Prime Site Research Articles

Mapping young stellar populations towards Orion with Gaia DR1

AbstractOB associations are prime sites for the study of star formation processes and of the interaction between young massive stars with the interstellar medium. Furthermore, the kinematics and structure of the nearest OB associations provide detailed insight into the properties and origin of the Gould Belt. In this context, the Orion complex has been extensively studied. However, the spatial distribution of the stellar population is still uncertain: in particular, the distances and ages of the various sub-groups composing the Orion OB association, and their connection to the surrounding interstellar medium, are not well determined. We used the first Gaia data release to characterize the stellar population in Orion, with the goal to obtain new distance and age estimates of the numerous stellar groups composing the Orion OB association. We found evidence of the existence of a young and rich population spread over the entire region, loosely clustered around some known groups. This newly discovered population of young stars provides a fresh view of the star formation history of the Orion region.

Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer.

ABSTRACTBacteria use a variety of DNA-mobilizing enzymes to facilitate environmental niche adaptation via horizontal gene transfer. This has led to real-world problems, like the spread of antibiotic resistance, yet many mobilization proteins remain undefined. In the study described here, we investigated the uncharacterized family of YhgA-like transposase_31 (Pfam PF04754) proteins. Our primary focus was the genetic and biochemical properties of the five Escherichia coli K-12 members of this family, which we designate RpnA to RpnE, where Rpn represents recombination-promoting nuclease. We employed a conjugal system developed by our lab that demanded RecA-independent recombination following transfer of chromosomal DNA. Overexpression of RpnA (YhgA), RpnB (YfcI), RpnC (YadD), and RpnD (YjiP) increased RecA-independent recombination, reduced cell viability, and induced the expression of reporter of DNA damage. For the exemplar of the family, RpnA, mutational changes in proposed catalytic residues reduced or abolished all three phenotypes in concert. In vitro, RpnA displayed magnesium-dependent, calcium-stimulated DNA endonuclease activity with little, if any, sequence specificity and a preference for double-strand cleavage. We propose that Rpn/YhgA-like family nucleases can participate in gene acquisition processes.IMPORTANCE Bacteria adapt to new environments by obtaining new genes from other bacteria. Here, we characterize a set of genes that can promote the acquisition process by a novel mechanism. Genome comparisons had suggested the horizontal spread of the genes for the YhgA-like family of proteins through bacteria. Although annotated as transposase_31, no member of the family has previously been characterized experimentally. We show that four Escherichia coli K-12 paralogs contribute to a novel RecA-independent recombination mechanism in vivo. For RpnA, we demonstrate in vitro action as a magnesium-dependent, calcium-stimulated nonspecific DNA endonuclease. The cleavage products are capable of providing priming sites for DNA polymerase, which can enable DNA joining by primer-template switching.

Motion of Fullerenes around Topological Defects on Metals: Implications for the Progress of Molecular Scale Devices.

Research on motion of molecules in the presence of thermal noise is central for progress in two-terminal molecular scale electronic devices. However, it is still unclear what influence imperfections in bottom metal electrode surface can have on molecular motion. Here, we report a two-layer crowding study, detailing the early stages of surface motion of fullerene molecules on Au(111) with nanoscale pores in a n-tetradecane chemical environment. The motion of the fullerenes is directed by crowding of the underlying n-tetradecane molecules around the pore fringes at the liquid-solid interface. We observe in real-space the growth of molecular populations around different pore geometries. Supported by atomic-scale modeling, our findings extend the established picture of molecular crowding by revealing that trapped solvent molecules serve as prime nucleation sites at nanopore fringes.

Research Article. A new gravity laboratory in Ny-Ålesund, Svalbard

Abstract The Norwegian Mapping Authority (NMA) has recently established a new gravity laboratory in Ny-Ålesund at Svalbard, Norway. The laboratory consists of three independent pillars and is part of the geodetic core station that is presently under construction at Brandal, approximately 1.5 km north of NMA’s old station. In anticipation of future use of the new gravity laboratory, we present benchmark gravity values, gravity gradients, and final coordinates of all new pillars. Test measurements indicate a higher noise level at Brandal compared to the old station. The increased noise level is attributed to higher sensitivity to wind.We have also investigated possible consequences of moving to Brandal when it comes to the gravitational signal of present-day ice mass changes and ocean tide loading. Plausible models representing ice mass changes at the Svalbard archipelago indicate that the gravitational signal at Brandal may differ from that at the old site with a size detectable with modern gravimeters. Users of gravity data from Ny-Ålesund should, therefore, be cautious if future observations from the new observatory are used to extend the existing gravity record. Due to its lower elevation, Brandal is significantly less sensitive to gravitational ocean tide loading. In the future, Brandal will be the prime site for gravimetry in Ny-Ålesund. This ensures gravity measurements collocated with space geodetic techniques like VLBI, SLR, and GNSS.

Enhancing Interleukin-6 and Interleukin-11 receptor cleavage

Proteolytic cleavage of the membrane-bound Interleukin-6 receptor (IL-6R) by the metalloprotease ADAM17 releases an agonistic soluble form of the IL-6R (sIL-6R), which is responsible for the pro-inflammatory trans-signaling branch of the cytokine's activities. This proteolytic step, which is also called ectodomain shedding, is critically regulated by the cleavage site within the IL-6R stalk, because mutations or small deletions within this region are known to render the IL-6R irresponsive towards proteolysis. In the present study, we employed cleavage site profiling data of ADAM17 to generate an IL-6R with increased cleavage susceptibility. Using site-directed mutagenesis, we showed that the non-prime sites P3 and P2 and the prime site P1′ were critical for this increase in proteolysis, whereas other positions within the cleavage site were of minor importance. Insertion of this optimized cleavage site into the stalk of the Interleukin-11 receptor (IL-11R) was not sufficient to enable ADAM17-mediated proteolysis, but transfer of different parts of the IL-6R stalk enabled shedding by ADAM17. These findings shed light on the cleavage site specificities of ADAM17 using a native substrate and reveal further differences in the proteolysis of IL-6R and IL-11R.

Molecular characterization of previously elusive badnaviruses associated with symptomatic cacao in the New World

Suspected virus-like symptoms were observed in cacao plants in Trinidad during 1943, and the viruses associated with these symptoms were designated as strains A and B of cacao Trinidad virus (CTV). However, viral etiology has not been demonstrated for either phenotype. Total DNA was isolated from symptomatic cacao leaves exhibiting the CTV A and B phenotypes and subjected to Illumina HiSeq and Sanger DNA sequencing. Based on de novo assembly, two apparently full-length badnavirus genomes of 7,533 and 7,454 nucleotides (nt) were associated with CTV strain A and B, respectively. The Trinidad badnaviral genomes contained four open reading frames, three of which are characteristic of other known badnaviruses, and a fourth that is present in only some badnaviruses. Both badnaviral genomes harbored hallmark caulimovirus-like features, including a tRNAMet priming site, a TATA box, and a polyadenylation-like signal. Pairwise comparisons of the RT-RNase H region indicated that the Trinidad isolates share 57-71% nt sequence identity with other known badnaviruses. Based on the system for badnavirus species demarcation in which viruses with less than 80% nt sequence identity in the RT-RNase gene are considered members of separate species, these isolates represent two previously unidentified badnaviruses, herein named cacao mild mosaic virus and cacao yellow vein banding virus, making them the first cacao-infecting badnaviruses identified thus far in the Western Hemisphere.

Mapping of Functional Subdomains in the Terminal Protein Domain of Hepatitis B Virus Polymerase.

HBV is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. One important feature of this virus is its polymerase, the enzyme used to create the DNA genome from a specific viral RNA by reverse transcription. One region of this polymerase, the TP domain, is required for association with the viral RNA and production of the DNA genome. Targeting the TP domain for antiviral development is difficult due to the lack of homology to other proteins and high-resolution structure. This study mapped the TP functions according to predicted secondary structure, where it folds into alpha helices or unstructured loops. Three predicted loops were found to be the most important regions functionally and the most conserved evolutionarily. Identification of these functional subdomains in TP will facilitate its targeting for antiviral development.

Preparing Fosmid Mate-Paired Libraries Using Cre-LoxP Recombination.

Fosmid end sequencing has been widely utilized in genome sequence assemblies and genome structural variation studies. We have developed a new approach to construct fosmid paired-end libraries that is suitable for Illumina sequencing platform. This approach employs a newly modified fosmid vector (pFosClip) which contains two loxP sites with identical orientation and two inverse Illumina adaptor priming sites flanking the cloning site. DNA prepared from the fosmid library constructed with pFosClip can be treated with the Cre recombinase to remove most of the vector DNA, leaving only 107bp of the vector sequence with insert DNA. Frequent cutting restriction enzymes and ligase are used to digest the fosmid DNA to small (less than 1Kb) fragments and recircularize the fosmid ends and all the internal fragments. Finally an inverse PCR step with the Illumina primers is used to enrich the fosmid paired ends (PEs) for sequencing. The advantages of this approach are the following: (1) the circularization of short fragments with sticky ends is efficient; therefore the success rate is higher than other approaches that attempt to join both blunt ends of large fosmid vectors; and (2) the restriction enzyme cutting generates an identifiable junction tag for splitting the paired reads. (3) Multiple restriction enzymes can be used to overcome possible enzyme-cutting bias. Our results have shown that this approach has produced mostly fosmid size (30-40Kb) pairs from the targeted fungi and plant genomes and has drastically increased the scaffold sizes in the assembled genomes.

Numerical Analysis of Fracture Behavior of Surgical Cement in THP

In this study, we use the finite element method to analyse the behaviour of cracks emanating from microcavities in the bone cement, binding the cup to the bone, according to their size and position around the cavity, the position of the patient, the cavity’s location and the inter-defects distance (cavity-crack, crack-crack). We show that the most unstable stress intensity factor, in mode I, when the crack located in the cement’s centre and propagating along this thickness. This instability is all the more important that its size increases, tends towards the cavity, the cracks are located in a vicinity one to other and that the patient is in a squatting position. The predominant fracture mode, in mode I and II, depends on the crack’s position priming site around the microcavities. This work allows the better understanding of the interconnection phenomena of the microcavities experimentally observed.

Detection of genotoxic effect of cadmium on tomato (Lycopersicon esculentum) using RAPD markers

Tomato (Lycopersicon esculentum) seeds were germinated in Peteri dishes for 7-10 days. Seedlings were transferred to pots and grown in greenhouse for two weeks. Cadmium treatments were applied with water with concentrations 0.0, 10.0, 50.0, 70.0 and 100.0 µM. Genomic DNA from tomato leaves was used for RAPD-PCR analysis using four random primers (OPB05, OPB07, OPB08 and OPB09). RAPD profiles showed great variations in banding patterns, particularly in intensity, number, thickness and mobility of the generated PCR fragments. Appearance of new PCR products may be occurred because some oligonucleotide priming sites could become accessible to primers due to changes in DNA sequence. Disappearance of some DNA fragments might be due to structural rearrangement in DNA caused by different types of DNA damage after exposure to cadmium pollution which can change the number of binding sites of Taq polymerase. Structural rearrangement may also results in an increase in the intensity and thickness of some DNA fragments. The change in the mobility of some DNA fragments might be due to Single Strand Conformational Polymorphism (SSCP) that reveals differences in electrophoretic mobility between normal and mutant single strands of DNA. These results indicated that RAPD analysis could be used as a useful biomarker assay for detection of genotoxic effects of cadmium. Cadmium pollution can cause genotoxic effects and tomato plants can be used as a bioindicator for evaluation of environmental pollution by heavy metals.

Assays for precise quantification of total (including short) and elongated HIV-1 transcripts

Despite intensive study, it is unclear which mechanisms are responsible for latent HIV infection in vivo. One potential mechanism is inhibition of HIV transcriptional elongation, which results in short abortive transcripts containing the trans-activation response (TAR) region. Because the relative levels of total (including short) and processive transcripts provide measures of HIV transcriptional initiation and elongation, there is a compelling need for techniques that accurately measure both. Nonetheless, prior assays for total transcripts have been semi-quantitative and have seen limited application to patient samples. This manuscript reports the validation of quantitative reverse transcription (RT) droplet digital PCR assays for measurement of total (TAR) and processive (R-U5/gag) HIV transcripts. Traditional RT priming strategies can efficiently detect the TAR region on long HIV transcripts but detect <4% of true short transcripts. The TAR assay presented here utilizes an initial polyadenylation step, which provides an accessible RT priming site and detects short and long transcripts with approximately equal efficiency (70%). By applying these assays to blood samples from 8 ART-treated HIV+ individuals, total HIV transcripts were detected at levels >10-fold higher than elongated transcripts, implying a substantial block to transcriptional elongation in vivo. This approach may be applied to other difficult-to-prime RNA targets.

Recent advances in understanding and managing Crohn's disease.

There is consensus that inflammatory bowel diseases (IBDs) are the result of “dysregulated” immune reactivity towards commensal microorganisms in the intestine. This gut microbiome is clearly altered in IBD, but its primary or secondary role is still debated. The focus has shifted from adaptive to innate immunity, with its multitude of receptor molecules (Toll-like and NOD receptors) and antibacterial effector molecules (defensins, cathelicidin, and others). The latter appear to be at least partly deficient at different intestinal locations. Host genetics also support the notion that microbe–host interaction at the mucosa is the prime site of pathogenesis. In contrast, even the latest therapeutic antibodies are directed against secondary targets like cytokines and integrins identified decades ago. These so-called “biologicals” have disappointing long-term results, with the majority of patients not achieving remission in the long run. A promising approach is the development of novel drugs like defensin-derived molecules that substitute for the missing endogenous antibacterials.

An innovative SNP genotyping method adapting to multiple platforms and throughputs.

An innovative genotyping method designated as semi-thermal asymmetric reverse PCR (STARP) was developed for genotyping individual SNPs with improved accuracy, flexible throughputs, low operational costs, and high platform compatibility. Multiplex chip-based technology for genome-scale genotyping of single nucleotide polymorphisms (SNPs) has made great progress in the past two decades. However, PCR-based genotyping of individual SNPs still remains problematic in accuracy, throughput, simplicity, and/or operational costs as well as the compatibility with multiple platforms. Here, we report a novel SNP genotyping method designated semi-thermal asymmetric reverse PCR (STARP). In this method, genotyping assay was performed under unique PCR conditions using two universal priming element-adjustable primers (PEA-primers) and one group of three locus-specific primers: two asymmetrically modified allele-specific primers (AMAS-primers) and their common reverse primer. The two AMAS-primers each were substituted one base in different positions at their 3' regions to significantly increase the amplification specificity of the two alleles and tailed at 5' ends to provide priming sites for PEA-primers. The two PEA-primers were developed for common use in all genotyping assays to stringently target the PCR fragments generated by the two AMAS-primers with similar PCR efficiencies and for flexible detection using either gel-free fluorescence signals or gel-based size separation. The state-of-the-art primer design and unique PCR conditions endowed STARP with all the major advantages of high accuracy, flexible throughputs, simple assay design, low operational costs, and platform compatibility. In addition to SNPs, STARP can also be employed in genotyping of indels (insertion-deletion polymorphisms). As vast variations in DNA sequences are being unearthed by many genome sequencing projects and genotyping by sequencing, STARP will have wide applications across all biological organisms in agriculture, medicine, and forensics.

Postcolonial and Liberation Theologies as Partners in Praxis Against Sin and Suffering: A Hermeneutical Approach in Asian Perspective

In their hermeneutical reading of the Bible, postcolonialism and liberationism have some differences. Liberationism can be seen as a ‘canon within canon approach’ because it has some certain favoured texts, such as the Exodus event and the Nazareth Manifesto. By contrast, postcolonialism can be seen as a ‘canonical approach’ since it is broader in its approach to Biblical interpretation. With a critical lens, the latter hermeneutics tries to read the whole Bible, including the imperial texts.1 Yet, both hermeneutics have common goals of liberation, working toward ending domination. Both endorse the oppressed as the prime site for theology and praxis.2 The main aim of this publication is to employ both hermeneutics as partners in praxis. Using postcolonial and liberation hermeneutics, this paper will explore a theological concept of sin and suffering and three aspects of liberation — holistic liberation, exclusive liberation and inclusive liberation. It will be affirmed that postcolonial theology of liberation is not just liberation of the oppressed, but it is liberation by the oppressed for the mutual benefits of both the oppressed and oppressors in a postcolonial Asia.

Mediterranean migration towards Europe: System failure?

The Mediterranean has historically been a space of exchange, contact, and conquest. Migration – in all directions – has always been part of the cultural, political and economic negotiation around “Mare Nostrum.” Few things, however, have thrown European identities and the European political project into question more than the recent movement of migrants and refugees across the Mediterranean. In 2014, more than 170,000 migrants reached Italian shores on maritime routes. Italy was the prime landing site for boats, departing mostly from Libya. Approximately a quarter of those crossing were Syrian refugees, while the remainder came from West Africa, Eastern Africa and the Horn of Africa. In 2015, the phenomenon transformed from a “Mediterranean problem” into a European-wide one, with a marked shift from the Central Mediterranean Route (from North Africa to Italy) to the Eastern Mediterranean Route (from Turkey towards Greece and along the Balkan route towards Central, Western and Northern Europe). Between January and mid-December 2015, more than 800,000 individuals arrived in Greece, compared to 150,000 in Italy during the same period. The distribution in 2016 to date has remained roughly the same with 147,000 arrivals in Greece and 13,000 in Italy (see infographic).

Subtype distribution of Blastocystis spp. isolated from children in Eskisehir, Turkey

Blastocystis spp. is the most common enteric protist found in human feces. The pathogenic role of Blastocystis remains controversial and it has been suggested that the symptomatology of Blastocystis is associated with its subtypes (ST). However, only few studies have investigated the relationship between the symptomatology and subtypes of Blastocystis in children. This study aimed to investigate the prevalence of Blastocystis in children aged 3 to 13years with or without gastrointestinal complaints and determine the distribution of the subtypes of Blastocystis. A total of 303 stool samples obtained from symptomatic (n=84) and asymptomatic (n=219) children were included in the study. The presence of Blastocystis was investigated using native-lugol examination, trichrome staining and real-time PCR method. Using the real-time PCR method, 115 samples were found positive for Blastocystis. Subtyping was successfully performed on 46 samples using sequenced-tagged site (STS) primers and PCR. The remaining 69 samples could not be subtyped. The most frequently detected subtype was ST3 (43.4%) followed by ST1 (26.1%), ST4 (10.9%) and ST2 (8.7%). The mixed subtypes were identified in five samples (10.9%) as; ST1+ST3 (n=3), ST1+ST2 (n=1) and ST2+ST3 (n=1). None of the samples had ST5, ST6 or ST7. No statistically significant difference was found between the symptomatic and asymptomatic groups in terms of the Blastocystis positivity and the distribution of subtypes (p>0.05). To our knowledge, this is the first study to investigate the subtype distribution of Blastocystis in children in Turkey and the results are in agreement with the related data available in Turkey.

Scientology and Sex

While the control and discipline of the body and human behavior is a perennial concern in all social orders, it is particularly acute within religions, both old and new. Religions typically regulate dress, social interaction, diet, and especially norms concerning sex, reproduction, and the family. To date, research on the Church of Scientology, founded by L. Ron Hubbard in 1954, has neglected the topic of sex. In this article, I remedy this lacuna by examining three areas linked by the theme of “attempted abortion.” First, I explore Hubbard’s biography in terms of sexual and familial experiences; second, I expound on his writings about sex and the doctrinal position of the Church of Scientology; and third, I examine recent allegations affecting the Sea Org due to defectors’ claims that pregnant women were forced to have abortions. Additionally, I adduce some comparative material from the biography of Sun Myung Moon, founder of the Unification Church, who manifested a similar disconnect between his personal life and his conservative teachings on sex. In the Church of Scientology, sexual orientation and activity are prime sites of control experienced by all its members, but in particular among the elite corps of the Sea Org.

Behavioural responses of talitrid amphipods to recreational pressures on oceanic tropical beaches with contrasting extension

Ocean sandy beaches are prime sites for human recreation. The integrity of these ecosystems may suffer greatly from tourism-related pressures. Behavioural adaptations of fauna are key traits as responses to environmental pressures and short time changes. In particular, orientation performance of talitrid amphipods to recover the optimal zone on the beach has been proposed as bioindicator of shoreline stability, mainly related to sedimentary dynamics and geomorphological changes. The question focused here was whether recreational activities and urbanisation may influence orientation performance of talitrids on oceanic tropical beaches with contrasting extension (beach length).Field orientation experiments were performed during Spring 2014 testing populations of the talitrid Atlantorchestoidea brasiliensis on four tropical beaches at Rio de Janeiro (Brazil), selected according to their human access (two with and two without public access) and length (two pocket and two extended beaches). The influence of landscape cues on the orientation of talitrids was experimentally tested in two etho-assay conditions: with and without the landscape vision. Talitrids used landscape cues and sun compass to orient seawards and the highest precision of orientation was recorded in the pocket beach without human access. A more scattered response was observed in the urbanised pocket beach under conditions of screened landscape and when the sun was veiled or covered by clouds, showing the importance of the local landscape features in these conditions. The populations from the extended beaches showed a similar and more scattered orientation, which may be interpreted as behavioural plasticity to cope with beach natural changes, disregarding human pressure on the beaches. The behavioural performances of talitrids on the four tropical beaches varied according to different human pressure conditions and beach extension, confirming the reliability of the use of talitrid orientation as bioindicator of beach changeability.

Subtype analysis of Blastocystis isolates using SSU rRNA-DNA sequencing in rural and urban population in southern Turkey

Blastocystis is a common and emerging parasite often seen in many studies conducted in urban population, with scanty reports on rural communities. However, little is known about the public health significance of Blastocystis infection. A total of 28 Blastocystis isolates from 17 (17/28, 60.71%) patients living in rural area and 11 (11/28, 39.29%) patients living in urban area were screened with seven kinds of sequenced-tagged site primers for identification of subtype. PCR products were sequenced with same combination of primers using the BigDye Terminator V 3.1 cycle sequencing kit, as per the manufacturers’ protocol on the 3730 DNA analyzer (Applied Biosystems, Carlsbad CA, USA). The cross-comparison of the Blastocystis sequences of samples were determined by the neighbor-joining method based on a distance matrix between sequence pairs to generate dendograms. The following subtypes were identified; subtype 1 (10/28, 35.7%), subtype 3 (7/28, 25.0%), subtype 2 (5/28, 17.8%), subtype 4 (3/28, 10.7%), subtype 5 (1/28, 3.6%), subtype 6 (1/28, 3.6%), and subtype 7 (1/28, 3.6%) in all DNA samples. The comparison of Blastocystis subtypes distribution among the patients from rural and urban area revealed subtype 5 (1/17, 5.9%), subtype 6 (1/17, 5.9%) and subtype 7 (1/17, 5.9%) from patients of rural area but not any of these subtypes in patients living urban area. This study is the first large-scale study to examine the occurrence of Blastocystis in Turkey to shed lights on the cosmopolitan distribution of Blastocystis subtypes in southern part of Turkey. Subtype 5, subtype 6 and subtype 7 were determined in only rural area. The findings of this study suggest that Blastocystis is transmitted from animal to human and possess a zoonotic potential.

Specificity characterization of the α-mating factor hormone by Kex2 protease.

Kex2 is a Ca2+-dependent serine protease from S.cerevisiae. Characterization of the substrate specificity of Kex2 is of particular interest because this protease serves as the prototype of a large family of eukaryotic subtilisin-related proprotein-processing proteases that cleave sites consisting of pairs or clusters of basic residues. Our goal was to study the prime region subsite S' of Kex2 because previous studies have only taken into account non-prime sites using AMC substrates but not the specificity of prime sites identified through structural modeling or predicted cleavage sites. Therefore, we used peptides derived from Abz-KR↓EADQ-EDDnp and Abz-YKR↓EADQ-EDDnp based on the pro-α-mating factor sequence. The specificity of Kex2 due to basic residues at P1' is affected by the type of residue in the P3 position. Some residues in P1' with large or bulky side chains yielded poor substrate specificity. The kcat/KM values for peptides with P2' substitutions containing Tyr in P3 were higher than those obtained for the peptides without Tyr. In fact, P' and P modifications mainly promoted changes in kcat and KM, respectively. The pH profile of Kex2 was fit to a double-sigmoidal pH-titration curve. The specificity results suggest that Kex2 might be involved in the processing of the putative cleavage sites in a polypeptide involved in cell elongation, hyphal formation and the processing of a toxin, which result in host cell lysis. In summary, the specificity of Kex2 is dependent on the set of interactions with prime and non-prime subsites, resulting in synergism.