bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Emerging Macrophage-Tropic HIV-1 R5 Variants in Brain Tissue of AIDS Patients without Severe Neurological Complications
Authors: Gonzalez-Perez Maria Paz , Peters Paul J. , O'Connell Olivia , Silva Nilsa , Harbison Carole , Cummings Macri Sheila , Kaliyaperumal Saravanan , Luzuriaga Katherine , Clapham Paul R.
Published: August 2017

Untreated HIV-positive (HIV-1
+
) individuals frequently suffer from HIV-associated neurocognitive disorders (HAND), with about 30% of AIDS patients suffering severe HIV-associated dementias (HADs). Antiretroviral therapy has greatly reduced the incidence of HAND and HAD. However, there is a continuing problem of milder neurocognitive impairments in treated HIV
+
patients that may be increasing with long-term therapy. In the present study, we investigated whether envelope (
env
) genes could be amplified from proviral DNA or RNA derived from brain tissue of 12 individuals with normal neurology or minor neurological conditions (N/MC individuals). The tropism and characteristics of the brain-derived Envs were then investigated and compared to those of Envs derived from immune tissue. We showed that (i) macrophage-tropic R5 Envs could be detected in the brain tissue of 4/12 N/MC individuals, (ii) macrophage-tropic Envs in brain tissue formed compartmentalized clusters distinct from non-macrophage-tropic (non-mac-tropic) Envs recovered from the spleen or brain, (iii) the evidence was consistent with active viral expression by macrophage-tropic variants in the brain tissue of some individuals, and (iv) Envs from immune tissue of the N/MC individuals were nearly all tightly non-mac-tropic, contrasting with previous data for neuro-AIDS patients where immune tissue Envs mediated a range of macrophage infectivities, from background levels to modest infection, with a small number of Envs from some patients mediating high macrophage infection levels. In summary, the data presented here show that compartmentalized and active macrophage-tropic HIV-1 variants are present in the brain tissue of individuals before neurological disease becomes overt or serious.

IMPORTANCE
The detection of highly compartmentalized macrophage-tropic R5 Envs in the brain tissue of HIV patients without serious neurological disease is consistent with their emergence from a viral population already established there, perhaps from early disease. The detection of active macrophage-tropic virus expression, and probably replication, indicates that antiretroviral drugs with optimal penetration through the blood-brain barrier should be considered even for patients without neurological disease (neuro-disease). Finally, our data are consistent with the brain forming a sanctuary site for latent virus and low-level viral replication in the absence of neuro-disease.
PGC1α Transcriptional Adaptor Function Governs Hepatitis B Virus Replication by Controlling HBcAg/p21 Protein-Mediated Capsid Formation
Authors: Shalaby Rasha E. , Iram Saira , Çakal Bülent , Oropeza Claudia E. , McLachlan Alan
Published: August 2017

In the human hepatoma cell line Huh7, the coexpression of the coactivators peroxisome proliferator-activated receptor γ coactivator 1α (PGC1α), cyclic AMP-responsive element binding protein binding protein (CBP), steroid receptor coactivator 1 (SRC1), and protein arginine methyltransferase 1 (PRMT1) only modestly increase hepatitis B virus (HBV) biosynthesis. However, by utilizing the human embryonic kidney cell line HEK293T, it was possible to demonstrate that PGC1α alone can support viral biosynthesis independently of the expression of additional coactivators or transcription factors. In contrast, additional coactivators failed to support robust HBV replication in the absence of PGC1α. These observations indicate that PGC1α represents a novel adaptor molecule capable of recruiting the necessary transcriptional machinery to the HBV nucleocapsid promoter to modestly enhance viral pregenomic 3.5-kb RNA synthesis. Although this change in transcription is associated with a similar modest change in hepatitis B virus core antigen polypeptide (HBcAg/p21) synthesis, it mediates a dramatic increase in viral capsid production and robust viral replication. Therefore, it is apparent that the synthesis of cytoplasmic HBcAg/p21 above a critical threshold level is required for the efficient assembly of HBV replication-competent viral capsids.

IMPORTANCE
Hepatitis B virus (HBV) is a major human pathogen, and novel targets for the development of additional therapeutic agents are urgently needed. Here we demonstrate that the coactivator peroxisome proliferator-activated receptor γ coactivator 1α (PGC1α) serves as a unique adaptor molecule for the recruitment of additional coactivator proteins, which can finely regulate HBV transcription. The consequence of this precise regulation of viral RNA levels by PGC1α is a subtle increase in cytoplasmic HBcAg/p21 polypeptide translation, which shifts the equilibrium from dimer formation dramatically in favor of viral capsid assembly. These findings suggest that both PGC1α and capsid assembly may represent attractive targets for the development of antiviral agents against chronic HBV infection.
Zinc Finger-Containing Cellular Transcription Corepressor ZBTB25 Promotes Influenza Virus RNA Transcription and Is a Target for Zinc Ejector Drugs
Authors: Chen Shu-Chuan , Jeng King-Song , Lai Michael M. C.
Published: August 2017

Influenza A virus (IAV) replication relies on an intricate interaction between virus and host cells. How the cellular proteins are usurped for IAV replication remains largely obscure. The aim of this study was to search for novel and potential cellular factors that participate in IAV replication. ZBTB25, a transcription repressor of a variety of cellular genes, was identified by an RNA interference (RNAi) genomic library screen. Depletion of ZBTB25 significantly reduced IAV production. Conversely, overexpression of ZBTB25 enhanced it. ZBTB25 interacted with the viral RNA-dependent RNA polymerase (RdRp) protein and modulated its transcription activity. In addition, ZBTB25 also functioned as a viral RNA (vRNA)-binding protein, binding preferentially to the U-rich sequence within the 5′ untranslated region (UTR) of vRNA. Both protein-protein and protein-RNA interactions involving ZBTB25 facilitated viral RNA transcription and replication. In addition, ZBTB25 suppressed interferon production, further enhancing viral replication. ZBTB25-associated functions required an intact zinc finger domain and posttranslational SUMO-1 modification of ZBTB25. Furthermore, treatment with disulfiram (a zinc ejector) of ZBTB25-overexpressing cells showed significantly reduced IAV production as a result of reduced RNA synthesis. Our findings indicate that IAV usurps ZBTB25 for IAV RNA synthesis and serves as a novel and potential therapeutic antiviral target.

IMPORTANCE
IAV-induced seasonal influenza causes severe illness and death in high-risk populations. However, IAV has developed resistance to current antiviral drugs due to its high mutation rate. Therefore, development of drugs targeting cellular factors required for IAV replication is an attractive alternative for IAV therapy. Here, we discovered a cellular protein, ZBTB25, that enhances viral RdRp activity by binding to both viral RdRp and viral RNA to stimulate viral RNA synthesis. A unique feature of ZBTB25 in the regulation of viral replication is its dual transcription functions, namely, promoting viral RNA transcription through binding to the U-rich region of vRNA and suppressing cellular interferon production. ZBTB25 contains a zinc finger domain that is required for RNA-inhibitory activity by chelating zinc ions. Disulfiram treatment disrupts the zinc finger functions, effectively repressing IAV replication. Based on our findings, we demonstrate that ZBTB25 regulates IAV RNA transcription and replication and serves as a promising antiviral target for IAV treatment.
Positive and Negative Regulation of Type I Interferons by the Human T Cell Leukemia Virus Antisense Protein HBZ
Authors: Narulla Manraj Singh , Alsairi Ahlam , Charmier Lucie , Noonan Stephen , Conroy David , Hall William W. , Sheehy Noreen
Published: August 2017

The pathogenesis of human T cell leukemia virus type 1 (HTLV-1) is strongly linked to the viral regulatory proteins Tax1 and HBZ, whose opposing functions contribute to the clinical outcome of infection. Type I interferons alpha and beta (IFN-α and IFN-β) are key cytokines involved in innate immunity, and IFN-α, in combination with other antivirals, is extensively used in the treatment of HTLV-1 infection. The relationship between HTLV-1 and IFN signaling is unclear, and to date the effect of HBZ on this pathway has not been examined. Here we report that HBZ significantly enhances interferon regulatory factor 7 (IRF7)-induced IFN-α- and IFN-stimulated response element (ISRE) promoter activities and IFN-α production and can counteract the inhibitory effect of Tax1. In contrast to this, we show that HBZ and Tax1 cooperate to inhibit the induction of IFN-β and ISRE promoters by IRF3 and IFN-β production. In addition, we reveal that HBZ enhances ISRE activation by IFN-α. We further show that HBZ enhances IRF7 and suppresses IRF3 activation by TBK1 and IKKε. We demonstrate that HBZ has no effect on virus-induced nuclear accumulation of IRF3, suggesting that it may inhibit IRF3 activity at a transcriptional level. We show that HBZ physically interacts with IRF7 and IKKε but not with IRF3 or TBK1. Overall, our findings suggest that both HBZ and Tax1 are negative regulators of immediate early IFN-β innate immune responses, while HBZ but not Tax1 positively regulates the induction of IFN-α and downstream IFN-α signaling.

IMPORTANCE
Type I interferons are powerful antiviral cytokines and are used extensively in the treatment of HTLV-1-induced adult T cell leukemia (ATL). To date, the relationship between HTLV-1 and the IFN pathway is poorly understood, and studies so far have focused on Tax1. Our study is unique in that it examined the effect of HBZ, alone or in combination with Tax1, on type I IFN signaling. This is important because HBZ is frequently the only viral protein expressed in infected cells, particularly at later stages of infection. A better understanding of the how HBZ regulates IFN signaling may lead to the development of therapeutics that can modify such responses and improve the clinical outcome for infected individuals.
Human Herpesvirus 8 Infects and Replicates in Langerhans Cells and Interstitial Dermal Dendritic Cells and Impairs Their Function
Authors: Rappocciolo Giovanna , Jais Mariel , Piazza Paolo A. , DeLucia Diana C. , Jenkins Frank J. , Rinaldo Charles R.
Published: August 2017

The predominant types of dendritic cells (DC) in the skin and mucosa are Langerhans cells (LC) and interstitial dermal DC (iDDC). LC and iDDC process cutaneous antigens and migrate out of the skin and mucosa to the draining lymph nodes to present antigens to T and B cells. Because of the strategic location of LC and iDDC and the ability of these cells to capture and process pathogens, we hypothesized that they could be infected with human herpesvirus 8 (HHV-8) (Kaposi's sarcoma [KS]-associated herpesvirus) and have an important role in the development of KS. We have previously shown that HHV-8 enters monocyte-derived dendritic cells (MDDC) through DC-SIGN, resulting in nonproductive infection. Here we show that LC and iDDC generated from pluripotent cord blood CD34+cell precursors support productive infection with HHV-8. Anti-DC-SIGN monoclonal antibody (MAb) inhibited HHV-8 infection of iDDC, as shown by low expression levels of viral proteins and DNA. In contrast, blocking of both langerin and the receptor protein tyrosine kinase ephrin A2 was required to inhibit HHV-8 infection of LC. Infection with HHV-8 did not alter the cell surface expression of langerin on LC but downregulated the expression of DC-SIGN on iDDC, as we previously reported for MDDC. HHV-8-infected LC and iDDC had a reduced ability to stimulate allogeneic CD4+T cells in the mixed-lymphocyte reaction. These results indicate that HHV-8 can target both LC and iDDC for productive infection via different receptors and alter their function, supporting their potential role in HHV-8 pathogenesis and KS.

IMPORTANCEHere we show that HHV-8, a DNA tumor virus that causes Kaposi's sarcoma, infects three types of dendritic cells: monocyte-derived dendritic cells, Langerhans cells, and interstitial dermal dendritic cells. We show that different receptors are used by this virus to infect these cells. DC-SIGN is a major receptor for infection of both monocyte-derived dendritic cells and interstitial dermal dendritic cells, yet the virus fully replicates only in the latter. HHV-8 uses langerin and the ephrin A2 receptor to infect Langerhans cells, which support full HHV-8 lytic replication. This infection of Langerhans cells and interstitial dermal dendritic cells results in an impaired ability to stimulate CD4+helper T cell responses. Taken together, our data show that HHV-8 utilizes alternate receptors to differentially infect and replicate in these tissue-resident DC and support the hypothesis that these cells play an important role in HHV-8 infection and pathogenesis.
Isolation and Characterization of Metallosphaera Turreted Icosahedral Virus, a Founding Member of a New Family of Archaeal Viruses
Authors: Wagner Cassia , Reddy Vijay , Asturias Francisco , Khoshouei Maryam , Johnson John E. , Manrique Pilar , Munson-McGee Jacob , Baumeister Wolfgang , Lawrence C. Martin , Young Mark J.
Published: August 2017

Our understanding of archaeal virus diversity and structure is just beginning to emerge. Here we describe a new archaeal virus, tentatively named Metallosphaera turreted icosahedral virus (MTIV), that was isolated from an acidic hot spring in Yellowstone National Park, USA. Two strains of the virus were identified and were found to replicate in an archaeal host species closely related to
Metallosphaera yellowstonensis
. Each strain encodes a 9.8- to 9.9-kb linear double-stranded DNA (dsDNA) genome with large inverted terminal repeats. Each genome encodes 21 open reading frames (ORFs). The ORFs display high homology between the strains, but they are quite distinct from other known viral genes. The 70-nm-diameter virion is built on a T=28 icosahedral lattice. Both single particle cryo-electron microscopy and cryotomography reconstructions reveal an unusual structure that has 42 turret-like projections: 12 pentameric turrets positioned on the icosahedral 5-fold axes and 30 turrets with apparent hexameric symmetry positioned on the icosahedral 2-fold axes. Both the virion structural properties and the genome content support MTIV as the founding member of a new family of archaeal viruses.

IMPORTANCE
Many archaeal viruses are quite different from viruses infecting bacteria and eukaryotes. Initial characterization of MTIV reveals a virus distinct from other known bacterial, eukaryotic, and archaeal viruses; this finding suggests that viruses infecting
Archaea
are still an understudied group. As the first known virus infecting a
Metallosphaera
sp., MTIV provides a new system for exploring archaeal virology by examining host-virus interactions and the unique features of MTIV structure-function relationships. These studies will likely expand our understanding of virus ecology and evolution.
Monoclonal Antibodies against Zika Virus: Therapeutics and Their Implications for Vaccine Design
Authors: Wang Qihui , Yan Jinghua , Gao George Fu
Published: August 2017

Zika virus (ZIKV) has caused global concern due to its association with neurological complications in newborns and adults. Although no vaccines or antivirals against ZIKV infection have been approved to date, hundreds of monoclonal antibodies (MAbs) have been developed in a short period. Here, we first present a complete picture of the ZIKV MAbs and then focus on the neutralizing mechanisms and immune hot spots uncovered through structural studies, which provide insight for therapeutics and vaccine design.
Kinase Activity of Fibroblast Growth Factor Receptor 3 Regulates Activity of the Papillomavirus E2 Protein
Authors: Xie Fang , DeSmet Marsha , Kanginakudru Sriramana , Jose Leny , Culleton Sara P. , Gilson Timra , Li Chengxin , Androphy Elliot J.
Published: August 2017

The papillomavirus (PV) E2 protein is a DNA binding, protein interaction platform that recruits viral and host factors necessary for transcription and replication. We recently discovered phosphorylation of a tyrosine (Y102) in bovine PV (BPV) E2. To identify the responsible factor, we tested several candidate tyrosine kinases that are highly expressed in keratinocytes for binding to BPV-1 E2. Fibroblast growth factor receptor 3 (FGFR3) coimmunoprecipitated with the BPV-1 E2 protein, as did human papillomavirus 31 (HPV-31) E2, which also colocalized with FGFR3 within the nucleus. A constitutively active mutant form of FGFR3 decreased BPV-1 and HPV-31 transient replication although this result also occurred in a BPV-1 E2 mutant lacking a previously identified phosphorylation site of interest (Y102). Furthermore, FGFR3 depletion in cell lines that maintain HPV-31 episomes increased viral copy number. These results suggest that FGFR3 kinase activity may regulate the PV reproductive program through phosphorylation of the E2 protein although this is unlikely to occur through the Y102 residue of HPV E2.

IMPORTANCE
The papillomavirus (PV) is a double-stranded DNA tumor virus infecting cervix, mouth, and throat tissues. The viral protein E2 is responsible for the replication of the virus. Understanding the mechanisms of the replicative life cycle of the virus may bring to light direct targets and treatments against viral infection. We recently found that the fibroblast growth factor receptor 3 (FGFR3) interacts with and mediates PV E2 function through phosphorylation of the E2 protein. Our study suggests that the function of the E2 protein may be regulated through a direct FGFR3 target during the maintenance stage of the PV life cycle.
Relevance of Assembly-Activating Protein for Adeno-associated Virus Vector Production and Capsid Protein Stability in Mammalian and Insect Cells
Authors: Grosse Stefanie , Penaud-Budloo Magalie , Herrmann Anne-Kathrin , Börner Kathleen , Fakhiri Julia , Laketa Vibor , Krämer Chiara , Wiedtke Ellen , Gunkel Manuel , Ménard Lucie , Ayuso Eduard , Grimm Dirk
Published: August 2017

The discovery that adeno-associated virus 2 (AAV2) encodes an eighth protein, called assembly-activating protein (AAP), transformed our understanding of wild-type AAV biology. Concurrently, it raised questions about the role of AAP during production of recombinant vectors based on natural or molecularly engineered AAV capsids. Here, we show that AAP is indeed essential for generation of functional recombinant AAV2 vectors in both mammalian and insect cell-based vector production systems. Surprisingly, we observed that AAV2 capsid proteins VP1 to -3 are unstable in the absence of AAP2, likely due to rapid proteasomal degradation. Inhibition of the proteasome led to an increase of intracellular VP1 to -3 but neither triggered assembly of functional capsids nor promoted nuclear localization of the capsid proteins. Together, this underscores the crucial and unique role of AAP in the AAV life cycle, where it rapidly chaperones capsid assembly, thus preventing degradation of free capsid proteins. An expanded analysis comprising nine alternative AAV serotypes (1, 3 to 9, and rh10) showed that vector production always depends on the presence of AAP, with the exceptions of AAV4 and AAV5, which exhibited AAP-independent, albeit low-level, particle assembly. Interestingly, AAPs from all 10 serotypes could cross-complement AAP-depleted helper plasmids during vector production, despite there being distinct intracellular AAP localization patterns. These were most pronounced for AAP4 and AAP5, congruent with their inability to rescue an AAV2/AAP2 knockout. We conclude that AAP is key for assembly of genuine capsids from at least 10 different AAV serotypes, which has implications for vectors derived from wild-type or synthetic AAV capsids.

IMPORTANCE
Assembly of adeno-associated virus 2 (AAV2) is regulated by the assembly-activating protein (AAP), whose open reading frame overlaps with that of the viral capsid proteins. As the majority of evidence was obtained using virus-like particles composed solely of the major capsid protein VP3, AAP's role in and relevance for assembly of genuine AAV capsids have remained largely unclear. Thus, we established a
trans
-complementation assay permitting assessment of AAP functionality during production of recombinant vectors based on complete AAV capsids and derived from any serotype. We find that AAP is indeed a critical factor not only for AAV2, but also for generation of vectors derived from nine other AAV serotypes. Moreover, we identify a new role of AAP in maintaining capsid protein stability in mammalian and insect cells. Thereby, our study expands our current understanding of AAV/AAP biology, and it concomitantly provides insights into the importance of AAP for AAV vector production.
Inactivated H7 Influenza Virus Vaccines Protect Mice despite Inducing Only Low Levels of Neutralizing Antibodies
Authors: Kamal Ram P. , Blanchfield Kristy , Belser Jessica A. , Music Nedzad , Tzeng Wen-Pin , Holiday Crystal , Burroughs Ashley , Sun Xiangjie , Maines Taronna R. , Levine Min Z. , York Ian A.
Published: August 2017

Avian influenza viruses of the H7 hemagglutinin (HA) subtype present a significant public health threat, as evidenced by the ongoing outbreak of human A(H7N9) infections in China. When evaluated by hemagglutination inhibition (HI) and microneutralization (MN) assays, H7 viruses and vaccines are found to induce lower level of neutralizing antibodies (nAb) than do their seasonal counterparts, making it difficult to develop and evaluate prepandemic vaccines. We have previously shown that purified recombinant H7 HA appear to be poorly immunogenic in that they induce low levels of HI and MN antibodies. In this study, we immunized mice with whole inactivated reverse genetics reassortant (RG) viruses expressing HA and neuraminidase (NA) from 3 different H7 viruses [A/Shanghai/2/2013(H7N9), A/Netherlands/219/2003(H7N7), and A/New York/107/2003(H7N2)] or with human A(H1N1)pdm09 (A/California/07/2009-like) or A(H3N2) (A/Perth16/2009) viruses. Mice produced equivalent titers of antibodies to all viruses as measured by enzyme-linked immunosorbent assay (ELISA). However, the antibody titers induced by H7 viruses were significantly lower when measured by HI and MN assays. Despite inducing very low levels of nAb, H7 vaccines conferred complete protection against homologous virus challenge in mice, and the serum antibodies directed against the HA head region were capable of mediating protection. The apparently low immunogenicity associated with H7 viruses and vaccines may be at least partly related to measuring antibody titers with the traditional HI and MN assays, which may not provide a true measure of protective immunity associated with H7 immunization. This study underscores the need for development of additional correlates of protection for prepandemic vaccines.

IMPORTANCE
H7 avian influenza viruses present a serious risk to human health. Preparedness efforts include development of prepandemic vaccines. For seasonal influenza viruses, protection is correlated with antibody titers measured by hemagglutination inhibition (HI) and virus microneutralization (MN) assays. Since H7 vaccines typically induce low titers in HI and MN assays, they have been considered to be poorly immunogenic. We show that in mice H7 whole inactivated virus vaccines (WIVs) were as immunogenic as seasonal WIVs, as they induced similar levels of overall serum antibodies. However, a larger fraction of the antibodies induced by H7 WIV was nonneutralizing
in vitro
. Nevertheless, the H7 WIV completely protected mice against homologous viral challenge, and antibodies directed against the HA head were the major contributor toward immune protection. Vaccines against H7 avian influenza viruses may be more effective than HI and virus neutralization assays suggest, and such vaccines may need other methods for evaluation.
Crystal Structure of the N-Terminal Half of the Traffic Controller UL37 from Herpes Simplex Virus 1
Authors: Koenigsberg Andrea L. , Heldwein Ekaterina E.
Published: August 2017

Inner tegument protein UL37 is conserved among all three subfamilies of herpesviruses. Studies of UL37 homologs from two alphaherpesviruses, herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV), have suggested that UL37 plays an essential albeit poorly defined role in intracellular capsid trafficking. At the same time, HSV and PRV homologs cannot be swapped, which suggests that in addition to a conserved function, UL37 homologs also have divergent virus-specific functions. Accurate dissection of UL37 functions requires detailed maps in the form of atomic-resolution structures. Previously, we reported the crystal structure of the N-terminal half of UL37 (UL37N) from PRV. Here, we report the crystal structure of HSV-1 UL37N. Comparison of the two structures reveals that UL37 homologs differ in their overall shapes, distributions of surface charges, and locations of projecting loops. In contrast, the previously identified R2 surface region is structurally conserved. We propose that within the N-terminal half of UL37, functional conservation is centered within the R2 surface region, whereas divergent structural elements pinpoint regions mediating virus-specific functions and may engage different binding partners. Together, the two structures can now serve as templates for a structure-guided exploration of both conserved and virus-specific functions of UL37.

IMPORTANCE
The ability to move efficiently within host cell cytoplasm is essential for replication in all viruses. It is especially important in the neuroinvasive alphaherpesviruses, such as human herpes simplex virus 1 (HSV-1), HSV-2, and veterinarian pseudorabies virus (PRV), that infect the peripheral nervous system and have to travel long distances along axons. Capsid movement in these viruses is controlled by capsid-associated tegument proteins, yet their specific roles have not yet been defined. Systematic exploration of the roles of tegument proteins in capsid trafficking requires detailed navigational charts in the form of their three-dimensional structures. Here, we determined the crystal structure of the N-terminal half of a conserved tegument protein, UL37, from HSV-1. This structure, along with our previously reported structure of the UL37 homolog from PRV, provides a much needed 3-dimensional template for the dissection of both conserved and virus-specific functions of UL37 in intracellular capsid trafficking.
Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information
Authors: Barberán Albert , Caceres Velazquez Hildamarie , Jones Stuart , Fierer Noah
Published: August 2017

Cultivation in the laboratory is key for understanding the phenotypic characteristics, growth requirements, metabolism, and environmental preferences of bacteria. However, oftentimes, phenotypic information is not easily accessible. Here, we compiled phenotypic and environmental tolerance information for >5,000 bacterial strains described in the
International Journal of Systematic and Evolutionary Microbiology
(IJSEM). We demonstrate how this database can be used to link bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and environmental preferences. The phenotypic database can be freely accessed (
https://doi.org/10.6084/m9.figshare.4272392
), and we have included instructions for researchers interested in adding new entries or curating existing ones.
Characterization of
Legionella
Species from Watersheds in British Columbia, Canada
Authors: Peabody Michael A. , Caravas Jason A. , Morrison Shatavia S. , Mercante Jeffrey W. , Prystajecky Natalie A. , Raphael Brian H. , Brinkman Fiona S. L.
Published: August 2017

Many species of
Legionella
can cause Legionnaires’ disease, a significant cause of bacterial pneumonia.
Legionella
in human-made water systems such as cooling towers and building plumbing systems are the primary sources of Legionnaires’ disease outbreaks. In this temporal study of natural aquatic environments,
Legionella
relative abundance was shown to vary in watersheds associated with different land uses. Analysis of the
Legionella
sequences detected at these sites revealed highly diverse populations that included potentially novel
Legionella
species. These findings have important implications for understanding the ecology of
Legionella
and control measures for this pathogen that are aimed at reducing human disease.
Amino Acid Differences in the 1753-to-1851 Region of TcdB Influence Variations in TcdB1 and TcdB2 Cell Entry
Authors: Hunt Jonathan J. , Larabee Jason L. , Ballard Jimmy D.
Published: August 2017

TcdB is a major virulence factor produced by
Clostridium difficile
, a leading cause of antibiotic-associated diarrhea. Hypervirulent strains of
C. difficile
encode a variant of TcdB (TcdB2) that is more toxic than toxin derived from historical strains (TcdB1). Though TcdB1 and TcdB2 exhibit 92% overall identity, a 99-amino-acid region previously associated with cell entry and spanning amino acids 1753 to 1851 has only 77% sequence identity. Results from the present study indicate that the substantial sequence variation in this region could contribute to the differences in cell entry between TcdB1 and TcdB2 and possibly explain TcdB2’s heightened toxicity. Finally, during the course of these studies, an unusual aspect of TcdB cell entry was discovered wherein cell binding appeared to depend on endocytosis. These findings provide insight into TcdB’s variant forms and their mechanisms of cell entry.
Nephrolithisis in a newborn: a rare case and review of literature
Authors: Singh Kawaljit , Sokhal Ashok Kumar , Sankhwar Satyanarayan , Purkait Bimalesh
Published: August 2017

Nephrolithiasis, although a common entity in adults, is less common in children and rare in newborns. The evaluation and management strategies of renal stones in neonates are unclear. We report a rare scenario of renal calculus in a newborn aged 3 days presenting with decreased urine output, fever and crying during micturition. Patient was thoroughly investigated and managed conservatively. Further follow-up showed increase in stone size with recurrent urinary tract infections, hence shock wave lithotripsy was performed to successfully break and clear the stone fragments. Patient recovered well and was doing fine until last follow-up.
Disseminated cryptococcal infection in a patient who had kidney transplant: discrepancy between clinical symptoms and microbiological findings
Authors: Dahdal Suzan , Kalicki Robert , Von Steiger Niklaus , Sendi Parham
Published: August 2017

A 29-year-old man complained of a 2-day history of frontal headache and new-onset fever but no other symptoms. Two months prior to admission, he underwent his third kidney transplantation. Clinical and laboratory examinations were unremarkable. Brain MRI showed a meningeal irritation consistent with viral meningitis. A diagnosis of cryptococcal meningitis and fungaemia was made after detection of a remarkably high and visible load ofCryptococcus neoformansin the cerebrospinal fluid.
Rare cause of respiratory failure in a young woman: isolated diffuse alveolar haemorrhage requiring extracorporeal membrane oxygenation
Authors: Kelly David , Makkuni Damodar , Ail Dhiraj
Published: August 2017

A previously healthy 21-year-old young woman presented with worsening dyspnoea and haemoptysis. Imaging was suggestive of widespread pulmonary haemorrhage. There was no other organ system involvement in particular no evidence of renal involvement. Raised antimyeloperoxidase titres allowed diagnosis of isolated diffuse alveolar haemorrhage (DAH) secondary to microscopic polyangiitis (MPA). The patient rapidly deteriorated with worsening respiratory failure despite invasive mechanical ventilation and required extracorporeal membrane oxygenation (ECMO). This maintained the patient long enough to allow aggressive therapy in the form of immunosuppression and plasma exchange. She made a remarkable recovery and is asymptomatic 2 years on. Isolated DAH in the absence of renal disease is an atypical presentation of MPA and can lead to diagnostic uncertainty. A literature review reveals increasing reports of successful use of ECMO in severe DAH due to pulmonary vasculitis. Despite this, the need for systemic anticoagulation in the presence of pre-existing haemorrhage remains a challenging dilemma.
Converting everolimus to mycophenolate mofetil ameliorated prolonged respiratory syncytial virus infection in a child after heart transplantation
Authors: Suginobe Hidehiro , Nawa Nobutoshi , Ishida Hidekazu , Kogaki Shigetoyo
Published: August 2017

In immunocompromised patients, respiratory syncytial virus (RSV) infections are known to be severe and prolonged, and have significant mortality and morbidity. However, little is known about the clinical courses and treatment strategy of RSV infection in heart transplant recipients. Here, we report a 6-year-old female with heart transplantation who had exhibited prolonged respiratory symptoms and shedding of RSV. She had received everolimus as an immunosuppressant. As immunosuppressants could have been responsible for the prolonged activation of RSV, we converted everolimus to mycophenolate mofetil. After the conversion, RSV promptly disappeared, and her symptoms improved. We speculate that converting the immunosuppressant may be effective for prolonged RSV infection due to the different immunosuppressive mechanisms.
POEMS syndrome in a patient with rheumatoid arthritis
Authors: Akagi Takahiko , Mukai Tomoyuki , Kodama Shoko , Morita Yoshitaka
Published: August 2017

Multiple myeloma has been reported to be associated with rheumatoid arthritis (RA). POEMS syndrome is a rare variant of multiple myeloma and is characterised by polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy and skin changes. We report the case of a 67-year-old patient with RA who developed numbness and tingling in both legs due to polyneuropathy. CT showed a massive right pleural effusion and a sclerotic lesion in the right ninth rib. Histopathological examination of the rib revealed IgA lambda-type plasmacytoma. Serum vascular endothelial growth factor was extremely high at 5530 pg/mL. We made a diagnosis of POEMS syndrome. A literature search of the PubMed database identified only two documented cases of POEMS syndrome in patients with RA. Neuropathies are reportedly more frequent in patients with RA than in the general population. Rheumatologists should consider POEMS syndrome in patients with RA and neurological symptoms.
Non-pseudomonal ecthyma gangrenosum caused by methicillin-resistant Staphylococcus aureus(MRSA) in a chronic alcoholic patient
Authors: R G Santhaseelan , Muralidhar Venkiteswaran
Published: August 2017

We report for the first time a case of non-pseudomonal ecthyma gangrenosum (EG) caused by methicillin-resistantStaphylococcus aureusin a chronic alcoholic without an associated immunocompromised state or disease. EG is an infection of the skin, commonly associated withPseudomonas aeruginosabacteraemia, though other organisms are also known to be causally related. It usually occurs in patients who are terminally ill and the immunocompromised. In our case, chronic alcoholism with suppression of innate immunity may have led to the development of the condition.
Room for improvement: a randomised controlled trial with nested qualitative interviews on space, place and treatment delivery
Authors: Sandal Louise F , Thorlund Jonas B , Moore Andrew J , Ulrich Roger S , Dieppe Paul A , Roos Ewa M
Published: August 2017

Objective

Healthcare-oriented design in hospitals can promote better clinical outcomes. Creating optimal facilities may increase treatment effects. We investigated the influence of the treatment room on effects of exercise therapy.

Methods

In a mixed-method randomised controlled double-blind trial, middle-aged individuals reporting knee or hip pain performed 8 weeks of exercise therapy in (1) a newly built physically enhanced environment, (2) a standard environment or (3) were waitlisted, receiving no intervention. Participants and therapists were blind to study aim. Primary outcome was participants’ Global Perceived Effect (GPE; seven-point Likert scale). Six nested focus group interviews with participants (n=25) and individual interviews with therapists (n=2) explored experiences of the environments.

Results

42 people exercised in the physically enhanced environment, 40 in the standard environment, 21 were waitlisted. Contrary to our hypothesis, the treatment response seemed greater in the standard environment for GPE (0.98, 95% CI0.5 to 1.4) than for the physically enhanced environment (0.37, 95% CI −0.2 to 0.9), between-group difference (0.61, 95% CI −0.1 to 1.3) did not reach statistical significance (p=0.07). Waitlist group reported no improvement (−0.05 95% CI −0.5 to 0.4). In interviews, participants from the standard environment expressed greater social cohesion and feeling at home. Qualitative themes identified; reflection, sense of fellowship and transition. Secondary patient-reported outcomes and qualitative findings supported the primary finding, while improvements in muscle strength and aerobic capacity did not differ between exercise groups.

Conclusion

Results suggest that the physical environment contributes to treatment response. Matching patients’ preferences to treatment rooms may improve patient-reported outcomes.

Trial registration number

ClinicalTrials.gov identifier:NCT02043613.
Factors influencing the reporting of adverse medical device events: qualitative interviews with physicians about higher risk implantable devices
Authors: Gagliardi Anna R , Ducey Ariel , Lehoux Pascale , Turgeon Thomas , Ross Sue , Trbovich Patricia , Easty Anthony , Bell Chaim , Urbach David
Published: August 2017

Background

Postmarket surveillance of medical devices is reliant on physician reporting of adverse medical device events (AMDEs). Little is known about factors that influence whether and how physicians report AMDEs, an essential step in developing behaviour change interventions. This study explored factors that influence AMDE reporting.

Methods

Qualitative interviews were conducted with physicians who differed by specialties that implant cardiovascular and orthopaedic devices prone to AMDEs, geography and years in practice. Participants were asked if and how they reported AMDEs, and the influencing factors. Themes were identified inductively using constant comparative technique, and reviewed and discussed by the research team on four occasions.

Results

Twenty-two physicians of varying specialty, region, organisation and career stage perceived AMDE reporting as unnecessary, not possible or futile due to multiple factors. Physicians viewed AMDEs as an expected part of practice that they could manage by switching to different devices or developing work-around strategies for problematic devices. Physician beliefs and behaviour were reinforced by limited healthcare system capacity and industry responsiveness. The healthcare system lacked processes and infrastructure to detect, capture, share and act on information about AMDEs, and constrained device choice through purchasing contracts. The device industry did not respond to reports of AMDEs from physicians or improve their products based on such reports. As a result, participants said they used devices that were less than ideal for a given patient, leading to suboptimal patient outcomes.

Conclusions

There may be little point in solely educating or incentivising individual physicians to report AMDEs unless environmental conditions are conducive to doing so. Future research should explore policies that govern AMDEs and investigate how to design and implement postmarket surveillance systems.
Supporting family carers in home-based end-of-life care: using participatory action research to develop a training programme for support workers and volunteers
Authors: Caswell Glenys , Hardy Beth , Ewing Gail , Kennedy Sheila , Seymour Jane
Published: August 2017

Background

Family carers are crucial in enabling dying people to stay at home, but are often not prepared for their caring role, receiving little support from formal health and social care services. It is increasingly likely that any help or support family carers receive will be provided by a third sector organisation on either a voluntary basis or by untrained carer support workers.

Objectives

To produce a training programme designed to equip carer support workers and volunteers with the basic skills and knowledge needed to support family carers.

Process of development

Participatory action research, a collaborative form of working in which those who are affected by an issue take a lead role in the research, was used. Bereaved carers acting as research partners, support workers and representatives of third sector organisations took an active part in designing, developing, piloting and refining the programme in a number of interlinked stages. During development, the programme was piloted on four occasions and evaluated by 36 trainees and 3 trainers.

Final training programme

The outcome of the project is an innovative, 1-day training programme, offering an introduction to supporting family carers who are looking after someone approaching the end of life. The use of participatory action research methods enabled the development of a programme that addresses support needs identified by bereaved carers and training needs identified by carer support workers.

The finished programme includes all the materials necessary to run a training day for support workers and volunteers: facilitator’s notes, trainee workbook, slides, promotional poster and pre-course reading for trainees. Knowledge of issues involved in end-of-life and palliative care is not required, although some experience in delivering training is advisable.

Conclusion

The programme evaluated well during development, but further research is required to examine the transfer of learning into the workplace.
Hb Baden: a rare high affinity haemoglobin variant and its management
Authors: Lee Joe , Harrison Claire N
Published: August 2017

Haemoglobin Baden is a rare variant haemoglobin which has only recently been clinically and functionally characterised. We present the case of a young adult male patient who presented with an erythrocytosis but was clinically asymptomatic. His mother was also diagnosed retrospectively having presented with erythrocytosis being treated with regular venesections. We discuss the management plan and potential significance of being a carrier of this rare haemoglobin variant.
Complementary and alternative treatments of multiple sclerosis: a review of the evidence from 2001 to 2016
Authors: Claflin Suzi B , van der Mei Ingrid A F , Taylor Bruce V
Published: August 2017

People with multiple sclerosis (PwMS) commonly use complementary and alternative medicines (CAM), but an understanding of their efficacy is lacking. Here, we quantitatively review the class I and class II studies of treatment efficacy for multiple sclerosis from January 2001 to January 2017, in order to assess the modern evidence for CAM use. The 38 studies included in this review are divided across five CAM types (cannabis, diet, exercise, psychological approaches and other). We found little evidence to support CAM efficacy. The studies contained little replication in intervention, primary outcomes or study design. Six of 16 CAMs included in this review were only researched in a single study. Future work in this area should build consensus around study methodologies and primary outcomes.
Fructose-rich diet differently affects angiotensin II receptor content in the nucleus and a plasma membrane fraction of visceral adipose tissue
Authors: Bundalo Maja , Djordjevic Ana , Bursac Biljana , Zivkovic Maja , Koricanac Goran , Stanković Aleksandra
Published: August 2017

The adipose tissue renin–angiotensin system (RAS) is proposed to be a pathophysiological link between adipose tissue dysregulation and metabolic disorders induced by a fructose-rich diet (FRD). RAS can act intracellularly. We hypothesized that adipocyte nuclear membranes possess angiotensin receptor types 1 and 2 (AT1R and AT2R), which couple to nuclear signaling pathways and regulate oxidative gene expression under FRD conditions. We analyzed the effect of consumption of 10% fructose solution for 9 weeks on biochemical parameters, adipocyte morphology, and expression of AT1R, AT2R, AT1R-associated protein (ATRAP), NADPH oxidase 4 (NOX4), matrix metalloproteinase-9 (MMP-9), and manganese superoxide dismutase (MnSOD) in adipose tissue of Wistar rats. We detected AT1R and AT2R in the nuclear fraction. FRD reduced the level of angiotensin receptors in the nucleus, while increased AT1R and decreased AT2R levels were observed in the plasma membrane. FRD increased the ATRAP mRNA level and decreased MnSOD mRNA and protein levels. No significant differences were observed for MMP-9 and NOX4 mRNA levels. These findings coincided with hyperleptinemia, elevated blood pressure and triglycerides, and unchanged visceral adipose tissue mass and morphology in FRD rats. Besides providing evidence for nuclear localization of angiotensin receptors in visceral adipose tissue, this study demonstrates the different effects of FRD on AT1R expression in different cellular compartments. Elevated blood pressure and decreased antioxidant capacity in visceral fat of fructose-fed rats were accompanied by an increased AT1R level in the plasma membrane, while upregulation of ATRAP and a decrease of nuclear membrane AT1R suggest an increased capacity for attenuation of excessive AT1R signaling and visceral adiposity.
Metabolic state can define the ovarian response to environmental contaminants and medicinal plants
Authors: Sirotkin Alexander V. , Fabian Dušan , Babel’ová (Kubandová) Janka , Vlčková Radoslava , Alwasel Saleh , Harrath Abdel Halim
Published: August 2017

Environmental contaminants and medicinal plants can affect reproductive processes. The aim of this study was to investigate the effect of maternal metabolic status on the response of mouse ovaries to the environmental contaminants benzene and xylene, as well as to extracts of the medicinal plant yucca. Ovaries isolated from normal-lean and slightly obese mice were cultured with or without 0.1% benzene or xylene for 24 h. Similarly, ovaries isolated from normal-lean, slightly obese, and significantly obese mice were cultured for 24 h with or without an extract of Yucca shidigera (YS, 10 μ g/mL). We found that the metabolic status did not influence the release of basal progesterone (P4), testosterone (T), or insulin-like growth factor I (IGF-I), but obesity influenced the effects of the environmental contaminants and YS. Benzene reduced P4 output in ovaries from obese but not normal-lean mice; it also reduced IGF-I (but not T) release from ovaries irrespective of the metabolic status. Xylene dramatically increased P4 and T (but not IGF-I) release by ovaries from normal-lean mice, but there were no changes in P4 and only small increases in T output in obese mice. YS increased P4 (but not T or IGF-I) release in normal-lean and slightly obese animal ovaries, whilst significant obesity was associated with a lack of P4 response to YS. Obesity might affect the basal ovarian release of T or IGF-I and increases the sensitivity of ovaries to the action of benzene but decreases their responsiveness to xylene and YS.