bluuebunny/crossref_metadata_2025 huggingface dataset:
Tools for Detection of Mycoplasma amphoriforme: a Primary Respiratory Pathogen?
Authors: Ling Clare L. , Oravcova Katarina , Beattie Thomas F. , Creer Dean D. , Dilworth Paul , Fulton Naomi L. , Hardie Alison , Munro Michelle , Pond Marcus , Templeton Kate , Webster David , Workman Sarita , McHugh Timothy D. , Gillespie Stephen H.
Published: January 2014

Mycoplasma amphoriforme
is a recently described organism isolated from the respiratory tracts of patients with immunodeficiency and evidence of chronic infection. Novel assays for the molecular detection of the organism by real-time quantitative PCRs (qPCRs) targeting the uracil DNA glycosylase gene (
udg
) or the 23S rRNA gene are described here. The analytical sensitivities are similar to the existing conventional
M. amphoriforme
16S rRNA gene PCR, with the advantage of being species specific, rapid, and quantitative. By using these techniques, we demonstrate the presence of this organism in 17 (19.3%) primary antibody-deficient (PAD) patients, 4 (5%) adults with lower respiratory tract infection, 1 (2.6%) sputum sample from a patient attending a chest clinic, and 23 (0.21%) samples submitted for viral diagnosis of respiratory infection, but not in normal adult control subjects. These data show the presence of this microorganism in respiratory patients and suggest that
M. amphoriforme
may infect both immunocompetent and immunocompromised people. Further studies to characterize this organism are required, and this report provides the tools that may be used by other research groups to investigate its pathogenic potential.
Real-Time PCR Assay for Detection of
blaZ
Genes in Staphylococcus aureus Clinical Isolates
Authors: Pereira Lynette A. , Harnett Gerald B. , Hodge Meredith M. , Cattell Julia A. , Speers David J.
Published: January 2014

The Clinical and Laboratory Standards Institute recommends consideration of
blaZ
gene testing for cases of serious
Staphylococcus aureus
infection. Conventional PCR methods have demonstrated superior sensitivity and specificity to phenotypic tests. To our knowledge, this is the first description of real-time PCR detection of the
blaZ
gene.
Molecular Characterization of Methicillin-Resistant Staphylococcus aureus Strains Isolated from Patients with Hospital Readmissions
Authors: Eghbaria Saleh , Schnitser Kathy , Danial-Farran Nada , Keness Yoram , Bisharat Naiel
Published: January 2014

It is unclear whether patients colonized with methicillin-resistant
Staphylococcus aureus
(MRSA) continue to harbor the same genotype during hospital readmissions. We characterized 140 MRSA strains isolated from 33 persistent MRSA carriers with hospital readmissions. Nearly half of the patients continued to harbor the same genotype, and the rest acquired different genotypes. Among 25 patients who received eradication therapy, 16 (64%) were colonized with MRSA strains exhibiting different genotypes from the preexisting one.
Specific Sequence of a Beta Turn in Human La Protein May Contribute to Species Specificity of Hepatitis C Virus
Authors: Kumar Anuj , Manna Asit Kumar , Ray Upasana , Mullick Ranajoy , Basu Gautam , Das Saumitra , Roy Siddhartha
Published: January 2014

Human La protein is known to be an essential host factor for translation and replication of hepatitis C virus (HCV) RNA. Previously, we have demonstrated that residues responsible for interaction of human La protein with the HCV internal ribosomal entry site (IRES) around the initiator AUG within stem-loop IV form a β-turn in the RNA recognition motif (RRM) structure. In this study, sequence alignment and mutagenesis suggest that the HCV RNA-interacting β-turn is conserved only in humans and chimpanzees, the species primarily known to be infected by HCV. A 7-mer peptide corresponding to the HCV RNA-interacting region of human La inhibits HCV translation, whereas another peptide corresponding to the mouse La sequence was unable to do so. Furthermore, IRES-mediated translation was found to be significantly high in the presence of recombinant human La protein
in vitro
in rabbit reticulocyte lysate. We observed enhanced replication with HCV subgenomic and full-length replicons upon overexpression of either human La protein or a chimeric mouse La protein harboring a human La β-turn sequence in mouse cells. Taken together, our results raise the possibility of creating an immunocompetent HCV mouse model using human-specific cell entry factors and a humanized form of La protein.

IMPORTANCE
Hepatitis C virus is known to infect only humans and chimpanzees under natural conditions. This has prevented the development of a small-animal model, which is important for development of new antiviral drugs. Although a number of human-specific proteins are responsible for this species selectivity and some of these proteins—-mostly entry factors—-have been identified, full multiplication of the virus in mouse cells is still not possible. In this study, we show that a turn in the human La protein that is responsible for the interaction with the viral RNA is highly specific for the human sequence. Replacement of the corresponding mouse sequence with the human sequence allows the mouse La to behave like its human counterpart and support viral growth in the mouse cell efficiently. This observation, in combination with previously identified cell entry factors, should open up the possibility of creating a mouse model of hepatitis C.
Inhibition of Hepatitis C Virus in Chimeric Mice by Short Synthetic Hairpin RNAs: Sequence Analysis of Surviving Virus Shows Added Selective Pressure of Combination Therapy
Authors: Dallas Anne , Ilves Heini , Ma Han , Chin Daniel J. , MacLachlan Ian , Klumpp Klaus , Johnston Brian H.
Published: January 2014

We have recently shown that a cocktail of two short synthetic hairpin RNAs (sshRNAs), targeting the internal ribosome entry site of hepatitis C virus (HCV) formulated with lipid nanoparticles, was able to suppress viral replication in chimeric mice infected with HCV GT1a by up to 2.5 log
10
(H. Ma et al., Gastroenterology 146:63–66.e5,
http://dx.doi.org/10.1053/j.gastro.2013.09.049
) Viral load remained about 1 log
10
below pretreatment levels 21 days after the end of dosing. We have now sequenced the HCV viral RNA amplified from serum of treated mice after the 21-day follow-up period. Viral RNA from the HCV sshRNA-treated groups was altered in sequences complementary to the sshRNAs and nowhere else in the 500-nucleotide sequenced region, while the viruses from the control group that received an irrelevant sshRNA had no mutations in that region. The ability of the most commonly selected mutations to confer resistance to the sshRNAs was confirmed
in vitro
by introducing those mutations into HCV-luciferase reporters. The mutations most frequently selected by sshRNA treatment within the sshRNA target sequence occurred at the most polymorphic residues, as identified from an analysis of available clinical isolates. These results demonstrate a direct antiviral activity with effective HCV suppression, demonstrate the added selective pressure of combination therapy, and confirm an RNA interference (RNAi) mechanism of action.

IMPORTANCE
This study presents a detailed analysis of the impact of treating a hepatitis C virus (HCV)-infected animal with synthetic hairpin-shaped RNAs that can degrade the virus's RNA genome. These RNAs can reduce the viral load in these animals by over 99% after 1 to 2 injections. The study results confirm that the viral rebound that often occurred a few weeks after treatment is due to emergence of a virus whose genome is mutated in the sequences targeted by the RNAs. The use of two RNA inhibitors, which is more effective than use of either one by itself, requires that any resistant virus have mutations in the targets sites of both agents, a higher hurdle, if the virus is to retain the ability to replicate efficiently. These results demonstrate a direct antiviral activity with effective HCV suppression, demonstrate the added selective pressure of combination therapy, and confirm an RNAi mechanism of action.
Role of Phosphatidylserine Receptors in Enveloped Virus Infection
Authors: Morizono Kouki , Chen Irvin S. Y.
Published: January 2014

We recently demonstrated that a soluble protein, Gas6, can facilitate viral entry by bridging viral envelope phosphatidylserine to Axl, a receptor tyrosine kinase expressed on target cells. The interaction between phosphatidylserine, Gas6, and Axl was originally shown to be a molecular mechanism through which phagocytes recognize phosphatidylserine exposed on dead cells. Since our initial report, several groups have confirmed that Axl/Gas6, as well as other phosphatidylserine receptors, facilitate entry of dengue, West Nile, and Ebola viruses. Virus binding by viral envelope phosphatidylserine is now a viral entry mechanism generalized to many families of viruses. In addition to Axl/Gas6, various molecules are known to recognize phosphatidylserine; however, the effects of these molecules on virus binding and entry have not been comprehensively evaluated and compared. In this study, we examined most of the known human phosphatidylserine-recognizing molecules, including MFG-E8, TIM-1, -3, and -4, CD300a, BAI1, and stabilin-1 and -2, for their abilities to facilitate virus binding and infection. Using pseudotyped lentiviral vectors, we found that a soluble phosphatidylserine-binding protein, MFG-E8, enhances transduction. Cell surface receptors TIM-1 and -4 also enhance virus binding/transduction. The extent of enhancement by these molecules varies, depending on the type of pseudotyping envelope proteins. Mutated MFG-E8, which binds viral envelope phosphatidylserine without bridging virus to cells, but, surprisingly, not annexin V, which has been used to block phagocytosis of dead cells by concealing phosphatidylserine, efficiently blocks these phosphatidylserine-dependent viral entry mechanisms. These results provide insight into understanding the role of viral envelope phosphatidylserine in viral infection.

IMPORTANCEEnvelope phosphatidylserine has previously been shown to be important for replication of various envelope viruses, but details of this mechanism(s) were unclear. We were the first to report that a bifunctional serum protein, Gas6, bridges envelope phosphatidylserine to a cell surface receptor, Axl. Recent studies demonstrated that many envelope viruses, including vaccinia, dengue, West Nile, and Ebola viruses, utilize Axl/Gas6 to facilitate their entry, suggesting that the phosphatidylserine-mediated viral entry mechanism can be shared by various enveloped viruses. In addition to Axl/Gas6, various molecules are known to recognize phosphatidylserine; however, the effects of these molecules on virus binding and entry have not been comprehensively evaluated and compared. In this study, we examined most human phosphatidylserine-recognizing molecules for their abilities to facilitate viral infection. The results provide insights into the role(s) of envelope phosphatidylserine in viral infection, which can be applicable to the development of novel antiviral reagents that block phosphatidylserine-mediated viral entry.
Development of Continuous Cell Culture of Brown Planthopper To Trace the Early Infection Process of Oryzaviruses in Insect Vector Cells
Authors: Chen Hongyan , Zheng Limin , Mao Qianzhuo , Liu Qifei , Jia Dongsheng , Wei Taiyun
Published: January 2014

Rice ragged stunt virus (RRSV), an oryzavirus in the family
Reoviridae
, is transmitted by the brown planthopper,
Nilaparvata lugens
, in a persistent-propagative manner. Here, we established a continuous cell line of brown planthopper to investigate the mechanism underlying the formation of the viroplasm, the putative site for viral replication and assembly, during infection of RRSV in its insect vector cells. Within 24 h of viral infection of cultured cells, the viroplasm had formed and contained the viral nonstructural proteins Pns6 and Pns10, known to be constituents of viroplasm. Core capsid protein P3, core particles, and newly synthesized viral RNAs were accumulated inside the viroplasm, while outer capsid protein P8 and virions were accumulated at the periphery of the viroplasm, confirming that the viroplasm induced by RRSV infection was the site for viral replication and assembly. Pns10 formed viroplasm-like inclusions in the absence of viral infection, suggesting that the viroplasm matrix was largely composed of Pns10. Pns6 was recruited in the viroplasm by direct interaction with Pns10. Core capsid protein P3 was recruited to the viroplasm through specific association with Pns6. Knockdown of Pns6 and Pns10 expression using RNA interference inhibited viroplasm formation, virion assembly, viral protein expression, and viral double-stranded RNA synthesis. Thus, the present study shows that both Pns6 and Pns10 of RRSV play important roles in the early stages of viral life cycle in its insect vector cells, by recruiting or retaining components necessary for viral replication and assembly.

IMPORTANCE
The brown planthopper, a commonly distributed pest of rice in Asia, is the host of numerous insect endosymbionts, and the major vector of two rice viruses (RRSV and rice grassy stunt virus). For the first time, we successfully established the continuous cell line of brown planthopper. The unique uniformity of brown planthopper cells in the monolayer can support a consistent, synchronous infection by endosymbionts or viral pathogens, improving our understanding of molecular insect-microbe interactions.
Resveratrol Inhibits the TRIF-Dependent Pathway by Upregulating Sterile Alpha and Armadillo Motif Protein, Contributing to Anti-Inflammatory Effects after Respiratory Syncytial Virus Infection
Authors: Liu Tiantian , Zang Na , Zhou Na , Li Wei , Xie Xiaohong , Deng Yu , Ren Luo , Long Xiaoru , Li Simin , Zhou Lili , Zhao Xiaodong , Tu Wenwei , Wang Lijia , Tan Bin , Liu Enmei
Published: January 2014

Respiratory syncytial virus (RSV) is the most important cause of lower respiratory tract infection in young children and the leading cause of infant hospitalization worldwide. Uncontrolled response to RSV is mediated by a toll-like receptor (TLR)-mediated immune response. Resveratrol possesses anti-RSV activity and is an inhibitor of the TRIF/TBK1/IRF-3 complex. We hypothesize that resveratrol inhibits the TRIF-dependent pathway through upregulation of SARM post-RSV infection. BALB/c mice were infected with RSV and were injected with resveratrol 1 h postinoculation. SARM short interfering RNA was administered to RSV-infected and resveratrol-treated mice. Lung function was measured by whole-body plethysmography, lung histopathology was examined, and lymphocytes in bronchoalveolar lavage fluid were quantified. SARM and TRIF protein expression were detected in the lung by Western blot analyses. The expression of gamma interferon in bronchoalveolar lavage fluid (BALF) was evaluated by enzyme-linked immunosorbent assay (ELISA). SARM expression was reduced and TRIF expression was increased after infection with RSV. Resveratrol increased SARM expression and decreased TRIF expression after RSV infection. SARM knockdown in resveratrol-treated mice enhanced gamma interferon production, RSV-induced airway inflammation, and airway hyperresponsiveness (AHR). Resveratrol decreased TRIF expression and prevented the RSV-mediated reduction of SARM expression. Resveratrol-mediated inhibition of the TRIF-dependent pathway may be dependent on SARM expression.

IMPORTANCE
Our study provides insights into the regulation of innate immunity in response to RSV infection. The results suggest that resveratrol-mediated alterations in SARM have therapeutic potential against RSV immunopathology caused by deregulation of the TLR-mediated immune response. Ultimately, improved insight into the complex interplay between TLR adaptor proteins and the occurrence of severe RSV infection might lead to novel therapeutic treatment strategies, such as TLR adjuvants.
The Influenza A Virus Protein NS1 Displays Structural Polymorphism
Authors: Carrillo Berenice , Choi Jae-Mun , Bornholdt Zachary A. , Sankaran Banumathi , Rice Andrew P. , Prasad B. V. Venkataram
Published: January 2014

NS1 of influenza A virus is a potent antagonist of host antiviral interferon responses. This multifunctional protein with two distinctive domains, an RNA-binding domain (RBD) and an effector domain (ED) separated by a linker region (LR), is implicated in replication, pathogenesis, and host range. Although the structures of individual domains of NS1 from different strains of influenza viruses have been reported, the only structure of full-length NS1 available to date is from an H5N1 strain (A/Vietnam/1203/2004). By carrying out crystallographic analyses of full-length H6N6-NS1 (A/blue-winged teal/MN/993/1980) and an LR deletion mutant, combined with mutational analysis, we show here that these full-length NS1 structures provide an exquisite structural sampling of various conformational states of NS1 that based on the orientation of the ED with respect to RBD can be summarized as “open,” “semi-open,” and “closed” conformations. Our studies show that preference for these states is clearly dictated by determinants such as linker length, residue composition at position 71, and a mechanical hinge, providing a structural basis for strain-dependent functional variations in NS1. Because of the flexibility inherent in the LR, any particular NS1 could sample the conformational space around these states to engage ED in different quaternary interactions so that it may participate in specific protein-protein or protein-RNA interactions to allow for the known multifunctionality of NS1. We propose that such conformational plasticity provides a mechanism for autoregulating NS1 functions, depending on its temporal distribution, posttranslational modifications, and nuclear or cellular localization, during the course of virus infection.

IMPORTANCE
NS1 of influenza A virus is a multifunctional protein associated with numerous strain-specific regulatory functions during viral infection, including conferring resistance to antiviral interferon induction, replication, pathogenesis, virulence, and host range. NS1 has two domains, an RNA-binding domain and an effector domain separated by a linker. To date, the only full-length NS1 structure available is that from an H5N1 strain (A/Vietnam/1203/2004). Here, we determined crystal structures of the wild type and a linker region mutant of the H6N6 NS1 (A/blue-winged teal/MN/993/1980), which together with the previously determined H5N1 NS1 structure show that NS1 exhibits significant strain-dependent structural polymorphism due to variations in linker length, residue composition at position 71, and a mechanical hinge. Such a structural polymorphism may be the basis for strain-specific functions associated with NS1.
Asymptomatic primary rectal neuroendocrine carcinoma presented as a large pelvic mass
Authors: Pittayanon Rapat , Pantongrag-Brown Linda , Wisedopas Naruemon , Rerknimitr Rungsun
Published: February 2014

A 55-year-old healthy Thai man presented with incidental finding of a well-circumscribed, 5.8×5.4 cm mass in the right side of the pelvic cavity with heterogeneous density by a CT scan performed for trauma. No other distant lesion was detected. The pathology from pelvic mass showed poorly differentiated neuroendocrine carcinoma (NEC). A submucosal mass of 10 cm from the anal verge was found at colonoscopy, and a biopsy showed the same histopathology as in the pelvic mass. Final diagnosis was poorly differentiated primary rectal NEC with metastasis to the right iliac node (by CT scan). Carboplatin and etoposide were given for six cycles and tumour size was decreased.
Myxoedema coma: an almost forgotten, yet still existing cause of multiorgan failure
Authors: Salomo Louise Havkrog , Laursen Adam Hoegsbro , Reiter Nanna , Feldt-Rasmussen Ulla
Published: January 2014

A 48-year-old man was admitted to department of emergency medicine at a tertiary referral hospital due to dizziness and fatigue. Clinical features on admission were non-pitting oedema, dry skin, very sparse hair, a hoarse voice, hypothermia (rectal temperature 28.7°C), macroglossia, sinus bradycardia and slow cerebration. Blood tests revealed severe hypothyroidism. During admission, the patient developed respiratory failure, renal failure, bleeding symptoms and diffuse colitis. The patient was treated with hydrocortisone and levothyroxine and he survived miraculously. This case describes a patient with myxoedema coma with severe hypothermia and cardiac involvement with development of multiorgan dysfunction all linked to the severe depletion of triiodothyronine.
Pleomorphic rhabdomyosarcoma of the cerebellopontine angle in an adult: a review of literature
Authors: Caporlingua Federico , Lapadula Gennaro , Antonelli Manila , Missori Paolo
Published: January 2014

Rhabdomyosarcoma (RMS) is a rare and aggressive neoplasm characterised by rapid growth and metastatic invasion. The most frequent localisation is the skeletal musculature of the limbs. The head and the neck are rarely involved. A 50-year-old woman presented to our attention because of a progressively increasing headache, ataxia and vomiting. MRI showed a lesion at the right cerebellopontine angle. Thereafter, the patient was submitted to a piece-meal removal of the neoplasm. Despite the postoperative MRI showed no signs of remnant, 7 months after the surgery, the disease recurred with multiple localisations, and the patient died a few days later. This report is the first description in the literature of a pleomorphic RMS of the cerebellopontine angle. This particular tumour carries a bad prognosis because of the vicinity of nervous structures and of the impossibility of achieving a one-piece resection. More than ever, the adjunctive treatments had to be effective against a potential remnant and in controlling recurrences.
Patterns of ALK expression in different human cancer types
Authors: Tennstedt Pierre , Strobel Gundula , Bölch Charlotte , Grob Tobias , Minner Sarah , Masser Sawinee , Simon Ronald
Published: January 2014

Aims

Oncogenic gene fusions involving the anaplastic lymphoma kinase (ALK) tyrosine kinase have been identified in several haematopoietic and sporadically also in solid tumour types. Preliminary results from clinical trials suggest that patients with ALK fusion positive cancers might optimally benefit from the tyrosine kinase inhibitor crizotinib, but a comprehensive analysis of solid tumour types for ALK fusion and fusion associated expression is lacking.

Methods

In order to identify human solid cancers carrying ALK alterations, we performed real-time PCR screening of 1000 tumour samples representing 29 different tumour entities. ALK-positive samples were then transferred into a tissue microarray format and subjected to ALK break-apart fluorescence in situ hybridisation (FISH) analysis and ALK immunohistochemistry (IHC) analysis.

Results

ALK expression was detected by real-time PCR in 260 of 896 (29%) interpretable tumour samples. FISH analysis was successful in 189 of 260 arrayed cancers but did not detect ALK rearrangement. There was also no ALK expression detectable by IHC.

Conclusions

Different levels of ALK expression can be found in various cancer types using sensitive methods like real-time PCR. However, such low-level expression is independent from oncogenic ALK fusions and cannot be detected with less-sensitive methods like IHC. ALK fusion is a rare event in human solid cancers.
β-Carotene autoxidation: oxygen copolymerization, non-vitamin A products, and immunological activity
Authors: Burton Graham W. , Daroszewski Janusz , Nickerson James G. , Johnston James B. , Mogg Trevor J. , Nikiforov Grigory B.
Published: February 2014

Carotenoids are reported to have immunological effects independent of vitamin A activity. Although antioxidant activity has been suggested as a basis of action, the ability of carotenoids to autoxidize to numerous non-vitamin A products with immunological activity is an alternative yet to be fully explored. We have undertaken a systematic study of β-carotene autoxidation and tested the product mixture for immunological activity. Autoxidation proceeds predominantly by oxygen copolymerization, leading to a defined, reproducible product corresponding to net uptake of almost 8 molar equivalents of oxygen. The product, termed OxC-beta, empirical formula C40H60O15versus C40H56for β-carotene, contains more than 30% oxygen (w/w) and 85% β-carotene oxygen copolymers (w/w) as well as minor amounts of many C8−C18 norisoprenoid compounds. No vitamin A or higher molecular weight norisoprenoids are present. The predominance of polymeric products has not been reported previously. The polymer appears to be a less polymerized form of sporopollenin, a biopolymer found in exines of spores and pollen. Autoxidations of lycopene and canthaxanthin show a similar predominance of polymeric products. OxC-beta exhibits immunological activity in a PCR gene expression array, indicating that carotenoid oxidation produces non-vitamin A products with immunomodulatory potential.
Super-radiance-cascades and multimode super-radiance oscillations in a cold 85Rb Rydberg gas
Authors: Han Jianing , Maeda H.
Published: January 2014

We report on super-radiance-cascades and multimode super-radiance in a cold Rydberg gas. Correctly matching the super-radiant radiation and the sample size, or mode-matching, is discussed. In addition, it is shown that the spontaneous emission rate and density determine how fast super-radiance happens and whether or not the multimode super-radiance is observable. The results reported here are essential steps toward super-radiance induced plasma formation and two-photon correlations.
Conservation genetics of the endangered Spotted Turtle (Clemmys guttata) illustrate the risks of “bottleneck tests”
Authors: Davy Christina M. , Murphy Robert W.
Published: January 2014

Studies of population genetics in turtles have suggested that turtles do not experience genetic impacts of bottlenecks as strongly as expected. However, recent studies cast doubt on two commonly used tests implemented in the program BOTTLENECK, suggesting that these findings should be re-evaluated. The Spotted Turtle (Clemmys guttata (Schneider, 1792)) is endangered both globally and within Canada, but genetic data required to develop effective recovery strategies are unavailable. Here, we conducted the first study of population genetic structure in C. guttata. We then used multiple small populations of C. guttata as replicates to test whether the commonly used program BOTTLENECK could detect the genetic signature of bottlenecks in our study populations, which are all thought to have experienced significant declines in the past 2–3 generations (75 years). Turtles (n = 256) were genotyped at 11 microsatellite loci. A suite of Bayesian population genetics analyses and a principal coordinates analysis identified a minimum of 6 distinct genetic populations and a maximum of 10 differentiated subpopulations across the sampled Canadian range of C. guttata, which corresponded to demographically independent units. BOTTLENECK failed to detect population declines. A literature review found that bottleneck tests in 17 of 18 previous genetic studies of tortoises and freshwater turtles were based on suboptimal sampling, potentially confounding their results. High retention of genetic diversity (allelic richness and heterozygosity) in isolated populations of C. guttata and other turtle species is encouraging for species recovery, but conclusions about the prevalence of genetic bottlenecks in such populations should be re-examined.
The legacy of early radiolarian taxonomists, with a focus on the species published by early German workers
Authors: Lazarus David
Published: January 2014

Abstract. Approximately one-third of the c. 1200 polycystine radiolarian names currently recognized as valid in deep-sea research (Cenozoic sediments and plankton) come from the first century of taxonomic studies (c. 1840–1930). German scientists dominated early research on radiolarian biology and taxonomy. C. G. Ehrenberg’s initial work was followed by E. Haeckel’s mammoth monographic works, particularly his Challenger report. Other important early workers were D. Rüst on Mesozoic and Palaeozoic forms and A. Popofsky on plankton and sediment materials, with smaller contributions by J. Müller, E. Stöhr, F. Dreyer and H. Mast. Excluding Haeckel, these workers together published over 2000 species names. A fraction (5–25%) of these names are still used today in deep-sea research, with a tendency for more prolific authors to have higher modern usage rates. Haeckel’s legacy is different. He published over 5000 species names, but only a few percent are still used. The reasons for his species names no longer being used seem to include both factors common to disuse of names from other early authors (inadequate text descriptions, poor or absent illustration, no preserved original materials) but also due to substantial duplication of species and genus names, created by imposition of a partially artificial high level taxonomy. Based on Haeckel’s own writings and by analogy to other parts of Haeckel’s work, it is suggested that Haeckel’s desire to discover and show evolutionary relationships lay behind this flawed approach to taxonomy.
Flow behaviour in the intra-caldera setting: an AMS study of the large (>1290 km
3
) Permian Ora ignimbrite
Authors: Willcock Madelaine A. W. , Mattei Massimo , Hasalová Pavlína , Giordano Guido , Cas Ray A. F. , Morelli Corrado
Published: January 2014

Anisotropy of magnetic susceptibility (AMS) data reveal heterogeneous pyroclastic flow processes and variable flow directions within the intra-caldera setting of the Permian rhyolitic welded Ora ignimbrite. Magnetic fabric is primary, orientated during the pyroclastic flow emplacement, and is controlled by paramagnetic and ferromagnetic mineral phases. The ignimbrite has typically weak mean magnetic susceptibilities (1.32–21.8×10
−4
SI) but with a large spread and low anisotropy degrees (1.003–1.023), which vary in different parts of the caldera. The intra-caldera magnetic fabric provides significant information on the dynamics of the intra-caldera setting, relating to changing vertical and lateral flow emplacement processes. AMS shape ellipsoids range from oblate to prolate; these are interpreted to reflect the heterogeneous nature of the flow resulting from the influence of underlying topography, constraints of the caldera walls, primary welding and post-emplacement mineral growth. We have identified different depositional units and possible eruptive source regions, indicating that more than one source fissure vent was active during eruption within this caldera system. The lateral variations demonstrate a meandering of flow pulses. The caldera margin acts as an obstacle in preventing and rebuffing certain flows from scaling the caldera margin.
EUK-134 ameliorates nNOSμ translocation and skeletal muscle fiber atrophy during short-term mechanical unloading
Authors: Lawler John M. , Kunst Mary , Hord Jeff M. , Lee Yang , Joshi Kumar , Botchlett Rachel E. , Ramirez Angelo , Martinez Daniel A.
Published: January 2014

Reduced mechanical loading during bedrest, spaceflight, and casting, causes rapid morphological changes in skeletal muscle: fiber atrophy and reduction of slow-twitch fibers. An emerging signaling event in response to unloading is the translocation of neuronal nitric oxide synthase (nNOSμ) from the sarcolemma to the cytosol. We used EUK-134, a cell-permeable mimetic of superoxide dismutase and catalase, to test the role of redox signaling in nNOSμ translocation and muscle fiber atrophy as a result of short-term (54 h) hindlimb unloading. Fischer-344 rats were divided into ambulatory control, hindlimb-unloaded (HU), and hindlimb-unloaded + EUK-134 (HU-EUK) groups. EUK-134 mitigated the unloading-induced phenotype, including muscle fiber atrophy and muscle fiber-type shift from slow to fast. nNOSμ immunolocalization at the sarcolemma of the soleus was reduced with HU, while nNOSμ protein content in the cytosol increased with unloading. Translocation of nNOS from the sarcolemma to cytosol was virtually abolished by EUK-134. EUK-134 also mitigated dephosphorylation at Thr-32 of FoxO3a during HU. Hindlimb unloading elevated oxidative stress (4-hydroxynonenal) and increased sarcolemmal localization of Nox2 subunits gp91phox (Nox2) and p47phox, effects normalized by EUK-134. Thus, our findings are consistent with the hypothesis that oxidative stress triggers nNOSμ translocation from the sarcolemma and FoxO3a dephosphorylation as an early event during mechanical unloading. Thus, redox signaling may serve as a biological switch for nNOS to initiate morphological changes in skeletal muscle fibers.
Phase-dependent resetting of the adrenal clock by ACTH in vitro
Authors: Yoder J. Marina , Brandeland Megan , Engeland William C.
Published: January 2014

The adrenal cortex has a molecular clock that generates circadian rhythms in glucocorticoids, yet how the clock is synchronized to the external environment is unknown. Using mPER2::Luciferase (mPER2Luc) knockin mice, in which luciferase is rhythmically expressed under the control of the mouse Per2 clock gene, we hypothesized that ACTH transmits entrainment signals to the adrenal. Adrenal explants were administered ACTH at different phases of the mPER2Luc rhythm. Treatment with ACTH 1–39 produced a phase delay that was phase-dependent, with a maximum at circadian time (CT)18; ACTH did not alter the period or amplitude of the rhythm. Forskolin produced a parallel response, suggesting that the phase delay was cAMP-mediated. The response to ACTH was concentration-dependent and peptide-specific. Pulse administration (60 min) of ACTH 1–39 also produced phase delays restricted to late CTs. In contrast to ACTH 1–39, other ACTH fragments, including α-melanocyte-stimulating hormone, which do not activate the melanocortin 2 (MC2/ACTH) receptor, had no effect. The finding that ACTH in vitro phase delays the adrenal mPER2luc rhythm in a monophasic fashion argues for ACTH as a key resetter, but not the sole entrainer, of the adrenal clock.
Supraoptic oxytocin and vasopressin neurons function as glucose and metabolic sensors
Authors: Song Zhilin , Levin Barry E. , Stevens Wanida , Sladek Celia D.
Published: January 2014

Neurons in the supraoptic nuclei (SON) produce oxytocin and vasopressin and express insulin receptors (InsR) and glucokinase. Since oxytocin is an anorexigenic agent and glucokinase and InsR are hallmarks of cells that function as glucose and/or metabolic sensors, we evaluated the effect of glucose, insulin, and their downstream effector ATP-sensitive potassium (KATP) channels on calcium signaling in SON neurons and on oxytocin and vasopressin release from explants of the rat hypothalamo-neurohypophyseal system. We also evaluated the effect of blocking glucokinase and phosphatidylinositol 3 kinase (PI3K; mediates insulin-induced mobilization of glucose transporter, GLUT4) on responses to glucose and insulin. Glucose and insulin increased intracellular calcium ([Ca2+]i). The responses were glucokinase and PI3K dependent, respectively. Insulin and glucose alone increased vasopressin release ( P < 0.002). Oxytocin release was increased by glucose in the presence of insulin. The oxytocin (OT) and vasopressin (VP) responses to insulin+glucose were blocked by the glucokinase inhibitor alloxan (4 mM; P ≤ 0.002) and the PI3K inhibitor wortmannin (50 nM; OT: P = 0.03; VP: P ≤ 0.002). Inactivating KATPchannels with 200 nM glibenclamide increased oxytocin and vasopressin release (OT: P < 0.003; VP: P < 0.05). These results suggest that insulin activation of PI3K increases glucokinase-mediated ATP production inducing closure of KATPchannels, opening of voltage-sensitive calcium channels, and stimulation of oxytocin and vasopressin release. The findings are consistent with SON oxytocin and vasopressin neurons functioning as glucose and “metabolic” sensors to participate in appetite regulation.
Biomarkers of vascular function in premenopausal and recent postmenopausal women of similar age: effect of exercise training
Authors: Nyberg Michael , Seidelin Kaare , Andersen Thomas Rostgaard , Overby Nickie Neumann , Hellsten Ylva , Bangsbo Jens
Published: January 2014

Menopause is associated with an accelerated decline in vascular function; however, whether this is an effect of age and/or menopause and how exercise training may affect this decline remains unclear. We examined a range of molecular measures related to vascular function in matched premenopausal and postmenopausal women before and after 12 wk of exercise training. Thirteen premenopausal and 10 recently postmenopausal [1.6 ± 0.3 (means ± SE) years after final menstrual period] women only separated by 3 yr (48 ± 1 vs. 51 ± 1 yr) were included. Before training, diastolic blood pressure, soluble intercellular adhesion molecule-1 (sICAM-1), and skeletal muscle expression of thromboxane A synthase were higher in the postmenopausal women compared with the premenopausal women, all indicative of impaired vascular function. In both groups, exercise training lowered diastolic blood pressure, the levels of sICAM-1, soluble vascular adhesion molecule-1 (sVCAM-1), as well as plasma and skeletal muscle endothelin-1. The vasodilator prostacyclin tended ( P = 0.061) to be higher in plasma with training in the postmenopausal women only. These findings demonstrate that already within the first years after menopause, several biomarkers of vascular function are adversely altered, indicating that these biomarker changes are more related to hormonal changes than aging. Exercise training appears to have a positive impact on vascular function, as indicated by a marked improvement in the biomarker profile, in both premenopausal and postmenopausal women.
Clopidogrel preserves whole kidney autoregulatory behavior in ANG II-induced hypertension
Authors: Osmond David A. , Zhang Shali , Pollock Jennifer S. , Yamamoto Tatsuo , De Miguel Carmen , Inscho Edward W.
Published: January 2014

This study tested the hypothesis that P2Y12receptor blockade with clopidogrel preserves renal autoregulatory ability during ANG II-induced hypertension. Clopidogrel was administered orally to male Sprague-Dawley rats chronically infused with ANG II. After 14 days of treatment, whole kidney autoregulation of renal blood flow was assessed in vivo in pentobarbital-anesthetized rats using an ultrasonic flow probe placed around the left renal artery. In ANG II-vehicle-treated rats, decreasing arterial pressure over a range from 160 to 100 mmHg resulted in a 25 ± 5% decrease in renal blood flow, demonstrating a significant loss of autoregulation with an autoregulatory index of 0.66 ± 0.15. However, clopidogrel treatment preserved autoregulatory behavior in ANG II-treated rats to levels indistinguishable from normotensive sham-operated (sham) rats (autoregulatory index: 0.04 ± 0.14). Compared with normotensive sham-vehicle-treated rats, ANG II infusion increased renal CD3-positive T cell infiltration by 66 ± 6%, induced significant thickening of the preglomerular vessels and glomerular basement membrane and increased glomerular collagen I deposition, tubulointerstitial fibrosis, damage to the proximal tubular brush border, and protein excretion. Clopidogrel significantly reduced renal infiltration of T cells by 39 ± 9% and prevented interstitial artery thickening, ANG II-induced damage to the glomerular basement membrane, deposition of collagen type I, and tubulointerstitial fibrosis, despite the maintenance of hypertension. These data demonstrate that systemic P2Y12receptor blockade with clopidogrel protects against impairment of autoregulatory behavior and renal vascular injury in ANG II-induced hypertension, possibly by reducing renal T cell infiltration.
Three-dimensional reconstruction of the rat nephron
Authors: Christensen Erik I. , Grann Birgitte , Kristoffersen Inger B. , Skriver Elisabeth , Thomsen Jesper S. , Andreasen Arne
Published: January 2014

This study gives a three-dimensional (3D) structural analysis of rat nephrons and their connections to collecting ducts. Approximately 4,500 2.5-μm-thick serial sections from the renal surface to the papillary tip were obtained from each of 3 kidneys of Wistar rats. Digital images were recorded and aligned into three image stacks and traced from image to image. Short-loop nephrons (SLNs), long-loop nephrons (LLNs), and collecting ducts (CDs) were reconstructed in 3D. We identified a well-defined boundary between the outer stripe and the inner stripe of the outer medulla corresponding to the transition of descending thick limbs to descending thin limbs and between the inner stripe and the inner medulla, i.e., the transition of ascending thin limbs into ascending thick limbs of LLNs. In all nephrons, a mosaic pattern of proximal tubule (PT) cells and descending thin limb (DTL) cells was observed at the transition between the PT and the DTL. The course of the LLNs revealed tortuous proximal “straight” tubules and winding of the DTLs within the outer half of the inner stripe. The localization of loop bends of SLNs in the inner stripe of the outer medulla and the bends of LLNs in the inner medulla reflected the localization of their glomeruli; i.e., the deeper the glomerulus, the deeper the bend. Each CD drained approximately three to six nephrons with a different pattern than previously established in mice. This information will provide a basis for evaluation of structural changes within nephrons as a result of physiological or pharmaceutical intervention.
Muscle activation patterns are bilaterally linked during split-belt treadmill walking in humans
Authors: MacLellan M. J. , Ivanenko Y. P. , Massaad F. , Bruijn S. M. , Duysens J. , Lacquaniti F.
Published: January 2014

There is growing evidence that human locomotion is controlled by flexibly combining a set of basic muscle activity patterns. To explore how these patterns are modified to cope with environmental constraints, 10 healthy young adults 1st walked on a split-belt treadmill at symmetric speeds of 4 and 6 km/h for 2 min. An asymmetric condition was then performed for 10 min in which treadmill speeds for the dominant (fast) and nondominant (slow) sides were 6 and 4 km/h, respectively. This was immediately followed by a symmetric speed condition of 4 km/h for 5 min. Gait kinematics and ground reaction forces were recorded. Electromyography (EMG) was collected from 12 lower limb muscles on each side of the body. Nonnegative matrix factorization was applied to the EMG signals bilaterally and unilaterally to obtain basic activation patterns. A cross-correlation analysis was then used to quantify temporal changes in the activation patterns. During the early (1st 10 strides) and late (final 10 strides) phases of the asymmetric condition, the patterns related to ankle plantar flexor (push-off) of the fast limb and quadriceps muscle (contralateral heel contact) of the slow limb occurred earlier in the gait cycle compared with the symmetric conditions. Moreover, a bilateral temporal alignment of basic patterns between limbs was still maintained in the split-belt condition since a similar shift was observed in the unilateral patterns. The results suggest that the temporal structure of these locomotor patterns is shaped by sensory feedback and that the patterns are bilaterally linked.
Fast feedback control involves two independent processes utilizing knowledge of limb dynamics
Authors: Kurtzer Isaac , Crevecoeur Frédéric , Scott Stephen H.
Published: January 2014

Corrective muscle responses occurring 50–100 ms after a mechanical perturbation are tailored to the mechanical features of the limb and its environment. For example, the evoked response by the shoulder's extensor muscle counters an imposed shoulder torque, rather than local shoulder motion, by integrating motion information from the shoulder and elbow appropriate for their dynamic interaction. Previous studies suggest that arm muscle activity within this epoch, alternately termed the R2/3 response, or long-latency reflex, reflects the summed result of two distinct components: an activity-dependent component which scales with the background muscle activity, and a task-dependent component which scales with the required vigor of the behavioral task. Here we examine how the knowledge of limb dynamics expressed during the shoulder muscle's R2/3 epoch is related to these two functional components. Subjects countered torque steps applied to their shoulder and/or elbow under different conditions of background torque and target size to recruit the activity-dependent and task-dependent component in varying degrees. Experiment 1 involved four torque perturbations, two levels of background torques and two target sizes; this design revealed that both background torque and target size impacted the shoulder's R2/3 activity, indicative of knowledge of limb dynamics. Experiment 2 involved two perturbation torques, five levels of background torque and two target sizes; this design demonstrated that the two factors had an independent impact on the R2/3 activity indicative of knowledge of limb dynamics. We conclude that a sophisticated feature of upper limb feedback control reflects the summation of two processes having a common capability.
Neonatal infraorbital nerve crush-induced CNS synaptic plasticity and functional recovery
Authors: Lo Fu-Sun , Zhao Shuxin , Erzurumlu Reha S.
Published: January 2014

Infraorbital nerve (ION) transection in neonatal rats leads to disruption of whisker-specific neural patterns (barrelettes), conversion of functional synapses into silent synapses, and reactive gliosis in the brain stem trigeminal principal nucleus (PrV). Here we tested the hypothesis that neonatal peripheral nerve crush injuries permit better functional recovery of associated central nervous system (CNS) synaptic circuitry compared with nerve transection. We developed an in vitro whisker pad-trigeminal ganglion (TG)-brain stem preparation in neonatal rats and tested functional recovery in the PrV following ION crush. Intracellular recordings revealed that 68% of TG cells innervate the whisker pad. We used the proportion of whisker pad-innervating TG cells as an index of ION function. The ION function was blocked by ∼64%, immediately after mechanical crush, then it recovered beginning after 3 days postinjury and was complete by 7 days. We used this reversible nerve-injury model to study peripheral nerve injury-induced CNS synaptic plasticity. In the PrV, the incidence of silent synapses increased to ∼3.5 times of control value by 2–3 days postinjury and decreased to control levels by 5–7 days postinjury. Peripheral nerve injury-induced reaction of astrocytes and microglia in the PrV was also reversible. Neonatal ION crush disrupted barrelette formation, and functional recovery was not accompanied by de novo barrelette formation, most likely due to occurrence of recovery postcritical period (P3) for pattern formation. Our results suggest that nerve crush is more permissive for successful regeneration and reconnection (collectively referred to as “recovery” here) of the sensory inputs between the periphery and the brain stem.