Species identification of archived fish bones collected from the Mediterranean Sea 100 years ago using molecular techniques

With the discovery that DNA can be successfully recovered from museum collections, a new source of genetic information has been provided to extend our comprehension of the evolutionary history of species. However, historical specimens are often mislabeled or report incorrect information of origin, thus accurate identification of specimens is essential. Due to the highly damaged nature of ancient DNA many pitfalls exist and particular precautions need to be considered in order to perform genetic analysis. In this study we analyze 208 historical remains of pelagic fishes collected in the beginning of the 20th century. Through the adaptation of existing protocols, usually applied to human remains, we manage to successfully retrieve valuable genetic material from almost all of the examined samples using a guanidine and silica column-based approach. The combined use of two mitochondrial markers cytochrome-oxidase-1(mtDNA COI) and Control Region (mtDNA CR), and the nuclear marker first internal transcriber space (ITS1) allowed us to identify the majority of the examined specimens using traditional PCR and Sanger sequencing techniques. The creation of primers capable of amplifying heavily degraded DNA have great potential for future uses, both in ancient and in modern investigation. The methodologies developed in this study can in fact be applied for other ancient fish specimens as well as cooked or canned samples.

A new information fusion method for land-use classification using high resolution satellite imagery

Satellite image classification involves designing and developing efficient image classifiers. With satellite image data and image analysis methods multiplying rapidly, selecting the right mix of data sources and data analysis approaches has become critical to the generation of quality land-use maps. In this study, a new postprocessing information fusion algorithm for the extraction and representation of land-use information based on high-resolution satellite imagery is presented. This approach can produce land-use maps with sharp interregional boundaries and homogeneous regions. The proposed approach is conducted in five steps. First, a GIS layer - ATKIS data - was used to generate two coarse homogeneous regions, i.e. urban and rural areas. Second, a thematic (class) map was generated by use of a hybrid spectral classifier combining Gaussian Maximum Likelihood algorithm (GML) and ISODATA classifier. Third, a probabilistic relaxation algorithm was performed on the thematic map, resulting in a smoothed thematic map. Fourth, edge detection and edge thinning techniques were used to generate a contour map with pixel-width interclass boundaries. Fifth, the contour map was superimposed on the thematic map by use of a region-growing algorithm with the contour map and the smoothed thematic map as two constraints. For the operation of the proposed method, a software package is developed using programming language C. This software package comprises the GML algorithm, a probabilistic relaxation algorithm, TBL edge detector, an edge thresholding algorithm, a fast parallel thinning algorithm, and a region-growing information fusion algorithm. The county of Landau of the State Rheinland-Pfalz, Germany was selected as a test site. The high-resolution IRS-1C imagery was used as the principal input data.

Prognostic importance of anaemia in patients with acute pulmonary embolism

Although associated with adverse outcomes in other cardiopulmonary diseases, limited evidence exists on the prognostic value of anaemia in patients with acute pulmonary embolism (PE). We sought to examine the associations between anaemia and mortality and length of hospital stay in patients with PE. We evaluated 14,276 patients with a primary diagnosis of PE from 186 hospitals in Pennsylvania, USA. We used random-intercept logistic regression to assess the association between anaemia at the time of presentation and 30-day mortality and discrete-time logistic hazard models to assess the association between anaemia and time to hospital discharge, adjusting for patient (age, gender, race, insurance type, clinical and laboratory variables) and hospital (region, size, teaching status) factors. Anaemia was present in 38.7% of patients at admission. Patients with anaemia had a higher 30-day mortality (13.7% vs. 6.3%; p <0.001) and a longer length of stay (geometric mean, 6.9 vs. 6.6 days; p <0.001) compared to patients without anaemia. In multivariable analyses, anaemia remained associated with an increased odds of death (OR 1.82, 95% CI: 1.60-2.06) and a decreased odds of discharge (OR 0.85, 95% CI: 0.82-0.89). Anaemia is very common in patients presenting with PE and is independently associated with an increased short-term mortality and length of stay.

Hybridization between distant lineages increases adaptive variation during a biological invasion: stickleback in Switzerland

The three-spined stickleback is a widespread Holarctic species complex that radiated from the sea into freshwaters after the retreat of the Pleistocene ice sheets. In Switzerland, sticklebacks were absent with the exception of the far northwest, but different introduced populations have expanded to occupy a wide range of habitats since the late 19th century. A well-studied adaptive phenotypic trait in sticklebacks is the number of lateral plates. With few exceptions, freshwater and marine populations in Europe are fixed for either the low plated phenotype or the fully plated phenotype, respectively. Switzerland, in contrast, harbours in close proximity the full range of phenotypic variation known from across the continent. We addressed the phylogeographic origins of Swiss sticklebacks using mitochondrial partial cytochrome b and control region sequences. We found only five different haplotypes but these originated from three distinct European regions, fixed for different plate phenotypes. These lineages occur largely in isolation at opposite ends of Switzerland, but co-occur in a large central part. Across the country, we found a strong correlation between a microsatellite linked to the high plate ectodysplasin allele and the mitochondrial haplotype from a region where the fully plated phenotype is fixed. Phylogenomic and population genomic analysis of 481 polymorphic amplified fragment length polymorphism loci indicate genetic admixture in the central part of the country. The same part of the country also carries elevated within-population phenotypic variation. We conclude that during the recent invasive range expansion of sticklebacks in Switzerland, adaptive and neutral between-population genetic variation was converted into within-population variation, raising the possibility that hybridization between colonizing lineages contributed to the ecological success of sticklebacks in Switzerland.

A high-resolution comparative radiation hybrid map of equine chromosome 4q12-q22

In this study, we present a comprehensive 5000-rad radiation hybrid map of a 40-cM region on equine chromosome 4 (ECA4) that contains quantitative trait loci for equine osteochondrosis. We mapped 29 gene-associated sequence tagged site markers using primers designed from equine expressed sequence tags or BAC clones in the ECA4q12-q22 region. Three blocks of conserved synteny, showing two chromosomal breakpoints, were identified in the segment of ECA4q12-q22. Markers from other segments of HSA7q mapped to ECA13p and ECA4p, and a region of HSA7p was homologous to ECA13p. Therefore, we have improved the resolution of the human-equine comparative map, which allows the identification of candidate genes underlying traits of interest.

Crystal structure of the platelet glycoprotein Ib(alpha) N-terminal domain reveals an unmasking mechanism for receptor activation

Glycoprotein Ib (GPIb) is a platelet receptor with a critical role in mediating the arrest of platelets at sites of vascular damage. GPIb binds to the A1 domain of von Willebrand factor (vWF-A1) at high blood shear, initiating platelet adhesion and contributing to the formation of a thrombus. To investigate the molecular basis of GPIb regulation and ligand binding, we have determined the structure of the N-terminal domain of the GPIb(alpha) chain (residues 1-279). This structure is the first determined from the cell adhesion/signaling class of leucine-rich repeat (LRR) proteins and reveals the topology of the characteristic disulfide-bonded flanking regions. The fold consists of an N-terminal beta-hairpin, eight leucine-rich repeats, a disulfide-bonded loop, and a C-terminal anionic region. The structure also demonstrates a novel LRR motif in the form of an M-shaped arrangement of three tandem beta-turns. Negatively charged binding surfaces on the LRR concave face and anionic region indicate two-step binding kinetics to vWF-A1, which can be regulated by an unmasking mechanism involving conformational change of a key loop. Using molecular docking of the GPIb and vWF-A1 crystal structures, we were also able to model the GPIb.vWF-A1 complex.

Large genomic fibrillin-1 (FBN1) gene deletions provide evidence for true haploinsufficiency in Marfan syndrome

Mutations in the FBN1 gene are the major cause of Marfan syndrome (MFS), an autosomal dominant connective tissue disorder, which displays variable manifestations in the cardiovascular, ocular, and skeletal systems. Current molecular genetic testing of FBN1 may miss mutations in the promoter region or in other noncoding sequences as well as partial or complete gene deletions and duplications. In this study, we tested for copy number variations by successively applying multiplex ligation-dependent probe amplification (MLPA) and the Affymetrix Human Mapping 500 K Array Set, which contains probes for approximately 500,000 single-nucleotide polymorphisms (SNPs) across the genome. By analyzing genomic DNA of 101 unrelated individuals with MFS or related phenotypes in whom standard genetic testing detected no mutation, we identified FBN1 deletions in two patients with MFS. Our high-resolution approach narrowed down the deletion breakpoints. Subsequent sequencing of the junctional fragments revealed the deletion sizes of 26,887 and 302,580 bp, respectively. Surprisingly, both deletions affect the putative regulatory and promoter region of the FBN1 gene, strongly indicating that they abolish transcription of the deleted allele. This expectation of complete loss of function of one allele, i.e. true haploinsufficiency, was confirmed by transcript analyses. Our findings not only emphasize the importance of screening for large genomic rearrangements in comprehensive genetic testing of FBN1 but, importantly, also extend the molecular etiology of MFS by providing hitherto unreported evidence that true haploinsufficiency is sufficient to cause MFS.

Pupil phase apodization for achromatic imaging of extra-solar planets

Direct imaging of extra-solar planets in the visible and infrared region has generated great interest among scientists and the general public as well. However, this is a challenging problem. Diffculties of detecting a planet (faint source) are caused, mostly, by two factors: sidelobes caused by starlight diffraction from the edge of the pupil and the randomly scattered starlight caused by the phase errors from the imperfections in the optical system. While the latter diffculty can be corrected by high density active deformable mirrors with advanced phase sensing and control technology, the optimized strategy for suppressing the diffraction sidelobes is still an open question. In this thesis, I present a new approach to the sidelobe reduction problem: pupil phase apodization. It is based on a discovery that an anti-symmetric spatial phase modulation pattern imposed over a pupil or a relay plane causes diffracted starlight suppression sufficient for imaging of extra-solar planets. Numerical simulations with specific square pupil (side D) phase functions, such as ... demonstrate annulling in at least one quadrant of the diffraction plane to the contrast level of better than 10^12 with an inner working angle down to 3.5L/D (with a = 3 and e = 10^3). Furthermore, our computer experiments show that phase apodization remains effective throughout a broad spectrum (60% of the central wavelength) covering the entire visible light range. In addition to the specific phase functions that can yield deep sidelobe reduction on one quadrant, we also found that a modified Gerchberg-Saxton algorithm can help to find small sized (101 x 101 element) discrete phase functions if regional sidelobe reduction is desired. Our simulation shows that a 101x101 segmented but gapless active mirror can also generate a dark region with Inner Working Distance about 2.8L/D in one quadrant. Phase-only modulation has the additional appeal of potential implementation via active segmented or deformable mirrors, thereby combining compensation of random phase aberrations and diffraction halo removal in a single optical element.

[Treatment of lymphangiomas with picibanil in the first year of life]

BACKGROUND: The therapeutic gold standard of cystic hygroma is its complete resection. Because of its growth pattern and its main location in the head and neck region complete resection is not always possible. An alternative is the local injection of Picibanil, but only few cases have been published about its use in infants. PATIENTS/METHOD: We retrospectively analyzed the data of 8 infants (age: 2 weeks-12 months) who got Picibanil therapy because of cystic hygroma in the time period 2002 until 2006. Follow up ranged from 3 months up to 3 years. RESULTS: During the postoperative period all patients had local swelling, in 4 cases accompanied with local inflammation and fever. Tumor reduction of >50% was obtained in 7 of 8 patients. CONCLUSIONS: Local injection of Picibanil in infants with cystic hygroma seems to be a safe alternative to surgical therapy, especially when complete tumor resection means damage of important neighbouring structures. Prospective trials are necessary to confirm the better outcome after therapy with Picibanil compare to primary surgery.

Role of the extraosseus blood supply in osteoarthritic femoral heads

Blood perfusion to the femoral head might be endangered during the surgical approach or the preparation of the femoral head or both in hip resurfacing arthroplasty. The contribution of the intramedullary blood supply to the femoral head in osteoarthritis is questionable. Therefore, the contribution of the extraosseous blood supply to osteoarthritic femoral heads was measured intraoperatively to question if there is measurable blood flow between the epiphysis and metaphysis in osteoarthritic hips in case of extraosseus vessel damage. At defined points during surgery we acquired the epiphyseal and metaphyseal femoral head perfusion by high-energy laser Doppler flowmetry. Complete femoral neck osteotomy sparing the retinacular vessels to simulate intraosseous blood disruption showed unchanged epiphyseal blood flow compared to initial measurement after capsulotomy. The pulsatile signal disappeared after transection of the retinacular vessels. Based on these acute measurements, we conclude intramedullary blood vessels to the femoral head do not provide measurable blood supply to the epiphysis once the medial femoral circumflex artery or the retinacular vessels have been damaged. We recommend the use of a safe surgical approach for hip resurfacing and careful implantation of the femoral component to respect blood supply to the femoral head and neck region in hip resurfacing arthroplasty.

Fog-water collection for community use

Fog is a potential source of water that could be exploited using the innovative technology of fog collection. Naturally, the potential of fog has proven its significance in cloud forests that are thriving from fog interception. Historically, the remains of artificial structures in different countries prove that fog has been collected as an alternative and/or supplementary water source. In the beginning of the 19th century, fog collection was investigated as a potential natural resource. After the mid-1980s, following success in Chile, fog-water collection commenced in a number of developing countries. Most of these countries are located in arid and semi-arid regions with topographic and climatic conditions that favour fog-water collection. This paper reviews the technology of fog collection with initial background information on natural fog collection and its historical development. It reviews the climatic and topographic features that dictate fog formation (mainly advection and orographic) and the innovative technology to collect it, focusing on the amount collected, the quality of fog water, and the impact of the technology on the livelihoods of beneficiary communities. By and large, the technology described is simple, cost-effective, and energy-free. However, fog-water collection has disadvantages in that it is seasonal, localised, and the technology needs continual maintenance. Based on the experience in several countries, the sustainability of the technology could be guaranteed if technical, economic, social, and management factors are addressed during its planning and implementation.

REGULATION OF THE EXPRESSION OF NAR OPERON ENCODING NITRATE REDUCTASE IN ESCHERICHIA COLI

The nar operon, which encodes the nitrate reductase in Escherichia coli, can be induced under anaerobic conditions without nitrate to a low level and with nitrate to a maximum level. The anaerobic formation of nitrate reductase is dependent upon the fnr gene product while the narL gene product is required for further induction by nitrate. The sequence was determined across the entire promoter and regulatory region of the nar operon. The translational start site of the first structural gene of the nar operon, narG gene, was established by identifying the nucleotide sequence for the first 20 N-terminal amino acid residues of the alpha subunit of nitrate reductase. The transcriptional start site and the level of the transcript was determined by S1 mapping procedure. One major transcript was identified which was initiated 50 base pair (bp) upstream from the translational start site of the first structural gene. The synthesis of the transcript was repressed aerobically, fully induced by nitrate anaerobically, and greatly reduced in a ${\rm Fnr\sp-}$ mutant. Deletions were created in the 5$\sp\prime$ nar regulatory sequence with either an intact nar operon or a nar::lacZ fusion. The expression of the plasmids with deletions were determined in a strain with wild type fnr and narL loci, a Fnr- mutant strain and a NarL- mutant strain. These experiments demonstrated that the $5\sp\prime$ limit of the nar operon lies at about $-210$ bp from the transcription start site. The region required for anaerobic induction by the fnr gene product is located around $-60$ bp. Two putative narL recognition sites were identified, one of which is around $-200$ and another immediately adjacent to the fnr recognition region. The deletion of the sequences around $-200$ rendered the remaining narL complex repressive and thus decreased the expression of nar operon, suggesting that the two potential narL sites interact with each other over a significant length of DNA. ^

Sampling strategies for capillary isoelectric focusing with electroosmotic zone mobilization assessed by high-resolution dynamic computer simulation

The impact of initial sample distribution on separation and focusing of analytes in a pH 3–11 gradient formed by 101 biprotic carrier ampholytes under concomitant electroosmotic displacement was studied by dynamic high-resolution computer simulation. Data obtained with application of the analytes mixed with the carrier ampholytes (as is customarily done), as a short zone within the initial carrier ampholyte zone, sandwiched between zones of carrier ampholytes, or introduced before or after the initial carrier ampholyte zone were compared. With sampling as a short zone within or adjacent to the carrier ampholytes, separation and focusing of analytes is shown to proceed as a cationic, anionic, or mixed process and separation of the analytes is predicted to be much faster than the separation of the carrier components. Thus, after the initial separation, analytes continue to separate and eventually reach their focusing locations. This is different to the double-peak approach to equilibrium that takes place when analytes and carrier ampholytes are applied as a homogenous mixture. Simulation data reveal that sample application between two zones of carrier ampholytes results in the formation of a pH gradient disturbance as the concentration of the carrier ampholytes within the fluid element initially occupied by the sample will be lower compared to the other parts of the gradient. As a consequence thereof, the properties of this region are sample matrix dependent, the pH gradient is flatter, and the region is likely to represent a conductance gap (hot spot). Simulation data suggest that sample placed at the anodic side or at the anodic end of the initial carrier ampholyte zone are the favorable configurations for capillary isoelectric focusing with electroosmotic zone mobilization.

Chronometric features of processing unpleasant stimuli: a functional MRI-based transcranial magnetic stimulation study.

The quick identification of potentially threatening events is a crucial cognitive capacity to survive in a changing environment. Previous functional MRI data revealed the right dorsolateral prefrontal cortex and the region of the left intraparietal sulcus (IPS) to be involved in the perception of emotionally negative stimuli. For assessing chronometric aspects of emotion processing, we applied transcranial magnetic stimulation above these areas at different times after negative and neutral picture presentation. An interference with emotion processing was found with transcranial magnetic stimulation above the dorsolateral prefrontal cortex 200-300 ms and above the left intraparietal sulcus 240/260 ms after negative stimuli. The data suggest a parallel and conjoint involvement of prefrontal and parietal areas for the identification of emotionally negative stimuli.

Atlanto-axial rotatory subluxations in postmortem CT: radiologists be aware of a common pitfall

The aim of the present study was to determine the frequency of atlanto-axial rotatory subluxations (AARS) in multi detector computed tomography (MDCT) performed on human corpses for forensic purposes and to investigate whether these are a physiological postmortem finding or indicate a trauma to the neck region. 80 forensic cases examined with MDCT from November 2003 to March 2007 were included in the study. The study was approved by the regional ethics committee. For each case volumes were rendered and investigated with reference to suspected AARS and any other anomalies of the head and neck region. The rotation of the head as well as in the atlanto-axial joint were measured and occurring AARS were judged according Fielding's classification. The finding of AARS was correlated to case criteria such as postmortem head rotation, sex, age, cause of death, time since death and further autopsy results. Statistical analysis was performed using Fisher's exact test, Wilcoxon's rank sums test and Chi-square test with Pearson approximation. 70% (n=56) of the cases included in the study presented with an AARS. A strong correlation (P<.0001) between suspected AARS and postmortem head rotation was found. Two cases presented with an atlanto-axial rotation greater than the head rotation. One showed an undiscovered lateral dislocation of the atlas, and one an unfused atlas-ring. There was no correlation to any further investigated case criteria. Ipsilateral AARS with head rotation alone does not indicate trauma to the neck. PmCT can substantially support forensic examinations of the skeleton, especially in body regions, which are elaborate to access at autopsy, such as the cervical spine. Isolated AARS (Fielding type I) on pmCT is usually a normal finding associated with ipsilateral head rotation.