bluuebunny/crossref_metadata_2025 huggingface dataset:
Overexpression of a diacylglycerol acyltransferase gene in Phaeodactylum tricornutum directs carbon towards lipid biosynthesis
Authors: Dinamarca Jorge , Levitan Orly , Kumaraswamy G. Kenchappa , Lun Desmond S. , Falkowski Paul G.
Published: January 2017

Under nutrient deplete conditions, diatoms accumulate between 15% to 25% of their dry weight as lipids, primarily as triacylglycerols (TAGs). As in most eukaryotes, these organisms produce TAGs via the acyl‐CoA dependent Kennedy pathway. The last step in this pathway is catalyzed by diacylglycerol acyltransferase (DGAT) that acylates diacylglycerol (DAG) to produce TAG. To test our hypothesis that DGAT plays a major role in controlling the flux of carbon towards lipids, we overexpressed a specific type II DGAT gene, DGAT2D, in the model diatom Phaeodactylum tricornutum. The transformants had 50‐ to 100‐fold higher DGAT2D mRNA levels and the abundance of the enzyme increased 30‐ to 50‐fold. More important, these cells had a 2‐fold higher total lipid content and incorporated carbon into lipids more efficiently than the wild type (WT) while growing only 15% slower at light saturation. Based on a flux analysis using 13C as a tracer, we found that the increase in lipids was achieved via increased fluxes through pyruvate and acetyl‐CoA. Our results reveal overexpression of DAGT2D increases the flux of photosynthetically fixed carbon towards lipids, and leads to a higher lipid content than exponentially grown WT cells.
Empowering Preschool Teachers to Identify Mental Health Problems: A Task‐Sharing Intervention in Ethiopia
Authors: Desta Menelik , Deyessa Negussie , Fish Irving , Maxwell Benjamin , Zerihun Tigist , Levine Saul , Fox Claire , Giedd Jay , Zelleke Tesfaye G. , Alem Atalay , F. Garland Ann
Published: January 2017

In Ethiopia there is a severe shortage of child mental health professionals. Identification and intervention for young children's mental health problems is crucial to improve developmental trajectories and reduce the severity of emotional and behavioral disorders. Teachers can play an important role in early problem detection. This role is particularly impactful in developing countries with limited mental health care resources. However, teachers' knowledge about mental health varies dramatically. This study tested the influence of a training intervention to improve teachers' ability to accurately identify preschool children's emotional and behavioral problems in 24 schools in Addis Ababa, Ethiopia. Sensitivity and specificity of teacher identification, and overall agreement with an established measurement criterion (Strengths and Difficulties Questionnaire) were examined 2 years following training compared to preintervention baseline, and a nonintervention control group of 12 schools. Results indicate that the teacher training was significantly associated with more accurate identification of children's problems.
From Birth to Death: The Life of the Standards Board for England
Authors: Lawton Alan , Macaulay Michael
Published: January 2017

Organizations wax and wane, and some cease to exist altogether. The Standards Board for England was abolished after a 10‐year life. Created to regulate the ethical behavior of local politicians in England, the ethics of politics was undermined by the politics of ethics. This article analyzes the life of the Standards Board initially through the lens of a life‐cycle approach to organizations but finds that a problem‐cluster approach provides a sharper picture. Over its lifetime, the Standards Board faced a number of crises; its failure to resolve these crises and an unfavorable political climate led to its demise.
Sequential augmentation reveals life history and suitable conditions for colonization of the rare mahogany mistletoe in South Florida
Authors: Duquesnel Janice A. , Maschinski Joyce , McElderry Robert , Gann George D. , Bradley Keith , Cowan Ernest
Published: January 2017

Successfully reintroducing rare plant populations to recover historical community composition may require multiple efforts and greater lengths of time than is typically devoted by researchers. To improve the probability of successful colonization and to learn about the life history of the regionally endangered mahogany mistletoe (Phoradendron rubrum) in the Florida Keys, United States, we conducted sequential augmentations for 10 years across two host tree sizes, two seed sources, and six recipient sites. Long‐term monitoring for 13 years revealed that sowing fresh seeds in dry periods from introduced versus wild plants onto small diameter trees (<20 cm diameter at breast height [dbh]) that had branch diameters 15–20 mm resulted in the greatest colonization success. An average of 38.7% of seeds germinated and 23.8% survived to 2015. Plant development was quite slow. Seeds required over 100 days to germinate, 1.6 years for cotyledon emergence, and over 4.7 years to produce fruit. We detected first recruitment nearly 8 years after installation. Population growth improved following multiple attempts and expanded spatial extent as is predicted by theory. Portions of the life cycle are undetectable and thus could give false indications of reintroduction success or failure. Achieving and documenting unequivocal success of this reintroduction has required over a decade.
Connecting Finite Element Modeling With Strengths of Materials and Vibrations Using Beam Experiments
Authors: Davis Julian L. , Smith Natasha L.
Published: January 2017

Students tend to compartmentalize individual classes throughout their time in school; associating that which is taught in one class with only that class. A finite element class offers a unique opportunity to illustrate the connection between several engineering topics through modeling and experiments since it is used to solve many different types of problems (e.g. force-deflection, stress-strain, heat transfer, fluid transport, and vibrations). In addition, providing hands-on experiments is an excellent way to illustrate concepts. Particularly, experiments can help students visualize the additional abstractions present in a finite element model while demonstrating the connections between several prerequisite engineering courses. Here we present experiments that connect finite element modeling with two classes: Strength of Materials and Vibrations. These experiments highlight the effects of finite element modeling choices and illustrate errors in the approximations.
Vocoded speech perception with simulated shallow insertion depths in adults and children
Authors: Waked Arifi , Dougherty Sara , Goupell Matthew J.
Published: January 2017

It is unclear how adults and children differ in their ability to learn distorted speech signals. Normal-hearing adults (≥18 years) and children (8–10 years) were repeatedly tested on vocoded speech perception with 0-, 3-, and 6-mm of frequency-to-place mismatch (i.e., shift). Between testing blocks, listeners were provided training blocks with feedback on the 6-mm shift condition. Adults performed better than children at 0-mm shift, but performed similarly at 3- and 6-mm shifts. Therefore, differences between adults and children in vocoded speech perception are dependent on the degree of distortion, and this difference seems unaltered by training with feedback.
Numerical study of Rayleigh wave propagation along a horizontal semi-infinite crack buried in half-space
Authors: Chakrapani Sunil Kishore
Published: January 2017

The present article investigates the propagation of Rayleigh waves along a horizontal semi-infinite crack, and its interaction with the crack tip. Finite element analysis was used to simulate wave propagation and study the interaction. An incident Rayleigh wave diffracts as bulk waves into the half-space upon interaction with the crack tip. It was observed that the diffracted bulk modes can interact with the half-space boundary, and mode converts into a Rayleigh wave traveling along the boundary. A qualitative analysis was performed to determine the effect of crack depth using transmission, reflection, and scattering coefficients. Moreover, the possibility of Lamb wave generation also arises since the crack face and boundary form a stress-free plate section. The source of the “turning” Lamb modes was also identified from the observations. The characteristics of the transmitted Rayleigh wave were also explored, and a certain degree of mode coupling between Rayleigh and shear waves was observed when the crack tip was farther away from the boundary.
Distraction distance and perceived disturbance by noise—An analysis of 21 open-plan offices
Authors: Haapakangas Annu , Hongisto Valtteri , Eerola Mervi , Kuusisto Tuomas
Published: January 2017

Previous research suggests that, in open-plan offices, noise complaints may be related to the high intelligibility of speech. Distraction distance, which is based on the Speech Transmission Index, can be used to objectively describe the acoustic quality of open-plan offices. However, the relation between distraction distance and perceived noise disturbance has not been established in field studies. The aim of this study was to synthesize evidence from separate studies covering 21 workplaces (N = 883 respondents) and a wide range of room acoustic conditions. The data included both questionnaire surveys and room acoustic measurements [ISO 3382-3 (2012) (International Organization for Standardization, Geneva, Switzerland]. Distraction distance, the spatial decay rate of speech, speech level at 4 m from the speaker, and the average background noise level were examined as possible predictors of perceived noise disturbance. The data were analyzed with individual participant data meta-analysis. The results show that distracting background speech largely explains the overall perception of noise. An increase in distraction distance predicts an increase in disturbance by noise, whereas the other quantities may not alone be associated with noise disturbance. The results support the role of room acoustic design, i.e., the simultaneous use of absorption, blocking, and masking in the attainment of good working conditions in open-plan offices.
Key role of the dopamine D
4
receptor in the modulation of corticostriatal glutamatergic neurotransmission
Authors: Bonaventura Jordi , Quiroz César , Cai Ning-Sheng , Rubinstein Marcelo , Tanda Gianluigi , Ferré Sergi
Published: January 2017

The function of the dopamine D
4
receptor and the product of a clinically significant gene polymorphic variant is revealed.
Life-saving diphtheria drug is running out
Authors: Kupferschmidt Kai
Published: January 2017

Two children's deaths in Europe spur search for new sources of antitoxin.
Webinar | Deciphering cancer: Modulating immunoregulatory pathways to treat tumors
Authors: Wolchok Jedd D. , Wherry E. John
Published: January 2017

In addition to being the first line of defense against pathogenic attack, the immune system seeks out aberrant cells within the body that may become cancerous. In response, precancerous and cancerous cells may exploit immune checkpoint pathways to evade immune detection and destruction. In order to block these tumorigenic cells, novel therapeutics that modulate immune checkpoint signaling have been developed, with some already available and others in clinical trials. Further development of effective therapeutics for use in personalized medicine requires the identification and characterization of a diverse range of immune checkpoint biomarkers. This webinar will explore recent progress and future directions in translational and clinical efforts centered on checkpoint modulators and combination therapies matched to the molecular profile of individual tumors and the genetic background of patients.

View the Webinar
Comment on “Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs”
Authors: Kawai Jun
Published: January 2017

Meinert
et al
. (Reports, 8 April 2016, p. 208) reported the formation of prebiotic molecules, including ribose, in an interstellar ice analog experiment. We show that if their experimental procedure is accurately described, much or most of their products may have been formed during their analysis process, not in the parent ice.
Principles for designing proteins with cavities formed by curved β sheets
Authors: Marcos Enrique , Basanta Benjamin , Chidyausiku Tamuka M. , Tang Yuefeng , Oberdorfer Gustav , Liu Gaohua , Swapna G. V. T. , Guan Rongjin , Silva Daniel-Adriano , Dou Jiayi , Pereira Jose Henrique , Xiao Rong , Sankaran Banumathi , Zwart Peter H. , Montelione Gaetano T. , Baker David
Published: January 2017

Designing proteins with cavities

In de novo protein design, creating custom-tailored binding sites is a particular challenge because these sites often involve nonideal backbone structures. For example, curved b sheets are a common ligand binding motif. Marcos
et al.
investigated the principles that drive β-sheet curvature by studying the geometry of β sheets in natural proteins and folding simulations. In a step toward custom design of enzyme catalysts, they used these principles to control β-sheet geometry and design proteins with differently shaped cavities.

Science
, this issue p.
201
A bacterial global regulator forms a prion
Authors: Yuan Andy H. , Hochschild Ann
Published: January 2017

Prions enter another domain of life

Prions are self-propagating protein aggregates, discovered in connection with the fatal transmissible spongiform encephalopathies in mammals. Prions have also been identified in fungi, where they act as protein-based elements of inheritance. Although prions have been uncovered in evolutionarily diverse eukaryotic species, it is not known whether prions exist in bacteria. Yuan and Hochschild report the identification of a bacterial protein—the transcription termination factor Rho from
Clostridium botulinum
—that exhibits the defining hallmarks of a prion-forming protein.

Science
, this issue p.
198
Putting the squeeze on superconductivity
Authors: Shen Kyle M.
Published: January 2017

The exotic superconductor Sr
2
RuO
4
yields new secrets under large uniaxial pressures
Causal neural network of metamemory for retrospection in primates
Authors: Miyamoto Kentaro , Osada Takahiro , Setsuie Rieko , Takeda Masaki , Tamura Keita , Adachi Yusuke , Miyashita Yasushi
Published: January 2017

Are you aware how well you remember?

Self-monitoring and evaluation of our own memory is a mental process called metamemory. For metamemory, we need access to information about the strength of our own memory traces. The brain structures and neural mechanisms involved in metamemory are completely unknown. Miyamoto
et al.
devised a test paradigm for metamemory in macaques, in which the monkeys judged their own confidence in remembering past experiences. The authors combined this approach with functional brain imaging to reveal the neural substrates of metamemory for retrospection. A specific region in the prefrontal brain was essential for meta mnemonic decision-making. Inactivation of this region caused selective impairment of metamemory, but not of memory itself.

Science
, this issue p.
188
A matter of tree longevity
Authors: Körner Christian
Published: January 2017

Tree longevity rather than growth rate controls the carbon capital of forests
Belowground drivers of plant diversity
Authors: van der Putten Wim H.
Published: January 2017

Feedbacks between soil microbes and plants affect the diversity of plant communities
Stability Studies on Dry Swabs and Wet Mailed Swabs for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Aptima Assays
Authors: Moncada Jeanne , Clark Carey B. , Holden Jeffrey , Hook Edward W. , Gaydos Charlotte A. , Schachter Julius
Published: January 2017

The Aptima Combo 2 (AC2) and Aptima CT (ACT) (Hologic Inc., San Diego, CA) are nucleic acid amplification tests (NAATs) that detect
Chlamydia trachomatis
. AC2 also detects
Neisseria gonorrhoeae
. Storage and temperature conditions may impact the utility of NAATs in some settings and screening programs. We evaluated specimen stability for use beyond the Aptima package insert specifications for temperature and duration of storage (between 2°C and 30°C and 60 days, respectively) in two studies: (i) dry
C. trachomatis
-seeded swabs were used with ACT after storage at 4°C, 23°C, or 36°C for up to 84 days and (ii) swabs seeded with
C. trachomatis
and
N. gonorrhoeae
and then placed in transport medium were tested with AC2, after being mailed via the U.S. Postal Service to three different sites. Prolonged storage of samples had no effect, and samples stored at 4°C, 23°C, and 36°C for up to 84 days yielded comparable ACT positivities, although there was a drop in signal intensity for virtually all specimens under all storage/shipping conditions after day 21. In the mailing study, 80%, 52% and 29% of seeded swabs were exposed to temperatures of >30°C during three rounds in transit, and 2% reached temperatures of >40°C. No evidence of signal degradation in the AC2 assay for detection of
C. trachomatis
or
N. gonorrhoeae
was observed, although some mailed swabs took more than 5 weeks to reach the laboratory site. These two studies support the potential use of swabs at temperatures above 36°C and storage beyond 60 days and provide confidence regarding this commercially available NAAT for testing of specimens after mailing.
Comparison of 11 Phenotypic Assays for Accurate Detection of Carbapenemase-Producing Enterobacteriaceae
Authors: Tamma Pranita D. , Opene Belita N. A. , Gluck Andrew , Chambers Krizia K. , Carroll Karen C. , Simner Patricia J.
Published: January 2017

Early identification of carbapenemase-producing
Enterobacteriaceae
(CPE) is essential to prevent their dissemination within health care settings. Our objective was to evaluate the accuracy of 11 phenotypic assays for the detection of CPE. Two collections of carbapenem-resistant
Enterobacteriaceae
(CRE) isolates were evaluated, including 191 retrospective isolates (122 CP-CRE and 69 non-CP isolates) as well as 45 prospective clinical isolates (15 CP-CRE and 30 non-CP-CRE) obtained over a 3-month period. The sensitivity and specificity of each test was determined, with molecular genotype serving as the gold standard. Among the retrospective cohort, sensitivities ranged from 72% for the boronic acid synergy test for the detection of KPC producers to ≥98% for the modified Carba NP, the Rapidec Carba NP, the manual Blue Carba, and the modified carbapenem inactivation method for the detection of any CPE. Sensitivity differed among tests across enzyme classes. All assays had excellent specificity exceeding 95%, with the exception of the boronic acid synergy test (88%) and modified Hodge test (91%). Prospectively, 45 CRE isolates were encountered over a 3-month period, including 15 CPE (33%) and 30 non-CP-CRE (67%). Results from the prospective cohort were similar. However, a decrease in specificity was observed across most tests, likely due to restricted inclusion of non-CP-CRE to assess the specificity of the assays. Overall, accuracy of CPE detection varied across phenotypic tests. Local epidemiology of CP genotypes, turnaround time, and ease of incorporation into the laboratory workflow should be considered when selecting a phenotypic assay for clinical use.
A New Development in Trypanosoma cruzi Detection
Authors: Tanowitz Herbert B. , Weiss Louis M.
Published: January 2017

Chagas disease is caused by the parasite
Trypanosoma cruzi
and is an important cause of morbidity and mortality in areas of Latin America where Chagas disease is endemic and among infected individuals who have migrated to nonendemic areas of North America and Europe. There are many diagnostic tests that are employed in the serological diagnosis of this infection. In this issue of the
Journal of Clinical Microbiology
, Bautista-López et al. provide characterization of excretory vesicles (EVs) from Vero cells infected with
T. cruzi
and provide data on the EVs produced by trypomastigotes and amastigotes (N. L. Bautista-López et al., J Clin Microbiol 55:744–758, 2017,
https://doi.org/10.1128/JCM.01649-16
). Their proteomic study defines potential targets to evaluate for improved diagnostic tests, effects on host cell biology that contribute to the pathogenesis of infection, and vaccine candidates. If any of the EV-associated proteins identified were to be correlated to cure of infection, this would be a major advance.
Sensitive Next-Generation Sequencing Method Reveals Deep Genetic Diversity of HIV-1 in the Democratic Republic of the Congo
Authors: Rodgers Mary A. , Wilkinson Eduan , Vallari Ana , McArthur Carole , Sthreshley Larry , Brennan Catherine A. , Cloherty Gavin , de Oliveira Tulio
Published: January 2017

As the epidemiological epicenter of the human immunodeficiency virus (HIV) pandemic, the Democratic Republic of the Congo (DRC) is a reservoir of circulating HIV strains exhibiting high levels of diversity and recombination. In this study, we characterized HIV specimens collected in two rural areas of the DRC between 2001 and 2003 to identify rare strains of HIV. Theenvgp41 region was sequenced and characterized for 172 HIV-positive specimens. Theenvsequences were predominantly subtype A (43.02%), but 7 other subtypes (33.14%), 20 circulating recombinant forms (CRFs; 11.63%), and 20 unclassified (11.63%) sequences were also found. Of the rare and unclassified subtypes, 18 specimens were selected for next-generation sequencing (NGS) by a modified HIV-switching mechanism at the 5′ end of the RNA template (SMART) method to obtain full-genome sequences. NGS produced 14 new complete genomes, which included pure subtype C (n= 2), D (n= 1), F1 (n= 1), H (n= 3), and J (n= 1) genomes. The two subtype C genomes and one of the subtype H genomes branched basal to their respective subtype branches but had no evidence of recombination. The remaining 6 genomes were complex recombinants of 2 or more subtypes, including subtypes A1, F, G, H, J, and K and unclassified fragments, including one subtype CRF25 isolate, which branched basal to all CRF25 references. Notably, all recombinant subtype H fragments branched basal to the H clade. Spatial-geographical analysis indicated that the diverse sequences identified here did not expand globally. The full-genome and subgenomic sequences identified in our study population significantly increase the documented diversity of the strains involved in the continually evolving HIV-1 pandemic.

IMPORTANCEVery little is known about the ancestral HIV-1 strains that founded the global pandemic, and very few complete genome sequences are available from patients in the Congo Basin, where HIV-1 expanded early in the global pandemic. By sequencing a subgenomic fragment of the HIV-1 envelope from study participants in the DRC, we identified rare variants for complete genome sequencing. The basal branching of some of the complete genome sequences that we recovered suggests that these strains are more closely related to ancestral HIV-1 strains than to previously reported strains and is evidence that the local diversification of HIV in the DRC continues to outpace the diversity of global strains decades after the emergence of the pandemic.
Identification of a Continuous Neutralizing Epitope within UL128 of Human Cytomegalovirus
Authors: Chiuppesi Flavia , Kaltcheva Teodora , Meng Zhuo , Barry Peter A. , Diamond Don J. , Wussow Felix
Published: January 2017

As human cytomegalovirus (HCMV) is the most common infectious cause of fetal anomalies during pregnancy, development of a vaccine that prevents HCMV infection is considered a global health priority. Although HCMV immune correlates of protection are only poorly defined, neutralizing antibodies (NAb) targeting the envelope pentamer complex (PC) composed of the subunits gH, gL, UL128, UL130, and UL131A are thought to contribute to the prevention of HCMV infection. Here, we describe a continuous target sequence within UL128 that is recognized by a previously isolated potent PC-specific NAb termed 13B5. By using peptide-based scanning procedures, we identified a 13-amino-acid-long target sequence at the UL128 C terminus that binds the 13B5 antibody with an affinity similar to that of the purified PC. In addition, the 13B5 binding site is universally conserved in HCMV, contains a previously described UL128/gL interaction site, and interferes with the 13B5 neutralizing function, indicating that the 13B5 epitope sequence is located within the PC at a site of critical importance for HCMV neutralization. Vaccination of mice with peptides containing the 13B5 target sequence resulted in the robust stimulation of binding antibodies and, in a subset of immunized animals, in the induction of detectable NAb, supporting that the identified 13B5 target sequence constitutes a PC-specific neutralizing epitope. These findings provide evidence for the discovery of a continuous neutralizing epitope within the UL128 subunit of the PC that could be an important target of humoral immune responses that are involved in protection against congenital HCMV infection.

IMPORTANCE
Neutralizing antibodies (NAb) targeting the human cytomegalovirus (HCMV) envelope pentamer complex (PC) are thought to be important for preventing HCMV transmission from the mother to the fetus, thereby mitigating severe developmental disabilities in newborns. However, the epitope sequences within the PC that are recognized by these potentially protective antibody responses are only poorly defined. Here, we provide evidence for the existence of a highly conserved, continuous, PC-specific epitope sequence that appears to be located within the PC at a subunit interaction site of critical importance for HCMV neutralization. These discoveries provide insights into a continuous PC-specific neutralizing epitope, which could be an important target for a vaccine formulation to interfere with congenital HCMV infection.
Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History
Authors: Tao Ying , Shi Mang , Chommanard Christina , Queen Krista , Zhang Jing , Markotter Wanda , Kuzmin Ivan V. , Holmes Edward C. , Tong Suxiang
Published: January 2017

Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating inTriaenopsbats and 229E-like viruses circulating inHipposiderosbats, with the breakpoint located near 5′ and 3′ ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination “hot spot” in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic diversity of bat CoVs is primarily structured by host species and subsequently by geographic distances.

IMPORTANCEUnderstanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated withTriaenops aferandHipposiderossp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential.
Studies on the Interaction of Tumor-Derived HD5 Alpha Defensins with Adenoviruses and Implications for Oncolytic Adenovirus Therapy
Authors: Vragniau Charles , Hübner Jens-Martin , Beidler Peter , Gil Sucheol , Saydaminova Kamola , Lu Zhuo-Zhuang , Yumul Roma , Wang Hongjie , Richter Maximilian , Sova Pavel , Drescher Charles , Fender Pascal , Lieber André
Published: January 2017

Defensins are small antimicrobial peptides capable of neutralizing human adenovirus (HAdV)
in vitro
by binding capsid proteins and blocking endosomal escape of virus. In humans, the alpha defensin HD5 is produced by specialized epithelial cells of the gastrointestinal and genito-urinary tracts. Here, we demonstrate, using patient biopsy specimens, that HD5 is also expressed as an active, secreted peptide by epithelial ovarian and lung cancer cells
in situ
. This finding prompted us to study the role of HD5 in infection and spread of replication-competent, oncolytic HAdV type 3 (HAdV3). HAdV3 produces large amounts of penton-dodecahedra (PtDd), virus-like particles, during replication. We have previously shown that PtDd are involved in opening epithelial junctions, thus facilitating lateral spread of
de novo
-produced virions. Here, we describe a second function of PtDd, namely, the blocking of HD5. A central tool to prove that viral PtDd neutralize HD5 and support spread of progeny virus was an HAdV3 mutant virus in which formation of PtDd was disabled (mut-Ad3GFP, where GFP is green fluorescent protein). We demonstrated that viral spread of mut-Ad3GFP was blocked by synthetic HD5 whereas that of the wild-type (wt) form (wt-Ad3GFP) was only minimally impacted. In human colon cancer Caco-2 cells, induction of cellular HD5 expression by fibroblast growth factor 9 (FGF9) significantly inhibited viral spread and progeny virus production of mut-Ad3GFP but not of wt-Ad3GFP. Finally, the ectopic expression of HD5 in tumor cells diminished the
in vivo
oncolytic activity of mut-Ad3GFP but not of wt-Ad3GFP. These data suggest a new mechanism of HAdV3 to overcome innate antiviral host responses. Our study has implications for oncolytic adenovirus therapy.

IMPORTANCE
Previously, it has been reported that human defensin HD5 inactivates specific human adenoviruses by binding to capsid proteins and blocking endosomal escape of virus. The central new findings described in our manuscript are the following: (i) the discovery of a new mechanism used by human adenovirus serotype 3 to overcome innate antiviral host responses that is based on the capacity of HAdV3 to produce subviral penton-dodecahedral particles that act as decoys for HD5, thus preventing the inactivation of virus progeny produced upon replication; (ii) the demonstration that ectopic HD5 expression in cancer cells decreases the oncolytic efficacy of a serotype 5-based adenovirus vector; and (iii) the demonstration that epithelial ovarian and lung cancers express HD5. The study improves our understanding of how adenoviruses establish infection in epithelial tissues and has implications for cancer therapy with oncolytic adenoviruses.
MAVS Is Essential for Primary CD4+T Cell Immunity but Not for Recall T Cell Responses following an Attenuated West Nile Virus Infection
Authors: Luo Huanle , Winkelmann Evandro , Xie Guorui , Fang Rong , Peng Bi-Hung , Li Li , Lazear Helen M. , Paessler Slobodan , Diamond Michael S. , Gale Michael , Barrett Alan D. , Wang Tian
Published: January 2017

The use of pathogen recognition receptor (PRR) agonists and the molecular mechanisms involved have been the major focus of research in individual vaccine development. West Nile virus (WNV) nonstructural (NS) 4B-P38G mutant has several features for an ideal vaccine candidate, including significantly reduced neuroinvasiveness, induction of strong adaptive immunity, and protection of mice from wild-type (WT) WNV infection. Here, we determined the role of mitochondrial antiviral signaling protein (MAVS), the adaptor protein for RIG-I-like receptor in regulating host immunity against the NS4B-P38G vaccine. We found thatMavs−/−mice were more susceptible to NS4B-P38G priming than WT mice.Mavs−/−mice had a transiently reduced production of antiviral cytokines and an impaired CD4+T cell response in peripheral organs. However, antibody and CD8+T cell responses were minimally affected. NS4B-P38G induced lower type I interferon (IFN), IFN-stimulating gene, and proinflammatory cytokine responses inMavs−/−dendritic cells and subsequently compromised the antigen-presenting capacity for CD4+T cells. Interestingly,Mavs−/−mice surviving NS4B-P38G priming were all protected from a lethal WT WNV challenge. NS4B-P38G-primedMavs−/−mice exhibited equivalent levels of protective CD4+T cell recall response, a modestly reduced WNV-specific IgM production, but more robust CD8+T cell recall response. Taken together, our results suggest that MAVS is essential for boosting optimal primary CD4+T cell responses upon NS4B-P38G vaccination and yet is dispensable for host protection and recall T cell responses during secondary WT WNV infection.

IMPORTANCEThe production of innate cytokines induced by the recognition of pathogen recognition receptors (PRRs) via their cognate ligands are critical for enhancing antigen-presenting cell functions and influencing T cell responses during microbial infection. The use of PRR agonists and the underlying molecular mechanisms have been the major focus in individual vaccine development. Here, we determined the role of mitochondrial antiviral-signaling protein (MAVS), the adaptor protein for RIG-I like receptor in regulating host immunity against the live attenuated West Nile virus (WNV) vaccine strain, the nonstructural (NS) 4B-P38G mutant. We found that MAVS is important for boosting optimal primary CD4+T cell response during NS4B-P38G vaccination. However, MAVS is dispensable for memory T cell development and host protection during secondary wild-type WNV infection. Overall, these results may be utilized as a paradigm to aid in the rational development of other efficacious live attenuated flavivirus vaccines.
SUN2 Silencing Impairs CD4 T Cell Proliferation and Alters Sensitivity to HIV-1 Infection Independently of Cyclophilin A
Authors: Donahue Daniel A. , Porrot Françoise , Couespel Norbert , Schwartz Olivier
Published: January 2017

Linker of nucleoskeleton and cytoskeleton (LINC) complexes connect the nucleus to the cytoskeleton in eukaryotic cells. We previously reported that the overexpression of SUN2, an inner nuclear membrane protein and LINC complex component, inhibits HIV infection between the steps of reverse transcription and nuclear import in a capsid-specific manner. We also reported that SUN2 silencing does not modulate HIV infection in several cell lines. Silencing of SUN2 was recently reported to decrease HIV infection of CD4 T cells, an effect which was suggested to result from modulation of cyclophilin A (CypA)-dependent steps of HIV infection. We confirm here that HIV infection of primary CD4 T cells is compromised in the absence of endogenous SUN2, and we extend these findings to additional viral strains. However, we find that CypA is not required for the decreased infection observed in SUN2-silenced cells and, conversely, that endogenous SUN2 is not required for the well-documented positive modulation of HIV infection by CypA. In contrast, CD4 T cells lacking SUN2 exhibit a considerable defect in proliferative capacity and display reduced levels of activation markers and decreased viability. Additionally, SUN2-silenced CD4 T cells that become infected support reduced levels of viral protein expression. Our results demonstrate that SUN2 is required for the optimal activation and proliferation of primary CD4 T cells and suggest that the disruption of these processes explains the contribution of endogenous SUN2 to HIV infection in primary lymphocytes.

IMPORTANCELinker of nucleoskeleton and cytoskeleton (LINC) complexes connect the nucleus to the cytoskeleton. We previously reported that the overexpression of the LINC complex protein SUN2 inhibits HIV infection by targeting the viral capsid and blocking infection before the virus enters the nucleus. A recent report showed that the depletion of endogenous SUN2 in primary CD4 T cells results in decreased HIV infection and that this involves cyclophilin A (CypA), a host protein that interacts with the capsid of HIV to promote infection. We confirm that HIV infection is reduced in CD4 T cells lacking SUN2, but we find no role for CypA. Instead, SUN2 silencing results in CD4 T cells with decreased viability and much lower proliferation rates. Our results show that SUN2 is required for optimal CD4 T cell activation and proliferation and explain the reduced level of HIV infection in the absence of SUN2.
Fungal Ecology: Principles and Mechanisms of Colonization and Competition by Saprotrophic Fungi
Authors: Boddy Lynne , Hiscox Jennifer
Published: January 2017

Decomposer fungi continually deplete the organic resources they inhabit, so successful colonization of new resources is a crucial part of their ecology. Colonization success can be split into (i) the ability to arrive at, gain entry into, and establish within a resource and (ii) the ability to persist within the resource until reproduction and dissemination. Fungi vary in their life history strategies, the three main drivers of which are stress (S-selected), disturbance (ruderal, or R-selected), and incidence of competitors (C-selected); however, fungi often have combinations of characteristics from different strategies. Arrival at a new resource may occur as spores or mycelium, with successful entry and establishment (primary resource capture) within the resource largely dependent on the enzymatic ability of the fungus. The communities that develop in a newly available resource depend on environmental conditions and, in particular, the levels of abiotic stress present (e.g., high temperature, low water availability). Community change occurs when these initial colonizers are replaced by species that are either more combative (secondary resource capture) or better able to tolerate conditions within the resource, either through changing abiotic conditions or due to modification of the resource by the initial colonizers. Competition for territory may involve highly specialized species-specific interactions such as mycoparasitism or may be more general; in both cases combat involves changes in morphology, metabolism, and reactive oxygen species production, and outcomes of these interactions can be altered under different environmental conditions. In summary, community development is not a simple ordered sequence, but a complex ever-changing mosaic.
The Complexity of Fungal Vision
Authors: Fischer Reinhard , Aguirre Jesus , Herrera-Estrella Alfredo , Corrochano Luis M.
Published: January 2017

Life, as we know it, would not be possible without light. Light is not only a primary source of energy, but also an important source of information for many organisms. To sense light, only a few photoreceptor systems have developed during evolution. They are all based on an organic molecule with conjugated double bonds that allows energy transfer from visible (or UV) light to its cognate protein to translate the primary physical photoresponse to cell-biological actions. The three main classes of receptors are flavin-based blue-light, retinal-based green-light (such as rhodopsin), and linear tetrapyrrole-based red-light sensors. Light not only controls the behavior of motile organisms, but is also important for many sessile microorganisms including fungi. In fungi, light controls developmental decisions and physiological adaptations as well as the circadian clock. Although all major classes of photoreceptors are found in fungi, a good level of understanding of the signaling processes at the molecular level is limited to some model fungi. However, current knowledge suggests a complex interplay between light perception systems, which goes far beyond the simple sensing of light and dark. In this article we focus on recent results in several fungi, which suggest a strong link between light-sensing and stress-activated mitogen-activated protein kinases.
Fungal Plant Pathogenesis Mediated by Effectors
Authors: De Wit Pierre J.G.M. , Testa Alison C. , Oliver Richard P.
Published: January 2017

The interactions between fungi and plants encompass a spectrum of ecologies ranging from saprotrophy (growth on dead plant material) through pathogenesis (growth of the fungus accompanied by disease on the plant) to symbiosis (growth of the fungus with growth enhancement of the plant). We consider pathogenesis in this article and the key roles played by a range of pathogen-encoded molecules that have collectively become known as effectors.
Dendritic Cells in the Immune System—History, Lineages, Tissues, Tolerance, and Immunity
Authors: Austyn Jonathan M.
Published: January 2017

The aim of this review is to provide a coherent framework for understanding dendritic cells (DCs). It has seven sections. The introduction provides an overview of the immune system and essential concepts, particularly for the nonspecialist reader. Next, the “History” section outlines the early evolution of ideas about DCs and highlights some sources of confusion that still exist today. The “Lineages” section then focuses on five different populations of DCs: two subsets of “classical” DCs, plasmacytoid DCs, monocyte-derived DCs, and Langerhans cells. It highlights some cellular and molecular specializations of each, and also notes other DC subsets that have been proposed. The following “Tissues” section discusses the distribution and behavior of different DC subsets within nonlymphoid and secondary lymphoid tissues that are connected by DC migration pathways between them. In the “Tolerance” section, the role of DCs in central and peripheral tolerance is considered, including their ability to drive the differentiation of different populations of regulatory T cells. In contrast, the “Immunity” section considers the roles of DCs in sensing of infection and tissue damage, the initiation of primary responses, the T-cell effector phase, and the induction of immunological memory. The concluding section provides some speculative ideas about the evolution of DCs. It also revisits earlier concepts of generation of diversity and clonal selection in terms of DCs driving the evolution of T-cell responses. Throughout, this review highlights certain areas of uncertainty and suggests some avenues for future investigation.
The Memory Immune Response to Tuberculosis
Authors: Kirman Joanna R. , Henao-Tamayo Marcela I. , Agger Else Marie
Published: January 2017

Immunological memory is a central feature of the adaptive immune system and a prerequisite for generating effective vaccines. Understanding long-term memory responses toMycobacterium tuberculosiswill thus provide us with valuable insights that can guide us in the search for a novel vaccine against tuberculosis (TB). For many years, triggering CD4 T cells and, in particular, those secreting interferon-γ has been the goal of most TB vaccine research, and numerous data from animals and humans support the key role of this subset in protective immunity. More recently, we have learned that the memory response required for effective control ofM. tuberculosisis much more complex, probably involving several phenotypically different CD4 T cell subsets as well as other cell types that are yet to be defined. Herein, we describe recent insights into memory immunity to TB in the context of both animal models and the human infection. With the increasing amount of data generated from clinical testing of novel TB vaccines, we also summarize recent knowledge of vaccine-induced memory immunity.
Innate Immune Responses to Tuberculosis
Authors: Schorey Jeffrey S. , Schlesinger Larry S.
Published: January 2017

Tuberculosis remains one of the greatest threats to human health. The causative bacterium,Mycobacterium tuberculosis, is acquired by the respiratory route. It is exquisitely adapted to humans and is a prototypic intracellular pathogen of macrophages, with alveolar macrophages being the primary conduit of infection and disease. However,M. tuberculosisbacilli interact with and are affected by several soluble and cellular components of the innate immune system which dictate the outcome of primary infection, most commonly a latently infected healthy human host, in whom the bacteria are held in check by the host immune response within the confines of tissue granuloma, the host histopathologic hallmark. Such individuals can develop active TB later in life with impairment in the immune system. In contrast, in a minority of infected individuals, the early host immune response fails to control bacterial growth, and progressive granulomatous disease develops, facilitating spread of the bacilli via infectious aerosols. The molecular details of theM. tuberculosis-host innate immune system interaction continue to be elucidated, particularly those occurring within the lung. However, it is clear that a number of complex processes are involved at the different stages of infection that may benefit either the bacterium or the host. In this article, we describe a contemporary view of the molecular events underlying the interaction betweenM. tuberculosisand a variety of cellular and soluble components and processes of the innate immune system.
Mycobacterium bovis
and Other Uncommon Members of the
Mycobacterium tuberculosis
Complex
Authors: Esteban Jaime , Muñoz-Egea Maria-Carmen
Published: January 2017

Since its discovery by Theobald Smith,
Mycobacterium bovis
has been a human pathogen closely related to animal disease. At present,
M. bovis
tuberculosis is still a problem of importance in many countries and is considered the main cause of zoonotic tuberculosis throughout the world. Recent development of molecular epidemiological tools has helped us to improve our knowledge about transmission patterns of this organism, which causes a disease indistinguishable from that caused by
Mycobacterium tuberculosis
. Diagnosis and treatment of this mycobacterium are similar to those for conventional tuberculosis, with the important exceptions of constitutive resistance to pyrazinamide and the fact that multidrug-resistant and extremely drug-resistant
M. bovis
strains have been described. Among other members of this complex,
Mycobacterium africanum
is the cause of many cases of tuberculosis in West Africa and can be found in other areas mainly in association with immigration.
M. bovis
BCG is the currently available vaccine for tuberculosis, but it can cause disease in some patients. Other members of the
M. tuberculosis
complex are mainly animal pathogens with only exceptional cases of human disease, and there are even some strains, like “
Mycobacterium canettii
,” which is a rare human pathogen that could have an important role in the knowledge of the evolution of tuberculosis in the history.