Potencial paleoecológico de los depósitos orgánicos marinos de Posidonia oceanica

XV lnternational A.P.L.E. Symposium of Palynolog

Experimental study of excited states of 62{}^{62}Ni via one-neutron (d,p)(d,p) transfer up to the neutron-separation threshold and characteristics of the pygmy dipole resonance states

The degree of collectivity of the Pygmy Dipole Resonance (PDR) is an open question. Recently, Ries {\it et al.} have suggested the onset of the PDR beyond $N=28$ based on the observation of a significant $E1$ strength increase in the Cr isotopes and proposed that the PDR has its origin in a few-nucleon effect. Earlier, Inakura {\it et al.} had predicted by performing systematic calculations using the random-phase approximation (RPA) with the Skyrme functional SkM* that the $E1$ strength of the PDR strongly depends on the position of the Fermi level and that it displays a clear correlation with the occupation of orbits with orbital angular momenta less than $3\hbar$ $(l \leq 2)$. To further investigate the microscopic structures causing the possible formation of a PDR beyond the $N=28$ neutron shell closure, we performed a $^{61}$Ni$(d,p){}^{62}$Ni experiment at the John D. Fox Superconducting Linear Accelerator Laboratory of Florida State University. To determine the angular momentum transfer populating possible $J^{\pi} = 1^-$ states and other excited states of ${}^{62}$Ni, angular distributions and associated single-neutron transfer cross sections were measured with the Super-Enge Split-Pole Spectrograph. A number of $J^{\pi} = 1^-$ states were observed below the neutron-separation threshold after being populated through $l=2$ angular momentum transfers. A comparison to available $(\gamma,\gamma')$ data for ${}^{58,60}$Ni provides evidence that the $B(E1)$ strength shifts further down in energy. The $(d,p)$ data clearly prove that $l=0$ strength, i.e., the neutron $(2p_{3/2})^{-1}(3s_{1/2})^{+1}$ one-particle-one-hole configuration plays only a minor role for $1^-$ states below the neutron-separation threshold in ${}^{62}$Ni.Comment: 15 pages, 8 figures, accepted for publication in Physical Review

Prevalence and Risk Factors of Sexually Transmitted Infections and Cervical Neoplasia in Women from a Rural Area of Southern Mozambique

There is limited information on the prevalence of sexually transmitted infections and the prevalence of cervical neoplasia in rural sub-Saharan Africa. This study describes the prevalence and the etiology of STIs and the prevalence of cervical neoplasia among women in southern Mozambique. An age-stratified cross-sectional study was performed where 262 women aged 14 to 61 years were recruited at the antenatal clinic (59%), the family-planning clinic (7%), and from the community (34%). At least one active STI was diagnosed in 79% of women. Trichomonas vaginalis was present in 31% of all study participants. The prevalence of Neisseria gonorrhea and Chlamydia trachomatis were 14% and 8%, respectively, and Syphilis was diagnosed in 12% of women. HPV DNA was detected in 40% of women and cervical neoplasia was diagnosed in 12% of all women. Risk factors associated with the presence of some of the STIs were being divorced or widowed, having more than one sexual partner and having the partner living in another area. A higher prevalence was observed in the reproductive age group and some of the STIs were more frequently diagnosed in pregnant women. STI control programs are a priority to reduce the STIs burden, including HIV and cervical neoplasia

A new approach to obtain pure and active proteins from Lactococcus lactis protein aggregates

The production of pure and soluble proteins is a complex, protein-dependent and time-consuming process, in particular for those prone-to-aggregate and/or difficult-to-purify. Although Escherichia coli is widely used for protein production, recombinant products must be co-purified through costly processes to remove lipopolysaccharide (LPS) and minimize adverse effects in the target organism. Interestingly, Lactococcus lactis, which does not contain LPS, could be a promising alternative for the production of relevant proteins. However, to date, there is no universal strategy to produce and purify any recombinant protein, being still a protein-specific process. In this context and considering that L. lactis is also able to form functional protein aggregates under overproduction conditions, we explored the use of these aggregates as an alternative source of soluble proteins. In this study, we developed a widely applicable and economically affordable protocol to extract functional proteins from these nanoclusters. For that, two model proteins were used: mammary serum amyloid A3 (M-SAA3) and metalloproteinase 9 (MMP-9), a difficult-to-purify and a prone-to-aggregate protein, respectively. The results show that it is possible to obtain highly pure, soluble, LPS-free and active recombinant proteins from L. lactis aggregates through a cost-effective and simple protocol with special relevance for difficult-to-purify or highly aggregated proteins

A Kernel for Open Source Drug Discovery in Tropical Diseases

Open source drug discovery, a promising alternative avenue to conventional patent-based drug development, has so far remained elusive with few exceptions. A major stumbling block has been the absence of a critical mass of preexisting work that volunteers can improve through a series of granular contributions. This paper introduces the results from a newly assembled computational pipeline for identifying protein targets for drug discovery in ten organisms that cause tropical diseases. We have also experimentally tested two promising targets for their binding to commercially available drugs, validating one and invalidating the other. The resulting kernel provides a base of drug targets and lead candidates around which an open source community can nucleate. We invite readers to donate their judgment and in silico and in vitro experiments to develop these targets to the point where drug optimization can begin

Purification and functional characterisation of rhiminopeptidase A, a novel aminopeptidase from the venom of Bitis gabonica rhinoceros

This study describes the discovery and characterisation of a novel aminopeptidase A from the venom of B. g. rhinoceros and highlights its potential biological importance. Similar to mammalian aminopeptidases, rhiminopeptidase A might be capable of playing roles in altering the blood pressure and brain function of victims. Furthermore, it could have additional effects on the biological functions of other host proteins by cleaving their N-terminal amino acids. This study points towards the importance of complete analysis of individual components of snake venom in order to develop effective therapies for snake bites

FLORA: a novel method to predict protein function from structure in diverse superfamilies

Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure embellishments to a common structural core. The majority of prediction algorithms employ local templates built on known or predicted functional residues. Here, we present a novel method (FLORA) that automatically generates structural motifs associated with different functional sub-families (FSGs) within functionally diverse domain superfamilies. Templates are created purely on the basis of their specificity for a given FSG, and the method makes no prior prediction of functional sites, nor assumes specific physico-chemical properties of residues. FLORA is able to accurately discriminate between homologous domains with different functions and substantially outperforms (a 2–3 fold increase in coverage at low error rates) popular structure comparison methods and a leading function prediction method. We benchmark FLORA on a large data set of enzyme superfamilies from all three major protein classes (α, β, αβ) and demonstrate the functional relevance of the motifs it identifies. We also provide novel predictions of enzymatic activity for a large number of structures solved by the Protein Structure Initiative. Overall, we show that FLORA is able to effectively detect functionally similar protein domain structures by purely using patterns of structural conservation of all residues

g9/2g_{9/2} neutron strength in the N=29N=29 isotones and the 52^{52}Cr(d,pd,p)53^{53}Cr reaction

We performed a measurement of the $^{52}$Cr$(d,p)^{53}$Cr reaction at 16 MeV using the Florida State University Super-Enge Split-Pole Spectrograph (SE-SPS) and observed 26 states. While all of the states observed here had been seen in previous $(d,p)$ experiments, we changed five $L$ assignments from those reported previously and determined $L$ values for nine states that had not had such assignments made previously. The $g_{9/2}$ neutron strength observed in $^{53}$Cr in the present work and in the $N=29$ isotones $^{49}$Ca, $^{51}$Ti, and $^{55}$Fe via $(d,p)$ reactions is much smaller than the sum rule for this strength. Most of the observed $L=4$ strength in these nuclei is located in states near 4 MeV excitation energy. The remaining $g_{9/2}$ strength may be located in the continuum or may be fragmented among many bound states. A covariant density functional theory calculation provides support for the hypothesis that the $g_{9/2}$ neutron orbit is unbound in $^{53}$Cr. The ($\alpha,^3$He) reaction may provide a more sensitive probe for the missing $g_{9/2}$ neutron strength. In addition, particle-$\gamma$ coincidence experiments may help resolve some remaining questions in this nucleus.Comment: 15 pages, 5 figures. arXiv admin note: text overlap with arXiv:2212.0438

Molecular interactions of ASPP1 and ASPP2 with the p53 protein family and the apoptotic promoters PUMA and Bax

The apoptosis stimulating p53 proteins, ASPP1 and ASPP2, are the first two common activators of the p53 protein family that selectively enable the latter to regulate specific apoptotic target genes, which facilitates yes yet unknown mechanisms for discrimination between cell cycle arrest and apoptosis. To better understand the interplay between ASPP- and p53-family of proteins we investigated the molecular interactions between them using biochemical methods and structure-based homology modelling. The data demonstrate that: (i) the binding of ASPP1 and ASPP2 to p53, p63 and p73 is direct; (ii) the C-termini of ASPP1 and ASPP2 interact with the DNA-binding domains of p53 protein family with dissociation constants, Kd, in the lower micro-molar range; (iii) the stoichiometry of binding is 1:1; (iv) the DNA-binding domains of p53 family members are sufficient for these protein–protein interactions; (v) EMSA titrations revealed that while tri-complex formation between ASPPs, p53 family of proteins and PUMA/Bax is mutually exclusive, ASPP2 (but not ASPP1) formed a complex with PUMA (but not Bax) and displaced p53 and p73. The structure-based homology modelling revealed subtle differences between ASPP2 and ASPP1 and together with the experimental data provide novel mechanistic insights

CCBuilder:An interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo . Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models. Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures. Availability and implementation: CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder