A global view of the nonprotein-coding transcriptome in Plasmodium falciparum

Nonprotein-coding RNAs (npcRNAs) represent an important class of regulatory molecules that act in many cellular pathways. Here, we describe the experimental identification and validation of the small npcRNA transcriptome of the human malaria parasite Plasmodium falciparum. We identified 630 novel npcRNA candidates. Based on sequence and structural motifs, 43 of them belong to the C/D and H/ACA-box subclasses of small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs). We further observed the exonization of a functional H/ACA snoRNA gene, which might contribute to the regulation of ribosomal protein L7a gene expression. Some of the small npcRNA candidates are from telomeric and subtelomeric repetitive regions, suggesting their potential involvement in maintaining telomeric integrity and subtelomeric gene silencing. We also detected 328 cis-encoded antisense npcRNAs (asRNAs) complementary to P. falciparum protein-coding genes of a wide range of biochemical pathways, including determinants of virulence and pathology. All cis-encoded asRNA genes tested exhibit lifecycle-specific expression profiles. For all but one of the respective sense–antisense pairs, we deduced concordant patterns of expression. Our findings have important implications for a better understanding of gene regulatory mechanisms in P. falciparum, revealing an extended and sophisticated npcRNA network that may control the expression of housekeeping genes and virulence factors

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Optical Diffraction Radiation Interference as a Non-Intercepting Emittance Measurement for Hight Brightness and High Repetition Rate Electron Beam

Conventional intercepting transverse electron beam diagnostics, as the one based on Optical Transition Radiation (OTR), cannot tolerate high power beams without significant mechanical damages of the diagnostics device. Optical Diffraction Radiation (ODR), instead, is an excellent candidate for the measurements of the transverse phase space parameters in a non-intercepting way. One of the main limitations of this method is the low signal to noise ratio, mainly due to the synchrotron radiation background. This problem can be overcome by using ODRI (ODR Interference). In this case the beam goes through slits opened in two metallic foils placed at a distance shorter than the radiationformation zone. Due to the shielding effect of the first screen a nearly background-free ODR interference pattern can be measured allowing the determination of the beam size and the angular divergence. We report here the result of the first measurements of the beam emittance using ODRI carried out at FLASH (DESY). Our result demonstrates the potential of this technique suitable to be used as non-intercepting diagnostic for accelerators operated with high brightness and high repetition rate electron beams

Adenylation-Dependent Conformation and Unfolding Pathways of the NAD(+)-Dependent DNA Ligase from the Thermophile Thermus scotoductus

In the last few years, an increased attention has been focused on NAD(+)-dependent DNA ligases. This is mostly due to their potential use as antibiotic targets, because effective inhibition of these essential enzymes would result in the death of the bacterium. However, development of an efficient drug requires that the conformational modifications involved in the catalysis of NAD(+)-dependent DNA ligases are understood. From this perspective, we have investigated the conformational changes occurring in the thermophilic Thermus scotoductus NAD(+)-DNA ligase upon adenylation, as well as the effect of cofactor binding on protein resistance to thermal and chemical (guanidine hydrochloride) denaturation. Our results indicate that cofactor binding induces conformational rearrangement within the active site and promotes a compaction of the enzyme. These data support an induced “open-closure” process upon adenylation, leading to the formation of the catalytically active enzyme that is able to bind DNA. These conformational changes are likely to be associated with the protein function, preventing the formation of nonproductive complexes between deadenylated ligases and DNA. In addition, enzyme adenylation significantly increases resistance of the protein to thermal denaturation and GdmCl-induced unfolding, establishing a thermodynamic link between ligand binding and increased conformational stability. Finally, chemical unfolding of deadenylated and adenylated enzyme is accompanied by accumulation of at least two equilibrium intermediates, the molten globule and premolten globule states. Maximal populations of these intermediates are shifted toward higher GdmCl concentrations in the case of the adenylated ligase. These data provide further insights into the properties of partially folded intermediates

First Experience with the Standard Diagnostics at the European XFEL Injector

International audienceThe injector of the European XFEL is in operation since December 2015. It includes, beside the gun and the accelerating section, containing 1.3 and a 3.9 GHz accelerating module, a variety of standard diagnostics systems specially designed for this facility. With very few exceptions, all types of diagnostics systems are installed in the injector. Therefore the operation of the injector is served to validate and prove the diagnostics characteristics for the complete European XFEL. Most of the standard diagnostics has been available for the start of beam operation and showed the evidence of first beam along the beam line. In the following months the diagnostics has been optimized and used for improvements of beam quality. First operational experiences and results from the standard beam diagnostics in the injector of the European XFEL will be reported in this contribution

Venous Thromboembolism Risk and Prophylaxis in the Acute Care Hospital Setting (ENDORSE Survey) Findings in Surgical Patients

Objective: To evaluate venous thromboembolism (VTE) risk in patients who underwent a major operation, including the use of, and factors influencing, American College of Chest Physicians-recommended types of VTE prophylaxis

Venous thromboembolism risk and prophylaxis in hospitalised medically ill patients The ENDORSE Global Survey

Limited data are available regarding the risk for venous thromboembolism (VIE) and VIE prophylaxis use in hospitalised medically ill patients. We analysed data from the global ENDORSE survey to evaluate VTE risk and prophylaxis use in this population according to diagnosis, baseline characteristics, and country. Data on patient characteristics, VIE risk, and prophylaxis use were abstracted from hospital charts. VTE risk and prophylaxis use were evaluated according to the 2004 American College of Chest Physicians (ACCP) guidelines. Multivariable analysis was performed to identify factors associated with use of ACCP-recommended prophylaxis. Data were evaluated for 37,356 hospitalised medical patients across 32 countries. VIE risk varied according to medical diagnosis, from 31.2% of patients with gastrointestinal/hepatobiliary diseases to 100% of patients with acute heart failure, active noninfectious respiratory disease, or pulmonary infection (global rate, 41.5%). Among those at risk for VTE, ACCP-recommended prophylaxis was used in 24.4% haemorrhagic stroke patients and 40-45% of cardiopulmonary disease patients (global rate, 39.5%). Large differences in prophylaxis use were observed among countries. Markers of disease severity, including central venous catheters, mechanical ventilation, and admission to intensive care units, were strongly associated with use of ACCP-recommended prophylaxis. In conclusion, VIE risk varies according to medical diagnosis. Less than 40% of at-risk hospitalised medical patients receive ACCP-recommended prophylaxis. Prophylaxis use appears to be associated with disease severity rather than medical diagnosis. These data support the necessity to improve implementation of available guidelines for evaluating VIE risk and providing prophylaxis to hospitalised medical patients