bluuebunny/crossref_metadata_2025 huggingface dataset:
NEUROPATHY, ATAXIA, AND RETINITIS PIGMENTOSA SYNDROME: A MULTIDISCIPLINARY DIAGNOSIS
Authors: Juaristi Leire , Irigoyen Cristina , Quiroga Jorge
Published: October 2018

Purpose:

To report a case of neuropathy, ataxia, and retinitis pigmentosa syndrome, a rare and undiagnosed disease in ophthalmology due to the need for multidisciplinary evaluation.

Methods:

Multimodal testing was performed, including neurologic, ophthalmologic, and genetic assessments. The neurologic tests comprised electromyogram and muscle biopsy; the ophthalmologic examination consisted of slit-lamp and fundus examinations, optical coherence tomography, visual field testing, and electrophysiology tests such as a full-field electroretinogram and multifocal electroretinogram; and genetic tests were performed for spinocerebellar ataxia. In addition, the patient underwent magnetic resonance imaging, an electrocardiogram, cerebrospinal fluid analysis with lactate levels, and a blood workup including antineuronal, antithyroid peroxidase, antinuclear, antimitochondrial, and antitransglutaminase antibodies and fat-soluble vitamins (A, D, E, K).

Results:

The ocular fundus examination showed bone spicules with retinal pigment epithelium alteration, optic nerve pallor, and arterial attenuation. Optical coherence tomography demonstrated macular atrophy. Visual field testing revealed concentric reduction. Electrophysiology examinations showed involvement of rods and cones in both eyes. The muscle biopsy was compatible with mitochondrial disease, and electromyogram demonstrated sensory axonal damage. However, genetic tests for spinocerebellar ataxia were negative. Magnetic resonance imaging showed cerebellar atrophy, whereas the electrocardiogram did not detect any abnormalities. Cerebrospinal fluid lactate levels were above normal but antibody levels in blood were normal.

Conclusion:

This is the first report of macular atrophy demonstrated by optical coherence tomography in a patient with neuropathy, ataxia, and retinitis pigmentosa syndrome. For the diagnosis, a multidisciplinary team including a neurologist, a geneticist, and an ophthalmologist was essential. Patients with suspected mitochondrial disease could greatly benefit from an ophthalmology examination like that conducted in this case because it was the key factor that led to the suspicion of syndromic disease, and ultimately the diagnosis.
Capnocytophaga Keratitis: Clinical Presentation and Use of Metagenomic Deep Sequencing for Diagnosis
Authors: Seitzman Gerami D. , Thulasi Praneetha , Hinterwirth Armin , Chen Cindi , Shantha Jessica , Doan Thuy
Published: October 2018

Purpose:

To report our experience with 2 cases of Capnocytophaga keratitis.

Methods:

This is a retrospective study of case reports. We present the clinical presentation, diagnosis, and treatment strategies of 2 patients who presented with Capnocytophaga keratitis.

Results:

Both patients had risk factors including systemic immune compromise and ocular trauma. Both patients had robust inflammatory keratitis with necrosis. Case 1 demonstrates identification of Capnocytophaga with traditional microbiologic techniques. Case 2 demonstrates the use of unbiased metagenomic deep sequencing for identification of this unusual corneal pathogen.

Conclusions:

Capnocytophaga is a rare and aggressive infection. Even when traditional culture identifies the pathogen rapidly, keratitis can progress to perforation. In cases of severe keratitis in which traditional culture methods are unrevealing, metagenomic deep sequencing has potential to provide actionable diagnoses.
Use of a Purpose-Built Impression Cytology Device for Gene Expression Quantification at the Ocular Surface Using Quantitative PCR and Droplet Digital PCR
Authors: Ganesalingam Kalaivarny , Ismail Salim , Craig Jennifer P. , Sherwin Trevor
Published: October 2018

Purpose:

To describe an impression cytology (IC) technique using a purpose-built, sterile, EYEPRIM IC device that can be coupled with a TRIzol reagent–based RNA extraction protocol to yield sufficient RNA for gene expression analysis.

Methods:

IC samples using the EYEPRIM device were collected from the bulbar conjunctiva, with and without topical anesthesia, and evaluated for RNA yield, the absence of polymerase chain reaction (PCR) inhibitors, and the ability to detect biomarkers by quantitative real-time PCR and droplet digital PCR. A technique for collecting IC samples in the clinic, while preserving RNA, and a protocol for subsequent laboratory analysis of RNA were developed.

Results:

The extracted RNA was free of PCR inhibitors and could be synthesized into complementary DNA and used for successful relative quantification of ocular surface biomarkers by quantitative real-time PCR. For gene targets present in low abundance, complementary DNA could also be used for quantification by the relatively new and emerging method of droplet digital PCR. The described method was successfully used to evaluate 3 biomarkers in a clinical trial assessing the tolerability of a proprietary eyelid therapy in 92 IC samples from a study population of 46 participants.

Conclusions:

IC is a recognized technique for ocular surface cell evaluation and protein biomarker quantification but is infrequently used for quantifying gene expression. The EYEPRIM device allows ease of use and impression-to-impression consistency while accurate gene expression data offers a highly specific and sensitive method of disease characterization for clinician scientists to use in diagnosis.
No Association Between Ljungan Virus Seropositivity and the Beta-cell Damaging Process in the Finnish Type 1 Diabetes Prediction and Prevention Study Cohort
Authors: Jääskeläinen Anne J. , Nurminen Noora , Kolehmainen Pekka , Smura Teemu , Tauriainen Sisko , Toppari Jorma , Ilonen Jorma , Veijola Riitta , Knip Mikael , Hyöty Heikki , Vapalahti Olli , Kallio-Kokko Hannimari
Published: October 2018

Background:

Ljungan virus (LV) has not confirmed to associate with any human disease, but a possible connection with type 1 diabetes has been suggested. LV is a rodent-borne picornavirus that induces a diabetes-like condition in rodents. Approximately 30% of adults and 60% of children are seropositive in Finland. The Finnish Type 1 Diabetes Prediction and Prevention study enabled the use of very well characterized sample panels from children seroconverted to positivity for multiple islet autoantibodies during their prospective observation from birth; in addition, samples from age, sex, human leukocyte antigen (HLA), and residence area matched control children.

Methods:

We analyzed LV IgG seroprevalence in 102 case children (65 had also developed type 1 diabetes), in addition to nondiabetic control children. LV and human parechovirus (HPeV) immunofluorescence assays were used to analyze LV and HPeV-specific IgG from 102 plasma samples taken at the time of islet autoantibody appearance and from 204 samples from the matched control children.

Results:

Altogether 46.1% of the case and 50.7% of the control children were positive for LV IgG (odds ratio 0.8; 95% confidence interval, 0.47–1.36; P = 0.416) and 67.6% versus 79.8% were positive for HPeV IgG, respectively (odds ratio 0.49, 0.27–0.9, P = 0.023).

Conclusions:

Thus, no risk associations between LV or HPeV-specific IgG and islet autoimmunity were observed. However, a trend for significantly higher prevalence of HPeV antibodies in control children (P = 0.023) suggests a possible protective association of this virus with islet autoimmunity.
Efficacy and Safety of a Rapid Intravenous Injection of Ketamine 0.5 mg/kg in Treatment-Resistant Major Depression
Authors: Vidal Sonia , Gex-Fabry Marianne , Bancila Victor , Michalopoulos Giorgio , Warrot Delphine , Jermann Françoise , Dayer Alexandre , Sterpenich Virginie , Schwartz Sophie , Vutskits Laszlo , Khan Nawaz , Aubry Jean-Michel , Kosel Markus
Published: October 2018

Background

Ketamine has been documented for its rapid antidepressant effects. However, optimal dose and delivery route have not yet been thoroughly investigated. The objectives of this study were to document the safety and test the antidepressant and antisuicidal effects of a single rapid 1-minute injection of ketamine 0.5 mg/kg in treatment-resistant depression (TRD).

Methods

Ten patients with TRD were included in an open, noncontrolled 4-week study and received a rapid intravenous dose of ketamine 0.5 mg/kg. Main outcome measure was the Montgomery-Åsberg Depression Rating Scale and suicidality was assessed using the Scale for Suicide Ideation.

Results

Rapid injection of ketamine elicited transient increase of blood pressure and altered states of consciousness in all patients and mild psychotomimetic effects in 4 patients, which all resolved without any intervention. Decrease of depression severity was observed from 40-minute postinjection until day 15. Eight patients became responders within 1 day and all were nonresponders after 4 weeks. The decrease of suicidal ideation was significant until day 7. Analysis indicated that higher severity of depression and anxiety at baseline predicted a larger Montgomery-Åsberg Depression Rating Scale decrease after 4 weeks.

Conclusions

This study suggests that in well-controlled medical settings with adequate monitoring, a single rapid 1-minute injection of ketamine 0.5 mg/kg can be well tolerated and is efficacious in rapidly reducing depression symptoms and suicidal thoughts in outpatients with TRD. These findings are relevant to the practice of general clinical psychiatry and emergency departments were ketamine can have a place in acute management of TRD. Larger studies are necessary to confirm these results.
“I Have Both Lost and Gained.” Norwegian Survivors’ Experiences of Coping 9 Years After Primary Breast Cancer Surgery
Authors: Drageset Sigrunn , Lindstrøm Torill Christine , Ellingsen Sidsel
Published: October 2018

Background

Increased breast cancer survival means that many women live with long-term consequences of their cancer and treatment. Knowledge about their coping is important.

Objective

This qualitative follow-up study describes survivors’ coping experiences 9 years after primary breast cancer surgery.

Methods

Seventeen of the 21 women interviewed 9 years earlier were invited to participate. Fifteen agreed and were interviewed individually between January and June 2015. Qualitative meaning condensation analysis was used.

Results

Three themes emerged: (1) Changed life: some felt healthy and beyond cancer; others suffered from reduced energy, joy of life, and self-esteem. Being affected by a life-threatening illness made their fundamental values clearer. Using cancer experiences to help others was emphasized. (2) Positive thinking, distancing the negative: striving to maintain positive thinking and distancing themselves from insecurity and fear of recurrence. A step-by-step strategy was important to cope with their new life situation. (3) Need for understanding and recognition: support was experienced as necessary and challenging. Recognition of posttreatment ailments was emphasized. Being more socially selective and preferring positive people were essential.

Conclusions

Cancer experiences changed the women’s lives. Their coping varied. Fewer but selected supporters were preferred. Understanding and recognition from others for the women’s changed life situation was essential.

Implications for Practice

Healthcare professionals should prepare women for a changed life situation because of illness experiences and the adverse effects of treatments. The support and information offered must be adjusted to each woman’s individual needs, coping capacity, and life situation. Further clinical intervention studies are needed.
Suicide by Detonation of Intraoral Firecracker
Authors: Hlavaty Leigh , Kasper William , Sung LokMan
Published: October 2018

Celebratory use of fireworks has been an integral part of human civilization for over millennia. While the majority of firework use is festive, their explosive nature can result in traumatic injuries and death. The authors present the death of a 21-year-old man found unresponsive on the floor of his parent's garage with extensive damage to his head after an explosion was heard. Firearms could not be found, but there were unexploded homemade and commercially produced firecrackers and components for the manufacture of additional firecrackers. The radial expansion of the blast wave formed by the intraoral explosion of a firecracker created injuries matching those of an intraoral shotgun wound.
An Unusual Foreign Object Attached to a Child's Finger
Authors: Kwan Stephanie , Shearin Jonathan W.
Published: October 2018

Strangulation injuries due to foreign objects are uncommon presentations of hand and finger injuries presenting to the emergency department (ED). Ring avulsion and hair tourniquet injuries are more commonly recognized mechanisms of strangulation, and algorithms for subsequent management and emergent treatment exist for these injuries. It is important to distinguish between hand injuries that can be managed in the setting of the ED and those that need emergent surgical management upon patient presentation. Nonemergent presentations of finger injuries include metallic bands or other objects trapped on digits without signs of neurovascular compromise. A 2-year-old girl presented to our ED with her right index finger trapped within a stainless steel salt shaker (2.55 in. H × 3.5 in. W × 4.9 in. D). The distal aspect of the digit was unable to be visualized, and communication with the patient was difficult secondary to distress and young age. Multiple attempts were made to remove the object in the ED by multiple health care providers, when concern for degloving injury prompted the patient to be taken to the operating room for removal with an electric saw by the hand surgeon and orthopedic team.
Bent Out of Shape
Authors: Chaganti Praneetha , Chao Jennifer H.
Published: October 2018

Spontaneous colon perforation is a known complication of vascular Ehlers-Danlos syndrome (vEDS) in the pediatric age group. The diagnosis of vEDS is often missed until the child presents to the pediatric emergency room with a complication like spontaneous arterial or colon rupture. These patients require immediate imaging and surgical attention to decrease morbidity and mortality. We present the case of a 9-year-old boy with abdominal pain and retching. An abdominal computed tomography revealed free air under the diaphragm, and surgical exploration showed perforation of the sigmoid colon. Ultimately, he was diagnosed with vEDS. We review the literature and discuss the clinical presentation, diagnosis, and life-threatening crises associated with vEDS.
Fertilizing riparian forests: nutrient repletion across ecotones with trophic rewilding
Authors: Bump Joseph K.
Published: October 2018

Trophic rewilding maintains that large mammals are functionally important to resource subsidies and nutrient repletion, yet this prediction is understudied. Here, I report on the potential magnitude and variability of nitrogen that moose populations move from aquatic to terrestrial ecosystems. My aim is to provide justified approximations of the role of moose in the flux of a limiting nutrient across ecotones and to illustrate how this role is linked to wolf predation and climate warming. Using Isle Royale and northeastern Minnesota, USA as contrasting focal systems, I found that the long-term annual N gain for riparian forests likely ranges from 1 to 10 kg N ha–1yr–1, depending on the heterogeneity of moose movements. For these systems, this range is equivalent to approximately 4–30% of net annual N mineralization, approximately 62–625% of annual N runoff, approximately 28–333% of annual atmospheric N deposition and approximately 31–312% of the N sequestered by trees. The N flux approximation is most sensitive to moose population levels and, as such, is influenced by wolves, climate warming and disease. The potential for other terrestrial ungulates that feed on aquatic plants to provide significant nutrient repletion across ecotones is unknown but important to examine in the context of trophic rewilding. The extent to which predators influence ungulate abundance indirectly impacts this nutrient repletion.

This article is part of the theme issue ‘Trophic rewilding: consequences for ecosystems under global change’.
Using species distribution modelling to determine opportunities for trophic rewilding under future scenarios of climate change
Authors: Jarvie Scott , Svenning Jens-Christian
Published: October 2018

Trophic rewilding, the (re)introduction of species to promote self-regulating biodiverse ecosystems, is a future-oriented approach to ecological restoration. In the twenty-first century and beyond, human-mediated climate change looms as a major threat to global biodiversity and ecosystem function. A critical aspect in planning trophic rewilding projects is the selection of suitable sites that match the needs of the focal species under both current and future climates. Species distribution models (SDMs) are currently the main tools to derive spatially explicit predictions of environmental suitability for species, but the extent of their adoption for trophic rewilding projects has been limited. Here, we provide an overview of applications of SDMs to trophic rewilding projects, outline methodological choices and issues, and provide a synthesis and outlook. We then predict the potential distribution of 17 large-bodied taxa proposed as trophic rewilding candidates and which represent different continents and habitats. We identified widespread climatic suitability for these species in the discussed (re)introduction regions under current climates. Climatic conditions generally remain suitable in the future, although some species will experience reduced suitability in parts of these regions. We conclude that climate change is not a major barrier to trophic rewilding as currently discussed in the literature.

This article is part of the theme issue ‘Trophic rewilding: consequences for ecosystems under global change’.
Loss of ZnT8 function protects against diabetes by enhanced insulin secretion
Authors: Dwivedi Om Prakash , Lehtovirta Mikko , Hastoy Benoit , Chandra Vikash , Kleiner Sandra , Jain Deepak , Richard Ann-Marie , Beer Nicola L. , Krentz Nicole A. J. , Prasad Rashmi B. , Hansson Ola , Ahlqvist Emma , Krus Ulrika , Artner Isabella , Gomez Daniel , Baras Aris , Abaitua Fernando , Champon Benoite , Payne Anthony J , Moralli Daniela , Thomsen Soren K. , Kramer Philipp , Spiliotis Ioannis , Ramracheya Reshma , Chabosseau Pauline , Theodoulou Andria , Cheung Rebecca , van de Bunt Martijn , Flannick Jason , Trombetta Maddalena , Bonora Enzo , Wolheim Claes B. , Sarelin Leena , Bonadonna Riccardo C. , Rorsman Patrik , Rutter Guy A , Davies Benjamin , Brosnan Julia , McCarthy Mark I. , Otonkoski Timo , Lagerstedt Jens O. , Gromada Jesper , Gloyn Anna L. , Tuomi Tiinamaija , Groop Leif
Published: October 2018

A rare loss-of-function variant p.Arg138* in SLC30A8 encoding the zinc transporter 8 (ZnT8) enriched in Western Finland protects against type 2 diabetes (T2D). We recruited relatives of the identified carriers and showed that protection was associated with better insulin secretion due to enhanced glucose responsiveness and proinsulin conversion, especially compared with individuals matched for the genotype of a common T2D risk variant in SLC30A8, p.Arg325. In genome-edited human IPS-derived β-like cells, we establish that the p.Arg138* variant results in reduced SLC30A8 expression due to haploinsufficiency. In human β-cells loss of SLC30A8 leads to increased glucose responsiveness and reduced KATP channel function, which was also seen in isolated islets from carriers of the T2D-protective allele p.Trp325. These data position ZnT8 as an appealing target for treatment aiming at maintaining insulin secretion capacity in T2D.
Sampling for disease absence—deriving informed monitoring from epidemic traits
Authors: Bourhis Yoann , Gottwald Timothy R. , Lopez-Ruiz Francisco J. , Patarapuwadol Sujin , van den Bosch Frank
Published: October 2018

Monitoring for disease requires subsets of the host population to be sampled and tested for the pathogen. If all the samples return healthy, what are the chances the disease was present but missed? In this paper, we developed a statistical approach to solve this problem considering the fundamental property of infectious diseases: their growing incidence in the host population. The model gives an estimate of the incidence probability density as a function of the sampling effort, and can be reversed to derive adequate monitoring patterns ensuring a given maximum incidence in the population. We then present an approximation of this model, providing a simple rule of thumb for practitioners. The approximation is shown to be accurate for a sample size larger than 20, and we demonstrate its use by applying it to three plant pathogens: citrus canker, bacterial blight and grey mould.
Evolution of hominin detoxification: Neanderthal and modern human AHR respond similarly to TCDD
Authors: Aarts Jac M.M.J.G. , Alink Gerrit M. , Franssen Henk J. , Roebroeks Wil
Published: October 2018

In studies of hominin adaptations to fire use, the role of the aromatic hydrocarbon receptor (AHR) in the evolution of hominin detoxification, especially regarding toxic smoke components, has been highlighted, including statements that the modern human AHR is significantly better at dealing with smoke toxins. We compared the AHR-controlled induction of cytochrome P450 1A1 (CYP1A1) in cultured cells transfected with an Altai-Neanderthal respectively a modern human reference AHR expression construct, and exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). We compared the complete AHR mRNA sequences including the untranslated regions (UTRs), maintaining the original codon usage, in HeLa human cervix epithelial adenocarcinoma cells. Our experiments complement a previous study of the AHR coding region optimized for mammalian codon usage and expressed in rat cells. Our results show no significant difference in CYP1A1 induction by TCDD between Neanderthal and modern human AHR (instead of a previously reported 150-1000 times difference range before), demonstrating that expression in a homologous cellular background is of major importance. The two dose-response curves almost coincide, except for a higher extrapolated maximum induction level for the Neanderthal AHR, possibly caused by a 5’-UTR G-variant known from modern humans (rs7796976). Our results are strongly at odds with a major role of the modern human AHR in the evolution of hominin detoxification of smoke components and consistent with our previous study which concluded that efficient detoxification alleles are more dominant in ancient hominins than in modern humans based on 18 relevant genes in addition to AHR.
Associations between environmental breast cancer risk factors and DNA methylation-based risk-predicting measures
Authors: Chen Minyuan , Wong Ee Ming , Nguyen Tuong L , Dite Gillian S , Stone Jennifer , Giles Graham G , Southey Melissa C , Hopper John L , Li Shuai
Published: October 2018

Background

Genome-wide average DNA methylation (GWAM) and epigenetic age acceleration have been suggested to predict breast cancer risk. We aimed to investigate the relationships between these putative risk-predicting measures and environmental breast cancer risk factors.

Methods

Using the Illumina HumanMethylation450K assay methylation data, we calculated GWAM and epigenetic age acceleration for 132 female twin pairs and their 215 sisters. Linear regression was used to estimate associations between these risk-predicting measures and multiple breast cancer risk factors. Within-pair analysis was performed for the 132 twin pairs.

Results

GWAM was negatively associated with number of live births, and positively with age at first live birth (both P<0.05). Epigenetic age acceleration was positively associated with body mass index (BMI), smoking, alcohol drinking and age at menarche, and negatively with age at first live birth (all P<0.05), and the associations with BMI, alcohol drinking and age at first live birth remained in the within-pair analysis.

Conclusions

This exploratory study shows that lifestyle and hormone-related breast cancer risk factors are associated with DNA methylation-based measures that could predict breast cancer risk. The associations of epigenetic age acceleration with BMI, alcohol drinking and age at first live birth are unlikely to be due to familial confounding.
A comprehensive framework to capture the arcana of neuroimaging analysis
Authors: Close Thomas G. , Ward Phillip G. D. , Sforazzini Francesco , Goscinski Wojtek , Chen Zhaolin , Egan Gary F.
Published: October 2018

Mastering the “arcana of neuroimaging analysis”, the obscure knowledge required to apply an appropriate combination of software tools and parameters to analyse a given neuroimaging dataset, is a time consuming process. Therefore, it is not typically feasible to invest the additional effort required generalise workflow implementations to accommodate for the various acquisition parameters, data storage conventions and computing environments in use at different research sites, limiting the reusability of published workflows.

We present a novel software framework, Abstraction of Repository-Centric ANAlysis (Arcana), which enables the development of complex, “end-to-end” workflows that are adaptable to new analyses and portable to a wide range of computing infrastructures. Analysis templates for specific image types (e.g. MRI contrast) are implemented as Python classes, which define a range of potential derivatives and analysis methods. Arcana retrieves data from imaging repositories, which can be BIDS datasets, XNAT instances or plain directories, and stores selected derivatives and associated provenance back into a repository for reuse by subsequent analyses. Workflows are constructed using Nipype and can be executed on local workstations or in high performance computing environments. Generic analysis methods can be consolidated within common base classes to facilitate code-reuse and collaborative development, which can be specialised for study-specific requirements via class inheritance. Arcana provides a framework in which to develop unified neuroimaging workflows that can be reused across a wide range of research studies and sites.
Tissue morphogenesis mediated by the Arabidopsis receptor kinase STRUBBELIG involves a clathrin-dependent process
Authors: Gao Jin , Chaudhary Ajeet , Vaddepalli Prasad , Nagel Marie-Kristin , Isono Erika , Schneitz Kay
Published: October 2018

Highlight

The Arabidopsis receptor kinase STRUBBELIG is internalized by clathrin-mediated endocytosis and affects clathrin-dependent processes in a tissue-dependent manner.

Signaling mediated by cell surface receptor kinases is central to the coordination of growth patterns during organogenesis. Receptor kinase signaling is in part controlled through endocytosis and subcellular distribution of the respective receptor kinase. For the majority of plant cell surface receptors the underlying trafficking mechanisms are not characterized. In Arabidopsis, tissue morphogenesis relies on the atypical receptor kinase STRUBBELIG (SUB). Here, we approach the endocytic mechanism of SUB. Our data reveal that a functional SUB:EGFP fusion is ubiquitinated in vivo. We further show that plasma membrane-bound SUB:EGFP becomes internalized in a clathrin-dependent fashion. We also find that SUB:EGFP associates with thetrans-Golgi network and accumulates in multivesicular bodies and the vacuole. Coimmunoprecipitation experiments reveal that SUB:EGFP and clathrin are present within the same protein complex. Our genetic analysis shows thatSUBandCLATHRIN HEAVY CHAIN 2promote root hair patterning. By contrast,SUBbehaves as a negative regulator of a clathrin-dependent process during floral development. Taken together, the data indicate that SUB undergoes clathrin-mediated endocytosis, that this process does not dependent on stimulation of SUB signaling by an exogenous agent, and thatSUBgenetically interacts with clathrin-dependent pathways in a tissue-specific manner.
Candidate Phyla Radiation Roizmanbacteria from hot springs have novel, unexpectedly abundant, and potentially alternatively functioning CRISPR-Cas systems
Authors: Chen Lin-Xing , Al-Shayeb Basem , Meheust Raphael , Li Wen-Jun , Doudna Jennifer A. , Banfield Jillian F.
Published: October 2018

The Candidate Phyla Radiation (CPR) comprises a huge group of bacteria that have small genomes that rarely encode CRISPR-Cas systems for phage defense. Consequently, questions remain about their mechanisms of phage resistance and the nature of phage that infect them. The compact CRISPR-CasY system (Cas12d) with potential value in genome editing was first discovered in these organisms. Relatively few CasY sequences have been reported to date, and little is known about the function and activity of these systems in the natural environment. Here, we conducted a genome-resolved metagenomic investigation of hot spring microbiomes and recovered CRISPR systems mostly from Roizmanbacteria that involve CasY proteins that are divergent from published sequences. Within population diversity in the spacer set indicates current in situ diversification of most of the loci. In addition to CasY, some Roizmanbacteria genomes also encode large type I-B and/or III-A systems that, based on spacer targeting, are used in phage defense. CRISPR targeting identified three phage represented by complete genomes and a prophage, which are the first reported for bacteria of the Microgenomates superphylum. Interestingly, one phage encodes a Cas4-like protein, a scenario that has been suggested to drive acquisition of self-targeting spacers. Consistent with this, the Roizmanbacteria population that it infects has a CRISPR locus that includes self-targeting spacers and a fragmented CasY gene (fCasY). Despite gene fragmentation, the PAM sequence is the same as that of other CasY reported in this study. Fragmentation of CasY may avoid the lethality of self-targeting spacers. However, the spacers may still have some biological role, possibly in genome regulation. The findings expand our understanding of CasY diversity, and more broadly, CRISPR-Cas systems and phage of CPR bacteria.
A global map of RNA binding protein occupancy guides functional dissection of post-transcriptional regulation of the T cell transcriptome
Authors: Litterman Adam J. , Zhu Wandi S. , Kageyama Robin , Zhao Wenxue , Zaitlen Noah , Erle David J. , Ansel K. Mark
Published: October 2018

RNA binding proteins (RBPs) mediate constitutive RNA metabolism and gene specific regulatory interactions. To identify RNA cis-regulatory elements, we developed GCLiPP, a biochemical technique for detecting RBP occupancy transcriptome-wide. GCLiPP sequence tags corresponded with known RBP binding sites, specifically correlating to abundant cytosolic RBPs. To demonstrate the utility of our occupancy profiles, we performed functional dissection of 3′ UTRs with CRISPR/Cas9 genome editing. Two RBP occupied sites in the CD69 3′ UTR destabilized the transcript of this key regulator of lymphocyte tissue egress. Comparing human Jurkat T cells and mouse primary T cells uncovered hundreds of biochemically shared peaks of GCLiPP signal across homologous regions of human and mouse 3′ UTRs, including a cis-regulatory element that governs the stability of the mRNA that encodes the proto-oncogene PIM3 in both species. Our GCLiPP datasets provide a rich resource for investigation of post-transcriptional regulation in the immune system.
sRNA-target Prediction Organizing Tool (SPOT) integrates computational and experimental data to facilitate functional characterization of bacterial small RNAs
Authors: King Alisa M. , Vanderpool Carin K. , Degnan Patrick H.
Published: October 2018

Small RNAs (sRNAs) post-transcriptionally regulate mRNA targets, typically under conditions of environmental stress. Although hundreds of sRNAs have been discovered in diverse bacterial genomes, most sRNAs remain uncharacterized, even in model organisms. Identification of mRNA targets directly regulated by sRNAs is rate-limiting for sRNA functional characterization. To address this, we developed a computational pipeline that we named SPOT for sRNA-targetPredictionOrganizingTool. SPOT incorporates existing computational tools to search for sRNA binding sites, allows filtering based on experimental data, and organizes the results into a standardized report. SPOT sensitivity (Correctly Predicted Targets/Total Known Targets) was equal to or exceeded any individual method when used on 12 characterized sRNAs. Using SPOT, we generated a set of target predictions for the sRNA RydC, which was previously shown to positively regulatecfamRNA, encoding cyclopropane fatty acid synthase. SPOT identifiedcfaalong with additional putative mRNA targets, which we then tested experimentally. Our results demonstrated that in addition tocfamRNA, RydC also regulatestrpEandpheAmRNAs, which encode aromatic amino acid biosynthesis enzymes. Our results suggest that SPOT can facilitate elucidation of sRNA target regulons to expand our understanding of the many regulatory roles played by bacterial sRNAs.

IMPORTANCE

Small RNAs (sRNAs) regulate gene expression in diverse bacteria by interacting with mRNAs to change their structure, stability or translation. Hundreds of sRNAs have been identified in bacteria, but characterization of their regulatory functions is limited by difficulty with sensitive and accurate identification of mRNA targets. Thus, new robust methods of bacterial sRNA target identification are in demand. Here, we describe ourSmall RNA-targetPredictionOrganizingTool, which streamlines the process of sRNA target prediction by providing a single pipeline that combines available computational prediction tools with customizable results filtering based on experimental data. SPOT allows the user to rapidly produce a prioritized list of predicted sRNA-target mRNA interactions that serves as a basis for further experimental characterization. This tool will facilitate elucidation of sRNA regulons in bacteria, allowing new discoveries regarding the roles of sRNAs in bacterial stress responses and metabolic regulation.
Sex differences in IL-17 determine chronicity in male versus female urinary tract infection
Authors: Scharff Anna Zychlinsky , Rousseau Matthieu , Mariano Livia Lacerda , Canton Tracy , Albert Matthew L , Fontes Magnus , Duffy Darragh , Ingersoll Molly A
Published: October 2018

Sex-based differences influence incidence and outcome of infectious disease. Women have a significantly greater incidence of urinary tract infection (UTI) than men, yet, conversely, male UTI is more persistent with greater associated morbidity. Mechanisms underlying these sex-based differences are unknown, in part due to a lack of experimental models. We optimized a model to transurethrally infect male mice and directly compared UTI in both sexes. Although both sexes were initially equally colonized by uropathogenicE. coli, only male and testosterone-treated female mice remained chronically infected for up to 4 weeks. Female mice had more robust innate responses, including higher IL-17 expression, and increased γδ T and LTi-like cells in the bladder following infection. Accordingly, neutralizing IL-17 abolished resolution in female mice, identifying the cytokine pathway necessary for bacterial clearance. Our findings support the concept that sex-based responses to UTI contribute to impaired innate immunity in males and provide a rationale for non-antibiotic-based immune targeting to improve the response to UTI.

One Sentence Summary

We investigated mechanisms underlying the clinical observation that while urinary tract infection is more prevalent in women, it is more severe in men, observing that in contrast to robust immune responses characterized by IL-17 in female animals, male mice develop chronic infection, following a failure to initiate innate immunity.
Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding
Authors: Tragin Margot , Vaulot Daniel
Published: October 2018

The Ocean Sampling Day (OSD) project provided metabarcoding data for the V4 hyper-variable regions of the 18S rRNA gene from 157 samples collected at 143 mostly coastal stations. In this paper we focus on the class Mamiellophyceae, which was found at nearly all OSD stations and represented 55 % of the green microalgae (Chlorophyta) reads in the 2014 OSD dataset. We performed phylogenetic analyses of unique OSD metabarcodes (ASV, amplicon single variants) and reference GenBank sequences from cultures and from the environment, focusing on the four most represented genera: Ostreococcus (45 % of the Mamiellophyceae reads), Micromonas (34 %), Bathycoccus (10 %) and Mantoniella (8.7 %). These analyses uncovered novel diversity within each genus except Bathycoccus. In Ostreococcus, a new clade (E) with 2 very clear base pair differences compared to the oceanic clade B in the V4 region was the second most represented clade after the coastal Ostreococcus “lucimarinus”. Within Micromonas, ten clades were found exceeding the 4 species and 2 candidate species already described. Finally, we found 2 new environmental clades of Mantoniella. Each Mamiellophyceae clade had a specific distribution in the OSD dataset suggesting that they are adapted to different ecological niches.
Targeted memory reactivation during sleep elicits neural signals related to learning content
Authors: Wang Boyu , Antony James , Lurie Sarah , Brooks Paula P , Paller Ken A , Norman Kenneth A
Published: October 2018

Reactivation of learning-related neural activity patterns is thought to drive memory stabilization. However, finding reliable, non-invasive, content-specific indicators of reactivation remains a central challenge. Here, we attempted to decode the content of reactivated memories in the electroencephalogram (EEG) during sleep. During encoding, human participants learned to associate spatial locations of visual objects with left- or right-hand movements, and each object was accompanied by an inherently related sound. During subsequent slow-wave sleep within an afternoon nap, we presented half of the sound cues that were associated (during wake) with left- and right-hand movements before bringing participants back for a final post-nap test. We trained a classifier on sleep EEG data (focusing on lateralized EEG features that discriminated left- vs. right-sided trials during wake) to predict learning content when we reactivated the memories during sleep. Discrimination performance was significantly above chance and predicted subsequent memory, supporting the idea that reactivation leads to memory stabilization. Moreover, these lateralized signals increased with post-cue spindle power, demonstrating that reactivation has a strong relationship with spindles. These results show that lateralized activity related to individual memories can be decoded from sleep EEG, providing an effective indicator of offline reactivation.
Epiblast formation by Tead-Yap-dependent expression of pluripotency factors and competitive elimination of unspecified cells
Authors: Hashimoto Masakazu , Sasaki Hiroshi
Published: October 2018

The epiblast is a pluripotent cell population first formed in preimplantation embryos and its quality is important for proper development. Here, we examined the mechanisms of epiblast formation and found that the Hippo pathway transcription factor Tead and its coactivator Yap regulate expression of pluripotency factors. After specification of the inner cell mass, Yap accumulates in the nuclei and activates Tead. Tead activity is required for strong expression of pluripotency factors and is variable in the forming epiblast. Cells showing low Tead activity are eliminated from the epiblast through cell competition. Pluripotency factor expression and Myc control cell competition downstream of Tead activity. Cell competition eliminates unspecified cells and is required for proper organization of the epiblast. These results suggest that induction of pluripotency factors by Tead activity and elimination of unspecified cells via cell competition ensure the production of an epiblast with naïve pluripotency.
Single-cell RNA-seq reveals that glioblastoma recapitulates normal brain development
Authors: Couturier Charles P. , Ayyadhury Shamini , Le Phuong U. , Monlong Jean , Riva Gabriele , Allache Redouane , Baig Salma , Yan Xiaohua , Bourgey Mathieu , Lee Changseok , Wang Yu Chang David , Yong V. Wee , Guiot Marie-Christine , Misic Bratislav , Antel Jack , Bourque Guillaume , Ragoussis Jiannis , Petrecca Kevin
Published: October 2018

Cancer stem cells are critical for cancer initiation, development, and resistance to treatments. Our understanding of these processes, and how they relate to glioblastoma heterogeneity, is limited. To overcome these limitations, we performed single-cell RNA-sequencing on 38 296 glioblastoma cells and 22 637 normal human fetal brain cells. Using an unbiased approach, we mapped the lineage hierarchy of the developing human brain and compared the transcriptome of each cancer cell to this roadmap. We discovered a conserved neural trilineage cancer hierarchy with glial progenitor-like cells at the apex. We also found that this progenitor population contains the majority of cancer’s cycling cells and is the origin of heterogeneity. Finally, we show that this hierarchal map can be used to identify therapeutic targets specific to progenitor cancer stem cells. Our analyses show that normal brain development reconciles glioblastoma development, unravels the origin of glioblastoma heterogeneity, and helps to identify cancer stem cell-specific targets.
Scaling principles of distributed circuits
Authors: Srinivasan Shyam , Stevens Charles F
Published: October 2018

Distributed circuits like the olfactory cortex, hippocampus, and cerebellum contain sub-circuits whose inputs distribute their axons over the entire circuit creating a puzzle of how information is encoded. One method for approaching the puzzle is to view them as scalable systems. In scalable systems the quantitative relationship between circuit components is conserved across brain sizes, and by mapping circuit size to functional abilities - e.g. visual acuity in the visual circuit - scientists have explained information encoding. This approach has not been applied to anti-map circuits as their scalability is unknown. To address this gap in knowledge, we obtained quantitative descriptions of the olfactory bulb and piriform cortex in six mammals using stereology techniques and light microscopy. We found that the olfactory circuit is scalable as it satisfies three requirements of scalable systems. First, quantitative relationships between circuit components are conserved: the number piriform neuronsnscales with bulb glomeruligasn∼g3/2. Second, the olfactory circuit has an invariant property: the average number of synapses between a bulb glomerulus and piriform neuron is one. Third, the olfactory circuit is symmorphic, i.e. olfactory ability improves with circuit size. Other distributed circuits with similar properties might also be scalable.
Impaired chromosome segregation results in sperms with excess centrosomes inemb-27APC6mutantC. elegans
Authors: Kondo Tomo , Kimura Akatsuki
Published: October 2018

The anaphase-promoting complex (APC) is a major regulator of chromosome segregation and is implicated in centriole engagement, whose de-regulation causes abnormal number of centrosomes. Theemb-27gene inC. elegansencodes a subunit of APC. The paternalemb-27mutant was reported to show cell division with multiple furrows, suggesting the presence of excess centrosomes. In this study, we examined the number of centrosomes and the mechanism underlying de-regulation of centrosome number inemb-27mutants. Our observations indicated excess centrosomes inemb-27sperms, which resulted in zygotes with excess centrosomes. Further, the secondary spermatocyte ofemb-27produced reduced number of spermatids, which is likely the direct cause of the excess number of centrosomes per sperm. We propose that a chromosome segregation defect inemb-27induced centrosome separation defect, resulting in reduced number of buds. Additionally, treatment with cytoskeletal inhibiting drugs indicated presence of three kinds of forces working in combination to move the centrosomes into the spermatids. The present study suggested a novel role of microtubule in the budding cytokinesis of spermatocytes.
Macrophage migration inhibitory factor of Syrian golden hamster has similar structure and function as human MIF and promotes pancreatic tumor growth
Authors: Dash Pujarini , Sundaram Rajivgandhi , Suresh Voddu , Sabat Surendra Chandra , Mohapatra Debasish , Mohanty Sneha , Vasudevan Dileep , Senapati Shantibhusan
Published: October 2018

Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine that increasingly is being studied in cancers and inflammatory diseases. Though murine models have been instrumental in understanding the functional role of MIF in different pathological conditions, the information obtained from these models is biased towards a specific species. In experimental science, results obtained from multiple clinically relevant animal models always provide convincing data that might recapitulate in humans. Syrian golden hamster (Mesocricetus auratus), is a clinically relevant animal model for multiple human diseases. Hence, the major objectives of this study were to characterize structure and function of hamster MIF, and finally evaluate its effect on pancreatic tumor growthin vivo. Initially, the recombinant hamster MIF (rha-MIF) was cloned, expressed and purified in bacterial expression system. The rha-MIF primary sequence, biochemical properties and crystal structure analysis showed a greater similarity with human MIF. The crystal structure of hamster MIF illustrates that it forms a homotrimer as known in human and mouse. However, hamster MIF exhibits some minor structural variations when compared to human and mouse MIF. Thein vitrofunctional studies show that rha-MIF has tautomerase activity and enhances activation and migration of hamster peripheral blood mononuclear cells (PBMCs). Interestingly, injection of rha-MIF into HapT1 pancreatic tumor bearing hamsters significantly enhanced the tumor growth and tumor associated angiogenesis. Together, the current study shows a structural and functional similarity between hamster and human MIF. Moreover, it has demonstrated that a high-level of circulating MIF originating from non-tumor cells might also promote pancreatic tumor growthin vivo.
Wakeful rest benefits memory when materials can be rehearsed
Authors: Millar Peter R. , Balota David A.
Published: October 2018

Wakeful rest is a brief (e.g., 10 minutes), quiet period of minimal stimulation, which has been shown to facilitate memory performance, compared to a distractor task. Researchers have argued that this benefit is driven by automatic consolidation during the wakeful rest period. However, prior studies have not fully ruled out a controlled rehearsal mechanism, which might also occur during wakeful rest. In the current study, we attempted to replicate the wakeful rest effect under conditions that more strictly limit the possibility of rehearsal. Across six experiments, we manipulated parameters of a standard wakeful rest paradigm, including the type of target materials (word lists or abstract shapes), intentionality of encoding (incidental or intentional), and final retrieval delay (immediate or delayed). Additionally, we tested both younger and older adults to test whether these effects are consistent across the adult lifespan. Importantly, we observed the expected wakeful rest memory benefit in recall for verbal targets, which are easily rehearseable, but not for abstract shapes, which cannot be readily rehearsed. This pattern occurred in both younger and older adults. These results place constraints on the generalizability of wakeful rest memory benefits and suggest that the effect may be at least partly driven by rehearsal processes, rather than an automatic consolidation process.