bluuebunny/crossref_metadata_2025 huggingface dataset:
Knockdown Resistance-Associated Mutations Dominate Populations of the Common Bed Bug (Hemiptera: Cimicidae) Across the South Central United States
Authors: Holleman Jeffrey G , Robison Grant A , Bellovich Ian J , Booth Warren
Published: June 2019

Despite awareness of the mutations conferring insecticide resistance in the bed bug, Cimex lectularius L. (Hemiptera: Cimicidae), within the United States few studies address the distribution and frequency of these. Within the United States, studies have focused on collections made along the East Coast and Midwest, documenting the occurrence of two mutations (V419L and L925I) within the voltage-gated sodium channel α-subunit gene shown to be associated with knockdown resistance (kdr) to pyrethroids. Here, the distribution and frequency of the V419L and L925I site variants is reported from infestations sampled within Oklahoma and its immediately adjacent states. Additionally, the presence of a mutation previously undocumented in the United States (I935F) is noted. While novel in the United States, this mutation has previously been reported in Australian and Old World populations. No infestations were found to harbor wild-type individuals, and hence susceptible, at each of the three sites. Instead, ~21% were found to possess the resistant mutation at the L925I site (haplotype B), ~77% had mutations at both the V419L and L925I sites (haplotype C), and 2% possessed the mutation at the L936F site (haplotype Ab). The high frequency of haplotype C corresponds to previous studies in the United States, and contrasts dramatically with those of the Old World and Australia. The data presented here provide insight into the contemporary occurrence of kdr-associated insecticide resistance in the South Central United States, a region for which data have previously been absent. These data suggest that New World and Old World/Australian infestations are likely to have originated from different origins.
Quality of Life During Palliative Systemic Therapy for Esophagogastric Cancer: Systematic Review and Meta-Analysis
Authors: van Kleef Jessy Joy , ter Veer Emil , van den Boorn Héctor G , Schokker Sandor , Ngai Lok Lam , Prins Mariska J , Mohammad Nadia Haj , van de Poll-Franse Lonneke V , Zwinderman Aeilko H , van Oijen Martijn G H , Sprangers Mirjam A G , van Laarhoven Hanneke W M
Published: June 2019

Background

Palliative systemic therapy can prolong life and reduce tumor-related symptoms for patients with advanced esophagogastric cancer. However, side effects of treatment could negatively affect health-related quality of life (HRQoL). Our aim was to review the literature and conduct a meta-analysis to examine the effect of palliative systemic therapy on HRQoL.

Methods

EMBASE, Medline, and Central were searched for phase II/III randomized controlled trials until April 2018 investigating palliative systemic therapy and HRQoL. Meta-analysis was performed on baseline and follow-up summary values of global health status (GHS) and other European Organisation for Research and Treatment of Cancer scales. A clinically relevant change and difference of 10 points (scale 0–100) was set to assess the course of HRQoL over time within treatment arms as well as between arms.

Results

We included 43 randomized controlled trials (N = 13 727 patients). In the first-line and beyond first-line treatment setting, pooled baseline GHS mean estimates were 54.6 (95% confidence interval = 51.9 to 57.3) and 57.9 (95% confidence interval = 55.7 to 60.1), respectively. Thirty-nine (81.3%) treatment arms showed a stable GHS over the course of time. Anthracycline-based triplets, fluoropyrimidine-based doublets without cisplatin, and the addition of trastuzumab to chemotherapy were found to have favorable HRQoL outcomes. HRQoL benefit was observed for taxane monotherapy and several targeted agents over best supportive care beyond first line.

Conclusions

Patients reported impaired GHS at baseline and generally remained stable over time. Anthracycline-based triplets and fluoropyrimidine-based doublets without cisplatin may be preferable first-line treatment options regarding HRQoL for HER2-negative disease. Taxanes and targeted agents could provide HRQoL benefit beyond first line compared with best supportive care.
Short-term results of total shoulder arthroplasty for ochronotic arthritis
Authors: Dorleijn Desiree , van Noort Arthur , Janus Guus
Published: June 2019

Alkaptonuria is a rare inherited autosomal recessive disorder resulting in large joint osteoarthritis with black discoloration of the cartilage. The glenohumeral is the third most affected joint. Two cases of ochronotic shoulder arthropathy with three shoulder joint replacements are presented. Stemless shoulder arthroplasty was implanted with moderate to good results up to 2 years follow-up regarding pain and range of motion.
The hazard from fragmenting comets
Authors: Napier W M
Published: June 2019

Comet disintegration proceeds both through sublimation and discrete splitting events. The cross-sectional area of material ejected by a comet may, within days, become many times greater than that of the Earth, making encounters with such debris much more likely than collisions with the nucleus itself. The hierarchic fragmentation and sublimation of a large comet in a short period orbit may yield many hundreds of such short-lived clusters. We model this evolution with a view to assessing the probability of an encounter which might have significant terrestrial effects, through atmospheric dusting or multiple impacts. Such an encounter may have contributed to the large animal extinctions and sudden climatic cooling of 12,900 years ago, and the near-simultaneous collapse of civilisations around 2350 BC.
Endoscopic Posterior Cervical Foraminotomy: 2-Dimensional Operative Video
Authors: Burkhardt Benedikt W , Oertel Joachim M
Published: June 2019

In the 1940s, the posterior cervical foraminotomy (PCF) was first described. At that time, this technique represented a big step ahead for the treatment of cervical radiculopathy. Rightly, a multitude of studies demonstrated that open microsurgical posterior foraminotomy is an effective treatment for cervical radiculopathy. Open posterior approaches have still the disadvantage of detaching the extensor cervical muscles from the laminae and the spinous processes, which can lead to severe collateral tissue and muscle damage, followed by postoperative complications, such as axial neck pain, shoulder pain, loss of lordosis, or even spinal instability. Minimally invasive techniques have been developed to reduce the approach related trauma. Initially, these techniques have been performed using endoscopic visualization and applied to the lumbar spine with great success. With this in mind, spine surgeons have extended the spectrum of indication and applied endoscopic techniques to treat degenerative cervical spine disorders. Indications for PCF are single-level or multilevel unilateral lateral disc herniation, osseous foraminal stenosis secondary to isolated facet hypertrophy, and persistent radicular symptoms following an anterior cervical spine procedure. Depending on the underlying pathology, clinical success rates from 75% to 96% for the treatment of cervical radiculopathy have been reported. Mainly, there are 2 different endoscopic techniques to perform PCF. The so-called full-endoscopic techniques are performed under continuous irrigation in single-handed technique. The endoscopic tubular assisted technique is performed in bimanual fashion with microsurgical instruments. The purpose of this video is to describe the endoscopic tubular assisted technique in detail. Patient consent was obtained prior to preparation of the video.
Living with ankylosing spondylitis: an open response survey exploring physical activity experiences
Authors: Rouse Peter C , Standage Martyn , Sengupta Raj
Published: June 2019

Objective

The aim was to gather in-depth, rich accounts of physical activity experiences of people living with AS, to include symptom management, consequences for symptoms, factors that encourage and disrupt physical activity, and motivations that underpin participation in physical activity.

Methods

Participants (n = 149; 60% female) completed a Bristol Online Survey that consisted of open questions to capture rich qualitative data. In total, 96% of participants self-reported having AS (1% other arthritis; 3% missing), and 51% had this diagnosis for >20 years. A content analysis was conducted to identify the key themes/factors from within the open question responses. A frequency analysis was used to ascertain the most commonly identified themes and factors.

Results

Fifty different physical activities were participated in over the previous month. Physical activity can improve and worsen arthritis symptoms, and fluctuations in participation exist even in the most active. Pain and fatigue were the two most frequently identified factors that stopped people with AS from being physically active. Participants reported more autonomously driven motivations than controlled motivations for participating in physical activity.

Conclusion

People with AS can and do participate in a diverse range of physical activities, but fluctuations in activity levels occur owing to disease- and non-disease-specific factors. Individually tailored plans and self-monitoring are important to optimize levels of physical activity and maximize benefits for people living with AS. Multiple reasons why AS patients participate in physical activity were revealed that included both adaptive (i.e. autonomous) and maladaptive (i.e. controlled) forms of motivation.
Anti-apolipoprotein A-1 autoantibodies correlate with disease activity in systemic lupus erythematosus
Authors: Nigolian Haïg , Ribi Camillo , Courvoisier Delphine S , Pagano Sabrina , Alvarez Montserrat , Trendelenburg Marten , Huynh-Do Uyen , Vuilleumier Nicolas , Dayer Jean-Michel , Chizzolini Carlo , Roux-Lombard Pascale
Published: June 2019

Objectives

Apolipoprotein A-1 (ApoA-1) is a protein fraction of the high-density lipoproteins with anti-inflammatory and antioxidant properties that play a major role in reverse cholesterol transport. The presence of anti-ApoA-1 IgG has been reported in SLE to be variably associated with disease activity or cardiovascular events (CVEs). We assessed the clinical performance of anti-ApoA-1 IgG and of antibodies directed against its immunodominant F3L1 peptide (F3L1 IgG) in a well-characterized Swiss SLE cohort study.

Methods

A total of 354 biological samples and interviews from 176 individuals were studied. SLEDAI, clinical characteristics, anamnestic CVEs and therapy details were recorded. Sera were tested for the presence of anti-ApoA-1 IgG, anti-F3L1 IgG, anti-dsDNA IgG and aPL.

Results

Anti-ApoA-1 and anti-F3L1 IgG positivity was associated with higher SLEDAI, mostly due to concomitant positivity of dsDNA IgG and low complement. Variations in time of anti-ApoA-1 IgG correlated positively with variations of anti-dsDNA IgG and inversely to variations of C3 levels. No cross-reactivity was found between anti-ApoA-1 and anti-dsDNA IgG. Positivity for anti-Apo-A1 IgG was more frequent in individuals receiving 10 mg/day or more of prednisone. We did not find any significant association between anti-ApoA-1 IgG positivity and CVEs.

Conclusion

Anti-ApoA-1 and anti-F3L1 IgG in SLE correlate strongly with laboratory markers of activity, particularly with the presence and titre of dsDNA IgG. These results confirm and extend previous findings and support the use of anti-ApoA1 IgG in the clinical setting. Their role in CVEs deserves further investigation.
A review of dengue diagnostics and implications for surveillance and control
Authors: Raafat Nader , Blacksell Stuart D , Maude Richard J
Published: June 2019

Dengue is the world’s most common arboviral infection, with almost 4 billion people estimated to be living at risk of dengue infection. A recently introduced vaccine is currently recommended only for seropositive individuals in a restricted age range determined by transmission intensity. With no effective dengue vaccine for the general population or any antiviral therapy, dengue control continues to rely heavily on vector control measures. Early and accurate diagnosis is important for guiding appropriate management and for disease surveillance to guide prompt dengue control interventions. However, major uncertainties exist in dengue diagnosis and this has important implications for all three. Dengue can be diagnosed clinically against predefined lists of signs and symptoms and by detection of dengue-specific antibodies, non-structural 1 antigen or viral RNA by reverse transcriptase–polymerase chain reaction. All of these methods have their limitations. This review aims to describe and quantify the advantages, uncertainties and variability of the various diagnostic methods used for dengue and discuss their implications and applications for dengue surveillance and control.
Genetic Diversity of Verticillium dahliae Isolates From Mint Detected with Genotyping by Sequencing
Authors: Dung Jeremiah K. S. , Knaus Brian J. , Fellows Henry L. S. , Grünwald Niklaus J. , Vining Kelly J.
Published: June 2019

Verticillium wilt is the most important disease threatening the commercial production of mint grown for essential oil. An important long-term goal for mint breeders is the production of cultivars with resistance to Verticillium wilt. Before that can be accomplished, a better understanding of the genetic variation within and among populations of Verticillium dahliae is needed. We characterized the extent of phenotypic and genetic diversity present in contemporary and archival populations of V. dahliae from mint fields in Oregon and other production regions of the United States using genotyping by sequencing, PCR assays for mating type and pathogenic race, vegetative compatibility group (VCG) tests, and aggressiveness assays. We report that the population in the Pacific Northwest can be described as one common genetic group and four relatively rare genetic groups. Eighty-three percent of the isolates belonged to VCG2B, and all isolates possessed the MAT1-2 idiomorph and were characterized as pathogenic race 2. These results indicate low levels of genetic diversity and a negligible risk of sexual recombination in populations of this host-adapted pathogen population. Knowledge of the genetic structure of V. dahliae in the Pacific Northwest will inform breeders about the diversity of pathogenicity factors that may need to be considered in their breeding programs.
Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma
Authors: Tanigawa Yosuke , Wainberg Michael , Karjalainen Juha , Kiiskinen Tuomo , Lemmelä Susanna , Turunen Joni A. , Graham Robert , Havulinna Aki S. , Perola Markus , Palotie Aarno ,   FinnGen, Daly Mark J. , Rivas Manuel A.
Published: June 2019

Protein-altering variants that are protective against human disease provide in vivo validation of therapeutic targets. Here we use genotyping data in UK Biobank and FinnGen to conduct a search for protein-altering variants conferring lower intraocular pressure (IOP) and protection against glaucoma. Through protein-altering variant association analysis we find a missense variant in UK Biobank (rs28991009 (MAF=0.8%) genotyped in 81,527 individuals with measured IOP and an independent set of 4,269 glaucoma patients and 251,355 controls) that significantly lowers IOP (β = −0.73 mmHg for heterozygotes, −2.96 mmHg for homozygotes, P = 1 × 10−13) and is associated with 34% reduced risk of glaucoma (P = 0.005). In FinnGen, we identify an ANGPTL7 missense variant at a greater than 50-fold increased frequency in Finland compared with other populations (rs147660927, p.Arg220Cys, MAF Finland = 4.1%), which was genotyped in 5,177 glaucoma patients and 130,461 controls and is associated with 30% lower glaucoma risk (P = 1 × 10−9). We further find three rarer variants in UK Biobank, including a protein-truncating variant, which confer a strong composite lowering of IOP (P = 0.002), suggesting the protective mechanism likely resides in the loss of an interaction or function. Our results support inhibition or down-regulation of ANGPTL7 as a therapeutic strategy for glaucoma
Cohesin removal reprograms gene expression upon mitotic entry
Authors: Perea-Resa Carlos , Bury Leah , Cheeseman Iain , Blower Michael D.
Published: June 2019

Entering mitosis, the genome is restructured to facilitate chromosome segregation, accompanied by dramatic changes in gene expression. However, the mechanisms that underlie mitotic transcriptional regulation are unclear. In contrast to transcribed genes, centromere regions retain transcriptionally active RNA Polymerase II (RNAPII) in mitosis. Here, we demonstrate that chromatin-bound cohesin is sufficient to retain RNAPII at centromeres while WAPL-mediated removal of cohesin during prophase is required for RNAPII dissociation from chromosome arms. Failure to remove cohesin from chromosome arms results in a failure to release elongating RNAPII and nascent transcripts from mitotic chromosomes and dramatically alters gene expression. We propose that prophase cohesin removal is the key step in reprogramming gene expression as cells transition from G2 to mitosis, and is temporally coupled with chromosome condensation to coordinate chromosome segregation with changes in gene expression.

Highlights

Mitotic centromere transcription requires cohesin

Cohesin removal releases elongating RNA Pol II and nascent RNA from chromatin

The prophase pathway reprograms gene expression during mitosis
Generation of Recombinant Rotavirus Expressing NSP3-UnaG Fusion Protein by a Simplified Reverse Genetics System
Authors: Philip Asha A. , Perry Jacob L. , Eaton Heather E. , Shmulevitz Maya , Hyser Joseph M. , Patton John T.
Published: June 2019

Rotavirus is a segmented double-stranded (ds)RNA virus that causes severe gastroenteritis in young children. We have established an efficient simplified rotavirus reverse genetics (RG) system that uses eleven T7 plasmids, each expressing a unique simian SA11 (+)RNA, and a CMV support plasmid for the African swine fever virus NP868R capping enzyme. With the NP868R-based system, we generated recombinant rotavirus (rSA11/NSP3-FL-UnaG) with a genetically modified 1.5-kB segment 7 dsRNA that encodes full-length NSP3 fused to UnaG, a 139-aa green fluorescent protein (FP). Analysis of rSA11/NSP3-FL-UnaG showed that the virus replicated efficiently and was genetically stable over 10 rounds of serial passage. The NSP3-UnaG fusion product was well expressed in rSA11/NSP3-FL-UnaG-infected cells, reaching levels similar to NSP3 in wildtype rSA11-infected cells. Moreover, the NSP3-UnaG protein, like functional wildtype NSP3, formed dimersin vivo. Notably, NSP3-UnaG protein was readily detected in infected cells via live cell imaging, with intensity levels ~3-fold greater than that of the NSP1-UnaG fusion product of rSA11/NSP1-FL-UnaG. Our results indicate that FP-expressing recombinant rotaviruses can be made through manipulation of the segment 7 dsRNA without deleting or interrupting any of the twelve open reading frames of the virus. Because NSP3 is expressed at levels higher than NSP1 in infected cells, rotaviruses expressing NSP3-based FPs may be a more sensitive tool for studying rotavirus biology than rotaviruses expressing NSP1-based FPs. This is the first report of a recombinant rotavirus containing a genetically engineered segment 7 dsRNA.

Importance

Previous studies have generated recombinant rotaviruses that express fluorescent proteins (FPs) by inserting reporter genes into the NSP1 open reading frame (ORF) of genome segment 5. Unfortunately, NSP1 is expressed at low levels in infected cells, making viruses expressing FP-fused NSP1 less than ideal probes of rotavirus biology. Moreover, FPs were inserted into segment 5 in such a way as to compromise NSP1, an interferon antagonist affecting viral growth and pathogenesis. We have identified an alternative approach for generating rotaviruses expressing FPs, one relying on fusing the reporter gene to the NSP3 ORF of genome segment 7. This was accomplished without interrupting any of the viral ORFs, yielding recombinant viruses likely expressing the complete set of functional viral proteins. Given that NSP3 is made at moderate levels in infected cells, rotavirus encoding NSP3-based FPs should be more sensitive probes of viral infection than rotaviruses encoding NSP1-based FPs.
Excess calorie intake early in life increases susceptibility to colitis in the adult
Authors: Al Nabhani Ziad , Dulauroy Sophie , Lécuyer Emelyne , Polomack Bernadette , Berard Marion , Eberl Gérard
Published: June 2019

Epidemiological data report an association between obesity and inflammatory bowel disease (IBD) 1–3. Furthermore, animal models demonstrate that maternal high fat diet (HFD) and maternal obesity increase susceptibility to IBD in the offsprings 4–8. However, the mechanisms that translate maternal obesity and HFD into increased susceptibility to IBD later in life remain unknown. Here we report that excess calorie intake by neonatal mice, as a consequence of maternal HFD, forced feeding of neonates or low litter competition, lead to an increase, during weaning, in intestinal permeability, expression of pro-inflammatory cytokines and hydrogen sulfide production by the microbiota. In this context, intestinal permeability, cytokine expression and hydrogen sulfide engaged in a mutual positive feedback that imprinted increased susceptibility to colitis in the adult. This pathological imprinting was prevented by the neutralization of IFNγ and TNFα, of the production of hydrogen sulphide, or by normalization of intestinal permeability during weaning. Thus, excessive calorie intake by neonates leads to multiple causally-linked perturbations in the intestine that imprint the individual with long term susceptibility to IBD.
binomialRF: Interpretable combinatoric efficiency of random forests to identify biomarker interactions
Authors: Zaim Samir Rachid , Kenost Colleen , Berghout Joanne , Chiu Wesley , Wilson Liam , Zhang Hao Helen , Lussier Yves A.
Published: June 2019

Background

In this era of data science-driven bioinformatics, machine learning research has focused on feature selection as users want more interpretation and post-hoc analyses for biomarker detection. However, when there are more features (i.e., transcript) than samples (i.e., mice or human samples) in a study, this poses major statistical challenges in biomarker detection tasks as traditional statistical techniques are underpowered in high dimension. Second and third order interactions of these features pose a substantial combinatoric dimensional challenge. In computational biology, random forest1(RF) classifiers are widely used2–7due to their flexibility, powerful performance, and robustness to “P predictors ≫subjects N” difficulties and their ability to rank features. We propose binomialRF, a feature selection technique in RFs that provides an alternative interpretation for features using a correlated binomial distribution and scales efficiently to analyze multiway interactions.

Methods

binomialRF treats each tree in a RF as a correlated but exchangeable binary trial. It determines importance by constructing a test statistic based on a feature’s selection frequency to compute its rank, nominal p-value, and multiplicity-adjusted q-value using a one-sided hypothesis test with a correlated binomial distribution. A distributional adjustment addresses the co-dependencies among trees as these trees subsample from the same dataset. The proposed algorithm efficiently identifies multiway nonlinear interactions by generalizing the test statistic to count sub-trees.

Results

In simulations and in the Madelon benchmark datasets studies, binomialRF showed computational gains (up to 30 to 600 times faster) while maintaining competitive variable precision and recall in identifying biomarkers’ main effects and interactions. In two clinical studies, the binomialRF algorithm prioritizes previously-published relevant pathological molecular mechanisms (features) with high classification precision and recall using features alone, as well as with their statistical interactions alone.

Conclusion

binomialRF extends upon previous methods for identifying interpretable features in RFs and brings them together under a correlated binomial distribution to create an efficient hypothesis testing algorithm that identifies biomarkers’ main effects and interactions. Preliminary results in simulations demonstrate computational gains while retaining competitive model selection and classification accuracies. Future work will extend this framework to incorporate ontologies that provide path-way-level feature selection from gene expression input data.

Availability

Github:https://github.com/SamirRachidZaim/binomialRF

Supplementary information

Supplementary analyses and results are available athttps://github.com/SamirRachidZaim/binomialRF_simulationStudy
Non-spatial features reduce the reliance on sustained spatial auditory attention
Authors: Bonacci Lia M. , Bressler Scott , Shinn-Cunningham Barbara G.
Published: June 2019

Top-down spatial attention is effective at selecting a target sound from a mixture. However, non-spatial features often distinguish sources in addition to location. This study explores whether redundant non-spatial features are used to maintain selective auditory attention for a spatially defined target. We recorded electroencephalography (EEG) while subjects focused attention on one of three simultaneous melodies. In one experiment, subjects (n = 17) were given an auditory cue indicating both the location and pitch of the target melody. In a second experiment (n = 17 subjects), the cue only indicated target location, and we compared two conditions: one in which the pitch separation of competing melodies was large, and one in which this separation was small. In both experiments, responses evoked by onsets of events in sound streams were modulated equally as strong by attention, suggesting that the target stimuli were correctly selected regardless of the cue or pitch information available. In all cases, parietal alpha was lateralized following the cue, but prior to melody onset, indicating that subjects always initially focused attention in space. During the stimulus presentation, however, this lateralization weakened when pitch cues were strong, suggesting that strong pitch cues reduced reliance on sustained spatial attention. These results demonstrate that once a well-defined target stream at a known location is selected, top-down spatial attention is unnecessary to filter out a segregated competing stream.
Episodic memory encoding by a place cell sub-population
Authors: Ormond Jake , Serka Simon A. , Johansen Joshua P.
Published: June 2019

Study of the hippocampal place cell system has greatly enhanced our understanding of memory encoding for distinct places, but how episodic memories for distinct experiences occurring within familiar environments are encoded is not clear. One possibility is that different place cell populations encode details of the novel experience or maintain the representation of the unchanged environment. We developed an aversive spatial decision making task which induced partial remapping in CA1, allowing us to identify both remapping and stable cell populations. We found that remapping cells exhibited distinct features not present in stable cells. During memory encoding, their theta phase preferences shifted to earlier phases, when CA3 inputs are strongest. Further, their recruitment into replay events increased during learning, unlike that of stable cells. Our demonstration of a sub-population of place cells identified on the basis of their degree of remapping and exhibiting unique changes in their spike firing properties with learning lend support to a model in which novel and familiar spatial/contextual information is encoded and maintained, respectively, by separate place cell populations.
Integrative analysis of proteome and transcriptome dynamics duringBacillus subtilisspore revival
Authors: Swarge Bhagyashree , Jonker Martijs , Abhyankar Wishwas , Hoefsloot Huub , de Koster Chris G. , Brul Stanley , de Koning Leo J.
Published: June 2019

Bacillus subtilisforms highly resistant, metabolically inactive dormant spores upon nutrient limitation. These endospores pose challenges to the food and medical sectors. Spores reactivate their metabolism upon contact with germinants and develop into vegetative cells. The activation of the molecular machinery that triggers the progress of germination and spore outgrowth is still unsettled. To gain further insight in spore germination and outgrowth processes, the transcriptome and proteome changeover during spore germination and outgrowth to vegetative cells, was analysed.B. subtilistranscriptome analysis allow us to trace the different functional groups of genes expressed. For each time-point sample, the change in the spore proteome was quantitatively monitored relative to the reference proteome of15N metabolically labelled vegetative cells. We observed until the phase transition, i.e. completion of germination, no significant change in the proteome. We have identified 36 transcripts present abundantly in the dormant spores. This number is in close agreement with the previous findings. These transcripts mainly belong to the genes encoding small acid soluble proteins (sspE, sspO, sspI, sspK, sspF) and proteins with uncharacterized functions. We observed in total 3152 differentially expressed genes, but ‘only’ 323 differentially expressed proteins (total 451 proteins identified and quantified). Our data shows that 173 proteins from dormant spores, both spore unique proteins and protein shared with vegetative cells, are lost during the phase transitioning period. This loss is in addition to the active protein degradation, undertaken by the spore proteases such as Gpr, as germination and outgrowth proceeds. Further analysis is required to functionally interpret the observed protein loss. The observed diverse timing of the synthesis of different protein sets reveals a putative core-strategy of the revival of ‘life’ starting from theB. subtilisspore.
Neonatal genetics of gene expression reveal the origins of autoimmune and allergic disease risk
Authors: Huang Qin Qin , Tang Howard H. F. , Teo Shu Mei , Ritchie Scott C. , Nath Artika P. , Brozynska Marta , Salim Agus , Bakshi Andrew , Holt Barbara J. , Mok Danny , Khor Chiea Chuen , Sly Peter D. , Holt Patrick G. , Holt Kathryn E. , Inouye Michael
Published: June 2019

Chronic immune-mediated diseases of adulthood often originate in early childhood. To investigate genetic associations between neonatal immunity and disease, we collected cord blood samples from a birth cohort and mapped expression quantitative trait loci (eQTLs) in resting monocytes and CD4+ T cells as well as in response to lipopolysaccharide (LPS) or phytohemagglutinin (PHA) stimulation, respectively. Cis-eQTLs were largely specific to cell type or stimulation, and response eQTLs were identified for 31% of genes with cis-eQTLs (eGenes) in monocytes and 52% of eGenes in CD4+ T cells. We identified trans-eQTLs and mapped cis regulatory factors which act as mediators of trans effects. There was extensive colocalisation of causal variants for cell type- and stimulation-specific neonatal cis-eQTLs and those of autoimmune and allergic diseases, in particular CTSH (Cathepsin H) which showed widespread colocalisation across diseases. Mendelian randomisation showed causal neonatal gene transcription effects on disease risk for BTN3A2, HLA-C and many other genes. Our study elucidates the genetics of gene expression in neonatal conditions and cell types as well as the aetiological origins of autoimmune and allergic diseases.
The effects of losing sex on the molecular evolution of plant defense
Authors: Carmona Diego , Hollister Jesse D. , Greiner Stephan , Wright Stephen I. , Ness Rob W. , Johnson Marc T.J.
Published: June 2019

It is hypothesized that the loss of sexual reproduction and reduced recombination rates decrease the ability for hosts to evolve in response to selection by parasites. Using transcriptomes from 32 species, we test whether repeated losses of sex in the plant genusOenotherahas resulted in changes to the evolution of defense genes against herbivores and pathogens. To achieve this, the function of 2,431Oenotheraorthologous genes was determined based on GO annotations fromArabidopsis thaliana. Phylogenetic Analysis by Maximum Likelihood (PAML) was then used to examine how the patterns of molecular evolution in 721 defense and 1,710 non-defense genes differ between sexual (16 spp.) and asexual (16 spp.) taxa. We test whether the relative rates of nonsynonymous to synonymous substitutions (ω = dN/dS) in proteins with defensive function were higher in lineages with sexual reproduction (ωsexual> ωa-sexual), and we asked if such patterns were exclusive for defense genes or not. We detected variability in the rate of amino acid replacements of proteins in >50% of genes and positive selection on 3% of the genes examined. Nevertheless, our results clearly show that on average, signatures of positive and purifying selection on defense and non-defense genes are similar and only a small number of specific genes related to plant immune function may be affected by a loss of sex.
Chemogenetic Control of Nanobodies
Authors: Farrants Helen , Tarnawski Miroslaw , Müller Thorsten G. , Otsuka Shotaro , Hiblot Julien , Koch Birgit , Kueblbeck Moritz , Kräusslich Hans-Georg , Ellenberg Jan , Johnsson Kai
Published: June 2019

We introduce an engineered nanobody whose affinity to green fluorescent protein (GFP) can be switched on and off with small molecules. By controlling the cellular localization of GFP fusion proteins, the engineered nanobody allows to study their role in basic biological processes, an approach that should be applicable to numerous previously described GFP fusions. We also outline how the binding affinities of other nanobodies can be controlled by small molecules.
The advantages of radial trajectories for vessel-selective dynamic angiography with arterial spin labeling
Authors: Berry Eleanor S. K. , Jezzard Peter , Okell Thomas W.
Published: June 2019

Object

To demonstrate the advantages of radial k-space trajectories over conventional Cartesian approaches for accelerating the acquisition of vessel-selective arterial spin labeling (ASL) dynamic angiograms, which are conventionally time-consuming to acquire.

Materials and Methods

Vessel-encoded pseudocontinuous ASL was combined with time-resolved balanced steady-state free precession (bSSFP) and spoiled gradient echo (SPGR) readouts to obtain dynamic vessel-selective angiograms arising from the four main brain-feeding arteries. Dynamic 2D protocols with acquisition times of one minute or less were achieved through radial undersampling or a Cartesian parallel imaging approach. For whole-brain dynamic 3D imaging, magnetic field inhomogeneity and the high acceleration factors required rule out the use of bSSFP and Cartesian trajectories, so the feasibility of acquiring 3D radial SPGR angiograms was tested.

Results

The improved SNR efficiency of bSSFP over SPGR was confirmed for 2D dynamic imaging. Radial trajectories had considerable advantages over a Cartesian approach, including a factor of two improvement in the measured SNR (p<0.00001, N=6), improved distal vessel delineation and the lack of a need for calibration data. The 3D radial approach produced good quality angiograms with negligible artifacts despite the high acceleration factor (R=13).

Conclusion

Radial trajectories outperform conventional Cartesian techniques for accelerated vessel-selective ASL dynamic angiography.
Early alterations in cortical and cerebellar regional brain growth in Down Syndrome: An in-vivo fetal and neonatal MRI assessment
Authors: Patkee Prachi A. , Baburamani Ana A. , Kyriakopoulou Vanessa , Davidson Alice , Avini Elhaam , Dimitrova Ralica , Allsop Joanna , Hughes Emer , Kangas Johanna , McAlonan Grainne , Rutherford Mary A.
Published: June 2019

Down Syndrome (DS) is the most frequent genetic cause of intellectual disability with a wide spectrum of neurodevelopmental outcomes. At present, the relationship between structural brain morphology and the spectrum of cognitive phenotypes in DS, is not well understood. This study aimed to quantify development of the fetal and neonatal brain in DS using dedicated, optimised and motion-corrected in-vivo magnetic resonance imaging (MRI). We detected deviations in development and altered regional brain growth in the fetus with DS from 21 weeks’ gestation, when compared to age-matched controls. Reduced cerebellar volume was apparent in the second trimester with significant alteration in cortical growth becoming evident during the third trimester. Developmental abnormalities in the cortex and cerebellum are likely substrates for later neurocognitive impairment, and ongoing studies will allow us to confirm the role of antenatal MRI as an early biomarker for subsequent cognitive ability in DS. In the era of rapidly developing technologies, it is hoped that the results of this study will assist counselling for prospective parents.
Behavioral training of marmosets and electrophysiological recording from the cerebellum
Authors: Sedaghat-Nejad Ehsan , Herzfeld David J. , Hage Paul , Karbasi Kaveh , Palin Tara , Wang Xiaoqin , Shadmehr Reza
Published: June 2019

The common marmoset (Callithrix Jacchus) is a promising new model for study of neurophysiological basis of behavior in primates. Like other primates, it relies on saccadic eye movements to monitor and explore its environment. Previous reports have demonstrated some success in training marmosets to produce goal-directed actions in the laboratory. However, the number of trials per session has been relatively small, thus limiting the utility of marmosets as a model for behavioral and neurophysiological studies. Here, we report the results of a series of new behavioral training and neurophysiological protocols aimed at increasing the number of trials per session while recording from the cerebellum. To improve the training efficacy, we designed a precisely calibrated food regulation regime that motivated the subjects to perform saccade tasks, resulting in about a thousand reward-driven trials on a daily basis. We then developed a multi-channel recording system that used imaging to target a desired region of the cerebellum, allowing for simultaneous isolation of multiple Purkinje cells in the vermis. In this report, we describe (1) the design and surgical implantation of a CT guided, subject specific head-post, (2) the design of a CT and MRI guided alignment tool for trajectory guidance of electrodes mounted on an absolute encoder microdrive, (3) development of a protocol for behavioral training of subjects, and (4) simultaneous recordings from pairs of Purkinje cells during a saccade task.

New and Noteworthy

Marmosets present the opportunity to investigate genetically based neurological disease in primates; in particular, diseases that affect social behaviors, vocal communication, and eye movements. All of these behaviors depend on the integrity of the cerebellum. Here, we present training methods that better motivate the subjects, allowing for improved performance, and also present electrophysiological techniques that precisely target the subject’s cerebellum, allowing for simultaneous isolation of multiple Purkinje cells.

In our parks, are there any trees more elegant and luxurious than the Purkinje cell from the cerebellum? Santiago Ramon y Cajal
Oropouche virus cases identified in Ecuador using an optimised rRT-PCR informed by metagenomic sequencing
Authors: Wise Emma L. , Márquez Sully , Mellors Jack , Paz Verónica , Atkinson Barry , Gutierrez Bernardo , Zapata Sonia , Coloma Josefina , Pybus Oliver G. , Jackson Simon K. , Trueba Gabriel , Fejer Gyorgy , Logue Christopher H. , Pullan Steven T.
Published: June 2019

Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published rRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an rRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68 - 99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens.
Recovery of glutamatergic and GABAergic protein expression in visual cortex after monocular deprivation
Authors: Balsor Justin L. , Jones David G. , Murphy Kathryn M.
Published: June 2019

A collection of glutamatergic and GABAergic proteins participate in regulating experience-dependent plasticity in the visual cortex (V1). Many studies have characterized changes to those proteins caused by monocular deprivation (MD) during the critical period (CP), but less is known about changes that occur when MD stops. We measured the effects of 3 types of visual experience after MD (n=24, 10 male and 14 female); reverse occlusion (RO), binocular deprivation (BD), or binocular vision, on the expression of synaptic proteins in V1 including glutamatergic and GABAergic receptor subunits. Synapsin expression was increased by RO but not affected by the other treatments. BD shifted the balance between glutamatergic and GABAergic receptor subunits to favor GABAAα1. In contrast, BV shifted expression to favor the glutamatergic mechanisms by increasing NMDAR and decreasing GABAAα1 subunits. None of the conditions returned normal expression levels to all of the proteins, but BV was the closest.
Variable Mutations at the p53-R273 Oncogenic Hotspot Position Leads to Altered Properties
Authors: Garg A , Hazra J P , Sannigrahi M K , Rakshit S , Sinha S
Published: June 2019

Mutations in p53 protein, especially in the DNA binding domain is one of the major hallmarks of cancer. The R273 position is a DNA contact position and has several oncogenic variants. Surprisingly, cancer patients carrying different mutant-variants of R273 in p53 have different survival rates indicating that the DNA contact inhibition may not be the sole reason for reduced survival with R273 variants. Here, we probed the structural properties of three major oncogenic variants of the R273: ([R273L], [R273H], and [R273C])p53. Using a series of biophysical, biochemical and theoretical simulation studies, we observe that these oncogenic variants of the p53 not only suffer a loss in DNA binding, but also show distinct structural stabilty, aggregation and toxicity profiles. [R273C]p53 shows maximum amyloidogenicity while [R273L]p53 shows maximum aggregation. Further probe in the aggregation mechanism show that [R273C]p53 aggregation is disulphide mediated whereas hydrophobic interactions dominate self-assembly in [R273L]p53. MD simulation studies clearly show that α-helical intermediates are observed in [R273C]p53 whereas β-sheets are observed for [R273L]p53. Our study indicates that each of the R273 variant has its own distinct property of stability and self-assembly, the molecular basis of which, may lead to different types of cancer pathogenesis in vivo. These studies will aid the design of therapeutic strategies for cancer using residue specific or process specific protein aggregation as target.

Statement of significance

The present work stems from an interesting observation that genetic mutations that results in switching of one amino acid to different variants at the same codon show different cancer cell progression. We are trying to understand the molecular reason behind the different gain-of-function opted by these variants. With the help of biophysical and biochemical experiments, and computational studies we have observed that the different thermal stability, unique mechanism of unfolding and self-assembly might be one of the crucial parameters for their different oncogenic effect. These studies thus call for the need of developing therapeutic strategies that consider the resultant mutant-variant as a target rather than mutation position. This is an important lead towards the understanding of cancer.
Label-free, real-time on-chip sensing of living cancer cell via grating-coupled surface plasmon resonance
Authors: Borile Giulia , Rossi Stefano , Filippi Andrea , Gazzola Enrico , Capaldo Pietro , Tregnago Claudia , Pigazzi Martina , Romanato Filippo
Published: June 2019

The application of nanotechnologies to address biomedical questions is a key strategy for innovation in biomedical research. Among others, a key point consists in the availability of nanotechnologies for monitoring cellular processes in a real-time and label-free approach. Here, we focused on a grating-coupled Surface Plasmon Resonance (GC-SPR) sensor exploiting phase interrogation. This sensor can be integrated in a microfluidic chamber that ensures cell viability and avoids cell stress. We report the calibration of the sensor response as a function of cell number and its application to monitor cell adhesion kinetics as well as cell response to an external stimulus. Our results show that GC-SPR sensors can offer a valuable alternative to prism-coupled or imaging SPR devices, amenable for microfluidic implementation.
Microenvironment-contextual cell signaling is attenuated with age
Authors: Ertsås Henriette C. , LaBarge Mark A. , Lorens James B
Published: June 2019

Post-menopausal women are more prone to breast cancer than younger women. The increased frequency of age-related breast cancers is likely due to interactions between acquired mutations and age-dependent epigenetic changes that affect mammary epithelial lineage fidelity. We hypothesized that the aging process fundamentally affects how human mammary epithelial cells (HMEC) respond to microenvironmental signals, resulting in increased susceptibility to oncogenic transformation. In order to measure microenvironmental cell signaling in normal finite lifespan HMEC, we applied a novel microsphere-based flow cytometry technology. The microsphere cytometry allows multiparametric single cell quantification of signaling pathway activity and lineage-specific marker expression in cells adhered to surface-functionalized microspheres that mimic specific microenvironments. Using this approach, we analyzed age-dependent changes in human mammary myoepithelial and luminal epithelial cells exposed to different ECM and growth factors. We found that ECM–mediated MAP kinase and PI3 kinase activation levels in HMEC were attenuated with age. Older luminal cells displayed higher surface integrin levels consistent with acquired basal identity, albeit with decreased integrin activation and increased Src-signaling relative to myoepithelial cells. We show that the diminished signaling magnitude in HMEC from older women correlated with reduced probability of activating oncogene-induced senescence. We propose that age-related changes in ECM-mediated epithelial cell regulation may impair protective tumor suppression mechanisms and increase breast cancer susceptibility.