bluuebunny/crossref_metadata_2025 huggingface dataset:
Once bitten, twice shy
Authors: Taylor Stuart
Published: March 2020

A 48yr old man presented with a 1-2 week history of diarrhoea and fever. He took occasional ibuprofen for migraines but took no regular medications and was fit and active. On presentation to A+E blood tests revealed severe AKI with hyperkalaemia, low platelets and anaemia with raised inflammatory markers. He complained of shortness of breath with a CXR consistent with ARDS. He was commenced on IV antibiotics and was transferred to ITU for further management. While on ITU his blood film revealed evidence of haemolysis, in addition to an LDH of >2600. He had persistenly low platelets (14 at its nadir), requiring platelet transfusion. His renal failure was managed with haemofiltration and he was transfused to maintain his Hb above 80. The diagnosis was of haemolytic uraemic syndrome due to a presumed infectious origin. Blood cultures came back positive for a fastidious, slow-growing Gram-negative rod, identified as Capnocytophaga canimorsus. Further questioning revealed the presence of a dog bite to his R. index finger two months previously. The patient's antibiotic regimen was changed to Ceftriaxone 2g IV OD and metronidazole 500mg IV TDS and he was transferred to the Royal Free Hospital to commence haemodilaysis and for specialist renal management.

Capnocytophaga canimorsus is an encapsulated organism known for its potential to cause disseminated and fatal infection in asplenic or immunocompromised patients, which were risk factors not present in our case. It is a rare cause of HUS and highlights the need for thorough history if an infective agent is presumed.
Carbapenem stewardship in a large teaching English hospital - are we improving?
Authors: Olusoga Abimbola , Howard Philip , Walker Caroline , Atack Kelly , Waterhouse Annabelle
Published: March 2020

Background:Overuse of antibiotics has been linked to the global growth of antimicrobial resistance (AMR). In 2018, increase in meropenem usage in our hospital revealed that we achieved the “Start Smart” but not “Then Focus” element. Following revised carbapenem stewardship, we aimed to evaluate the adherence to guidelines, by monitoring patients initiated on meropenem.

Methods:As part of the antimicrobial stewardship (AMS) at our 1800-bed teaching hospital, carbanepem stewardship was revised in September 2018 and required consultant approval for all carbapenem initiation or continuation following specialist advice. Meropenem prescriptions in adult and paediatric patients were generated from the electronic prescription system and reviewed daily for one week in August 2019 to ascertain if prescribed in line with guideline recommendations or on the advice of microbiology or infectious diseases.

Results:Sixty patients were reviewed. Microbiology or Infectious Diseases recommendation was obtained in 37% of patients. 95% had samples taken where blood cultures accounted for 85% but over a third of these had no growth reported. Meropenem was initiated empirically in 50% of patients mainly for neutropenic sepsis while 28% were culture directed. 35% of patients were escalated from piperacillin-tazobactam of which 57% had neutropenia while de-escalation occurred in 10%.

Conclusion:AMR is related directly to antibiotic use at a patient level. Our revised strategy resulted in a reduction of total carbapenem DDD/1000 Admission from 128 (June 2018) to 87 (June 2019) through improved adherence to guideline and infection specialists recommendations however more work is required to promote switch to narrower-spectrum choice.
Antibiotics & adjuvant corticosteroids in management of pneumococcal meningitis: a retrospective case-notes audit
Authors: Barr Andrew , Schwab Uli
Published: March 2020

Background

Pneumococcus remains the most common cause of bacterial meningitis with high morbidity and mortality. Adjuvant corticosteroids with early antibiotics have been shown to reduce the neurological morbidity and mortality respectively and this is reflected in British Infection Society (BIS) guidance.

Aim

To assess how closely BIS guidelines were followed regarding antibiotic and adjuvant corticosteroid administration in management of pneumococcal meningitis.

Methods

Newcastle Upon Tyne Hospital case-notes of pneumococcal meningitis from a 7-year-period(2012-2019) were audited. Patients were identified using microbiological records and case-notes. Data was collected on intervals from initial-assessment to commencing antibiotics and corticosteroids.

Results

Eighteen cases were identified of whom three(17%) presented with the classic triad (fever, meningism, reduced GCS). All patients received appropriate antibiotics: 3/18(17%) within first hour of assessment. The median time to antibiotics was 5h 8mins (range:21-7129min). Eight patients(44%) received antibiotics >6h after assessment. Twelve patients(67%) received corticosteroids; only six(33%) at the recommended dose and duration. Mean time from antibiotics to corticosteroids was 6h1min. Five deaths occurred in the cohort with three attributable to pneumococcal sepsis (all had late presentations). 6/18 had significant neurological sequelae, irrespective of whether they received corticosteroids.

Discussion

The significant morbidity and mortality of pneumococcal meningitis demands a high index of suspicion. BIS guideline targets are repeatedly not met; long delays exist between assessment and antibiotic and corticosteroid administration. Integrated electronic prescribing and clinical Early Warning Systems have potential to ameliorate this with meningitis-tailored order sets to prompt consideration of meningitis and guide correct prescribing.
Managing seasonal influenza in hospitalized patients - without an influenza point-of-care test
Authors: Hills George , Kennedy Matthew , Ahmed Osama , Tang Julian
Published: March 2020

Background: National guidelines recommend isolation and commencing empirical antiviral therapy for suspected influenza in the inpatient setting, however this is not always done in practice. There are many reasons why influenza may be diagnosed late, and in order to minimise potential harm, rapid results are therefore required.

Methods: During the 2018-19 influenza season, we instigated a policy of calling out all new influenza positives during normal working hours. As well as informing clinical teams of results, we also recorded clinical information, including whether the patient was:

* isolated,

* already on antivirals,

* discharged (and if so on what therapy)

Results: In the peak season (January 1st - March 31st 2019), 179 calls to clinical teams were made. The median time from sample collection to reporting was 28 hours and 33 minutes. 44% of patients were not on antivirals at the time of the result, and 28% were not isolated. Based on these numbers, we estimated that 141-235 inpatients may have been exposed to influenza on our wards. 25% of a total of 309 positive influenza samples were from patients who were discharged at the time of the result. 65% of these patients were discharged with antibiotics, 54% with antivirals, and 37% with both antivirals and antibiotics.

Conclusion: Based on our data, and that of other studies, we hypothesise that rapid influenza results would lead to better infection control practices, reduced spread of infection, and improved antimicrobial stewardship. Molecular point-of-care tests have the potential to resolve some of the issues with late influenza diagnosis.
Real-time Monitoring of Aerosols Generated from Toilet Flushing
Authors: Fennelly Mehael , Hellebust Stig , Sodeau John , Prentice Michael
Published: March 2020

Flushing toilets generate visible droplets from turbulent flow, but also produce numerous smaller airborne droplets (∼micrometres in size) through atomisation. Flushing may aerosolise pathogens from stool or urine, spreading disease. This study continuously monitored aerosols in a shared office lavatory over a week using a biological particle detector, the Wideband Integrated Bioaerosol Sensor (WIBS). This instrument monitors individual particle sizes and numbers and identifies fluorescent particles likely to be droplets containing bacteria.

The toilet was a standard wash-down design, (Armitage Shanks), with a lid. No statistically significant variation between fluorescent particle counts was found between periods prior to flushing. Fluorescent particle numbers and intensity increased with toilet flushing, remaining above background for 5 minutes post-flushing on average. Placing the toilet lid down significantly (P<0.001) reduced total and fluorescent particle counts during and after flushing by 30-50%. Lid usage significantly increased (P<0.001) particle diameter from 1.5 μm to 2.1 μm and increased particle fluorescence intensity (P<0.001) during flushing and after flushing, intensity remaining above background for 16 minutes.

This suggests standard lid usage reduces but does not eliminate flush-related bioaerosols. Lid-use changes their characteristics and apparently prolongs their residence time in room air. The aerosol change could represent particle agglomeration by a pressure-related Kelvin effect or particle re-aerosolisation from different surfaces in the toilet rather than exclusively originating from droplet generation. Previous studies reporting the effect of toilet lids have found that they prevent the spread of visible droplets on flushing, however the effect on smaller particles is less clear cut.
Pneumococcal 13-valent polysaccharide vaccination (PCV13) response in patients with pulmonary aspergillosis
Authors: Aggarwal Sunil , Kosmidis Chris , Denning David
Published: March 2020

Background

Response to pneumococcal 23-valent polysaccharide vaccine (PPV23) is poor in patients with pulmonary aspergillosis, pneumococcal 13-valent polysaccharide vaccine (PCV13) is believed to be more antigenic. Thus practice at the national aspergillosis centre (NAC), Manchester University NHS foundation trust (MFT) is to give PCV13. However, response to PCV13 has not been studied.

Methods

We conducted a retrospective, observational study of patients with pulmonary aspergillosis at the NAC, MFT. Patients who had non-protective pre-vaccine levels, and received PCV13 between January-2015 and July-2019 with serology available within 3 months after vaccination were included.

Serotype-specific pneumococcal IgG antibodies were quantified for 12 pneumococcal serotypes. Non-protective immunity was defined as pre-vaccine level <0.35μg/mL to >
6 out of 12 serotypes. Protective response was defined as level >1.3μg/mL, or an increase in concentration ≥4-fold for at least 9 of 12 serotypes within 3 months.

Results

47 of 144 patients receiving PCV13 had non-protective pre-vaccination levels and repeat serology within 3 months post-vaccination. 52% and 20%, of patients who received 2 and 1 doses (respectively) developed protective immunity; χ2(1)=2.987,p= 0.084. 42.86%, 69.23%, 42.86%, 50%, and 0% of patients with chronic pulmonary aspergillosis (CPA), allergic bronchopulmonary aspergillosis (ABPA), severe asthma with fungal sensitisation, aspergillus bronchitis, and mixed ABPA and CPA developed protective immunity; χ2(4)=6.329,p=0.176.

Conclusion

Patients with CPA respond poorly to PCV13 compared to ABPA. Response to two doses of PCV13 is comparable to one dose of PPV-231. Patients with pulmonary aspergillosis should receive two doses of PCV13 rather than one dose.
Unaccountable use of systemic antifungal treatment leads to change in guidelines and stewardship in a district general hospital
Authors: David Kate , Patel Trupti , Lim Ai-nee , Kelsey Michael
Published: March 2020

Background

Antifungal resistance is a global emergency of increasing prevalence, yet only 11% of NHS Trusts have an antifungal stewardship programme. Given the high mortality and cost associated with invasive fungal infections, it is paramount to optimise investigations and judicious use of systemic antifungals. Hospital guidelines often focus on empirical treatment, omitting diagnostics.

Methods

Patients prescribed systemic antifungals were identified using pharmacy records over a 1 year period in a district general hospital in London. Electronic patient records were interrogated for microbiological, serological, histopathological and radiological investigations based on national recommendations. Audit standards were designed to meet the NHS England Medicines Optimisation and Stewardship CQUIN.

Results

31 adult patients were identified. Microbiological evidence of fungal infection was demonstrated in 15/31 patients (48%). 60% were speciated and 47% underwent susceptibility testing. Three patients had beta-D-glucan tests; two patients had histopathological testing; 19 patients underwent imaging, of which 42% were reported as consistent with possible fungal infection.

Conclusion

9 (29%) patients had no obvious indication for antifungal treatment. Systemic antifungal treatment is not without toxicity and cost and contributes to resistance. In view of this, we updated the hospital guideline to include a guide to diagnostics, incorporated antifungals into our antimicrobial stewardship ward round and submitted this audit to NHS England CQUIN. Further work will evaluate whether these changes impact upon current practice.

References

Micallef C et al.
Med. Microbiol. 2017;66(11):1581-1589

Fisher MC et al. Science 2018;360(6390):739-742

Schelenz S et al. Lancet Infect Dis 2015;15(4):461–74
Theoretical approaches in the development and evaluation of behaviour change interventions that improve clinicians’ antimicrobial prescribing: a systematic review
Authors: Talkhan Hend , Stewart Derek , McIntosh Trudi , Rouf Palli Valappila Abdul , Al-Hail Moza , Cunningham Scott , Ziglam Hisham
Published: March 2020

Many countries have developed antimicrobial stewardship programmes with strategies to optimise antimicrobial prescribing. There remains a need for behaviour change interventions at clinician level to promote appropriate prescribing. Theories should be used for developing and evaluating interventions to change human behaviour.

Aim / Objectives:The aim of this review was to critically appraise, synthesise and present the available evidence for theoretical approaches in the development and evaluation of behaviour change interventions designed to improve clinicians' antimicrobial prescribing.

Design & Methodology:

The systematic review protocol was developed and registered with the International Prospective Register of Systematic Reviews (CRD42018098586).

Two review authors independently extracted data and assessed study quality. Clinical and methodological heterogeneity limited data synthesis.

Results

The searches resulted in 4227 relevant articles after duplicates removal. Screening of titles/abstracts led to retrieval and dual assessment of 38 full-text articles. Of those, a total of 10 studies met the inclusion criteria.

The majority of studies were carried out in primary care settings (n = 9) targeting upper respiratory tract infections (n = 8). Use of theory varied considerably across studies included. Theory of Planned Behaviour, Social Cognitive Theory and Operant Learning Theory were the most common theories used to inform the design and choice of interventions.

Conclusion / Discussion

It is feasible to develop and evaluate theoretically based interventions to improve professional practice. The findings of this systematic review will inform understanding of the theoretical basis of behaviour change interventions which contribute to contain AMR rates and prevent the world entering a “post-antibiotic era”.
Characteristics of patients admitted to Intensive care units with severe Influenza and management outcome at a large district general hospital in East of England, UK
Authors: Patel Jignna , Vaghela Tejal , Kandil Hala
Published: March 2020

Background:

Influenza pneumonia can be challenging to treat particularly in critically ill patients. The aim of this study is to review the risk factors for severe influenza infection, the course of the disease, the choice of antivirals and the management outcome in patients admitted with complicated influenza illness to ICU

Method

Sixteen patients who were admitted to ICU at West Hertfordshire hospitals NHS Trust with severe influenza illness were reviewed between 20th December 2018 and 14th February 2019. Data on Demographics, vaccination status, viral strain and clinical outcome were collected and analysed.

Results

High proportion of patients were below the age of 65 (n=9).The predominant strain was A(H1N1) pdm09 (n=10), followed by A(H3N2) (n=5) and 1 patient had no strain reported. All patients were initiated on Oseltamivir. Six patients developed multi-organ failure and were switched to IV Zanamivir. None of the latter were severely immunosuppressed. 56.25% (n=9) were not vaccinated and third with unknown status (n=5). 66% of the patients below the age of 65 were not vaccinated and had to switch to Zanamavir. Fourteen patients made good recovery and 2 died while on Zanamavir

Conclusion:

Our result suggest that the majority of patients admitted to ICU did not carry risk factor for complications and were below the age of 65, but were unvaccinated and infected with A(H1N1)pdm09 strain. Larger study is required to fully understand the risk factors for ICU admission including vaccination status in this group of patients and the optimum antiviral choice.
Microbulbifer harenosus sp. nov., an alginate-degrading bacterium isolated from coastal sand
Authors: Huang Huiqin , Mo Kunlian , Hu Yonghua , Liu Min , Zhu Jun , Zou Xiaoxiao , Bao Shixiang
Published: March 2020

A Gram-stain-negative, aerobic, rod-shaped bacterium with peritrichous flagella, designated strain HB161719T, was isolated from coastal sand collected from Tanmen Port in Hainan, PR China. The isolate was found to grow with 2–11 % (w/v) NaCl, at 15–45 °C and pH 6.0–10.0, with an optima of 2–3 % NaCl, 37 °C and pH 7.0, respectively. Chemotaxonomic analysis showed that Q-8 was detected as the sole respiratory quinone and that iso-C15 : 0 and summed features 3, 8 and 9 were the major cellular fatty acids. The G+C content of the genomic DNA was 58.2 mol%. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus

Microbulbifer

, sharing 98.7, 98.4, 97.8 and 97.8 % sequence similarities to the closest relatives of

Microbulbifer okinawensis

ABABA23T,

Microbulbifer pacificus

SPO729T,

Microbulbifer taiwanensis

CC-LN1-12T and

Microbulbifer gwangyangensis

GY2T, respectively. Low DNA–DNA hybridization values showed that it formed a distinct genomic species. The combined phenotypic and molecular features supported that strain HB161719T represents a novel species of the genus

Microbulbifer

, for which the name Microbulbifer harenosus sp. nov. is proposed. The type strain is HB161719T (=CGMCC 1.13584T=JCM 32688T).
An assessment of genome annotation coverage across the bacterial tree of life
Authors: Lobb Briallen , Tremblay Benjamin Jean-Marie , Moreno-Hagelsieb Gabriel , Doxey Andrew C.
Published: March 2020

Although gene-finding in bacterial genomes is relatively straightforward, the automated assignment of gene function is still challenging, resulting in a vast quantity of hypothetical sequences of unknown function. But how prevalent are hypothetical sequences across bacteria, what proportion of genes in different bacterial genomes remain unannotated, and what factors affect annotation completeness? To address these questions, we surveyed over 27 000 bacterial genomes from the Genome Taxonomy Database, and measured genome annotation completeness as a function of annotation method, taxonomy, genome size, 'research bias' and publication date. Our analysis revealed that 52 and 79 % of the average bacterial proteome could be functionally annotated based on protein and domain-based homology searches, respectively. Annotation coverage using protein homology search varied significantly from as low as 14 % in some species to as high as 98 % in others. We found that taxonomy is a major factor influencing annotation completeness, with distinct trends observed across the microbial tree (e.g. the lowest level of completeness was found in the Patescibacteria lineage). Most lineages showed a significant association between genome size and annotation incompleteness, likely reflecting a greater degree of uncharacterized sequences in 'accessory' proteomes than in 'core' proteomes. Finally, research bias, as measured by publication volume, was also an important factor influencing genome annotation completeness, with early model organisms showing high completeness levels relative to other genomes in their own taxonomic lineages. Our work highlights the disparity in annotation coverage across the bacterial tree of life and emphasizes a need for more experimental characterization of accessory proteomes as well as understudied lineages.
The need to unravel the twisted nature of the Borrelia burgdorferi sensu lato complex across Europe
Authors: Strnad Martin , Rego Ryan O.M.
Published: March 2020

Lyme borreliosis is a vector-borne infection caused by bacteria under theBorrelia burgdorferisensu lato complex, both in Europe and North America. Differential gene expression at different times throughout its infectious cycle allows the spirochete to survive very diverse environments within different mammalian hosts as well as the tick vector. To date, the vast majority of data about spirochetal proteins and their functions are from genetic studies carried out on North American strains of a single species, i.e.B. burgdorferi sensu stricto. The whole-genome sequences recently obtained for several European species/strains make it feasible to adapt and use genetic techniques to study inherent differences between them. This review highlights the crucial need to undertake independent studies of genospecies within Europe, given their varying genetic content and pathogenic potential, and differences in clinical manifestation.
Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemia
Authors: Yang Hongbo , Zhang Hui , Luan Yu , Liu Tingting , Roberts Kathryn G , Qian Mao-xiang , Zhang Bo , Yang Wenjian , Perez-Andreu Virginia , Xu Jie , Iyyanki Sriranga , Kuang Da , Reshmi Shalini C. , Gastier-Foster Julie , Smith Colton , Pui Ching-Hon , Evans William E , Hunger Stephen P , Platanias Leonidas C. , Relling Mary V , Mullighan Charles G , Loh Mignon L , Yue Feng , Yang Jun J
Published: March 2020

Inherited non-coding genetic variants confer significant disease susceptibility in many cancers. However, the molecular processes of by which germline variants contribute to somatic lesions are poorly understood. We performed targeted sequencing in 5,008 patients and identified a key regulatory germline variant in GATA3 strongly associated with Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL). By creating an isogenic cellular model with CRISPR-Cas9 system, we showed that this variant activated a strong enhancer that significantly upregulated GATA3 transcription, which in turn reshaped the global chromatin accessibility and 3D genome organization. Remarkably, this genotype switch induced a chromatin loop between the CRLF2 oncogene and a distal enhancer, similar to the somatically acquired super-enhancer hijacking event in patients. GATA3 genotype-related alterations in transcriptional control and 3D chromatin organization were further validated in Ph-like ALL patients. Finally, we showed that GATA3 directly regulates CRLF2 and potentiates the oncogenic effects of JAK-STAT signaling in leukemogenesis. Altogether, our results provide evidence for a novel mechanism by which a germline non-coding variant contributes to oncogene activation epigenetic regulation and 3D genome reprogramming.
Strategies for vaccine design for corona virus using Immunoinformatics techniques
Authors: Basu Anamika , Sarkar Anasua , Maulik Ujjwal
Published: March 2020

The cutting-edge technology vaccinomics is the combination of two topics immunogenetics and immunogenomics with the knowledge of systems biology and immune profiling for designing vaccine against infectious disease. In our present study, an epitope-based peptide vaccine against nonstructural protein 4 of beta coronavirus, using a combination of B cell and T cell epitope predictions, followed by molecular docking methods are performed. Here, protein sequences of homologous nonstructural protein 4 of beta coronavirus are collected and conserved regions present in them are investigated via phylogenetic study to determine the most immunogenic part of protein. From the identified region of the target protein, the peptide sequence IRNTTNPSAR from the region ranging from 38-47 and the sequence PTDTYTSVYLGKFRG from the positions of 76-90 are considered as the most potential B cell and T cell epitopes respectively. Furthermore, this predicted T cell epitopes PTDTYTSVY and PTDTYTSVYLGKFRG interacted with MHC allelic proteins HLA-A*01:01 and HLA-DRB5*01:01 respectively with the low IC50values. These epitopes are perfectly fitted into the epitope binding grooves of alpha helix of MHC I molecule and MHC II molecule with binding energy scores −725.0 Kcal/mole and −786.0 Kcal/mole respectively, showing stability in MHC molecules binding. This MHC restricted epitope PTDTYTSVY also showed a good conservancy of 50.16% in world population coverage. This MHC I HLA-A*01:01 allele is present among 58.87% of Chinese population also. Therefore, the epitopes IRNTTNPSAR and PTDTYTSVYLGKFRG may be considered as potential peptides for peptide-based vaccine for coronavirus after further experimental study.
Highly ACE2 Expression in Pancreas May Cause Pancreas Damage After SARS-CoV-2 Infection
Authors: Liu Furong , Long Xin , Zou Wenbin , Fang Minghao , Wu Wenjuan , Li Wei , Zhang Bixiang , Zhang Wanguang , Chen Xiaoping , Zhang Zhanguo
Published: March 2020

The ongoing outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) started in the end of 2019 in China has triggered a global public health crisis. Previous studies have shown that SARS-CoV-2 infects cells by binding angiotensin-converting enzyme 2 (ACE2), which is the same as SARS-CoV. The expression and distribution of ACE2 in the pancreas are unknown. At the same time, the injury of pancreas after SARS-CoV-2 infection has not been concerned. Here, we collected public datasets (bulk RNA-seq and single-cell RNA-seq) to indicate the expression and the distribution of ACE2 in pancreas (in both exocrine glands and islets). And further, clinical data including mild and severe patients with COVID-19 demonstrated there existed mild pancreatitis. In the 67 severe cases, 11 patients (16.41%) showed elevated levels of both amylase and lipase, and 5 patients (7.46%) showed imaging alterations. Only one patient (1.85%) showed elevated levels of both amylase and lipase in 54 mild cases, without imaging changes. Our study revealed the phenomenon and possible cause of mild pancreatic injury in patients with COVID-19. This suggests that pancreatitis after SARS-CoV-2 infection should also be paid attention in clinical work.
In Arabidopsis, low blue light enhances phototropism by releasing cryptochrome 1-mediated inhibition ofPIF4expression
Authors: Boccaccini Alessandra , Legris Martina , Krahmer Johanna , Allenbach-Petrolati Laure , Goyal Anupama , Galvan-Ampudia Carlos , Vernoux Teva , Karayekov Elisabeth , Casal Jorge , Fankhauser Christian
Published: March 2020

Shade-avoiding plants includingArabidopsis thalianadisplay a number of growth responses elicited by shade cues including elongation of stem-like structures and repositioning of leaves. Shade also promotes phototropism of de-etiolated seedlings through repression of phytochrome B (phyB) presumably to enhance capture of unfiltered sunlight. Light cues indicative of shade include a reduction in the blue and red portions of the solar spectrum and a low red to far-red ratio. Here we show that in Arabidopsis seedlings both low blue and a low red to far-red ratio are required to rapidly enhance phototropism. However, prolonged low blue treatments through reduced cryptochrome 1 (cry1) activation are sufficient to promote phototropism. The enhanced phototropic response ofcry1mutants in the lab and in response to natural canopies depends onPHYTOCHROME INTERACTING FACTORs(PIFs). In favorable light conditions, cry1 limits the expression ofPIF4while in low blue light PIF4 expression increases, which contributes to phototropic enhancement. The analysis of a quantitative DII auxin reporter indicates that low blue light leads to enhanced auxin levels in the hypocotyl and, upon phototropic stimulation, a steeper auxin gradient across the hypocotyl. We conclude that phototropic enhancement by canopy shade results from the combined activities of phytochrome B and cry1 that converge on PIF regulation.

ONE SENTENCE SUMMARY

The persistent depletion of blue light in natural canopy shade relieves the inhibitory effect of cryptochrome 1 on PIF4, enhancing phototropism in de-etiolated Arabidopsis seedlings.

Financial support

This work was supported by the University of Lausanne and a grant from the Swiss National Science foundation (n° 310030B_179558 to C.F.); Human Frontier Science Program organization (HFSP) Grant RPG0054-2013, ANR-12-BSV6-0005 grant (AuxiFlo) to T.V.; The University of Buenos Aires (Grant 20020100100437 to J. J. C.), andAgencia Nacional de Promoción Científica y Tecnológica of Argentina(Grant PICT-2018-01695 to J. J. C.). Alessandra Boccaccini and Martina Legris are funded by Marie Curie fellowships H2020-MSCA-IF-2017 grants CRoSh 796283 and Flat-Leaf 796443 respectively.
SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements
Authors: Barbera Pierre , Czech Lucas , Lutterop Sarah , Stamatakis Alexandros
Published: March 2020

Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogenetic identity of the anonymous environmental sequences in a sample by means of a given phylogenetic reference tree. However, assessing the diversity of a sample remains challenging, as traditional methods do not scale well with the increasing data volumes and/or do not leverage the phylogenetic placement information.

Here, we presentSCRAPP, a highly parallel and scalable tool that uses a molecular species delimitation algorithm to quantify the diversity distribution over the reference phylogeny for a given phylogenetic placement of the sample.SCRAPPemploys a novel approach to cluster phylogenetic placements, called placement space clustering, to efficiently perform dimensionality reduction, so as to scale on large data volumes. Furthermore, it utilizes the phylogeny-aware molecular species delimitation methodmPTPto quantify diversity.

We evaluatedSCRAPPusing both, simulated and empirical datasets. We use simulated data to verify our approach. Tests on an empirical dataset show that SCRAPP-derived metrics can classify samples by their diversity-correlated features equally well or better than existing, commonly used approaches.

SCRAPPis available athttps://github.com/pbdas/scrapp
Persistence and stability of interacting species in response to climate warming: The role of trophic structure
Authors: Kaur Taranjot , Dutta Partha Sharathi
Published: March 2020

Over the past century, the Earth has experienced roughly 0.4–0.8°C rise in the average temperature and which is projected to increase between 1.4–5.8°C by the year 2100. The increase in the Earth’s temperature directly influences physiological traits of individual species in ecosystems. However, the effect of these changes in community dynamics, so far, remains relatively unknown. Here we show that the consequences of warming (i.e., increase in the global mean temperature) on the interacting species persistence or extinction are correlated with their trophic complexity and community structure. In particular, we investigate different nonlinear bioenergetic tri-trophic food web modules, commonly observed in nature, in the order of increasing trophic complexity; a food chain, a diamond food web and an omnivorous interaction. We find that at low temperatures, warming can destabilize the species dynamics in the food chain as well as the diamond food web, but it has no such effect on the trophic structure that involves omnivory. In the diamond food web, our results indicate that warming does not support top-down control induced co-existence of intermediate species. However, in all the trophic structures warming can destabilize species up to a threshold temperature. Beyond the threshold temperature, warming stabilizes species dynamics at the cost of the extinction of higher trophic species. We demonstrate the robustness of our results when a few system parameters are varied together with the temperature. Overall, our study suggests that variations in the trophic complexity of simple food web modules can influence the effects of climate warming on species dynamics.
Charge-Altering Releasable Transporters Enable Specific Phenotypic Manipulation of Resting Primary Natural Killer Cells
Authors: Wilk Aaron J. , Benner Nancy L. , Vergara Rosemary , Haabeth Ole A.W. , Levy Ronald , Waymouth Robert M. , Wender Paul A. , Blish Catherine A.
Published: March 2020

Natural killer (NK) cells are capable of rapid and robust cytotoxicity, making them excellent tools for immunotherapy. However, their recalcitrance to standard transfection techniques has limited both mechanistic studies and clinical applications. Current approaches for NK cell manipulation rely on viral transduction or methods requiring NK cell activation, which can alter NK cell function. Here, we report that non-viral Charge-Altering Releasable Transporters (CARTs) efficiently transfect primary human NK cells with mRNA without relying on NK cell activation. Compared to electroporation, CARTs transfect NK cells two orders of magnitude more efficiently, better preserve cell viability, and cause minimal reconfiguration of NK cell phenotype and function. Finally, we use CARTs to generate highly cytotoxic primary human chimeric antigen receptor NK cells, indicating potential therapeutic utility of this technique. To our knowledge, CARTs represent the first efficacious transfection technique for resting primary NK cells that preserves NK cell phenotype, and can drive new biological discoveries and clinical applications of this understudied lymphocyte subset.
Drivers of large-scale spatial demographic variation in a perennial plant
Authors: Römer Gesa , Christiansen Ditte M. , de Buhr Hendrik , Hylander Kristoffer , Jones Owen R. , Merinero Sonia , Reitzel Kasper , Ehrlén Johan , Dahlgren Johan P.
Published: March 2020

To understand how the environment drives spatial variation in population dynamics, we need to assess the effects of a large number of potential drivers on the vital rates (survival, growth and reproduction), and explore these relationships over large geographical areas and long environmental gradients. In this study, we examined the effects of a broad variety of abiotic and biotic environmental factors, including intraspecific density, on the demography of the forest understory herbActaea spicatabetween 2017 and 2019 at 40 sites across Sweden, including the northern range margin of its distribution. We assessed the effect of potential environmental drivers on vital rates using generalized linear mixed models (GLMMs), and then quantified the impact of each important driver on population growth rate (λ) using integral projection models (IPMs). Population dynamics ofA. spicatawere mostly driven by environmental factors affecting survival and growth, such as air humidity, soil depth and forest tree species composition, and thus those drivers jointly determined the realized niche of the species. Soil pH had a strong effect on the flowering probability, while the effect on population growth rate was relatively small. In addition to identifying specific drivers forA. spicata’spopulation dynamics, our study illustrates the impact that spatial variation in environmental conditions can have on λ. Assessing the effects of a broad range of potential drivers, as done in this study, is important not only to quantify the relative importance of different drivers for population dynamics but also to understand species distributions and abundance patterns.
The immune system fails to mount a protective response to Gram-positive or Gram-negative bacterial prostatitis
Authors: Lupo Federico , Rousseau Matthieu , Canton Tracy , Ingersoll Molly A.
Published: March 2020

Bacterial prostatitis affects 1% of men, with increased incidence in the elderly. It is defined by the frequency and urgency to urinate, localized pain, and positive bacterial cultures in expressed seminal fluids. Acute bacterial prostatitis frequently progresses to chronicity, which is marked by recurrent acute episodes interspersed with asymptomatic periods of variable duration. Up to 80% of bacterial prostatitis cases are caused by Gram-negative uropathogenicE. coli(UPEC) or Gram-positiveE. faecalis. Antibiotic treatment is standard of care, however, global dissemination of antimicrobial resistant uropathogens threatens efficacy of therapy. Thus, development of non-antibiotic-based approaches to treat bacterial prostatitis is a priority. One challenge is that the immune response to infection in the prostate is incompletely understood. We used a mouse model of transurethral bacterial instillation to study the immune response to UPEC orE. faecalisprostate infection. Both uropathogens exhibited tropism for the prostate over the bladder early post-infection. UPEC infection induced greater proinflammatory cytokine expression and neutrophil and monocyte infiltration compared toE. faecalisinfection. Following challenge infection, cytokine responses and myeloid cell infiltration were largely comparable to primary infection. Characteristic of memory responses, more lymphoid cells infiltrating the prostate in the second infection compared to the primary infection. Unexpectedly, however, bacterial burden in prostates challenged with either UPEC orE. faecaliswas equal or greater than in primary infection, despite that an adaptive response to UPEC infection was evident in the bladder of the same animals. Thus, an immune response to primary infection is initiated, however it does not protect against reinfection. Our findings support the idea that chronic or recurrent prostatitis develops in the absence of efficacious immunity to infection. A greater understanding of the mechanisms underlying this observation may point to actionable targets for immunotherapy.
Morphological pseudotime ordering and fate mapping reveals diversification of cerebellar inhibitory interneurons
Authors: Wang Wendy Xueyi , Lefebvre Julie L.
Published: March 2020

Understanding how diverse neurons are assembled into circuits requires a framework for describing cell types and their developmental trajectories. Here, we combined genetic fate mapping and pseudo-temporal profiling to resolve the diversification of cerebellar inhibitory interneurons based on morphology. The molecular layer interneurons (MLIs) derive from a common progenitor but comprise a diverse population of dendritic-, somatic-, and axon initial segment-targeting interneurons. MLIs are classically divided into two types. However, their morphological heterogeneity suggests an alternate model of one continuously varying population. Through clustering and trajectory inference of 811 MLI reconstructions at maturity and during development, we show that MLIs divide into two discrete classes but also present significant within-class heterogeneity. Pseudotime trajectory mapping uncovered the emergence of distinct phenotypes during migration and axonogenesis, well before neurons reach their final positions. Our study illustrates the utility of quantitative single-cell methods to morphology for defining the diversification of neuronal subtypes.
An Inherent Structural Difference Between Serine and Threonine Phosphorylation: Phosphothreonine Prefers an Ordered, Compact, Cyclic Conformation
Authors: Pandey Anil K. , Ganguly Himal K. , Sinha Sudipta Kumar , Daniels Kelly E. , Yap Glenn P. A. , Patel Sandeep , Zondlo Neal J.
Published: March 2020

Phosphorylation and dephosphorylation of proteins by kinases and phosphatases are central to cellular responses and function. The structural effects of serine and threonine phosphorylation were examined in peptides and in proteins, by circular dichroism, NMR spectroscopy, bioinformatics analysis of the PDB, small-molecule X-ray crystallography, and computational investigations. Phosphorylation of both serine and threonine residues induces substantial conformational restriction in their physiologically more important dianionic forms. Threonine exhibits a particularly strong disorder-to-order transition upon phosphorylation, with dianionic phosphothreonine preferentially adopting a cyclic conformation with restrictedϕ(ϕ∼ –60°) stabilized by three noncovalent interactions: a strong intraresidue phosphate-amide hydrogen bond, an n→π* interaction between consecutive carbonyls, and an n→σ* interaction between the phosphate Oγ lone pair and the antibonding orbital of C–Hβ that restricts theχ2side chain conformation. Proline is unique among the canonical amino acids for its covalent cyclization on the backbone. Phosphothreonine can mimic proline’s backbone cyclization via noncovalent interactions. The preferred torsions of dianionic phosphothreonine areϕ,ψ= polyproline helix or α-helix (ϕ∼ –60°);χ1=g−;χ2= eclipsed C–H/O–P bonds. This structural signature is observed in diverse proteins, including the activation loops of protein kinases and protein-protein interactions. In total, these results suggest a structural basis for the differential use and evolution of threonine versus serine phosphorylation sites in proteins, with serine phosphorylation typically inducing smaller, rheostat-like changes, versus threonine phosphorylation promoting larger, step function-like switches, in proteins.
Identification, presence, and possible multifunctional regulatory role of invertebrate gonadotropin-releasing hormone/corazonin molecule in the great pond snail (Lymnaea stagnalis)
Authors: Fodor István , Zrinyi Zita , Urbán Péter , Herczeg Róbert , Büki Gergely , Koene Joris M. , Tsai Pei-San , Pirger Zsolt
Published: March 2020

In the last years, the interpretation of gonadotropin-releasing hormone (GnRH) neuropeptide superfamily has changed tremendously. One main driver is the investigation of functions and evolutionary lineage of previously identified molluscan GnRH molecules. Emerging evidence suggests not only reproductive, but also diverse biological effects of these molecules and proposes they should most likely be called corazonin (CRZ). Clearly, a more global understanding necessitates further exploration of species-specific functions and structure of invGnRH/CRZ peptides. Towards this goal, we have identified the full-length cDNA of invGnRH/CRZ peptide in an invertebrate model species, the great pond snailLymnaea stagnalis, termed ly-GnRH/CRZ, and characterized the transcript and peptide distribution in the central nervous system (CNS) and peripheral organs. Our results are consistent with previous data that molluscan GnRHs are more related to CRZs and serve diverse functions. For this, our findings support the notion that peptides originally termed molluscan GnRH are multifunctional modulators and that nomenclature change should be taken into consideration.
The genomic landscapes of individual melanocytes from human skin
Authors: Tang Jessica , Fewings Eleanor , Chang Darwin , Zeng Hanlin , Liu Shanshan , Jorapur Aparna , Belote Rachel L. , McNeal Andrew S. , Yeh Iwei , Arron Sarah T. , Judson-Torres Robert L. , Bastian Boris C. , Shain A. Hunter
Published: March 2020

Every cell in the human body has a unique set of somatic mutations, yet it remains difficult to comprehensively genotype an individual cell. Here, we developed solutions to overcome this obstacle in the context of normal human skin, thus offering the first glimpse into the genomic landscapes of individual melanocytes from human skin. We comprehensively genotyped 133 melanocytes from 19 sites across 6 donors. As expected, sun-shielded melanocytes had fewer mutations than sun-exposed melanocytes. However, within sun-exposed sites, melanocytes on chronically sun-exposed skin (e.g. the face) displayed a lower mutation burden than melanocytes on intermittently sun-exposed skin (e.g. the back). Melanocytes located adjacent to a skin cancer had higher mutation burdens than melanocytes from donors without skin cancer, implying that the mutation burden of normal skin can be harnessed to measure cumulative sun damage and skin cancer risk. Moreover, melanocytes from healthy skin commonly harbor pathogenic mutations, likely explaining the origins of the melanomas that arise in the absence of a pre-existing nevus. Phylogenetic analyses identified groups of related melanocytes, suggesting that melanocytes spread throughout skin as fields of clonally related cells, invisible to the naked eye. Overall, our study offers an unprecedented view into the genomic landscapes of individual melanocytes, revealing key insights into the causes and origins of melanoma.
The lateral hypothalamus and orexinergic transmission in the paraventricular thalamus promote the attribution of incentive salience to reward-associated cues
Authors: Haight Joshua L , Campus Paolo , Maria-Rios Cristina E , Johnson Allison M , Klumpner Marin S , Kuhn Brittany N , Covelo Ignacio R , Morrow Jonathan D , Flagel Shelly B
Published: March 2020

Rationale

Prior research suggests that inputs from the lateral hypothalamic area (LHA) to the paraventricular nucleus of the thalamus (PVT) contribute to the attribution of incentive salience to Pavlovian-conditioned reward cues. However, a causal role for the LHA in this phenomenon has not been demonstrated. In addition, it is unknown which hypothalamic neurotransmitter or peptide system(s) are involved in mediating incentive salience attribution.

Objectives

To examine: 1) the role of the LHA in the propensity to attribute incentive salience to reward cues, and 2) the role of orexinergic signaling in the PVT on the expression of Pavlovian conditioned approach (PavCA) behavior, a reflection of incentive salience attribution.

Methods

Male Sprague-Dawley rats received bilateral excitotoxic lesions of the LHA prior to the acquisition of Pavlovian conditioned approach (PavCA) behavior. A separate cohort of male rats acquired PavCA behavior and were characterized as sign-trackers (STs) or goal-trackers (GTs) based on their conditioned response. The orexin 1 receptor (OX1r) antagonist SB-334867, or the orexin 2 receptor (OX2r) antagonist TCS-OX2-29, were then administered directly into the PVT to assess the effects of these pharmacological agents on the expression of PavCA behavior and on the conditioned reinforcing properties of the Pavlovian reward cue.

Results

Lesions of the LHA before training attenuated the development of lever-directed (sign-tracking) behaviors in the PavCA paradigm, without affecting magazine-directed (goal-tracking) behaviors. In STs, administration of the OX1r antagonist into the PVT reduced lever-directed behaviors and increased magazine-directed behaviors; while administration of the OX2r antagonist only reduced lever-directed behaviors. Further, OX2r, but not OX1r, antagonism was able to reduce the incentive motivational value of the conditioned stimulus on a conditioned reinforcement test in STs. The behavior of GTs was unaffected by orexinergic antagonism in the PVT.

Conclusions

The LHA is necessary for the attribution of incentive salience to reward cues and, thereby, the development of a sign-tracking conditioned response. Furthermore, blockade of orexin signaling in the PVT attenuates the incentive value of a Pavlovian reward cue. These data suggest that hypothalamic orexin inputs to the PVT are a key component of the circuitry that encodes the incentive motivational value of reward cues and promotes maladaptive cue-driven behaviors.