bluuebunny/crossref_metadata_2025 huggingface dataset:
A Meta-Analysis and Systematic Review of Perioperative Outcomes of Laparoscopic-assisted Rectal Resection (LARR) Versus Open Rectal Resection (ORR) for Carcinoma
Authors: Memon Muhammed A. , Yunus Rossita M. , Memon Breda , Awaiz Aiman , Khan Shahjahan
Published: October 2018

Aims and Objectives:

The aim was to conduct a systematic review and meta-analysis of the randomized evidence to determine the relative merits of perioperative outcomes of laparoscopic-assisted (LARR) versus open rectal resection (ORR) for proven rectal cancer.

Materials and Methods:

A search of the Medline, Embase, Science Citation Index, Current Contents and PubMed databases identified English-language randomized clinical trials comparing LARR and ORR. The meta-analysis was prepared in accordance with the PRISMA statement. Thirteen outcome variables were analyzed. Random effects meta-analyses were performed due to heterogeneity.

Results:

A total of 14 randomized clinical trials that included 3843 rectal resections (LARR 2096, ORR 1747) were analyzed. The summary point estimates favored LARR for the intraoperative blood loss, commencement of oral intake, first bowel movement, and length of hospital stay. There was significantly longer duration of operating time of 38.29 minutes for the LARR group. Other outcome variables such as total complications, postoperative pain, postoperative ileus, abdominal abscesses, postoperative anastomotic leak, reintervention and postoperative mortality rates were found to have comparable outcomes for both cohorts.

Conclusions:

LARR was associated with significantly reduced blood loss, quicker resumption of oral intake, earlier return of gastrointestinal function, and shorter length of hospital stay at the expense of significantly longer operating time. Postoperative morbidity and mortality and analgesia requirement for both these groups were comparable. LARR seems to be a safe and effective alternative to ORR; however, it needs to be performed in established colorectal units with experienced laparoscopic surgeons.
Hypoxia weakens mussel attachment by interrupting DOPA cross-linking during adhesive plaque curing
Authors: George Matthew N. , Pedigo Benjamin , Carrington Emily
Published: October 2018

Marine mussels (Mytilusspp.) attach to a wide variety of surfaces underwater using a network of byssal threads, each tipped with a protein-based adhesive plaque that uses the surrounding seawater environment as a curing agent. Plaques undergo environmental post-processing, requiring a basic seawater pH be maintained for up to 8 days for the adhesive to strengthen completely. Given the sensitivity of plaques to local pH conditions long after deposition, we investigated the effect of other aspects of the seawater environment that are known to vary in nearshore habitats on plaque curing. The effect of seawater temperature, salinity and dissolved oxygen concentration were investigated using tensile testing, atomic force microscopy and amino acid compositional analysis. High temperature (30°C) and hyposalinity (1 PSU) had no effect on adhesion strength, while incubation in hypoxia (0.9 mg l−1) caused plaques to have a mottled coloration and prematurely peel from substrates, leading to a 51% decrease in adhesion strength. AFM imaging of the plaque cuticle found that plaques cured in hypoxia had regions of lower stiffness throughout, indicative of reductions in DOPA cross-linking between adhesive proteins. A better understanding of the dynamics of plaque curing could aid in the design of better synthetic adhesives, particularly in medicine where adhesion must take place within wet body cavities.
The cost of infection:Argulus foliaceusand its impact on the swimming performance of the three-spined stickleback (Gasterosteus aculeatus)
Authors: Stewart A. , Hunt R. , Mitchell R. , Muhawenimana V. , Wilson C. A. M. E. , Jackson J. A. , Cable J.
Published: October 2018

For fish, there can be multiple consequences of parasitic infections, including the physical impacts on swimming and the pathological costs of infection. This study used the three-spined stickleback (Gasterosteus aculeatus) and the ectoparasitic fish louse,Argulus foliaceus, to assess both physical (including form drag and mass) and pathological effects of infection. Both sustained (prolonged swimming within an open channel flume) and burst (C-start) swimming performance were measured on individual fish before (trials 1–2) and after infection (trials 3–5). Experimental infection occurred shortly before the third trial, when the physical impacts of infection could be separated from any subsequent pathology as transmission of adult parasites causes instantaneous drag effects prior to observable pathology. Despite the relatively large size of the parasite and corresponding increase in hydrodynamic drag for the host, there were no observable physical effects of infection on either sustained or burst host swimming. By contrast, parasite-induced pathology is the most probable explanation for reduced swimming performance across both tests. All sticklebacks displayed a preference for flow refugia, swimming in low-velocity regions of the flume, and this preference increased with both flow rate and infection time. This study suggests that even with large, physically demanding parasites their induced pathology is of greater concern than direct physical impact.
Living in a trash can: turbulent convective flows impairDrosophilaflight performance
Authors: Ortega-Jiménez Victor Manuel , Combes Stacey A.
Published: October 2018

Turbulent flows associated with thermal convection are common in areas where the ground is heated by solar radiation, fermentation or other processes. However, it is unknown how these flow instabilities affect the locomotion of small insects, like fruit flies, that inhabit deserts and urban landscapes where surface temperatures can reach extreme values. We quantified flight performance of fruit flies (Drosophila melanogaster) traversing a chamber through still air and turbulent Rayleigh–Bénard convection cells produced by a vertical temperature gradient. A total of 34% of individuals were unable to reach the end of the chamber in convection, although peak flow speeds were modest relative to typical outdoor airflow. Individuals that were successful in convection were faster fliers and had larger wing areas than those that failed. All flies displayed higher pitch angles and lower mean flight speeds in convection. Successful individuals took longer to cross the chamber in convection, due to lower flight speeds and greater path sinuosity. All individuals displayed higher flapping frequencies in convection, and successful individuals also reduced stroke amplitude. Our results suggest that thermal convection poses a significant challenge for small fliers, resulting in increased travel times and energetic costs, or in some cases precluding insects from traversing these environments entirely.
Seeing is believing: methods to monitor vertebrate autophagy
in vivo
Authors: Lopez Ana , Fleming Angeleen , Rubinsztein David C.
Published: October 2018

Autophagy is an intracellular clearance pathway that delivers cytoplasmic contents to the lysosome for degradation. It plays a critical role in maintaining protein homeostasis and providing nutrients under conditions where the cell is starved. It also helps to remove damaged organelles and misfolded or aggregated proteins. Thus, it is not surprising that defects in this pathway are associated with a variety of pathological conditions, such as neurodegeneration, cancer and infection. Pharmacological upregulation of autophagy is considered a promising therapeutic strategy for the treatment of neurodegenerative and infectious diseases. Studies in knockout mice have demonstrated that autophagy is essential for nervous system function, and data from invertebrate and vertebrate models suggest that the efficiency of autophagic processes generally declines with age. However, much of our understanding of the intracellular regulation of autophagy comes from
in vitro
studies, and there is a paucity of knowledge about how this process is regulated within different tissues and during the processes of ageing and disease. Here, we review the available tools to probe these questions
in vivo
within vertebrate model systems. We discuss how these tools have been used to date and consider future avenues of research.
Vertebral morphometrics and lung structure in non-avian dinosaurs
Authors: Brocklehurst Robert J. , Schachner Emma R. , Sellers William I.
Published: October 2018

The lung-air sac system of modern birds is unique among vertebrates. However, debate surrounds whether an avian-style lung is restricted to birds or first appeared in their dinosaurian ancestors, as common osteological correlates for the respiratory system offer limited information on the lungs themselves. Here, we shed light on these issues by using axial morphology as a direct osteological correlate of lung structure, and quantifying vertebral shape using geometric morphometrics in birds, crocodilians and a wide range of dinosaurian taxa. Although fully avian lungs were a rather late innovation, we quantitatively show that non-avian dinosaurs and basal dinosauriforms possessed bird-like costovertebral joints and a furrowed thoracic ceiling. This would have immobilized the lung's dorsal surface, a structural prerequisite for a thinned blood-gas barrier and increased gas exchange potential. This could have permitted high levels of aerobic and metabolic activity in dinosaurs, even in the hypoxic conditions of the Mesozoic, contributing to their successful radiation.
A two-step probing method to compare lysine accessibility across macromolecular complex conformations
Authors: MacRae Andrew J. , Coltri Patricia , Hrabeta-Robinson Eva , Chalkley Robert J. , Burlingame A.L. , Jurica Melissa S.
Published: October 2018

Structural models of multi-megadalton molecular complexes are appearing in increasing numbers, in large part because of technical advances in cryo-electron microscopy realized over the last decade. However, the inherent complexity of large biological assemblies comprising dozens of components often limits the resolution of structural models. Furthermore, multiple functional configurations of a complex can leave a puzzle as to how one intermediate moves to the next stage. Orthogonal biochemical information is crucial to understanding the molecular interactions that drive those rearrangements. We present a two-step method for chemical probing detected by tandem mass-spectrometry to globally assess the reactivity of lysine residues within purified macromolecular complexes. Because lysine side chains often balance the negative charge of RNA in ribonucleoprotein complexes, the method is especially powerful for detecting changes in protein-RNA interactions. Probing the E. coli 30S ribosome subunit showed that the reactivity pattern of lysine residues quantitatively reflects structure models from X-ray crystallography. We assessed differences in two conformations of purified human spliceosomes. Our results demonstrate that this method supplies powerful biochemical information that aids in functional interpretation of atomic models of macromolecular complexes at the intermediate resolution often provided by cryo-electron microscopy.
Liver ultrasound elastography for the evaluation of periportal fibrosis in schistosomiasis mansoni: A cross-sectional study
Authors: Santos Joelma Carvalho , Batista Andrea Dória , Vasconcelos Carla Maria Mola , Lemos Roberto Souza , de Souza Valter Romão , Dessein Alain , Dessein Hélia , Montenegro Silvia Maria Lucena , Almeida Lopes Edmundo Pessoa , Domingues Ana Lúcia Coutinho
Published: October 2018

Background

ARFI elastrography has been used as a noninvasive method to assess the severity of liver fibrosis in viral hepatitis, although with few studies in schistosomiasis mansoni. We aimed to evaluate the performance of point shear wave elastography (pSWE) for predicting significant periportal fibrosis (PPF) in schistosomotic patients and to determine its best cutoff point.

Methodology/Principal findings

This cross-sectional study included 358 adult schistosomotic patients subjected to US and pSWE on the right lobe. Two hundred two patients (62.0%) were women, with a median age of 54 (ranging 18-92) years. The pSWE measurements were compared to the US patterns of PPF, as gold standard, according to the Niamey classification. The performance of pSWE was calculated as the area under the ROC curve (AUC). Patients were further classified into two groups: 86 patients with mild PPF and 272 patients with significant PPF. The median pSWE of the significant fibrosis group was higher (1.40 m/s) than that of mild fibrosis group (1.14 m/s, p<0.001). AUC was 0.719 with ≤1.11 m/s as the best cutoff value for excluding significant PPF. Sensitivity and negative predictive values were 80.5% and 40.5%, respectively. Whereas, for confirming significant PPF, the best cutoff value was >1.39 m/s, with specificity of 86.1% and positive predictive value of 92.0%.

Conclusions/Significance

pSWE was able to differentiate significant from mild PPF, with better performance to predict significant PPF.

Author summary

In the developing world, over 207 million people are infected with parasitic Schistosoma worms. Among the species of Schistosoma that infect humans Schistosoma mansoni is one of the most common causes of illness. Here, we investigated the performance of point shear wave elastography (pSWE) for predicting significant periportal fibrosis (PPF) in schistosomotic patients and to determine its best cutoff point. We examined 358 people from northeast of Brazil for Schistosoma infections. The present study showed that pSWE was able to differentiate significant from mild PPF, with better performance to predict significant PPF.
MR-PET head motion correction based on co-registration of multi-contrast MR images
Authors: Chen Zhaolin , Sforazzini Francesco , Baran Jakub , Close Thomas , Jon Shah N. , Egan Gary F.
Published: October 2018

Head motion is a major source of image artefacts in neuroimaging studies and can lead to degradation of the quantitative accuracy of reconstructed PET images. Simultaneous Magnetic Resonance-Positron Emission Tomography (MR-PET) makes it possible to estimate head motion information from high-resolution MR images and then correct motion artefacts in PET images. In this paper, we introduce a fully automated PET motion correction method, MR-guided MAF, based on the co-registration of multi-contrast MR images. The performance of the MR-guided MAF method was evaluated using MR-PET data acquired from a cohort of ten healthy participants who received a slow infusion of fluorodeoxyglucose ([18-F]FDG). Compared with conventional methods, MR guided PET image reconstruction can reduce head motion introduced artefacts and improve the image sharpness and quantitative accuracy of PET images acquired using simultaneous MR-PET scanners. The fully automated motion estimation method has been implemented as a publicly available web-service.
Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy byStreptomyces
Authors: Avalos Mariana , Garbeva Paolina , Raaijmakers Jos M. , van Wezel Gilles P.
Published: October 2018

Soil-inhabiting streptomycetes are Nature’s medicine makers, producing over half of all known antibiotics and many other bioactive natural products. However, these bacteria also produce many volatile compounds, and research into these molecules and their role in soil ecology is rapidly gaining momentum. Here we show that streptomycetes have the ability to kill bacteria over long distances via air-borne antibiosis. Our research shows that streptomycetes do so by producing surprisingly high amounts of the low-cost volatile antimicrobial ammonia, which travels over long distances and antagonises both Gram-positive and Gram-negative bacteria. Glycine is required as precursor to produce ammonia, and inactivation of the glycine cleavage system annihilated air-borne antibiosis. As a resistance strategy,E. colicells acquired mutations resulting in reduced expression of the porin master regulator OmpR and its cognate kinase EnvZ, which was just enough to allow them to survive. We further show that ammonia enhances the activity of the more costly canonical antibiotics, suggesting that streptomycetes adopt a low-cost strategy to sensitize competitors for antibiosis over longer distances.
Learning of distant state predictions by the orbitofrontal cortex in humans
Authors: Wimmer G. Elliott , Büchel Christian
Published: October 2018

Representations of our future environment are essential for planning and decision making. Previous research in humans has demonstrated that the hippocampus is a critical region for forming and retrieving associations, while the medial orbitofrontal cortex (OFC) is an important region for representing information about recent states. However, it is not clear how the brain acquires predictive representations during goal-directed learning. Here, we show using fMRI that while participants learned to find rewards in multiple different Y-maze environments, hippocampal activity was highest during initial exposure and then decayed across the remaining repetitions of each maze, consistent with a role in rapid encoding. Importantly, multivariate patterns in the OFC-VPFC came to represent predictive information about upcoming states approximately 30 seconds in the future. Our findings provide a mechanism by which the brain can build models of the world that span long-timescales to make predictions.
Massive gene amplification on a recently formed Drosophila Y chromosome
Authors: Bachtrog Doris , Mahajan Shivani , Bracewell Ryan
Published: October 2018

Widespread loss of genes on the Y is considered a hallmark of sex chromosome differentiation. Here we show that the initial stages of Y evolution are driven by massive amplification of distinct classes of genes. The neo-Y chromosome ofDrosophila mirandainitially contained about 3000 protein-coding genes, but has gained over 3200 genes since its formation about 1.5 MY ago, primarily by tandem amplification of protein-coding genes ancestrally present on this chromosome. We show that distinct evolutionary processes may account for this drastic increase in gene number on the Y. Testis-specific and dosage sensitive genes appear to have amplified on the Y to increase male fitness. A distinct class of meiosis-related multi-copy Y genes independently co-amplified on the X, and their expansion is likely driven by conflicts over segregation. Co-amplified X/Y genes are highly expressed in testis, enriched for meiosis and RNAi functions, and are frequently targeted by small RNAs in testis. This suggests that their amplification is driven by X vs. Y antagonism for increased transmission, where sex chromosome drive suppression is likely mediated by sequence homology between the suppressor and distorter, through RNAi mechanism. Thus, our analysis suggests that newly emerged sex chromosomes are a battleground for sexual and meiotic conflict.
Integration of heterogeneous functional genomics data in gerontology research identifies genes and pathway underlying aging across species
Authors: Bubier Jason A , Sutphin George L , Reynolds Timothy J , Korstanje Ron , Fuksman-Kumpa Axis , Baker Erich J , Langston Michael A , Chesler Elissa J
Published: October 2018

Understanding the biological mechanisms behind aging, lifespan and healthspan is becoming increasingly important as the proportion of the world's population over the age of 65 grows, along with the cost and complexity of their care. BigData oriented approaches and analysis methods for integrative functional genomics enable current and future bio-gerontologists to synthesize, distill and interpret vast, heterogeneous data. GeneWeaver is an analysis system for integration of data that allows investigators to store, search, and analyze immense amounts of data including user-submitted experimental data, data from primary publications, and data in other databases. Aging related genome-wide gene sets from primary publications were curated into this system in concert with data from other model-organism and aging-specific databases, and used in several application using GeneWeavers analysis tools. For example, we identified Cd63 as a frequently represented gene among aging-related genome-wide results. To evaluate the role of Cd63 in aging, we performed RNAi knockdown of the C. elegans ortholog, tsp-7, demonstrating that this manipulation is capable of extending lifespan. The tools in GeneWeaver enable aging researchers to make new discoveries into the associations between the genes, normal biological processes, and diseases that affect aging, healthspan, and lifespan.
Ask1 and Akt act synergistically to promote ROS-dependent regeneration in Drosophila
Authors: Santabárbara-Ruiz Paula , Esteban-Collado José , Pérez Lidia , Viola Giacomo , Milán Marco , Corominas Montserrat , Serras Florenci
Published: October 2018

The mechanism by which apoptotic cells release signals that induce undamaged neighbor cells to proliferate and regenerate missing parts remains elusive. Oxidative stress originated by dying or damaged cells can be propagated to neighboring cells, which then promote regeneration. We investigated the nature of the stress sensing mechanism by which neighboring cells are recruited. We found that Drosophila apoptosis signal-regulating kinase 1 (Ask1) senses reactive oxygen species (ROS) differently in stressed dying cells and unstressed neighboring cells and this differential sensing is pivotal for tissue repair. In undamaged cells, this activity is attenuated, but not abolished, by Akt1 phosphorylation, which thus acts as a survival signal that results in the tolerable levels of p38 and JNK necessary for regeneration. These observations demonstrate that the non-autonomous activation of the ROS-sensing mechanism by Ask1 and Akt1 in neighboring unstressed cells. Collectively, these results provide the basis for understanding the molecular mechanism of communication between dying and living cells that triggers regeneration.

Author summary

One of the early events that occur after tissue damage is oxidative stress production that signals to initiate wound healing and regeneration. Several signaling pathways, such as JNK and p38, respond to oxidative stress and are necessary for regeneration. We decided to explore the mechanism that links the oxidative stress and the activation of these pathways. We used epithelia of Drosophila to genetically direct cell death in specific zones of the tissue as means of experimentally controlled cell damage. We found that the Ask1 protein, which is sensitive to oxidative stress, is a key player in this scenario. Actually it acts as an intracellular sensor that upon damage activates those signaling pathways. However, high activity of Ask1 can be toxic for the cell. This is controlled by Akt, an enzyme dowstream the insulin pathway, with attenuates the activity of Ask1 to tolerable levels. In conclusion, Ask1 and Akt act synergistically to respond to the stress generated after tissue damage and drive regeneration. In other words, we found that the link between oxidative stress and nutrition is key for tissue regeneration.
Bioinspired Design of Lysolytic Triterpenoid-peptide Conjugates that Kill African Trypanosomes
Authors: Leeder W.-Matthias , Giehler Fabian , Joswig Juliane , Göringer H. Ulrich
Published: October 2018

Humans have evolved a natural immunity against Trypanosoma brucei infections, which is executed by two serum (lipo)protein complexes known as trypanolytic factors (TLF). Active TLF-ingredient is the primate-specific apolipoprotein L1 (ApoL1). The protein has a pore-forming activity that kills parasites by lysosomal and mitochondrial membrane fenestration. Of the many trypanosome subspecies only two are able to counteract the activity of ApoL1, which illustrates its evolutionary optimized design and trypanocidal potency. Here we ask the question whether a synthetic (syn)TLF can be synthesized using the design principles of the natural TLF-complexes but relying on different chemical building blocks. We demonstrate the stepwise development of triterpenoid-peptide conjugates, in which the triterpenoids act as a cell binding, uptake and lysosomal transport-moduls and the synthetic peptide GALA as a pH-sensitive, pore-forming lysolytic toxin. As designed, the conjugate kills infective-stage African trypanosomes through lysosomal lysis demonstrating proof-of-principle for the bioinspired, forward-design of a synTLF.
INPP5E controls ciliary localization of phospholipids and odor response kinetics in a mouse model of Joubert syndrome
Authors: Ukhanov Kirill , Uytingco Cedric , Green Warren , Zhang Lian , Schurmans Stephane , Martens Jeffrey R.
Published: October 2018

Ciliopathies manifested in part by a dysfunction of several phosphoinositide 5’phosphatases constitute Lowes, Dent disease 2 and Joubert syndromes through critical involvement of properly functioning primary cilia (PC). We showed that deletion of INPP5E under the control of OMP-Cre in mature mouse olfactory sensory neurons (OSNs) led to a dramatic redistribution of PI(4,5)P2 (PIP2) in cilia, significant reduction of PI(3,4)P2 and enrichment of PI(3,4,5)P3in knobs. Redistribution of the phospholipids accompanied marked elongation of cilia in INPP5E-OMP knockout (KO) OSNs. Such a dramatic remodeling of phospholipid composition however did not affect other integral membrane lipids (cholesterol, sphingomyelin, glycosylated phosphaditylinositol, phosphatidylserine). Proteins known to bind with high affinity PIP2 entered the cilia of the KO OSNs. Loss of INPP5E did not affect ciliary localization of endogenous olfactory receptor M71/M72 or distribution and movement of IFT122 particles implicating independent of phospholipids mechanism of retrograde protein transport in cilia of mature OSNs. Net odor sensitivity and response magnitude as measured by EOG was not affected by the mutation. However, odor adaptation in the KO mouse was significantly impaired resulting in less efficient recovery and altered inactivation kinetics of the odor response at the EOG and single-cell level. These findings implicate phosphoinositide-dependent regulation of active Ca2+extrusion in OSNs whereby controlling the rate of sensory adaptation.

Significance statement

Currently there are little if any available treatment to cure congenital ciliopathies. This is in part due to lack of basic knowledge of cilia biology. Olfactory cilia as well as primary cilia appear to be a phospholipid privileged organelle distinct from the rest of plasma membrane albeit sharing its continuity. We characterized distribution of several critically important for cell biology phospholipids and showed that their balance, especially of PIP2, is disrupted in Joubert syndrome animal model and has functional implications. Virally assisted delivery of wild typeINPP5Eto the mutant OSNs was able to restore localization of PIP2 and rescued impaired response to odor.
Loss ofTP73function contributes to amyotrophic lateral sclerosis pathogenesis
Authors: Downie Jonathan M. , Gibson Summer B. , Tsetsou Spyridoula , Russell Kristi L. , Keefe Matthew D. , Figueroa Karla P. , Bromberg Mark B. , Murtaugh L. Charles , Bonkowsky Joshua L. , Pulst Stefan M. , Jorde Lynn B.
Published: October 2018

Much remains unknown about the genetics and pathophysiology underlying the neurodegenerative disease amyotrophic lateral sclerosis (ALS). We analyzed exome sequences from a cohort of 87 sporadic ALS (SALS) patients and 324 healthy individuals.TP73, a homolog of theTP53tumor suppressor gene, had five rare deleterious protein-coding variants; in a separate collection of >2,900 ALS patients we identified an additional 19 rare deleterious variants inTP73. Anin vitroC2C12 myoblast growth assay confirmed that these variants impair or alterTP73function.In vivomutagenesis of zebrafishtp73using CRISPR led to impaired motor neuron development and abnormal axonal morphology, concordant with ALS pathology. Together, these results demonstrate thatTP73is a risk factor for ALS, and identifies a novel dysfunctional cellular process in the pathogenesis of ALS.
Draft genome of the liver fluke Fasciola gigantica
Authors: Tripathi Tripti , Ghosh Arpita , Todur Vivek N , Kalita Parismita , Vijayakumar R , Kalita Jupitara , Shukla Rohit , Chetri Purna B , Shukla Harish , Sonkar Amit , Lyngdoh Denzelle Lee , Singh Radhika , Chikara Surendra K , Tripathi Timir
Published: October 2018

Fascioliasis is a neglected food-borne disease caused by liver flukes (genus Fasciola) and affects more than 200 million people worldwide. Despite technological advances, little is known about the molecular biology and biochemistry of the fluke. We present the draft genome of Fasciola gigantica for the first time. The assembled draft genome has a size of ~1.04 Gb with an N50 of 129 kb. A total of 20,858 genes were predicted. The de novo repeats identified in the draft genome were 46.85%. In pathway analysis, all the genes of glycolysis, Kreb’s cycle and fatty acid metabolism were found to be present, but the key genes for fatty acid production in fatty acid biosynthesis were missing. This indicates that the fatty acid required for the survival of the fluke may be acquired from the host bile. The genomic information will provide a comprehensive resource to facilitate the development of novel interventions for fascioliasis control.
Sperm gatekeeping: 3D imaging reveals a constricted entrance to zebra finch sperm storage tubules
Authors: Mendonca T. , Cadby A. J. , Hemmings N.
Published: October 2018

Females across many internally fertilising taxa store sperm, often in specialised storage organs in their reproductive tracts. In birds, several hundred sperm storage tubules exist in the utero-vaginal junction of the oviduct and there is growing evidence that sperm storage in these tubules is selective. The mechanisms underlying female sperm storage in birds remain unknown due to our limited ability to make three dimensional, live observations inside the large, muscular avian oviduct. Here, we describe a new application of fluorescence selective plane illumination microscopy to optically section oviduct tissue from zebra finchTaeniopygia guttatafemales label-free, by harnessing tissue autofluorescence. Our data provide the first description of the 3D structure of sperm storage organs in any vertebrate and reveal the presence of gate-like constricted openings that may play a role in sperm selection.

Statement of Significance

Female birds can store sperm in microscopic tubular structures in their reproductive tract for up to several months, depending on species. Studying these sperm storage tubules has been a major challenge due to the muscular and opaque nature of reproductive tracts in birds. We have developed a new method for imaging live reproductive tract tissue using selective plane illumination microscopy, a fluorescence microscopy technique. From these images, we could extract three-dimensional measurements of sperm storage tubules and found these structures to have a gate-like constriction, providing evidence that females can actively select sperm at storage and ultimately influence the paternity of her offspring. Understanding these reproductive adaptations can help improve captive breeding programs and similar conservation strategies.
Fragmentation of pooled PCR products for highly multiplexed TILLING
Authors: Tramontano Andrea , Jarc Luka , Jankowicz-Cieslak Joanna , Hofinger Bernhard J. , Gajek Katarzyna , Szurman-Zubrzycka Miriam , Szarejko Iwona , Inglebrecht Ivan , Till Bradley J.
Published: October 2018

Improvements to massively parallel sequencing have allowed the routine recovery of natural and induced sequence variants. A broad range of biological disciplines have benefited from this, ranging from plant breeding to cancer research. The need for high sequence coverage to accurately recover single nucleotide variants and small insertions and deletions limits the applicability of whole genome approaches. This is especially true in organisms with a large genome size or for applications requiring the screening of thousands of individuals, such as the reverse-genetic technique known as TILLING, where whole genome approaches become cost prohibitive. Using PCR to target and sequence chosen genomic regions provides an attractive alternative as the vast reduction in interrogated bases means that sample size can be dramatically increased through amplicon multiplexing and multidimensional sample pooling while maintaining suitable coverage for recovery of small mutations. Direct sequencing of PCR products is limited, however, due to limitations in read lengths of many next generation sequencers. In the present study we show the optimization and use of ultrasonication for the simultaneous fragmentation of multiplexed PCR amplicons for TILLING highly pooled samples. Thirty-two PCR products were produced from genomic DNA pools representing 265 pooled barley mutant lines. Mutant lines were produced with the chemical mutagen ethyl methanesulfonate. Samples were subjected to 2×300PE illumina sequencing. Evaluation of read coverage and base quality across amplicons suggests this approach is suitable for high-throughput TILLING and other applications employing highly pooled complex sampling schemes. Induced mutations previously identified in a traditional TILLING screen were recovered in this dataset further supporting the efficacy of the approach.
Discovery of the role of a SLOG superfamily biological conflict systems associated protein IodA (YpsA) in oxidative stress protection and cell division inhibition in Gram-positive bacteria
Authors: Brzozowski Robert S. , Graham Gianni , Burroughs A. Maxwell , Huber Mirella , Walker Merryck , Alva Sameeksha S. , Aravind L. , Eswara Prahathees J.
Published: October 2018

Bacteria adapt to different environments by regulating cell division and several conditions that modulate cell division have been documented. Understanding how bacteria transduce environmental signals to control cell division is critical to comprehend the global network of cell division regulation. In this article we describe a role forBacillus subtilisYpsA, an uncharacterized protein of the SLOG superfamily of nucleotide and ligand-binding proteins, in cell division. We observed that YpsA provides protection against oxidative stress as cells lackingypsAshow increased susceptibility to hydrogen peroxide treatment. We found that increased expression ofypsAleads to cell division inhibition due to defective assembly of FtsZ, the tubulin-like essential protein that marks the sites of cell division. We showed that cell division inhibition by YpsA is linked to glucose availability. We generated YpsA mutants that are no longer able to inhibit cell division. Finally, we show that the role of YpsA is possibly conserved in Firmicutes, as overproduction of YpsA inStaphylococcus aureusalso impairs cell division. Therefore, we proposeypsAto be renamed asiodAforinhibitorofdivision.

IMPORTANCE

Although key players of cell division in bacteria have been largely characterized, the factors that regulate these division proteins are still being discovered and evidence for the presence of yet-to-be discovered factors has been accumulating. How bacteria sense the availability of nutrients and how that information is used to regulate cell division positively or negatively is less well-understood even though some examples exist in the literature. We discovered that a protein of hitherto unknown function belonging to the SLOG superfamily of nucleotide/ligand-binding proteins, YpsA, influences cell division inBacillus subtilisby integrating metabolic status such as the availability of glucose. We showed that YpsA is important for oxidative stress response inB. subtilis. Furthermore, we provide evidence that cell division inhibition function of YpsA is also conserved in another FirmicuteStaphylococcus aureus. This first report on the role of YpsA (IodA) brings us a step closer in understanding the complete tool set that bacteria have at their disposal to regulate cell division precisely to adapt to varying environmental conditions.
ATR and mTOR regulate F-actin to alter nuclear architecture and repair replication stress
Authors: Lamm Noa , Masamsetti V. Pragathi , Read Mark N. , Biro Maté , Cesare Anthony J.
Published: October 2018

“Replication stress” describes phenomena that alter DNA replication rates 1–3. Multiple architectural challenges within the confined nuclear volume must be navigated during replication to prevent or repair replication stress. Cellular mechanisms potentiating changes in nuclear architecture that facilitate DNA replication remain unclear. Here we show that the ATR, IPMK and mTOR kinases regulate actin polymerisation in human cells to alter nuclear architecture and promote replication fork repair. We demonstrate that replication stress activates mTOR, in an ATR and IPMK-dependent manner, to induce polymerisation of nuclear filamentous actin (F-actin). mTOR and ATR then counteract replication stress-induced nuclear envelope deformation and increase nuclear volume through their regulation of actin dynamics. Additionally, we reveal that FANCD2 labelled replication forks colocalise with actin filaments in late S-phase. mTOR and ATR then regulate the mobility, speed and directionality of stalled replication foci within the three-dimensional nuclear architecture. Importantly, we find nuclear F-actin also acts as a substrate for the directed migration of stalled replication foci to the nuclear periphery. Suppressing mTOR and ATR-dependent actin forces prevents replication fork restart and promotes chromosome segregation errors in primary and cancer cell lines. Together, these data reveal that ATR and mTOR regulate actin dynamics in the replication stress response to alter nuclear architecture and maintain genome stability.
Origins and Evolution of the Global RNA Virome
Authors: Wolf Yuri I. , Kazlauskas Darius , Iranzo Jaime , LucÍa-Sanz Adriana , Kuhn Jens H. , Krupovic Mart , Dolja Valerian V. , Koonin Eugene V.
Published: October 2018

Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches, 2 of which include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded (ds) RNA viruses, and 2 consist of dsRNA and negative-sense (−) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas -RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, particularly, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy.

IMPORTANCE

The majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than what was attainable previously. This reconstruction reveals the relationships between different Baltimore Classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.
Ranking noncanonical 5′ splice site usage by genome-wide RNA-seq analysis and splicing reporter assays
Authors: Erkelenz Steffen , Theiss Stephan , Kaisers Wolfgang , Ptok Johannes , Walotka Lara , Müller Lisa , Hillebrand Frank , Brillen Anna-Lena , Sladek Michael , Schaal Heiner
Published: October 2018

Most human pathogenic mutations in 5′ splice sites affect the canonical GT in positions +1 and +2, leading to noncanonical dinucleotides. On the other hand, noncanonical dinucleotides are observed under physiological conditions in ∼1% of all human 5′ss. It is therefore a challenging task to understand the pathogenic mutation mechanisms underlying the conditions under which noncanonical 5′ss are used. In this work, we systematically examined noncanonical 5′ splice site selection, both experimentally using splicing competition reporters and by analyzing a large RNA-seq data set of 54 fibroblast samples from 27 subjects containing a total of 2.4 billion gapped reads covering 269,375 exon junctions. From both approaches, we consistently derived a noncanonical 5′ss usage ranking GC > TT > AT > GA > GG > CT. In our competition splicing reporter assay, noncanonical splicing was strictly dependent on the presence of upstream or downstream splicing regulatory elements (SREs), and changes in SREs could be compensated by variation of U1 snRNA complementarity in the competing 5′ss. In particular, we could confirm splicing at different positions (i.e., −1, +1, +5) of a splice site for all noncanonical dinucleotides “weaker” than GC. In our comprehensive RNA-seq data set analysis, noncanonical 5′ss were preferentially detected in weakly used exon junctions of highly expressed genes. Among high-confidence splice sites, they were 10-fold overrepresented in clusters with a neighboring, more frequently used 5′ss. Conversely, these more frequently used neighbors contained only the dinucleotides GT, GC, and TT, in accordance with the above ranking.
Towards synchrotron phase-contrast lung imaging in patients – a proof-of-concept study on porcine lungs in a human-scale chest phantom
Authors: Wagner Willi L. , Wuennemann Felix , Pacilé Serena , Albers Jonas , Arfelli Fulvia , Dreossi Diego , Biederer Jürgen , Konietzke Philip , Stiller Wolfram , Wielpütz Mark O. , Accardo Agostino , Confalonieri Marco , Cova Maria , Lotz Joachim , Alves Frauke , Kauczor Hans-Ulrich , Tromba Giuliana , Dullin Christian
Published: October 2018

In-line free propagation phase-contrast synchrotron tomography of the lungs has been shown to provide superior image quality compared with attenuation-based computed tomography (CT) in small-animal studies. The present study was performed to prove the applicability on a human-patient scale using a chest phantom with ventilated fresh porcine lungs. Local areas of interest were imaged with a pixel size of 100 µm, yielding a high-resolution depiction of anatomical hallmarks of healthy lungs and artificial lung nodules. Details like fine spiculations into surrounding alveolar spaces were shown on a micrometre scale. Minor differences in artificial lung nodule density were detected by phase retrieval. Since we only applied a fraction of the X-ray dose used for clinical high-resolution CT scans, it is believed that this approach may become applicable to the detailed assessment of focal lung lesions in patients in the future.
A new hexamolybdate-based copper–2,2′-biimidazole coordination polymer serving as an acid catalyst and support for enzyme immobilization
Authors: Sang Xiao-Jing , Feng Shu-Li , Lu Ying , Zhang Yue-Xian , Su Fang , Zhang Lan-Cui , Zhu Zai-Ming
Published: October 2018

The hydrothermal reaction of (NH4)3[CoMo6O24H6]·7H2O (CoMo6
), CuCl2·2H2O and 2,2′-biimidazole (H2biim) led to the formation of a new coordination polymer, namely poly[diaquabis(2,2′-biimidazole)hexa-μ3-oxo-octa-μ2-oxo-hexaoxodicopper(II)hexamolybdate(VI)], [Cu2Mo6O20(C6H6N4)2(H2O)2]
n
(Cu-Mo6O20
), at pH 2–3. It is obvious that in the formation of crystalline Cu-Mo6O20
, the original Anderson-type skeleton of heteropolymolybdate CoMo6
was broken and the new isopolyhexamolybdate Mo6O20 unit was assembled. In Cu-Mo6O20
, one Mo6O20 unit connects four [Cu(H2biim)(H2O)]2+ ions in a pentacoordinate mode via four terminal O atoms, resulting in a tetra-supported structure, and each CuII ion is shared by two adjacent Mo6O20 units. Infinite one-dimensional chains are established by linkage between two adjacent Mo6O20 units and two CuII ions, and these chains are further packed into a three-dimensional framework by hydrogen bonds, π–π interactions and electrostatic attractions. The catalytic performance of this crystalline material used as an efficient and reusable heterogeneous acid catalyst for carbonyl-group protection is discussed. In addition, Cu-Mo6O20
was applied as a new support for enzyme (horseradish peroxidase, HRP) immobilization, forming immobilized enzyme HRP/Cu-Mo6O20
. HRP/Cu-Mo6O20
showed good catalytic activity and could be reused.
Structural and electrochemical comparison of trinuclear ruthenium oxo clusters [Ru3(OAc)6O(L)3]+and [Ru3(OAc)6O(L)2(CO)] (L = imidazole, benzimidazole, and 4-phenylpyridine)
Authors: Derstine Brandon , Chamberlain Carmen , Glover Morgan , Porter Lindsey , Eckermann Amanda
Published: October 2018

The triruthenium oxo clusters [Ru3(OAc)6O(L)3]+ and [Ru3(OAc)6O(L)2(CO)] possess unique electronic characteristics that vary based on the ligands L. Here we report an investigation of the structural, electrochemical, and optical properties of clusters with imidazole, benzimidazole, and 4-phenylpyridine ligands. The complexes [Ru3(OAc)6O(L)3]+ [1+
: L = imidazole (im); 2+
: L = benzimidazole (benzim); 3+
: L = 4-phenylpyridine (4PP)] and [Ru3(OAc)6O(L)2(CO)] (1-CO and 3-CO) were synthesized by reaction of either [Ru3(OAc)6O(MeOH)3]+ or [Ru3(OAc)6O(MeOH)2(CO)], respectively, with the corresponding heterocycle. We further discovered that [3]OAc could be reduced to the mixed-valence neutral state 3 by refluxing the complex under nitrogen in methanol. Single-crystal X-ray structure analysis of hexa-μ2-acetato-μ3-oxido-tris(1H-imidazole)triruthenium hexafluorophosphate acetonitrile hemisolvate, [Ru3(C2H3O2)6O(C3H4N2)3]PF6·0.5CH3CN, [1]PF6
, hexa-μ2-acetato-carbonylbis(1H-imidazole)-μ3-oxido-triruthenium methanol monosolvate, [Ru3(C2H3O2)6O(C3H4N2)(CO)]·CH3OH, 1-CO, hexa-μ2-acetato-μ3-oxido-tris(4-phenylpyridine)triruthenium pentahydrate, [Ru3(C2H3O2)6O(C11H9N)3]·5H2O, 3, and hexa-μ2-acetato-carbonyl-μ3-oxido-bis(4-phenylpyridine)triruthenium methanol monosolvate, [Ru3(C2H3O2)6O(C11H9N)2(CO)]·CH3OH, 3-CO, show the expected triruthenium μ3-oxo core and N-coordination of the ligands. Cyclic voltammetry revealed quasi-reversible and irreversible redox couples in [1]PF6
, 1-CO, and [2]PF6
, while [3]PF6
and 3-CO exhibit reversible redox couples. The optical properties of these richly colored species were investigated using UV–Vis spectroscopy.