands (Majorca, Minorca, and Ibiza). Ibiza shows the lowest intra-population variability and the highest level of linkage disequilibrium together with an important genetic distance with regard to the geographically close populations, which is consistent with the historical evidence for long-term demographic isolation and its different matrilineal background.

New data on Perkinsus mediterraneus in the Balearic Archipelago: locations and affected species.

Perkinsus mediterraneus, a protozoan parasite that can cause perkinsosis (marine mollusc disease), was first detected in oysters Ostrea edulis from Mahon (Minorca, Balearic Islands, Spain) in 2004. Several years later it was also found in Andratx Harbour (Majorca, Balearic Islands) and in the Gulf of Manfredonia (Adriatic coast of Italy) in oyster populations. Since 2007, Perkinsus surveys have been conducted in different localities and shellfish species in the Balearic Archipelago. In the present work, we found P. mediterraneus in the Balearic Islands infecting oyster and other shellfish species. We describe infection with P. mediterraneus for the first time in Arca noae and Mimachlamys varia. The detection was carried out using Ray's fluid thioglycolate medium (RFTM), histology and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methodologies. The internal transcribed spacer (ITS) region (including ITS1, 5.8S and ITS2) of P. mediterraneus ribosomal DNA was sequenced from infected bivalve gills (or from the body in Chamelea gallina) from Balearic Archipelago localities. Twelve haplotypes with a strong genetic similarity between them (97-100%) were observed in our samples. These data were completed with 12 more haplotypes from GenBank sequences. The phylogenetic relationship between Balearic P. mediterraneus haplotypes found in this study, those previously obtained in Mahon Harbour, and the Perkinsus spp. sequences available in GenBank clearly grouped the different Perkinsus spp. in distinct clades supported by strong bootstrap values. Moreover, these analyses detected different P. mediterraneus groups in O. edulis from Minorca Island. No abnormal mortalities or decline in populations were detected during the survey, except for C. gallina, which is also affected by Marteilia refringens.

Multilocus genetic diversity and historical biogeography of the endemic wall lizard from Ibiza and Formentera, Podarcis pityusensis (Squamata: Lacertidae).

Two monophyletic sister species of wall lizards inhabit the two main groups of Balearic Islands: Podarcis lilfordi from islets and small islands around Mallorca and Menorca and Podarcis pityusensis from Ibiza, Formentera and associated islets. Genetic diversity within the endangered P. lilfordi has been well characterized, but P. pityusensis has not been studied in depth. Here, 2430 bp of mtDNA and 15 microsatellite loci were analysed from P. pityusensis populations from across its natural range. Two main genetic groupings were identified, although geographical structuring differed slightly between the mtDNA and the nuclear loci. In general, individuals from islets/islands adjacent to the main island of Ibiza were genetically distinct from those from Formentera and the associated Freus islands for both mtDNA and the nuclear loci. However, most individuals from the island of Ibiza were grouped with neighbouring islets/islands for nuclear loci, but with Formentera and Freus islands for the mitochondrial locus. A time-calibrated Bayesian tree was constructed for the principal mitochondrial lineages within the Balearics, using the multispecies coalescent model, and provided statistical support for divergence of the two main P. pityusensis lineages 0.111-0.295 Ma. This suggests a mid-late Pleistocene intraspecific divergence, compared with an early Pleistocene divergence in P. lilfordi, and postdates some major increases in sea level between 0.4 and 0.6 Ma, which may have flooded Formentera. The program IMa2 provided a posterior divergence time of 0.089-0.221 Ma, which was similar to the multispecies coalescent tree estimate. More significantly, it indicated low but asymmetric effective gene copy migration rates, with higher migration from Formentera to Ibiza populations. Our findings suggest that much of the present-day diversity may have originated from a late Pleistocene colonization of one island group from the other, followed by allopatric divergence of these populations. Subsequent gene flow between these insular groups seems likely to be explained by recent human introductions. Two evolutionary significant units can be defined for P. pityusensis but these units would need to exclude the populations that have been the subjects of recent admixture.

Balearic archipelago: three islands, three beta-thalassemia population patterns.

The mutation spectrum of 175 ß-thalassemia (ß-thal) carriers, identified in pilot carrier screening on 22,713 individuals from Balearic Islands (Spain), is reported. The ß(0) CD39 (C>T) mutation is the most frequent (61.1%), followed by ß(+) IVS-I-110 (G>A) (12.0%), ß(+) IVS-I-6 (T>C) and ß(0) IVS-1-1 (G>A) (3.4% both) and eight other rare mutations (2.9-0.6%); with a distinct prevalence and distribution between islands. Minorca shows the highest prevalence in Iberian populations, with a single mutation, CD39 (C>T), present in most ß-thal carriers. Ibiza is the only Western Mediterranean population where the most frequent ß-thal mutation is IVS-I-110 (G>A). These results can be explained by a combination of historical-demographic characteristics together with evolutionary forces such as founder effect, genetic drift and probably selection by malaria. Knowledge of the mutational spectrum in the Balearic Islands will enable to optimize mutation detection strategy for genetic diagnosis of ß-thal in these islands.

Improving sodium dodecyl sulfate polyacrylamide gel electrophoresis detection of low-abundance protein samples by rapid freeze centrifugation.

This work presents a rapid and simple freeze centrifugation method to concentrate dilute protein solutions for detection by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) Coomassie blue staining. Moreover, a simple way to assemble a cryoconcentration device is presented, and its use is discussed. Commercial purified protein standard and an enzyme with high fructosyltransferase (FTase) activity, coming from target fractions obtained by chromatographic separation, were used as an example. FTase, coming directly from the chromatographic fractions, was difficult to view through SDS-PAGE analysis; however, it was easily visualized, and its activity was enhanced, after the application of the freeze centrifugation protocol presented here.

[Translated article] Preoperative assessment and surgical indications: Separation surgery.

Neurological compression occurs in 10%-20% of patients who develop spinal metastases. In the last decade, the evolution of oncological diagnostic and medical techniques, the change from conventional external radiation to radiosurgery and the new surgical instruments have meant that the treatment of these patients must be indicated in a personalized manner and by consensus, multidisciplinary way, in specific commissions. Today, the biological state of the patient, the presence of mechanical instability, the neurological assessment and degree of epidural compression, as well as the best prognostic categorization of the tumor, are established as decision factors prior to the indication of surgical treatment, treatment that has passed from a cytoreductive concept to that of a spinal cord release from tumor in order to ensure safe radiosurgery.

Preoperative assessment and surgical indications: Separation surgery. / Valoración e indicaciones quirúrgicas: cirugía separación.

Neurological compression occurs in 10%-20% of patients who develop spinal metastases. In the last decade, the evolution of oncological diagnostic and medical techniques, the change from conventional external radiation to radiosurgery and the new surgical instruments have meant that the treatment of these patients must be indicated in a personalized manner and by consensus, multidisciplinary way, in specific commissions. Today, the biological state of the patient, the presence of mechanical instability, the neurological assessment and degree of epidural compression, as well as the best prognostic categorization of the tumor, are established as decision factors prior to the indication of surgical treatment, treatment that has passed from a cytoreductive concept to that of a spinal cord release from tumor in order to ensure safe radiosurgery.

Method to concentrate protein solutions based on dialysis-freezing-centrifugation: enzyme applications.

One of the recurrent methodological problems in preparative biochemical work is the concentration of dilute protein solutions, including culture supernatants resulting from biotechnological processes. A procedure was developed to concentrate enzymes by a novel cryoconcentration system. This approach includes a new device that facilitates the sample freezing and the subsequent solute elution from the frozen matrix by centrifugation. The optimal centrifugation conditions for this cryoconcentration system were obtained using whey protein solution as a model. The procedure was applied to concentrate dilute solutions of commercial pectinase, measuring the endopolygalacturonase (EPG) activity of this enzyme in the concentrate by a method based on the on-line torque measurement, and of recombinant fructan:fructan 1-fructosyltransferase (1-FFT) protein of Pichia pastoris from a culture in a bioreactor, as an expression system. The optimal centrifugation speed, time, and temperature were 6150 g, 20 min, and 4 °C, respectively. The concentration factors for the dilute protein solutions were 9.2-, 11.2-, and 17.1-fold for 1-FFT, whey, and commercial pectinase, respectively. Recoveries ranged from 87% to 93%. The procedure allowed concentrating proteins efficiently without affecting their enzymatic activity.

Mitochondrial DNA effects on fitness in Drosophila subobscura.

We tested different fitness components on a series of conspecific mtDNA haplotypes, detected by RFLPs in Drosophila subobscura. Additionally, haplotype VIII, endemic to the Canary Islands, was tested upon its own native nuclear DNA background and upon that of the rest of mtDNAs tested herein. We found that both nuclear and mitochondrial DNA can have a significant effect upon their hosts' fitness, and that negative selection is one of the mechanisms that can intervene in this species' mtDNA haplotype pattern. We discuss the importance of this mechanism in relation to genetic drift, in the form of periodic population bottlenecks, and how the latter can enhance the former. We also detected a significant positive effect of haplotype VIII upon fitness that could explain in part the dominance of this endemic haplotype on some of the Canary Islands, and a mitochondrial heterosis involving this haplotype when on a foreign nuclear DNA background.

Alloreactive cytolytic T cell clones with dual recognition of HLA-B27 and HLA-DR2 antigens. Selective involvement of CD8 in their class I--directed cytotoxicity.

HLA-B27- responder cells were stimulated in vitro with HLA-B27.1+ lymphoblastoid cell lines, and alloreactive CTL clones were obtained by limiting dilution. Three of these clones specifically lysed B27.1+ targets. In addition, they also lysed homozygous DR2 targets with various degrees of efficiency, depending on the Dw specificity of the target cell. All three clones possessed a homogeneous CD3+,CD8+,CD4- phenotype and were also homogeneous upon subcloning. Cold-target inhibition analyses showed mutual inhibition of B27.1 target lysis by DR2 targets and vice versa. Lysis of B27.1 targets was selectively inhibited by anti-class I mAbs. In contrast, lysis of DR2 targets was inhibited only by anti-class II and anti-DR monomorphic antibodies, but not by anti-class I, anti-DQw1, or anti-DP antibodies. The results indicate that these clones display dual recognition for HLA-B27.1 and for HLA-DR2 and suggest that HLA-B27.1 may share at least one epitope that is closely related to some stimulatory Dw determinants present on the HLA-DR2 antigens. Lysis of both B27+ and DR+ targets was inhibited by an anti-CD3 mAb. In contrast, an anti-CD8 antibody selectively inhibited the B27- but not the DR2-directed killing by these clones. The data support a stabilizing role of CD8 through its binding to the same class I (but not class II) molecule on the target cell bound by the T cell antigen receptor.

T cell receptor V beta gene usage in a human alloreactive response. Shared structural features among HLA-B27-specific T cell clones.

A strategy, based on using V beta family-specific oligonucleotides, was developed for specific amplification and direct sequencing of human TCR V beta genes. With this strategy, it was possible to undertake a structural analysis of TCRs from human T cell clones in specific responses. 12 HLA-B27-specific cytotoxic clones were examined. The results reveal a nonrandom use of V beta gene diversity in this alloreactive response in that: (a) the clones express a restricted number of V beta segments, including a subset of V beta families that are significantly more related to one another than to most other V beta families; (b) five of seven clones having a particular reaction pattern with HLA-B27 subtypes possess Alanine at the D-J junction; and (c) identical J beta segments are found associated in several instances with identical or highly homologous V beta gene segments. In addition, two new V beta 13 members are reported.

Changes in the repertoire of peptides bound to HLA-B27 subtypes and to site-specific mutants inside and outside pocket B.

HLA-B27 subtypes share many structural features, including their pocket B, which interacts with a conserved Arg residue at the second position of B*2705-bound peptides. Subtypes differ among each other at other locations in the peptide binding site. In this study, metabolic labeling and radiochemical pool sequencing were used to address the following issues: (a) presence of the Arg 2 (R2) motif among peptides bound to the various HLA-B27 subtypes; (b) influence of mutations inside and outside pocket B on this motif; and (c) the degree of similarity among the peptide pools bound to the various B27 subtypes. Sequencing of Arg-labeled peptide pools extracted from B*2701 to B*2706, and from two site-directed mutants of B*2705 with changes outside pocket B, indicated that all of these molecules bind peptides with Arg at position 2. Peptides from several mutants with changes altering the structure of pocket B, and from one mutant at the pocket B rim, also retained the R2 motif. However, this was absent in the peptide pool extracted from the M45 mutant, in which the negative charge of pocket B, conferred to HLA-B27 by Glu45, was canceled. These results indicate that alterations outside pocket B, and even disruption of the network of hydrogen bonds that stabilizes Arg binding in pocket B, do not impair binding of peptides bearing the R2 motif, but a nonconservative substitution at position 45 does. As a substantial fraction of anti-B*2705 cytotoxic T lymphocyte (CTL) clones crossreact with the M45 mutant (Villadangos, J., B. Galocha, D. López, V. Calvo, and J. A. López de Castro. 1992. J. Immunol. 149:505) this result suggest that determinant mimicry by nonidentical peptides may frequently account for unexpected CTL crossreactions. Metabolic labeling with various other amino acids and radiochemical sequencing revealed similarities, but also substantial differences, among the peptide pools from the various HLA-B27 subtypes. This strongly suggests that many peptides bind to multiple subtypes, but significant subsets of peptides bound to a given HLA-B27 subtype do not bind to other subtypes or do so with greatly altered efficiency. These results indicate the importance of polymorphism outside pocket B in modulating peptide binding to HLA-B27.

An N-acetylated natural ligand of human histocompatibility leukocyte antigen (HLA)-B39. Classical major histocompatibility complex class I proteins bind peptides with a blocked NH(2) terminus in vivo.

Sequence-independent interactions involving the free peptidic NH(2) terminus are thought to be an essential feature of peptide binding to classical major histocompatibility complex (MHC) class I proteins. Challenging this paradigm, a natural Nalpha-acetylated ligand of human histocompatibility leukocyte antigen (HLA)-B39 was identified in this study. It matched the NH(2)-terminal sequence of two human helicases, was resistant to aminopeptidase M, and was produced with high yield from a synthetic 30 mer with the sequence of the putative parental protein by the 20S proteasome. This is the first reported natural ligand of classical MHC class I antigens that has a blocked NH(2) terminus.

HLA-B27 and ankylosing spondylitis: tales from China.

The two most frequent HLA-B27 subtypes worldwide are B*2704 and B*2705. In the Han population of China B*2704 and, to a lower extent, B*2705 are found with significant frequency, and both are associated to ankylosing spondylitis (AS). Two articles in this issue report that the association to AS in this ethnic group is stronger for B*2704 than for B*2705. Thus, at least among the Han, B*2704 would be the strongest known susceptibility factor for AS.

Real-time PCR in clinical practice: a powerful tool for evaluating Leishmania chagasi loads in naturally infected dogs.

The performance of the less expensive SYBR-Green-based PCR assay, for quantifying Leishmania chagasi in smears of bone-marrow aspirates from naturally infected, mongrel dogs, was recently compared with that of a similar PCR based on TaqMan chemistry. Aspirates were obtained from 36 infected dogs and examined for parasites by direct examination, culture, and quantitative PCR (qPCR) using specific primers (based on the parasite's kinetoplast DNA), DNA extracted from a smear, and either the SYBR-Green or TaqMan chemistries. Every aspirate smear was found PCR-positive for L. chagasi (whether the assay employed SYBR Green or TaqMan) but only 74% of the aspirates were found positive by culture and only 33% by direct, microscopical examination. There was no evidence of PCR inhibition when the DNA was collected from smears, and the parasite loads estimated using the SYBR-Green PCR were almost identical to those estimated using the TaqMan PCR (r=0.99). As a method for quantifying parasite loads in dogs infected with L. chagasi (and, probably, other mammals infected with other leishmanial parasites), PCR based on SYBR Green may therefore be an appropriate and inexpensive alternative to PCR based on TaqMan, and a reliable clinical tool.