bluuebunny/crossref_metadata_2025 huggingface dataset:
Janthinobacterium violaceinigrum sp. nov., Janthinobacterium aquaticum sp. nov. and Janthinobacterium rivuli sp. nov., isolated from a subtropical stream in China
Authors: Lu Huibin , Deng Tongchu , Cai Zhipeng , Liu Feifei , Yang Xunan , Wang Yonghong , Xu Meiying
Published: March 2020

Four strains assigned the names FT13WT, FT14W, FT58WT and FT68WT were isolated from a subtropical stream in PR China. All the strains were Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile with flagella. Comparisons based on 16S rRNA gene sequences showed that strains FT13WT, FT14W, FT58WT and FT68WT belonged to genus

Janthinobacterium

and shared 16S rRNA gene similarities in the range of 98.8–99.7 % with

Janthinobacterium lividum

DSM 1522T,

Janthinobacterium agaricidamnosum

DSM 9628T and ‘Janthinobacterium svalbardensis JA-1', respectively. The calculated pairwise average nucleotide identity (ANI) values among the genomes of above seven strains were in the range of 79.0–92.2 %, except that the ANI value was 96.8 % between strain FT13WT and FT14W. The respiratory quinone of strains FT13WT, FT14W, FT58WT and FT68WT was determined to be Q-8. The major fatty acids were C16 : 1 ω7c, C16 : 0, C18 : 1 ω7c and C12 : 0. The polar lipids included phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. The genome sizes of strains FT13WT, FT14W, FT58WT and FT68WT were 6.45, 6.38, 5.73 and 6.37 Mbp with G+C contents of 63.4, 63.7, 61.6 and 63.1 mol%, respectively. Combining phenotypic, biochemical, genotypic and ANI data, strain FT13WT and FT14W should belong to the same species. The four strains were considered to represent three novel species within genus

Janthinobacterium

, for which the names Janthinobacterium violaceinigrum sp. nov. (type strain FT13WT=GDMCC 1.1638T=KACC 21319T), Janthinobacterium aquaticum sp. nov. (FT58WT=GDMCC 1.1676T=KACC 21468T) and Janthinobacterium rivuli sp. nov. (FT68WT=GDMCC 1.1677T=KACC 21469T) are proposed.
Methylotenera oryzisoli sp. nov., a lanthanide-dependent methylotrophic bacteria isolated from rice field soil
Authors: Lv Haoxin , Sahin Nurettin , Tani Akio
Published: March 2020

A new lanthanide (Ln3+)-dependent methanol-utilizing bacterial strain, La3113T, was isolated from rice field soil and its taxonomic position was investigated using polyphasic approaches. The strain was aerobic, Gram-stain-negative, strongly motile, catalase-positive and cytochrome oxidase-positive. It could neither catalyse the hydrolysis of urea nor reduce nitrate to nitrite. Growth was observed within a temperature range of 10–40 °C and a pH range of 6–8, with optimum growth at 28 °C and pH 7. Methylamine was utilized as the single source of energy, carbon and nitrogen, and it was oxidized by methylamine dehydrogenase. C16 : 1
 ω7c, C16 : 1
 ω6c and C16 : 0 were the dominant cellular fatty acids. Its draft genome (2.67 Mbp and 44.9 mol% G+C content) encodes genes including three Ln3+-dependent methanol dehydrogenase (XoxF-type MDH) genes, those for formaldehyde assimilation (ribulose monophosphate pathway), formate dehydrogenases and methylamine dehydrogenases, but not Ca2+-dependent MDH (MxaFI-MDH), which characterizes the species as a Ln3+-dependent methylotroph. The 16S rRNA gene sequence showed that strain La3113T belongs to the genus

Methylotenera

and is closely related to

Methylotenera mobilis

JLW8T (98.29 % identity). The digital DNA–DNA hybridization (dDDH) values (less than 30 %) and average nucleotide identity (ANI) values (less than 85 %) between genomes of strain La3113T and related type strains were lower than the thresholds for species delineation (70 % for dDDH and 95–96 % for ANI). On the basis of these polyphasic approaches, we propose a novel

Methylotenera

species, Methylotenera oryzisoli sp. nov. (type strain La3113T=NBRC 111954T=DSM 103219T).
Streptomyces cahuitamycinicus sp. nov., isolated from desert soil and reclassification of Streptomyces galilaeus as a later heterotypic synonym of Streptomyces bobili
Authors: Saygin Hayrettin , Ay Hilal , Guven Kiymet , Cetin Demet , Sahin Nevzat
Published: March 2020

A novel actinobacterial strain, designated 13K301T, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan. The taxonomic position of strain 13K301T was revealed by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain 13K301T belongs to the genus

Streptomyces

and had highest sequence similarity to ‘Streptomyces qaidamensis’ S10T (99.2 %),

Streptomyces flavovariabilis

NRRL B-16367T (98.9 %) and

Streptomyces phaeoluteigriseus

DSM 41896T (98.8 %), but the strain formed a distinct clade in the phylogenetic tree. The DNA–DNA relatedness and average nucleotide identity values as well as evolutionary distances based on multilocus (atpD, gyrB, recA, rpoB and trpB) sequences between strain 13K301T and closely related type strains were significantly lower than the recommended threshold values. The cell wall contained ll-diaminopimelic acid and the whole-cell hydrolysates were glucose and ribose. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were determined as the predominant polar lipids. The major menaquinones were identified as MK-9(H8) and MK-9(H6). On the basis of these genotypic and phenotypic data, it is proposed that strain 13K301T should be classified as representative of a novel species of the genus

Streptomyces

, for which the name Streptomyces cahuitamycinicus sp. nov. is proposed. The type strain is 13K301T (=DSM 106873T=KCTC 49110T). In addition, the whole genome-based comparisons as well as the multilocus sequence analysis revealed that the type strains of

Streptomyces galilaeus

and

Streptomyces bobili

belong to a single species. It is, therefore, proposed that

S. galilaeus

be recognised as a heterotypic synonym of

S. bobili

for which an emended description is given.
Strongly heterogeneous transmission of COVID–19 in mainland China: local and regional variation
Authors: Wang Yuke , Teunis Peter
Published: March 2020

Background

The outbreak of novel coronavirus disease 2019 (COVID-19) started in the city of Wuhan, China, with a period of rapid initial spread. Transmission on a regional and then national scale was promoted by intense travel during the holiday period of the Chinese New Year. We studied the variation in transmission of COVID-19, locally in Wuhan, as well as on a larger spatial scale, among different cities and even among provinces in mainland China.

Methods

In addition to reported numbers of new cases, we have been able to assemble detailed contact data for some of the initial clusters of COVID-19. This enabled estimation of the serial interval for clinical cases, as well as reproduction numbers for small and large regions.

Findings

We estimated the average serial interval was 4·8 days. For early transmission in Wuhan, any infectious case produced as many as four new cases, transmission outside Wuhan was less intense, with reproduction numbers below two. During the rapid growth phase of the outbreak the region of Wuhan city acted as a hot spot, generating new cases upon contact, while locally, in other provinces, transmission was low.

Interpretation

COVID-19 is capable of spreading very rapidly. The sizes of outbreak in provinces of mainland China mainly depended on the numbers of cases imported from Wuhan as the local reproduction numbers were low. The COVID-19 epidemic should be controllable with appropriate interventions.

Funding

No specific funding.
Relationship between the ABO Blood Group and the COVID-19 Susceptibility
Authors: Zhao Jiao , Yang Yan , Huang Hanping , Li Dong , Gu Dongfeng , Lu Xiangfeng , Zhang Zheng , Liu Lei , Liu Ting , Liu Yukun , He Yunjiao , Sun Bin , Wei Meilan , Yang Guangyu , Wang Xinghuan , Zhang Li , Zhou Xiaoyang , Xing Mingzhao , Wang Peng George
Published: March 2020

The novel coronavirus disease-2019 (COVID-19) has been spreading around the world rapidly and declared as a pandemic by WHO. Here, we compared the ABO blood group distribution in 2,173 patients with COVID-19 confirmed by SARS-CoV-2 test from three hospitals in Wuhan and Shenzhen, China with that in normal people from the corresponding regions. The results showed that blood group A was associated with a higher risk for acquiring COVID-19 compared with non-A blood groups, whereas blood group O was associated with a lower risk for the infection compared with non-O blood groups. This is the first observation of an association between the ABO blood type and COVID-19. It should be emphasized, however, that this is an early study with limitations. It would be premature to use this study to guide clinical practice at this time, but it should encourage further investigation of the relationship between the ABO blood group and the COVID-19 susceptibility.
Reported symptoms differentiate diagnoses in children with exercise-induced respiratory problems: findings from the Swiss Paediatric Airway Cohort (SPAC)
Authors: Pedersen Eva SL , de Jong Carmen CM , Ardura-Garcia Cristina , Mallet Maria Christina , Barben Juerg , Casaulta Carmen , Hoyler Karin , Jochmann Anja , Moeller Alexander , Mueller-Suter Dominik , Regamey Nicolas , Singer Florian , Goutaki Myrofora , Kuehni Claudia E.
Published: March 2020

Background

Exercise-induced breathing problems with similar clinical presentations can have different aetiologies. This makes distinguishing common diagnoses such as asthma, extrathoracic and thoracic dysfunctional breathing (DB), insufficient fitness, and chronic cough difficult.

Objective

We studied which parent-reported, exercise-induced symptoms (EIS) can help distinguish diagnoses of EIS in children seen in respiratory outpatient clinics.

Methods

This study was nested in the Swiss Paediatric Airway Cohort (SPAC), an observational study of children aged 0-17 years referred to paediatric respiratory outpatient clinics in Switzerland. We studied children aged 6-17 years and compared information on EIS from parent-completed questionnaires between children with different diagnoses. We used multinomial regression to analyse whether parent-reported symptoms differed between diagnoses (asthma as base).

Results

Among 1109 children, EIS were reported for 732 (66%) (mean age 11 years, 318 of 732 [43%] female). Among the symptoms, dyspnoea best distinguished thoracic DB (relative risk ratio [RRR] 5.4, 95%CI 1.3-22) from asthma. Among exercise triggers, swimming best distinguished thoracic DB (RRR 2.4, 95%CI 1.3-6.2) and asthma plus DB (RRR 1.8, 95%CI 0.9-3.4) from asthma only. Late onset of EIS was less common for extrathoracic DB (RRR 0.1, 95%CI 0.03-0.5) and thoracic DB (RRR 0.4, 95%CI 0.1-1.2) compared with asthma. Localisation of dyspnoea (throat vs. chest) differed between extrathoracic DB (RRR 2.3, 95%CI 0.9-5.8) and asthma. Reported respiration phase (inspiration or expiration) did not help distinguish diagnoses.

Conclusion

Parent-reported symptoms help distinguish different diagnoses in children with EIS. This highlights the importance of physicians obtaining detailed patient histories.

Highlights box

What is already known about this topic?

Experts suggest that information about the symptoms and their onset and duration can assist accurate diagnosis of children with exercise-induced respiratory problems, but no original studies have tested this. (29/35 words)

What does this article add to our knowledge?

Exercise-induced symptoms reported by parents and further information about their onset, triggers, and effects of treatment help differentiate diagnoses in children with exercise-induced respiratory problems. (25/35 words)

How does this study impact current management guidelines?

Our results emphasize the importance of taking detailed symptom histories of children with exercise-induced problems, and suggest which questions are most helpful.
Impact assessment of non-pharmaceutical interventions against COVID-19 and influenza in Hong Kong: an observational study
Authors: Cowling Benjamin J. , Ali Sheikh Taslim , Ng Tiffany W. Y. , Tsang Tim K. , Li Julian C. M. , Fong Min Whui , Liao Qiuyan , Kwan Mike YW , Lee So Lun , Chiu Susan S. , Wu Joseph T. , Wu Peng , Leung Gabriel M.
Published: March 2020

Background

A range of public health measures have been implemented to delay and reduce local transmission of COVID-19 in Hong Kong, and there have been major changes in behaviours of the general public. We examined the effect of these interventions and behavioral changes on the incidence of COVID-19 as well as on influenza virus infections which may share some aspects of transmission dynamics with COVID-19.

Methods

We reviewed policy interventions and measured changes in population behaviours through two telephone surveys, on January 20-23 and February 11-14. We analysed data on laboratory-confirmed COVID-19 cases, influenza surveillance data in outpatients of all ages, and influenza hospitalisations in children. We estimated the daily effective reproduction number (Rt), for COVID-19 and influenza A(H1N1).

Findings

COVID-19 transmissibility has remained at or below 1, indicating successful containment to date. Influenza transmission declined substantially after the implementation of social distancing measures and changes in population behaviours in late January, with a 44% (95% confidence interval, CI: 34% to 53%) reduction in transmissibility in the community, and a 33% (95% CI: 24% to 43%) reduction in transmissibility based on paediatric hospitalization rates. In the two surveys we estimated that 74.5% and 97.5% of the general adult population wore masks when going out, and 61.3% and 90.2% avoided going to crowded places, respectively.

Implications

Containment measures, social distancing measures and changes in population behaviour have successfully prevented spread of COVID-19. The social distancing measures and behavioural changes led to a substantial reduction in influenza transmission in early February 2020. However, it may be challenging to avoid fatigue and sustain these measures and population behaviours as COVID-19 continues to spread globally.

Funding

Health and Medical Research Fund, Hong Kong
The first report of the prevalence of COVID-19 in Chronic myelogenous leukemia patients in the core epidemic area of China: multicentre, cross-sectional survey
Authors: Wang Dan-Yu , Guo Jing-Ming , Yang Zhuang-Zhi , Yuan Guo-Lin , Meng Li , Li Wei-Ming
Published: March 2020

Background

Since late December 2019, the outbreak of the novel coronavirus disease, COVID-19, that began in Wuhan, has become endemic in China and more than 100 countries and regions in the world. So far, there is rare data on the prevalence of COVID-19 in patients with chronic myelogenous leukemia (CML). We aimed to describe the clinical course, outcomes of CML patients with COVID-19 and prevalence of COVID-19 in CML patients.

Methods

In this multicentre, cross-sectional survey, the clinical data of CML patients with COVID-19 in each center were collected. Simultaneously, an online survey was conducted for information about the CML patients under the management at each center by asking the CML patients to complete a questionnaire,from February 15, 2020 to February 21, 2020. The questionnaire includes demographic data, place of residence, smoking status, CML diagnosis and treatment, comorbidities, combined medications, epidemiological history, symptoms(fever, cough, shortness of breath, etc) during the epidemic. Additional clinical data was collected on respondents suspected or confirmed to have COVID-19. We described and analyzed the prevalence of COVID-19 in CML patients, and focus on the clinical characteristics and outcomes of COVID-19 patients. Data were compared between the CML patients with optimal response and those with non-optimal response. The primary outcome was prevalence of COVID-19 in CML patients, as of Feb 21, 2020. Secondary outcomes included the history of epidemiology of CML patients, the clinical characteristics and outcomes of CML patients with COVID-19.

Findings

Of 392 respondents, 223(56.9%) were males, and 240(61.2%) were 50 years or younger. Only 10 patients took drugs irregularly due to the influence of the epidemic because of traffic control, pharmacies unable to operate normally, etc. In the history of epidemiology, there were 4 patients with definite contact with COVID-19, of which 3 were remote contact and 1 was close contact. 12 respondents had fever, cough or shortness of breath during the epidemic, 1 case (common type) was confirmed with COVID-19 and cured after treatment. 1 patient was clinically diagnosed and succumbed. 1 of 299 (0.3%) patients with an optimal response was diagnosed with COVID-19. Of the 50 patients who failed to respond to CML treatment or had a poor response, 1 patient (2%) had a clinical diagnosis of COVID-19.

Interpretation

While the 392 CML respondents required regular referrals to hospitals, they did not have much contact with COVID-19 patients during the outbreak. Patients who failed to achieved an optimal response to CML therapy appear more likely to have a symptomatic infection with SARS-CoV-2. Older patients with comorbidities are at increased risk of death.

Funding

This work was supported by grants from the National Natural Science Foundation of China(NSFC)(81873440&81700142).
Safety and acceptability of clozapine and risperidone in progressive multiple sclerosis: a phase 1, randomized, blinded, placebo-controlled trial
Authors: La Flamme Anne Camille , Abernethy David , Sim Dalice , Goode Liz , Lockhart Michelle , Bourke David , Milner Imogen , Garrill Toni-Marie , Joshi Purwa , Watson Eloise , Smyth Duncan , Lance Sean , Connor Bronwen
Published: March 2020

Objective

Because clozapine and risperidone have been shown to reduce neuroinflammation in humans and mice, the CRISP trial was conducted to determine whether clozapine and risperidone are suitable for progressive multiple sclerosis (pMS).

Methods

The CRISP trial (ACTRN12616000178448) was a blinded, randomized, placebo-controlled trial with three parallel arms (n=12/arm). Participants with pMS were randomized to clozapine (100 to 150 mg/day), risperidone (2 to 3.5 mg/day), or placebo for six months. The primary outcome measures were safety (adverse events/serious adverse events) and acceptability (TSQM-9).

Results

An interim analysis (n=9) revealed significant differences in the time-on-trial between treatment groups and placebo (p=0.030 and 0.025, clozapine and risperidone, respectively) with all participants receiving clozapine being withdrawn during the titration period (mean dose=35±15 mg/day). Participants receiving clozapine or risperidone reported a significantly higher rate of adverse events than placebo (p=0.00001) but not serious adverse events. Specifically, low doses of clozapine appeared to cause an acute and dose-related intoxicant effect in patients with pMS, who had fairly severe chronic spastic ataxic gait and worsening over all mobility, which resolved on drug cessation.

Interpretation

The CRISP trial results suggest that pMS patients may experience increased sensitivity to clozapine and risperidone and indicate that the dose and/or titration schedule developed for schizophrenia may not be suitable for pMS. While these findings do not negate the potential of these drugs to reduce MS-associated neuroinflammation, they highlight the need for further research to understand the pharmacodynamic profile and effect of clozapine and risperidone in pMS patients.
Influence factors of death risk among COVID-19 patients in Wuhan, China: a hospital-based case-cohort study
Authors: Fu Lin , Fei Jun , Xiang Hui-Xian , Xiang Ying , Tan Zhu-Xia , Li Meng-Die , Liu Fang-Fang , Liu Hong-Yan , Zheng Ling , Li Ying , Zhao Hui , Xu De-Xiang
Published: March 2020

Background

Coronavirus disease 2019 (COVID-19) triggered by infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been widely pandemic all over the world. The aim of this study was to analyze the influence factors of death risk among 200 COVID-19 patients.

Methods

Two hundred patients with confirmed SARS-CoV-2 infection were recruited. Demographic data and clinical characteristics were collected from electronic medical records. Biochemical indexes on admission were measured and patient’s prognosis was tracked. The association of demographic data, clinical characteristics and biochemical indexes with death risk was analyzed.

Results

Of 200 COVID-19 patients, 163 (81.5%) had at least one of comorbidities, including diabetes, hypertension, hepatic disease, cardiac disease, chronic pulmonary disease and others. Among all patients, critical cases, defined as oxygenation index lower than 200, accounted for 26.2%. Severe cases, oxygenation index from 200 to 300, were 29.7%. Besides, common cases, oxygenation index higher than 300, accounted for 44.1%. At the end of follow-up, 34 (17%) were died on mean 10.9 day after hospitalization. Stratified analysis revealed that older ages, lower oxygenation index and comorbidities elevated death risk of COVID-19 patients. On admission, 85.5% COVID-19 patients were with at least one of extrapulmonary organ injuries. Univariable logistic regression showed that ALT and TBIL, two indexes of hepatic injury, AST, myoglobin and LDH, AST/ALT ratio, several markers of myocardial injury, creatinine, urea nitrogen and uric acid, three indexes of renal injury, were positively associated with death risk of COVID-19 patients. Multivariable logistic regression revealed that AST/ALT ratio, urea nitrogen, TBIL and LDH on admission were positively correlated with death risk of COVID-19 patients.

Conclusion

Older age, lower oxygenation index and comorbidities on admission elevate death risk of COVID-19 patients. AST/ALT ratio, urea nitrogen, TBIL and LDH on admission may be potential prognostic indicators. Early hospitalization is of great significance to prevent multiple organ damage and improve the survival of COVID-19 patients.

In this hospital-based case-cohort study, we found that serum urea nitrogen, TBIL, LDH and AST/ALT ratio, several markers of extrapulmonary organ injuries, were positively correlated with death risk of COVID-19 patients. We provide evidence for the first time that multiple organ damage on admission influences the prognosis of COVID-19 patients. Early hospitalization is beneficial for elevating the survival rate of COVID-19 patients especially critical ill patients.
Vibrio Cholerae O1 Transmission in Bangladesh: Insights from a Nationally-Representative Serosurvey
Authors: Azman Andrew S , Lauer Stephen , Rahman Bhuiyan M. Taufiqur , Luquero Francisco J , Leung Daniel T , Hegde Sonia , Harris Jason , Paul Kishor Kumar , Khaton Fatema , Ferdous Jannatul , Lessler Justin , Salje Henrik , Qadri Firdausi , Gurley Emily S
Published: March 2020

Background

Pandemic Vibrio cholerae from cholera-endemic countries around the Bay of Bengal regularly seed epidemics globally. Without reducing cholera in these countries, including Bangladesh, global cholera control may never be achieved. Little is known about the geographic distribution and magnitude of V. cholerae O1 transmission nationally. Here we use recent advances in cholera seroepidemiology to describe infection risk across Bangladesh overcoming many of the limitations of current clinic-based surveillance.

Methods

We tested serum from a nationally-representative serosurvey in Bangladesh of 2,778 participants with eight V. cholerae-specific assays. Using these data with a previously validated machine learning model we estimate the annual seroincidence rate and use Bayesian geostatistical models to create high-resolution national maps of infection risk.

Findings

We estimate a national seroincidence rate of 19.1% (95% CI 12.2-26.9%). Our high-resolution maps reveal large heterogeneity of infection risk, with community-level annual infection risk within the sampled population ranging from 2.4-69.0%. Across the country, we estimate that 31.0 million (95% CI 19.8-43.7 million) occurred in the year before the survey with most of these infections occurring in urban areas, including Dhaka, the capital.

Interpretation

Serosurveillance provides an avenue for identifying areas with high V. cholerae O1 transmission and exploring key risk factors for infection across geographic scales. This may serve as an important tool for countries to plan and monitor progress towards 2030 cholera elimination goals.
Laser capture microdissection-based single-cell RNA sequencing reveals optic nerve crush-related early mRNA alterations in retinal ganglion cells
Authors: Pan Dongyan , Xu Mengqiao , Chang Xin , Xia Mao , Fang Yibin , Fu Yinghua , Shen Wei , Wang Yue , Sun Xiaodong
Published: March 2020

Retinal ganglion cells (RGC) are the primary cell type injured in a variety of diseases of the optic nerve, and the early changes of RGC’s RNA profiling may be important to understand the mechanism of optic nerve injury and axon regeneration. Here we employed the optic nerve crush (ONC) model to explore early mRNA alterations in RGCs using laser capture microdissection (LCM) and single-cell RNA sequencing. We successfully established an optimal LCM protocol using 30 μm-thick retinal tissue sections mounted on glass slides and laser pressure catapulting (LPC) to collect RGCs and obtain high-quality RNA for single-cell sequencing. Based on our protocol, we identified 8744 differentially expressed genes that were involved in ONC-related early mRNA alterations in RGCs. Candidate genes included Atf3, Lgals3, LOC102551701, Plaur, Tmem140 and Maml1. The LCM-based single-cell RNA sequencing allowed new insights into the early mRNA changes in RGCs, highlighting new molecules associated with ONC.
DeepDigest: prediction of protein proteolytic digestion with deep learning
Authors: Yang Jinghan , Gao Zhiqiang , Ren Xiuhan , Sheng Jie , Xu Ping , Chang Cheng , Fu Yan
Published: March 2020

In shotgun proteomics, it is essential to accurately determine the proteolytic products of each protein in the sample for subsequent identification and quantification, because these proteolytic products are usually taken as the surrogates of their parent proteins in the further data analysis. However, systematical studies about the commonly used proteases in proteomics research are insufficient, and there is a lack of easy-to-use tools to predict the digestibilities of these proteolytic products. Here, we propose a novel sequence-based deep learning model – DeepDigest, which integrates convolutional neural networks and long-short term memory networks for digestibility prediction of peptides. DeepDigest can predict the proteolytic cleavage sites for eight popular proteases including trypsin, ArgC, chymotrypsin, GluC, LysC, AspN, LysN and LysargiNase. Compared with traditional machine learning algorithms, DeepDigest showed superior performance for all the eight proteases on a variety of datasets. Besides, some interesting characteristics of different proteases were revealed and discussed.
Human-derived NLS enhance the gene transfer efficiency of chitosan
Authors: Bitoque Diogo B. , Morais Joana , Oliveira Ana V. , Sequeira Raquel L. , Calado Sofia M. , Fortunato Tiago M. , Simão Sónia , da Costa Ana M. Rosa , Silva Gabriela A.
Published: March 2020

Nuclear import is considered one of the major limitations for non-viral gene delivery systems and the incorporation of nuclear localization signals (NLS) that mediate nuclear intake can be used as a strategy to enhance internalization of exogenous DNA. In this work, human-derived endogenous NLS peptides based on Insulin Growth Factor Binding Proteins (IGFBP), namely IGFBP-3 and IGFBP-5, were tested for their ability to improve nuclear translocation of genetic material by non-viral vectors. Several strategies were tested to determine their effect on chitosan mediated transfection efficiency: co-administration with polyplexes, co-complexation at the time of polyplex formation, and covalent ligation to chitosan. Our results show that co-complexation and covalent ligation of human-derived NLS peptides to chitosan polyplexes yields a 2-fold increase in transfection efficiency.

These results indicate that the integration of IGFBP-NLS peptides into polyplexes has potential as a strategy to enhance the efficiency of non-viral vectors.
A 2,000-year-old specimen with intraerythrocyticBartonella quintana
Authors: Barbieri R , Mai B-H-A , Chenal T , Bassi M-L , Gandia D , Camoin-Jau L , Lepidi H , Aboudharam G , Drancourt M
Published: March 2020

Photogrammetry and cascading microscopy investigations of dental pulp specimens collected from 2,000-year-old individuals buried in a Roman necropolis in Besançon, France, revealed unprecedented preserved tissular and cellular morphology. Photogrammetry yielded 3-D images of the smallest archaeological human remain ever recovered. Optical microscopy examinations after standard hematoxylin-phloxine-saffron staining and anti-glycophorin A immunohistochemistry exposed dental pulp cells, in addition erythrocytes were visualized by electron microscopy, which indicated that the ancient dental pulp trapped a blood drop. Fluorescencein situhybridization applied on red blood cells revealed the louse-borne pathogenBartonella quintana, a finding confirmed by polymerase chain reaction assays. Through paleohistology and paleocytology, we demonstrate that ancient dental pulp preserved intact blood cells at the time of the individual’s death, offering an unprecedented opportunity to engage in direct and indirect tests to diagnose pathogens in ancient buried individuals.
Impact of Cannabinoid Type 1 Receptor Modulation on Risky Decision-Making
Authors: Freels Timothy G. , Liley Anna E. , Gabriel Daniel B. K. , Simon Nicholas W.
Published: March 2020

Recent changes in policy regarding cannabis in the U.S. have been accompanied by an increase in the prevalence of cannabis use and a reduction in the perceived harms associated with consumption. However, little is understood regarding the effects of cannabinoids on cognitive processes. Given that deficient risk-taking is commonly observed in individuals suffering from substance use disorders (SUDs), we assessed the impact of manipulating cannabinoid type 1 receptors (CB1Rs; the primary target for Δ9-tetrahydrocannabinol in the brain) on punishment-based risk-taking using the risky decision-making task (RDT) in male Long-Evans rats. The RDT measures preference for small, safe rewards over large, risky rewards associated with an escalating chance of foot shock. Systemic bidirectional CB1R manipulation with a CB1R agonist, CB1R antagonist, and FAAH inhibitor (which increases overall endocannabinoid tone) did not alter overt risk-taking in the RDT. Interestingly, direct CB1R agonism, but not indirect CB1R stimulation or CB1R blockade, resulted in reduction in latency to make risky choices while not altering safe choice latency. Our findings suggest that CB1R activation expedites engagement in punishment based risk-taking without affecting overall preference for risky vs. safe options. This indicates that risk preference and rate of deliberation for risk-taking are influenced by distinct neural substrates, an important consideration for development of precise treatments targeting the aberrant risk-taking typical of SUD symptomology.
Five millennia ofBartonella quintanabacteremia
Authors: Mai Ba-Hoang-Anh , Barbieri Rémi , Chenal Thomas , Castex Dominique , Jonvel Richard , Tanasi Davide , Georges-Zimmerman Patrice , Dutour Olivier , Perissinotto David , Demangeot Coralie , Drancourt Michel , Aboudharam Gérard
Published: March 2020

Bartonella quintanacaused trench fever in the framework of two World Wars and is now recognized as an agent of re-emerging infection. Many reports indicated the popularity ofB. quintanaexposure since the 90s. For evaluating its prevalence in ancient populations, we used real-time PCR to detectB. quintanaDNA in 400 teeth collected from 145 individuals dating from the 1st to 19th centuries in nine archeological sites with the presence of negative controls. Fisher’s exact test was used to compare the prevalence ofB. quintanadetection in civil and military populations.B. quintana DNAwas confirmed in a total of 28/145 (19.3%) individuals, comprising 78 citizens and 67 soldiers, 20.1% and 17.9% of which were positive forB. quintanabacteremia, respectively. This study collected previous studies on these ancient samples and showed that the presence ofB. quintanainfection followed the course of time in human history; a total of 14/15 sites from five European countries had a positive prevalence. The positive rate in soldiers was higher than those of citizens, with 20% and 18.8%, respectively, in the 18th - 19th centuries, but the difference in frequency was not significant. These results confirmed the role of dental pulp in diagnosingB. quintanabacteremia in ancient populations and showed the incidence ofB. quintanain both citizens and soldiers. Many recent findings contributed to understanding the coevolution of the relationship betweenB. quintanaand humans.
Synthesis of Glycoconjugates Utilizing the Regioselectivity of a Lytic Polysaccharide Monooxygenase
Authors: Westereng Bjørge , Kračun Stjepan K. , Leivers Shaun , Ø. Arntzen Magnus , Aachmann Finn L. , Eijsink Vincent G. H.
Published: March 2020

Polysaccharides from plant biomass are the most abundant renewable chemicals on Earth and can potentially be converted to a wide variety of useful glycoconjugates. While anomeric hydroxyl groups of carbohydrates are amenable to a variety of useful chemical modifications, selective cross-coupling to non-reducing ends has remained challenging. Several lytic polysaccharide monooxygenases (LPMOs), powerful enzymes known for their application in cellulose degradation, specifically oxidize non-reducing ends, introducing carbonyl groups that can be utilized for chemical coupling. This study provides a simple and highly specific approach to produce oxime-based glycoconjugates from LPMO-functionalized oligosaccharides. The products are evaluated by HPLC, mass spectrometry and NMR. Furthermore, we demonstrate potential biodegradability of these glycoconjugates using selective enzymes.
Methylphenidate normalizes aberrant beta oscillations and reduces alpha power during retention in children with ADHD
Authors: Mazzetti C. , ter Huurne N. , Buitelaar J.K. , Jensen O.
Published: March 2020

Attention Deficit-Hyperactivity Disorder (ADHD) has been intensively studied in neurodevelopmental research, with the aim to identify the neural substrates of the disorder. Prior studies have established that brain oscillations in specific frequency ranges associated with attention and motor tasks are altered in ADHD patients as compared to typically developing (TD) peers. We hypothesized that the behavioral improvement following medication in ADHD patients should be accompanied by a normalization in the modulation of such oscillations. We hence implemented a double-blind placebo-controlled crossover design, where boys diagnosed with ADHD underwent behavioral and MEG measurements during a spatial attention task while on and off stimulant medication (methylphenidate, MPH). Results were compared with an age/IQ-matched TD group performing the same task, to assess the effect of MPH on oscillatory activity in the alpha (7 – 13Hz) and beta (15 – 30Hz) bands. We observed that depression of beta band oscillation over motor cortex in preparation to the response in ADHD boys on placebo were significantly lower as compared to the TD group. Importantly MPH resulted in a normalization of the beta depression, which then reached the same levels as in the control subjects. Furthermore, alpha power increased during the preparation interval in the ADHD control group, supposedly reflecting working memory maintenance of the cue information. This increase was significantly reduced in the ADHD group on MPH, reflecting a reduced impact on working memory load. This is the first MEG study showing task related changes in brain oscillations with MPH in children with ADHD.

Significance statement

Brain oscillations in the alpha (7-13Hz) and beta (15-30Hz) frequency bands are thought to underly different aspects of attentional processing and their aberrant modulation has been reported in ADHD. Here, we used a child-friendly adaptation of a Posner cueing paradigm to investigate such oscillations in children with and without a diagnosis of ADHD, and further examined the effects of methylphenidate (MPH) in the latter group. We showed that MPH restores aberrant patterns of beta desynchronization and reduces alpha power during retention in the ADHD group, concomitant to an improvement in behavioural performance.
Distinct neural mechanisms construct classical versus extraclassical inhibitory surrounds in an inhibitory nucleus in the midbrain attention network
Authors: Schryver Hannah M. , Lim Jing Xuan , Mysore Shreesh P.
Published: March 2020

Inhibitory neurons in the midbrain spatial attention network, called isthmi pars magnocellularis (Imc), control stimulus selection by the sensorimotor and attentional hub, the optic tectum (OT). Here, we investigate in the barn owl how classical as well as extraclassical (global) inhibitory surrounds of Imc receptive fields (RFs), fundamental units of Imc computational function, are constructed. We find that focal, reversible blockade of GABAergic input onto Imc neurons disconnects their extraclassical inhibitory surrounds, but, surprisingly, leaves intact their classical surrounds. Subsequently, with paired recordings and iontophoresis, first at spatially aligned site-pairs in Imc and OT, and then, at mutually distant site-pairs within Imc, we demonstrate that classical inhibitory surrounds of Imc RFs are inherited from OT, but their extraclassical inhibitory surrounds are constructed within Imc. These results reveal key design principles of the midbrain spatial attention circuit, and attest to the critical importance of competitive interactions within Imc for its operation.
Evolutionary divergence of novel open reading frames in cichlids speciation
Authors: Puntambekar Shraddha , Newhouse Rachel , Navas Jaime San Miguel , Chauhan Ruchi , Vernaz Grégoire , Willis Thomas , Wayland Matthew T. , Urmania Yagnesh , Miska Eric A. , Prabakaran Sudhakaran
Published: March 2020

Novel open reading frames (nORFs) with coding potential may arise from noncoding DNA. Not much is known about their emergence, functional role, fixation in a population or contribution to adaptive radiation. Cichlids fishes exhibit extensive phenotypic diversification and speciation. Encounters with new environments alone are not sufficient to explain this striking diversity of cichlid radiation because other taxa coexistent with the Cichlidae demonstrate lower species richness. Wagner et al analyzed cichlid diversification in 46 African lakes and reported that both extrinsic environmental factors and intrinsic lineage-specific traits related to sexual selection have strongly influenced the cichlid radiation1, which indicates the existence of unknown molecular mechanisms responsible for rapid phenotypic diversification, such as emergence of novel open reading frames (nORFs). In this study, we integrated transcriptomic and proteomic signatures from two tissues of two cichlids species, identified nORFs and performed evolutionary analysis on these nORF regions. Our results suggest that the time scale of speciation of the two species and evolutionary divergence of these nORF genomic regions are similar and indicate a potential role for these nORFs in speciation of the cichlid fishes.
MetaGenomic analysis of short and long reads
Authors: Manske Felix , Grundmann Norbert , Makalowski Wojciech
Published: March 2020

Identifying single organisms in environmental samples is one of the key tasks of metagenomics. During the last few years, third generation sequencing technologies have enabled researchers to sequence much longer molecules, but at the expense of sequencing accuracy. Thus, new algorithms needed to be developed to cope with this new type of data. With this in mind, we developed a tool called MetaG. An intuitive web interface makes the software accessible to a vast range of users, including those without extensive bioinformatic expertise. Evaluation of MetaG’s performance showed that it makes nearly perfect classifications of viral isolates using simulated short and long reads. MetaG also outperformed current state-of-the-art algorithms on data from targeted sequencing of the 16S and 28S rRNA genes. Since MetaG’s output is also supplemented with information about hosts and antibiotic resistances of pathogens, we expect it to be especially useful to the healthcare sector. Moreover, the outstanding accuracy of the taxonomic assignments will make MetaG a serious alternative for anyone working with metagenomic sequences. MetaG can be accessed athttp://bioinformatics.uni-muenster.de/tools/metag/.
Spectral harmonicity distinguishes two types of ictal phase-amplitude cross frequency couplings in patients candidate to epilepsy surgery
Authors: Dellavale Damián , Urdapilleta Eugenio , Cámpora Nuria , Velarde Osvaldo Matías , Kochen Silvia , Mato Germán
Published: March 2020

Objective

Spectral harmonicity of the ictal activity was analyzed regarding two clinically relevant aspects, (1) as a confounding factor producing ‘spurious’ phase-amplitude couplings (PAC) which may lead to wrong conclusions about the underlying ictal mechanisms, and (2) its role in how good PAC is in correspondence to the seizure onset zone (SOZ) classification performed by the epileptologists.

Methods

PAC patterns observed in intracerebral electroencephalography (iEEG) recordings were retrospectively studied during seizures of seven patients with pharmacoresistant focal epilepsy. The time locked index (TLI) measure was introduced to quantify the degree of harmonicity between frequency bands associated to the emergence of PAC during epileptic seizures.

Results

(1) Harmonic and non harmonic PAC patterns coexist during the seizure dynamics in iEEG recordings with macroelectrodes. (2) Harmonic PAC patterns are an emergent property of the periodic non sinusoidal waveform constituting the epileptiform activity. (3) The TLI metric allows to distinguish the non harmonic PAC pattern, which has been previously associated with the ictal core through the paroxysmal depolarizing shifts mechanism of seizure propagation.

Conclusions

Our results suggest that the spectral harmonicity of the ictal activity plays a relevant role in the visual analysis of the iEEG recordings performed by the epileptologists to define the SOZ, and that it should be considered for the proper interpretation of ictal mechanisms.

Significance

The proposed harmonicity analysis can be used to improve the delineation of the SOZ by reliably identifying non harmonic PAC patterns emerging from fully recruited cortical and subcortical areas.

Highlights

Harmonic and non harmonic phase-amplitude couplings coexist in epileptiform local field potentials.

The time locked index quantitatively differentiates harmonic and non harmonic ictal PAC patterns.

Spectral harmonicity plays a relevant role in the interpretation of underlying ictal mechanisms.
Efficient Generation of Isogenic Primary Human Myeloid Cells using CRISPR-Cas9 Ribonucleoproteins
Authors: Hiatt Joseph , Cavero Devin A. , McGregor Michael J. , Gordon David E. , Zheng Weihao , Budzik Jonathan M. , Roth Theodore L. , Haas Kelsey M. , Rathore Ujjwal , Meyer-Franke Anke , Bouzidi Mohamed S. , Hultquist Judd F. , Wojcechowskyj Jason A. , Fontaine Krystal A. , Pillai Satish K. , Cox Jeffery S. , Ernst Joel D. , Krogan Nevan J. , Marson Alexander
Published: March 2020

Genome engineering of primary human cells with CRISPR-Cas9 has revolutionized experimental and therapeutic approaches to cell biology, but human myeloid-lineage cells have remained largely genetically intractable. We present a method for delivery of CRISPR-Cas9 ribonucleoprotein (RNP) complexes by nucleofection directly into CD14+ human monocytes purified from peripheral blood, leading to high rates of precise gene knockout. These cells can be efficiently differentiated into monocyte-derived macrophages or dendritic cells. This process yields genetically-edited cells that retain critical markers of both myeloid differentiation and phagocytic function. Genetic ablation of the restriction factor SAMHD1 increased HIV-1 infection more than fifty-fold, demonstrating the power of this system for genotype-phenotype interrogation. This fast, flexible and scalable platform can be used for genetic studies of human myeloid cells in immune signaling, inflammation, cancer immunology, host-pathogen interactions, and beyond, and could facilitate development of novel myeloid cellular therapies.
Discrimination amongCryptococcus deneoformans, C. neoformansand interspecies hybrids using MALDI-TOF Mass Spectrometry
Authors: Zvezdanova Margarita Estreya , Arroyo Manuel J. , Méndez Gema , Guinea Jesús , Mancera Luis , Muñoz Patricia , Rodríguez-Sánchez Belén , Escribano Pilar
Published: March 2020

Background

Differentiation of the species within theCryptococcus neoformanscomplex (C. deneoformans, C. neoformansandC. neoformansinterspecies hybrids –C. deneoformansxC. neoformans-) is important to define the epidemiology of the infection.

Objectives

In this study we attempted the discrimination of threeC. neoformansspecies using MALDI-TOF MS coupled with an in-house library.

Methods

AllCryptococcusspp. isolates were identified by AFLP markers. An in-house database was constructed 26 well characterizedC. deneoformans, C. neoformansand interspecies hybrids. Forty-fourCryptococcusspp. isolates were blindly identified using MALDI-TOF MS (Bruker Daltonics) and the expanded library. Their protein spectra were also submitted to hierarchical clustering and the resulting species were verified via Partial Least Squares Differential Analysis (PLS-DA) and Support-Vector Machine (SVM).

Results

MALDI-TOF MS coupled with the in-house library allowed 100% correct identification ofC. deneoformansandC. neoformansbut misidentified the interspecies hybrids. The same level of discrimination amongC. deneoformansandC. neoformanswas achieved applying SVM. The application of the PLS-DA and SVM algorithms in a two-step analysis allowed 96.95% and 96.55% correct discrimination ofC. neoformansfrom the interspecies hybrids, respectively. Besides, PCA analysis prior to SVM provided 98.45% correct discrimination of the 3 species analysed in a one-step analysis.

Conclusions

Our results indicate that MALDI-TOF MS could be a rapid and reliable tool for the correct discrimination ofC. deneoformansandC. neoformans. The correct identification of the interspecies hybrids could only be achieved by hierarchical clustering with other protein spectra from the same species.