Cytomegalovirus sequence variability, amplicon length, and DNase-sensitive non-encapsidated genomes are obstacles to standardization and commutability of plasma viral load results

Background: Cytomegalovirus (CMV) management post-transplantation relies on quantification in blood, but inter-laboratory and inter-assay variability impairs commutability. An international multicenter study demonstrated that variability is mitigated by standardizing plasma volumes, automating DNA extraction and amplification, and calibration to the 1st-CMV-WHO-International-Standard as in the FDA-approved Roche-CAP/CTMCMV. However, Roche-CAP/CTM-CMV showed under-quantification and false-negative results in a quality assurance program (UK-NEQAS-2014). Objectives: To evaluate factors contributing to quantification variability of CMV viral load and to develop optimized CMV-UL54-QNAT. Study design: The UL54 target of the UK-NEQAS-2014 variant was sequenced and compared to 329 available CMV GenBank sequences. Four Basel-CMV-UL54-QNAT assays of 361 bp, 254 bp, 151 bp, and 95 bp amplicons were developed that only differed in reverse primer positions. The assays were validated using plasmid dilutions, UK-NEQAS-2014 sample, as well as 107 frozen and 69 prospectively collected plasma samples from transplant patients submitted for CMV QNAT, with and without DNase-digestion prior to nucleic acid extraction. Results: Eight of 43 mutations were identified as relevant in the UK-NEQAS-2014 target. All Basel-CMV-UL54 QNATs quantified the UK-NEQAS-2014 but revealed 10-fold increasing CMV loads as amplicon size decreased. The inverse correlation of amplicon size and viral loads was confirmed using 1st-WHO-International-Standard and patient samples. DNase pre-treatment reduced plasma CMV loads by > 90% indicating the presence of unprotected CMV genomic DNA. Conclusions: Sequence variability, amplicon length, and non-encapsidated genomes obstruct standardization and commutability of CMV loads needed to develop thresholds for clinical research and management. Besides regular sequence surveys, matrix and extraction standardization, we propose developing reference calibrators using 100 bp amplicons.Peer reviewe

Female bone physiology resilience in 750-300 BP ‘Polynesian Outlier’ community

Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in n = 69 individuals from 750 – 300 BP Taumako in Solomon Islands, a remote ‘Polynesian Outlier’ island in Melanesia. We tested whether bone remodelling indicators differed between age-at-death groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-to-osteon (~10%) did not differ between the sexes. Compared to males, the femora of Taumako females experienced higher frequencies of remodelling events, which mirrors bone health paradigms through the life-course today. However, contrary to modern populations, female femoral bone tissue did not decline with age. This matches findings in other archaeological samples, and is testament to ancient female bone physiology resilience also in the Pacific region.Introduction - The importance of bone remodelling through human life-course - Bone remodelling in archaeological humans Results - Trends in bone remodelling at Taumako Discussion - Sex-specific trends in cortical bone remodelling - Bone remodelling with age at Taumako Limitations and remarks on temporal and spatial data Conslusions Materials and Method

Female bone physiology resilience in a past Polynesian Outlier community

Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in 69 individuals from ca. 440–150 BP Taumako in Solomon Islands, a remote ‘Polynesian Outlier’ island in Melanesia. We tested whether bone remodelling indicators differed between age groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-osteon (~ 8%) did not differ between the sexes. Our results indicate that, compared to males, localised femoral bone tissue of the Taumako females did not drastically decline with age, contrary to what is often observed in modern populations. However, our results match findings in other archaeological samples—a testament to past female bone physiology resilience, also now observed in the Pacific region.Introduction - Bone remodelling through human life‑course. - Bone remodelling in archaeological humans. Results - Femoral vascular porosity and bone remodelling indicators at Taumako. Discussion - Sex and cortical bone histology at Taumako. - The effect of age on bone histology at Taumako. Remarks on temporal and spatial bone histology data Limitations Conclusions Materials and method

Magnetic state of plutonium ion in metallic Pu and its compounds

By LDA+U method with spin-orbit coupling (LDA+U+SO) the magnetic state and electronic structure have been investigated for plutonium in \delta and \alpha phases and for Pu compounds: PuN, PuCoGa5, PuRh2, PuSi2, PuTe, and PuSb. For metallic plutonium in both phases in agreement with experiment a nonmagnetic ground state was found with Pu ions in f^6 configuration with zero values of spin, orbital, and total moments. This result is determined by a strong spin-orbit coupling in 5f shell that gives in LDA calculation a pronounced splitting of 5f states on f^{5/2} and f^{7/2} subbands. A Fermi level is in a pseudogap between them, so that f^{5/2} subshell is already nearly completely filled with six electrons before Coulomb correlation effects were taken into account. The competition between spin-orbit coupling and exchange (Hund) interaction (favoring magnetic ground state) in 5f shell is so delicately balanced, that a small increase (less than 15%) of exchange interaction parameter value from J_H=0.48eV obtained in constrain LDA calculation would result in a magnetic ground state with nonzero spin and orbital moment values. For Pu compounds investigated in the present work, predominantly f^6 configuration with nonzero magnetic moments was found in PuCoGa5, PuSi2, and PuTe, while PuN, PuRh2, and PuSb have f^5 configuration with sizeable magnetic moment values. Whereas pure jj coupling scheme was found to be valid for metallic plutonium, intermediate coupling scheme is needed to describe 5f shell in Pu compounds. The results of our calculations show that both spin-orbit coupling and exchange interaction terms in the Hamiltonian must be treated in a general matrix form for Pu and its compounds.Comment: 20 pages, LaTeX; changed discussion on reference pape

Absence of system xc⁻ on immune cells invading the central nervous system alleviates experimental autoimmune encephalitis

Background: Multiple sclerosis (MS) is an autoimmune demyelinating disease that affects the central nervous system (CNS), leading to neurodegeneration and chronic disability. Accumulating evidence points to a key role for neuroinflammation, oxidative stress, and excitotoxicity in this degenerative process. System x(c)- or the cystine/glutamate antiporter could tie these pathological mechanisms together: its activity is enhanced by reactive oxygen species and inflammatory stimuli, and its enhancement might lead to the release of toxic amounts of glutamate, thereby triggering excitotoxicity and neurodegeneration. Methods: Semi-quantitative Western blotting served to study protein expression of xCT, the specific subunit of system x(c)-, as well as of regulators of xCT transcription, in the normal appearing white matter (NAWM) of MS patients and in the CNS and spleen of mice exposed to experimental autoimmune encephalomyelitis (EAE), an accepted mouse model of MS. We next compared the clinical course of the EAE disease, the extent of demyelination, the infiltration of immune cells and microglial activation in xCT-knockout (xCT(-/-)) mice and irradiated mice reconstituted in xCT(-/-) bone marrow (BM), to their proper wild type (xCT(+/+)) controls. Results: xCT protein expression levels were upregulated in the NAWM of MS patients and in the brain, spinal cord, and spleen of EAE mice. The pathways involved in this upregulation in NAWM of MS patients remain unresolved. Compared to xCT(+/+) mice, xCT(-/-) mice were equally susceptible to EAE, whereas mice transplanted with xCT(-/-) BM, and as such only exhibiting loss of xCT in their immune cells, were less susceptible to EAE. In none of the above-described conditions, demyelination, microglial activation, or infiltration of immune cells were affected. Conclusions: Our findings demonstrate enhancement of xCT protein expression in MS pathology and suggest that system x(c)- on immune cells invading the CNS participates to EAE. Since a total loss of system x(c)- had no net beneficial effects, these results have important implications for targeting system x(c)- for treatment of MS

Acclimation in plants - the Green Hub consortium

Acclimation is the capacity to adapt to environmental changes within the lifetime of an individual. This ability allows plants to cope with the continuous variation in ambient conditions to which they are exposed as sessile organisms. Because environmental changes and extremes are becoming even more pronounced due to the current period of climate change, enhancing the efficacy of plant acclimation is a promising strategy for mitigating the consequences of global warming on crop yields. At the cellular level, the chloroplast plays a central role in many acclimation responses, acting both as a sensor of environmental change and as a target of cellular acclimation responses. In this Perspective article, we outline the activities of the Green Hub consortium funded by the German Science Foundation. The main aim of this research collaboration is to understand and strategically modify the cellular networks that mediate plant acclimation to adverse environments, employing Arabidopsis, tobacco (Nicotiana tabacum) and Chlamydomonas as model organisms. These efforts will contribute to 'smart breeding' methods designed to create crop plants with improved acclimation properties. To this end, the model oilseed crop Camelina sativa is being used to test modulators of acclimation for their potential to enhance crop yield under adverse environmental conditions. Here we highlight the current state of research on the role of gene expression, metabolism and signalling in acclimation, with a focus on chloroplast-related processes. In addition, further approaches to uncovering acclimation mechanisms derived from systems and computational biology, as well as adaptive laboratory evolution with photosynthetic microbes, are highlighted

Comparative descriptions of eggs from three species of Rhodnius (Hemiptera: Reduviidae: Triatominae)

The authors describe and compare the morphological and ultrastructural characteristics of eggs from the three most recent described species of the genus Rhodnius Stål, 1859, which have not previously been studied. These species are Rhodnius colombiensis (Mejia, Galvão & Jurberg 1999), Rhodnius milesi (Carcavallo, Rocha, Galvão & Jurberg 2001) and Rhodnius stali (Lent, Jurberg & Galvão 1993). The results revealed that there are similarities in the exochorial architecture of optical microscopy and scanning electron microscopy; these include the predominance of hexagonal cells that are common to all Rhodnius species and variable degrees of lateral flattening, which is common not only to species of this genus, but also to the Rhodniini tribe. Differences in overall colour, the presence of a collar in R. milesi, a longitudinal bevel in R. stali and the precise length of R. colombiensis can be useful distinguishing features. As a result of this study, the key for egg identification proposed by Barata in 1981 can be updated.European Community - Chagas Disease Intervention ActivitiesCNPqCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES

Ultrafast All-Polymer Paper-Based Batteries

Conducting polymers for battery applications have been subject to numerous investigations during the last two decades. However, the functional charging rates and the cycling stabilities have so far been found to be insufficient for practical applications. These shortcomings can, at least partially, be explained by the fact that thick layers of the conducting polymers have been used to obtain sufficient capacities of the batteries. In the present letter, we introduce a novel nanostructured high-surface area electrode material for energy storage applications composed of cellulose fibers of algal origin individually coated with a 50 nm thin layer of polypyrrole. Our results show the hitherto highest reported charge capacities and charging rates for an all polymer paper-based battery. The composite conductive paper material is shown to have a specific surface area of 80 m2 g-1 and batteries based on this material can be charged with currents as high as 600 mA cm-2 with only 6 % loss in capacity over 100 subsequent charge and discharge cycles. The aqueous-based batteries, which are entirely based on cellulose and polypyrrole and exhibit charge capacities between 25 and 33 mAh g-1 or 38-50 mAh g-1 per weight of the active material, open up new possibilities for the production of environmentally friendly, cost efficient, up-scalable and lightweight energy storage systems. There is currently a great interest in the development of thin, flexible, lightweight, and environmentally friendly batteries and supercapacitors.1 In this process, the preparation of novel redox polymer and electronically conducting polymer-base

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

A contiguous assembly of the inbred ‘EL10’ sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly was 540 Mb, of which 96.2% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNA-seq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals producing estimates from 633 to 875 Mb/1C. Read-depth mapping with short-read whole-genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation

CXCL12-Mediated Guidance of Migrating Embryonic Stem Cell-Derived Neural Progenitors Transplanted into the Hippocampus

Stem cell therapies for neurodegenerative disorders require accurate delivery of the transplanted cells to the sites of damage. Numerous studies have established that fluid injections to the hippocampus can induce lesions in the dentate gyrus (DG) that lead to cell death within the upper blade. Using a mouse model of temporal lobe epilepsy, we previously observed that embryonic stem cell-derived neural progenitors (ESNPs) survive and differentiate within the granule cell layer after stereotaxic delivery to the DG, replacing the endogenous cells of the upper blade. To investigate the mechanisms for ESNP migration and repair in the DG, we examined the role of the chemokine CXCL12 in mice subjected to kainic acid-induced seizures. We now show that ESNPs transplanted into the DG show extensive migration through the upper blade, along the septotemporal axis of the hippocampus. Seizures upregulate CXCL12 and infusion of the CXCR4 antagonist AMD3100 by osmotic minipump attenuated ESNP migration. We also demonstrate that seizures promote the differentiation of transplanted ESNPs toward neuronal rather than astrocyte fates. These findings suggest that ESNPs transplanted into the adult rodent hippocampus migrate in response to cytokine-mediated signals