bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of SARS-CoV-2 in Different Human Biofluids Using the Loop-Mediated Isothermal Amplification Assay: A Prospective Diagnostic Study in Fortaleza, Brazil
Authors: Clementino Marco , Cavalcante Karene Ferreira , Feitosa Viana Vania Angelica , Silva Dayara de Oliveira , Damasceno Caroline Rebouças , de Souza Jessica Fernandes , Gondim Rafhaella Nogueira Della Guardia , Jorge Daniel Macedo de Melo , Magalhães Lyvia Maria Vasconcelos Carneiro , de Arruda Érico Antônio Gomes , Neto Roberto da Justa Pires , Medeiros Melissa Soares , dos Santos Armênio Aguiar , Magalhães Pedro Jorge Caldas , Perdigão Mello Liana , Arruda Eurico , Moreira Lima Aldo Ângelo , Havt Alexandre
Published: January 2022

We adopted the reverse transcriptase - loop mediated isothermal amplification (RT-LAMP) to detect SARS-Cov-2 in patient samples. Two primer sets for genes N and Orf1ab were designed to detect SARS-CoV-2, and one primer set was designed to detect the human gene Actin. We collected prospective 138 nasopharyngeal swabs, 70 oropharyngeal swabs, 69 saliva, and 68 mouth saline wash samples from patients suspected to have severe acute respiratory syndrome (SARS) caused by SARS-CoV-2 to test the RT-LAMP in comparison with the golden standard technique RT-qPCR. Accuracy of diagnosis using both primers, N5 and Orf9, was evaluated. Sensitivity and specificity for diagnosis was 96% (95% CI 87-99) and 85% (95% CI 76-91) in 138 samples, respectively. Accurate diagnosis results were obtained only in nasopharyngeal swab processed via extraction kit. Accurate and rapid diagnosis could aid COVID-19 pandemic management by identifying, isolating, and treating patients rapidly.

Highlights

New nucleic acid amplification test for the diagnosis of SARS-CoV-2 using the RT-LAMP

N5 primer set showed mutations in strains of interest, such as the gamma strain (P.1) of SARS-CoV-2

When evaluated in combination N5 and Orf9 primer sets maintained high sensitivity and specificity
RBDAct: Home screening of REM sleep behaviour disorder based on wrist actigraphy in Parkinson’s patients
Authors: Raschellà Flavio , Scafa Stefano , Puiatti Alessandro , Martin Moraud Eduardo , Ratti Pietro-Luca
Published: January 2022

Background

REM sleep behaviour disorder (RBD) is a disabling, often overlooked sleep disorder affecting up to 70% of patients with Parkinson’s disease. Identifying and treating RBD is critical to prevent severe sleep-related injuries, both to patients and bedpartners. Current diagnosis relies on nocturnal video-polysomnography, which is an expensive and cumbersome exam requiring specific clinical expertise.

Objectives

To design, optimise, and validate a novel home-screening tool, termed RBDAct, that automatically identifies RBD in Parkinson’s patients based on wrist actigraphy only.

Methods

Twenty-six Parkinson’s patients underwent two-week home wrist actigraphy worn on their more affected arm, followed by two non-consecutive in-lab evaluations. Patients were classified as RBD versus non-RBD based on dream enactment history and video-polysomnography. We characterised patients’ movement patterns during sleep using raw tri-axial accelerometer signals from wrist actigraphy. Machine learning classification algorithms were then trained to discriminate between patients with or without RBD using actigraphic features that described patients’ movements. Classification performance was quantified with respect to clinical diagnosis, separately for in-lab and at-home recordings.

Results

Classification performance from in-lab actigraphic data reached an accuracy of 92.9±8.16% (sensitivity 94.9±7.4%, specificity 92.7±13.8%). When tested on home recordings, accuracy rose to 100% over the two-week window. Features showed robustness across tests and conditions.

Conclusions

RBDAct provides reliable predictions of RBD in Parkinson’s patients based on home wrist actigraphy only. These results open new perspectives for faster, cheaper and more regular screening of sleep disorders, both for routine clinical practice and for clinical trials.
Proteostasis is differentially modulated by inhibition of translation initiation or elongation
Authors: Clay Khalyd J. , Yang Yongzhi , Petrascheck Michael
Published: January 2022

Recent work has revealed an increasingly important role for mRNA translation in maintaining proteostasis. Inhibiting translation protects from various proteostatic insults, including heat, expression of aggregation-prone proteins, or aging. However, multiple studies have come to differing conclusions about the mechanisms underlying the protective effects of translation inhibition. Here, we systematically lower translation either by pharmacologically inhibiting translation initiation or elongation and show that each step activates distinct protective responses in Caenorhabditis elegans. Targeting initiation triggers an HSF-1 dependent mechanism that protects from heat and age-associated protein misfolding but not from proteotoxicity caused by proteasome dysfunction. Conversely, targeting elongation triggers an HSF-1 independent mechanism that protects from heat and proteasome dysfunction but not from age-associated protein aggregation. Furthermore, while inhibiting translation initiation increases lifespan in wild-type worms, inhibiting translation elongation only extends lifespan when the animals exhibit preexisting proteotoxic stress—either as a result of aggregation-prone protein expression or hsf-1 deficiency. Together our findings suggest that organisms evolved complementary mechanisms that the mRNA translation machinery can trigger to restore proteostasis.
FiMO: Inferring the Temporal Order of Mutations on Clonal Phylogeny under Finite-sites Models
Authors: Agrawal Avesh Kumar , Zafar Hamim
Published: January 2022

Determining the temporal order of somatic mutations that drives cancer progression is essential for understanding the intra-tumor heterogeneity (ITH) and designing personalized therapy. Recently emerged single-cell DNA sequencing (SCS) technologies provide high-resolution datasets suitable for elucidating the temporal order of mutation. However, this task is challenged by technical artifacts associated with single-cell sequencing. While computational methods have been developed to account for these errors, these methods rely on using infinite sites assumption which gets violated in human cancers due to deletion, loss of heterozygosity and parallel mutations. Here, we propose a novel method FiMO, which employs a Bayesian frameowrk for inferring the temporal order of somatic mutations from noisy SCS mutational profiles under tumor evolutionary models that account for mutation recurrence and losses. Using synthetic datasets generated under a wide variety of settings, we show that FiMO outperforms the state-of-the-art methods in inferring the temporal order of mutations. We also applied FiMO on two experimental colon cancer datasets for inferring the temporal order of somatic mutations and quantifying their posterior probability. FiMO is publicly available at https://github.com/aveshag/FiMO.
Genome-wide association analysis identifies ancestry-specific genetic variation associated with medication response in the Study to Understand the Genetics of the Acute Response to Metformin and Glipizide in Humans (SUGAR-MGH)
Authors: Li Josephine H. , Brenner Laura N. , Kaur Varinderpal , Figueroa Katherine , Udler Miriam S. , Leong Aaron , Investigators MAGIC , Mercader Josep M. , Florez Jose C.
Published: January 2022

Background

Characterization of genetic variation that influences response to glucose-lowering medications is instrumental to precision medicine for treatment of type 2 diabetes (T2D). SUGAR-MGH examined the acute response to two anti-diabetes medications in order to understand the functional relevance of known T2D- and glycaemic trait-associated genetic loci.

Methods

1,000 participants at risk for T2D from diverse ancestries underwent sequential glipizide and metformin challenges. A genome-wide association study was performed using the Illumina Multi-Ethnic Genotyping Array. Imputation was performed with the TOPMed reference panel. Multiple linear regression using an additive model tested for association between variants and primary endpoints of drug response. We evaluated the influence of 804 unique T2D and glycaemic trait-associated variants on SUGAR-MGH outcomes and performed colocalization analyses to identify shared genetic signals.

Findings

Five genome-wide significant variants were associated with metformin or glipizide response. The strongest association was between an African ancestry-specific variant (minor allele frequency=0·026) at rs149403252 and lower fasting glucose following metformin, adjusted for baseline glucose (p=1·9×10−9), with a 0·94 mmol/L larger decrease in fasting glucose after metformin. We identified associations between T2D-associated variants and glycaemic response, including the T2D-protective C allele of rs703972 near ZMIZ1 and increased levels of active GLP-1 (p=1·6×10−5), supporting the role of alterations in incretin levels in T2D pathophysiology.

Interpretation

We present a well phenotyped, densely genotyped, multi-ancestry resource to study gene-drug interactions, uncover novel variation associated with response to common anti-diabetes medications, and provide insight into mechanisms of action of T2D-related variation.

Funding

US National Institutes of Health.
Over- and under-estimation of vaccine effectiveness
Authors: De-Leon Hilla , Aran Dvir
Published: January 2022

Background

The effectiveness of SARS-CoV-2 vaccines has been a subject of debate, with varying results reported in different studies, ranging from 60-95% vaccine effectiveness (VE). This range is striking when comparing two studies conducted in Israel at the same time, as one study reported VE of 90-95%, while the other study reported only ~80%. We argue that this variability is due to inadequate accounting for indirect protection provided by vaccines, which can block further transmission of the virus

Materials and Methods

We developed a novel analytic heterogenous infection model and extended our agent-based model of disease spread to allow for heterogenous interactions between vaccinated and unvaccinated across close-contacts and regions. We applied these models on real-world regional data from Israel from early 2021 to estimate VE using two common study designs: population-based and secondary infections

Results

Our results show that the estimated VE of a vaccine with efficacy of 85% can range from 70-95% depending on the interactions between vaccinated and unvaccinated individuals. Since different study designs capture different levels of interactions, we suggest that this interference explains the variability across studies. Finally, we propose a methodology for more accurate estimation without knowledge of interactions

Discussions and Conclusions

Our study highlights the importance of considering indirect protection when estimating vaccine effectiveness, explains how different study designs may report biased estimations, and propose a method to overcome this bias. We hope that our models will lead to more accurate understanding of the impact of vaccinations and inform public health policy.
Development and validation of personalised risk prediction models for early detection and diagnosis of primary liver cancer among the English primary care population using the QResearch® database: research protocol and statistical analysis plan
Authors: Liao Weiqi , Jepsen Peter , Coupland Carol , Innes Hamish , Matthews Philippa C. , Campbell Cori , Barnes Eleanor , Hippisley-Cox Julia ,   DeLIVER consortium
Published: January 2022

Background and research aim

The incidence and mortality of liver cancer have been increasing in recent years in the UK. However, liver cancer is still under-studied. The Early Detection of Hepatocellular Liver Cancer (DeLIVER-QResearch) project aims to address the research gap and generate new knowledge to improve early detection and diagnosis of primary liver cancer from general practice and at the population level. There are three research objectives: (1) to understand the current epidemiology of primary liver cancer in England, (2) to identify and quantify the symptoms and comorbidities associated with liver cancer, and (3) to develop and validate prediction models for early detection of liver cancer suitable for implementation in clinical settings.

Methods

This population-based study uses the QResearch® database (version 46) and includes patients aged 25-84 years old and without a diagnosis of liver cancer at the cohort entry (study period: 1 January 2008 to 31 December 2020). The team conducted a literature review (with additional clinical input) to inform the inclusion of variables for data extraction from the QResearch database. A wide range of statistical techniques will be used for the three research objectives, including descriptive statistics, multiple imputation for missing data, conditional logistic regression to investigate the association between the clinical features (symptoms and comorbidities) and the outcome, fractional polynomial terms to explore the non-linear relationship between continuous variables and the outcome, and Cox regression for the prediction model. We have a specific focus on the 1-year, 5-year, and 10-year absolute risks of developing liver cancer, as risks at different time points have different clinical implications. The internal-external validation approach will be used, and the discrimination and calibration of the prediction model will be evaluated.

Discussion

The DeLIVER-QResearch project uses large-scale representative population-based data to address the most relevant research questions for early detection and diagnosis of primary liver cancer in England. This project has great potential to inform the national cancer strategic plan and yield substantial public and societal benefits.

Medical Subject Headings (MeSH)

Liver Neoplasms; Carcinoma, Hepatocellular; Cholangiocarcinoma; Clinical Decision Rules; Early Detection of Cancer; Early Diagnosis; Symptom Assessment; Comorbidity
Comprehensive analysis of Histone deacetylases genes in the prognosis and immune infiltration of glioma patients
Authors: Liu Aibin , Li Yanyan , Shen Lin , Li Na , Shen Liangfang , Li Zhanzhan
Published: January 2022

The occurrence and development of tumors are closely related to histone deacetylases (HDACs). However, the overall biology and prognosis are still unknown in glioma. In the present study, we comprehensively explored the biology function and prognosis of eleven HDAC genes in glioma, which may contribute the more understanding of molecular mechanisms and potential therapeutic targets for glioma patients.We systematically described the expression files, molecular subtypes, prognostic value, immune filtration and tumor microenvironment and gene alteration, function and pathways enrichment, and drug sensitivity using TCGA and CGGA datasets. We developed and validated the prognostic model based on HDACs genes in glioma using LASSO, univariate, and multivariate cox regression. Receiver operating characteristic analyses were used for model evaluating. We also validated the expressions of HDACs genes included in the model in non-tumor and glioma tissues samples. Glioma patients can be divided into two subclasses based on eleven HDAC genes, and patients from two subclasses had markedly different survival outcomes. Then, using six HDAC genes (HDAC1, HDAC3, HDAC4, HDAC5, HDAC7, and HDAC9), we established a prognostic model in glioma patients, and this prognostic model was well validated in an independent cohort population. Furthermore, the calculated risk score from six HDACA genes expression was suggested to be an independent prognostic factor, which can predict the five-year overall survival of glioma patients well. High-risk patients can be attributed to multiple complex function and molecular signaling pathways, and the genes alterations of high- and low-risk patients were significantly different. We also found that different survival outcomes of high- and low-risk patients could be involved in the differences of immune filtration level and tumor microenvironment. Subsequently, we identified several small molecular compounds that could be favorable for glioma patients’ treatment. And finally, the expression levels of HDAC genes from prognostic model were validated in glioma and non-tumor tissues samples.Our results revealed the clinical utility and potential molecular mechanisms of HDAC genes in glioma. Model based on six HDAC genes can predict the overall survival of glioma patients well, which can be served as potential therapeutic targets.
Emergence of glycogen synthase kinase-3 interaction domain enhances phosphorylation of SARS-CoV-2 nucleocapsid protein
Authors: Yun Jun Seop , Kim Nam Hee , Song Hyeeun , Cha So Young , Hwang Kyu Ho , Lee Jae Eun , Jeong Cheol-Hee , Song Sang Hyun , Kim Seonghun , Cho Eunae Sandra , Kim Hyun Sil , Yook Jong In
Published: January 2022

A structural protein of SARS-CoV-2, nucleocapsid (N) protein is abundantly expressed during viral replication. The N protein is phosphorylated by glycogen synthase kinase (GSK)-3 on the serine/arginine (SR) rich motif located in disordered regions. Although phosphorylation by GSK-3β constitutes a critical event for viral replication, the molecular mechanism underlying N phosphorylation is not well understood. In this study, we found the putative alpha-helix L/FxxxL/AxxRL motif known as the GSK-3 interacting domain (GID), commonly found in many endogenous GSK-3β binding proteins, such as Axins, FRATs, WWOX and GSKIP. Indeed, N interacts with GSK-3β similarly to Axin, and Leu to Glu substitution of the GID abolished the interaction, with loss of N phosphorylation. Unlike with endogenous GID proteins, the N interaction neither disturbs endogenous GSK-3 activity nor regulates subsequent canonical Wnt activity and the Snail-EMT program. Notably, N abundance in SARS-CoV-2 is incomparably high compared to other coronaviruses, such as 229E, OC43 and HKU1. Compared to other coronaviruses, N harbors a CDK1 primed phosphorylation site and Gly-rich linker for enhanced phosphorylation by GSK-3β. Furthermore, we found that the S202R mutant found in Delta and R203K/G204R mutant found in the Omicron variant allows increased abundance and hyper-phosphorylation of N. Our observations suggest that the emergence of GID and mutations for increased phosphorylation in N may have contributed to the emergence of SARS-CoV-2 and evolution of variants, respectively. Further study, especially in a BSL3-equipped facility, is required to elucidate the functional importance of GID and N phosphorylation in SARS-CoV-2 and variants.
P38 kinases mediate NLRP1 inflammasome activation after ribotoxic stress response and virus infection
Authors: Jenster Lea-Marie , Lange Karl-Elmar , Normann Sabine , vom Hemdt Anja , Wuerth Jennifer D. , Schiffelers Lisa D.J. , Tesfamariam Yonas M. , Gohr Florian N. , Klein Laura , Kaltheuner Ines H. , Lapp Dorothee J. , Mayer Jacob , Moecking Jonas , Ploegh Hidde L. , Latz Eicke , Geyer Matthias , Kümmerer Beate M. , Schmidt Florian I.
Published: January 2022

Inflammasomes integrate cytosolic evidence of infection or damage to mount inflammatory responses. The inflammasome sensor NLRP1 is expressed in human keratinocytes and coordinates inflammation in the skin. We found that diverse stress signals converge on the activation of p38 kinases to initiate human NLRP1 inflammasome assembly: UV irradiation and microbial molecules that initiate the ribotoxic stress response critically relied on the MAP3 kinase ZAKα to activate p38 and ultimately human NLRP1. Infection with insect-transmitted alphaviruses, including Semliki Forest, Ross River, and Chikungunya virus, also activated NLRP1 in a p38-dependent manner. In the absence on ZAKα, inflammasome assembly was maintained, although at reduced levels, indicating contribution of other upstream kinases. NLRP1 activation by direct nanobody-mediated ubiquitination was independent of p38 activity. Stimulation of p38 by overexpression of MAP2 kinases MKK3 or MKK6 is sufficient for NLRP1 activation, and NLRP1 is directly phosphorylated by p38. Taken together, we define p38 activation as a unifying signaling hub that controls NLRP1 inflammasome activation by integrating a variety of cellular stress signals relevant to the skin.
The temporal and contextual stability of activity levels in hippocampal CA1 cells
Authors: Hayashi Yuichiro , Kobayakawa Ko , Kobayakawa Reiko
Published: January 2022

Recent long-term optical imaging studies have demonstrated that the activity levels of hippocampal neurons in a familiar environment change on a daily to weekly basis. However, it is unclear whether there is any time-invariant property in the cells’ neural representations. In this study, using miniature fluorescence microscopy, we measured the neural activity of the mouse hippocampus in four different environments every 3 days. Although the activity level of hippocampal neurons fluctuated greatly in each environment across days, we found a significant correlation between the activity levels for different days, and the correlation was higher for averaged activity levels across multiple environments. When the number of environments used for averaging was increased, a higher activity correlation was observed. Furthermore, the number of environments in which a cell showed activity was preserved. Cells that showed place cell activity in many environments had greater spatial information content, and thus carried a higher amount of information about the current position. In contrast, cells that were active only in a small number of environments provided sparse representation for the environment. These results suggest that each cell has not only an inherent activity level but also play a characteristic role in the coding of space.

Significance Statement

Recent studies have revealed that place cell activity in the hippocampal CA1 cells exhibit instability on a daily to weekly scale. However, it is unclear whether there is any invariant property in the activity of the cells. In this study, we found that, although the activity level of CA1 neurons fluctuated greatly in one environment, the mean activity level across multiple environments was more stable. Furthermore, the number of environments in which a cell showed activity was preserved over time. These results suggest that even though the spatial code changes dynamically, each cell has an inherent activity level and plays a characteristic role in spatial coding.
A novel neuroelectrophysiological age index implicates brain health and sleep disorders
Authors: Yook Soonhyun , Park Hea Ree , Park Claire , Park Gilsoon , Lim Diane C. , Kim Jinyoung , Joo Eun Yeon , Kim Hosung
Published: January 2022

Sleep architecture and microstructures alter with aging and sleep disorder-led accelerated aging. We proposed a sleep electroencephalogram (EEG) based brain age prediction model using convolutional neural networks. We then associated the estimated brain age index (BAI) with brain structural aging features, sleep disorders and various sleep parameters. Our model also showed a higher BAI (predicted brain age minus chronological age) is associated with cortical thinning in various functional areas. We found a higher BAI for sleep disorder groups compared to healthy sleepers, as well as significant differences in the spectral pattern of EEG among different sleep disorders (lower power in slow and ϑ waves for sleep apnea vs. higher power in β and σ for insomnia), suggesting sleep disorder-dependent pathomechanisms of aging. Our results demonstrate that the new EEG-BAI can be a biomarker reflecting brain health in normal and various sleep disorder subjects, and may be used to assess treatment efficacy.
Crystal structure of an RNA/DNA strand exchange junction
Authors: Cofsky Joshua C. , Knott Gavin J. , Gee Christine L. , Doudna Jennifer A.
Published: January 2022

Short segments of RNA displace one strand of a DNA duplex during diverse processes including transcription and CRISPR-mediated immunity and genome editing. These strand exchange events involve the intersection of two geometrically distinct helix types—an RNA:DNA hybrid (A-form) and a DNA:DNA homoduplex (B-form). Although previous evidence suggests that these two helices can stack on each other, it is unknown what local geometric adjustments could enable A-on-B stacking. Here we report the X-ray crystal structure of an RNA-5’/DNA-3’ strand exchange junction at an anisotropic resolution of 1.6 to 2.2 Å. The structure reveals that the A-to-B helical transition involves a combination of helical axis misalignment, helical axis tilting and compression of the DNA strand within the RNA:DNA helix, where nucleotides exhibit a mixture of A- and B-form geometry. These structural principles explain previous observations of conformational stability in RNA/DNA exchange junctions, enabling a nucleic acid architecture that is repeatedly populated during biological strand exchange events.
Genome-wide analysis identifies Homothorax and Extradenticle as regulators of insulin in Drosophila Insulin-Producing cells
Authors: Winant M. , Buhler K. , Clements J. , De Groef S. , Hens K. , Vulsteke V , Callaerts P.
Published: January 2022

Drosophila Insulin-Producing Cells (IPCs) are the main production site of the Drosophila Insulin-like peptides or Dilps which have key roles in regulating growth, development, reproduction, lifespan and metabolism. To better understand the signalling pathways and transcriptional networks that are active in the IPCs we queried publicly available transcriptome data of over 180 highly inbred fly lines for dilp expression and used this as the input for a Genome-wide association study (GWAS). This resulted in the identification of variants in 125 genes that were associated with variation in dilp expression. The function of 57 of these genes in the IPCs was tested using an RNAi-based approach. We found that IPC-specific depletion of most genes resulted in differences in expression of one or more of the dilps. We then elaborated further on homothorax, one of the candidate genes with the strongest effect on dilp expression. We found that Homothorax and its binding partner Extradenticle are involved in regulating dilp2, -3 and -5 expression and that genetic depletion of both transcription factors leads to phenotypes associated with reduced insulin signalling. Furthermore, we provide evidence that other transcription factors involved in eye development are also functional in the IPCs. In conclusion, we showed that this GWAS approach using gene expression levels as input identified genetic regulators implicated in IPC function and dilp expression.
Structural and mechanistic basis of σ-dependent transcriptional pausing
Authors: Pukhrambam Chirangini , Molodtsov Vadim , Kooshbaghi Mahdi , Tareen Ammar , Vu Hoa , Skalenko Kyle S. , Su Min , Zhou Yin , Winkelman Jared T. , Kinney Justin B. , Ebright Richard H. , Nickels Bryce E.
Published: January 2022

In σ-dependent transcriptional pausing, the transcription initiation factor σ, translocating with RNA polymerase (RNAP), makes sequence-specific protein-DNA interactions with a promoter-like sequence element in the transcribed region, inducing pausing. It has been proposed that, in σ-dependent pausing, the RNAP active center can access off-pathway “backtracked” states that are substrates for the transcript-cleavage factors of the Gre family, and on-pathway “scrunched” states that mediate pause escape. Here, using site-specific protein-DNA photocrosslinking to define positions of the RNAP trailing and leading edges and of σ relative to DNA at the λPR’ promoter, we show directly that σ-dependent pausing in the absence of GreB in vitro predominantly involves a state backtracked by 2-4 bp, and that σ-dependent pausing in the presence of GreB in vitro and in vivo predominantly involves a state scrunched by 2-3 bp. Analogous experiments with a library of 47 (∼16,000) transcribed-region sequences show that the state scrunched by 2-3 bp--and only that state--is associated with the consensus sequence, T-3N-2Y-1G+1, (where -1 corresponds to the position of the RNA 3’ end), which is identical to the consensus for pausing in initial transcription, and which is related to the consensus for pausing in transcription elongation. Experiments with heteroduplex templates show that sequence information at position T-3 resides in the DNA nontemplate strand. A cryo-EM structure of a complex engaged in σ-dependent pausing reveals positions of DNA scrunching on the DNA nontemplate and template strands and suggests that position T-3 of the consensus sequence exerts its effects by facilitating scrunching.
Biodiversity of the Genus Trichoderma in the Rhizosphere of Coffee (Coffea arabica) Plants in Ethiopia and their Potential Use in Biocontrol of Coffee Wilt Disease
Authors: Mulatu Afrasa , Megersa Negussie , Abena Tariku , Kanagarajan Selvaraju , Liu Qinsong , Alemu Tesfaye , Vetukuri Ramesh R.
Published: January 2022

The present study investigated the distribution status and biodiversity of Trichoderma species surveyed from coffee rhizosphere soil samples from Ethiopia and their potential for biocontrol of coffee wilt disease (CWD) caused by Fusarium xylarioides. Trichoderma isolates were identified based on molecular approaches and morphological characteristics followed by biodiversity analysis using different biodiversity indices. The antagonistic potential of Trichoderma isolates was evaluated against F. xylarioides using the dual confrontation technique and agar diffusion bioassays. A relatively high diversity of species was observed including 16 taxa and 11 undescribed isolates. Trichoderma asperellum, T. asperelloides and T. longibrachiatum were classified as abundant species, with dominance (Y) values of 0.062, 0.056 and 0.034, respectively. Trichoderma asperellum was the most abundant species (comprising 39.6% of all isolates) in all investigated coffee ecosystems. Shannon’s biodiversity index (H), the evenness (E), Simpson’s biodiversity index (D), and the abundance index (J) were calculated for each coffee ecosystem, revealing that species diversity and evenness were highest in the Jimma zone (H =1.97, E = 0.76, D = 0.91, J = 2.73). The average diversity values for Trichoderma species originating from the coffee ecosystem were H = 1.77, D = 0.7, E = 0.75 and J = 2.4. In vitro confrontation experiments revealed that T. asperellum AU131 and T. longibrachiatum AU158 reduced the mycelial growth of F. xylarioides by over 80%. The potential use of these Trichoderma species for disease management of F. xylarioides and to reduce its impact on coffee cultivation is discussed in relation to Ethiopia’s ongoing coffee wilt disease crisis.
Analysis of non-coding RNAs in Methylorubrum extorquens reveals a novel small RNA specific to Methylobacteriaceae
Authors: Boutet Emilie , Djerroud Samia , Smail Katia , Lorain Marie-Josée , Wu Meiqun , Lamarche Martin , Imane Roqaya , Miguez Carlos , Perreault Jonathan
Published: January 2022

Methylorubrum extorquens metabolizes methanol, a cheap raw material that can be derived from waste. It is a facultative methylotroph, making it a model organism to study the metabolism of one carbon compounds. Despite a considerable interest to exploit this bacteria as a biotechnological tool in a methanol-based bioeconomy, little is known about its non-coding sRNA. Small RNAs play well-documented essential roles in Escherichia coli for post-transcriptional regulation; and have important functions in many bacteria, including other Alphaproteobacteria like Agrobacterium tumefaciens. M. extorquens is expected to contain many sRNAs, especially since it also encodes for the protein Hfq, a chaperone protein important in the interaction between sRNAs and their target, but also critical for the stabilization of sRNAs themselves. Few sRNAs are annotated in the genome of this Alphaproteobacteria and they were never validated. In this study, formerly annotated sRNAs ffh, CC2171, BjrC1505 were confirmed by Northern blot, validating the expression of sRNAs in M. extorquens. Moreover, analysis of RNA-sequencing data established a considerable list of potential sRNAs. Interesting candidates selected after bioinformatic analysis were tested by Northern blot, revealing a novel sRNA specific to Methylobacteriaceae, sRNA Met2624. Its expression patterns and genomic context were analyzed. This research is the first experimental validation of sRNAs in M. extorquens and paves the way for other sRNA discoveries.
Hippocampal delta oscillations entrain neuronal activity, modulate gamma amplitude and convey information about running speed on a treadmill
Authors: Furtunato Alan MB , Pedrosa Rafael , Lobão-Soares Bruno , Tort Adriano BL , Belchior Hindiael
Published: January 2022

Locomotion has long been associated with rhythmic oscillations in the rat hippocampus. Running speed and acceleration affect the spectral density at the theta (6-10 Hz) and gamma (30-150 Hz) bands and the rhythmic entrainment of neuronal activity. However, less is known about other oscillatory rhythms. Recent studies have shown that oscillatory activity in the delta (1-4 Hz) band also relates to locomotion in stationary conditions, such as running on a treadmill or in a running wheel. To further investigate the effects of stationary running on hippocampal oscillations, we recorded CA1 local field potentials and neuronal activity while rats ran at different speed protocols on a treadmill. We found a remarkable oscillatory activity at 2 Hz that was strongly modulated by running speed. Delta power and peak frequency were highest at the fastest running speed, both in constant and progressively increasing speed protocols. Delta and theta oscillations co-occurred and showed independent relationships in their instantaneous power and frequency. Moreover, the delta phase modulated the amplitude of low-gamma (20-50 Hz) oscillations and the spiking activity of putative pyramidal neurons in a speed-dependent manner. Finally, spectral components in the delta frequency range, but not theta, predicted running speed using a naive Bayes classifier. In summary, our study shows that locomotion-related delta oscillations convey information about stationary running speed and coordinate hippocampal rhythmic activity in a speed-dependent manner.

Statement of significance

Theta and gamma oscillations are hallmarks of rhythmic activity in the rat hippocampus during locomotion and exploratory behaviors, but less is known about other oscillatory rhythms. This study shows the emergence of delta (∼2 Hz) oscillations in the dorsal CA1 of rats running on a treadmill. Locomotion-related delta oscillations are independent of the concomitant theta activity and convey information about running speed. Delta waves modulate low-gamma oscillations and the spiking activity of pyramidal neurons in a speed-dependent way. These results suggest that oscillatory activity in the delta band aids rhythmic coordination during stationary locomotor behaviors.
Cullin-5 regulates nuclear positioning and reveals insights on the sensing of the nuclear-to-cytoplasmic ratio in Drosophila embryogenesis
Authors: Hayden Luke , Chao Anna , Deneke Victoria E. , Puliafito Alberto , Di Talia Stefano
Published: January 2022

In most metazoans, early embryonic development is characterized by rapid division cycles which pause before gastrulation at the mid-blastula transition (MBT).1 These early cleavage divisions are accompanied by cytoskeletal rearrangements which ensure proper nuclear positioning. Yet, the molecular mechanisms controlling nuclear positioning are not fully elucidated. In Drosophila, early embryogenesis unfolds in a multinucleated syncytium, and nuclei rapidly move across the anterior-posterior (AP) axis at cell cycles 4-6 in a process driven by actomyosin contractility and cytoplasmic flows.2,3 Previously, shackleton (shkl) mutants were identified in which this axial spreading is impaired.4 Here, we show that shkl mutants carry mutations in the cullin-5 (cul-5) gene. Live imaging experiments show that Cul-5 is downstream of the cell cycle but required for cortical actomyosin contractility. The nuclear spreading phenotype of cul-5 mutants can be rescued by reducing Src activity genetically, suggesting that a major target of Cul-5 is Src kinase. cul-5 mutants display gradients of nuclear density across the AP axis at the MBT which we exploit to study cell cycle control as a function of the N/C ratio. We found that the N/C ratio is sensed collectively in neighborhoods of about 100μm and such collective sensing is required for a precise MBT in which all the nuclei in the embryo pause their division cycle. Moreover, we found that the response to the N/C ratio is slightly graded along the AP axis. These two features can be linked to the spatiotemporal regulation of Cdk1 activity. Collectively, our results reveal a new pathway controlling nuclear spreading and provide a quantitative dissection of how nuclear cycles respond to the N/C ratio.
Manganese excess and deficiency affects photosynthesis and metabolism in Marchantia polymorpha
Authors: Messant Marine , Hennebelle Thaïs , Guérard Florence , Gakière Bertrand , Gall Andrew , Thomine Sébastien , Krieger-Liszkay Anja
Published: January 2022

Manganese is an essential metal for plant growth. The most important Mn-containing enzyme is the Mn4CaO5 cluster that catalyses water oxidation in Photosystem II. Mn deficiency primarily affects photosynthesis, while Mn excess is generally toxic. Mn excess and deficiency were studied in the liverwort Marchantia polymorpha, an emerging model ideally suited for analysis of metal stress since it accumulates rapidly toxic substances due to the absence of well-developed vascular and radicular systems and a reduced cuticle. We established growth conditions for Mn excess and deficiency, performed analysis of metal content in thalli and isolated chloroplasts and determined metabolites. Metabolome analysis revealed a strong accumulation of N-methylalanine upon exposure to Mn excess and a different response of Marchantia to heavy metal stress than that known for higher plants. We investigated photosynthetic performance by chlorophyll fluorescence at room temperature and at 77K, P700 absorption and by studying the susceptibility of thalli to photoinhibition. In vivo super-resolution fluorescence microscopy was used to visualize changes in the organization of the thylakoid membrane under Mn excess and deficiency. Non-optimal Mn concentrations changed the ratio of photosystem I to photosystem II and altered the organisation of thylakoid membranes. Mn deficiency seems to favour cyclic electron flow around photosystem I protecting thereby photosystem II against photoinhibition.
Variability in sampling of cortex-wide neural dynamics explains individual differences in functional connectivity and behavioral phenotype
Authors: MacDowell Camden J. , Briones Brandy A. , Lenzi Michael J. , Gustison Morgan L. , Buschman Timothy J.
Published: January 2022

Individual differences in behavior are associated with changes in the correlation of neural activity between brain areas. Such differences in ‘functional connectivity’ are thought to reflect individual differences in brain structure that alter the flow of neural activity between regions. Here, in contrast, we show that individual differences in functional connectivity and behavior can be explained by differences in how frequently an individual expresses distinct cortex-wide spatiotemporal patterns of neural activity. This suggests variability in sampling of cortex-wide neural dynamics may underlie individuals’ unique behavioral phenotypes.
Modeling the longitudinal changes of ancestry diversity in the Million Veteran Program
Authors: Wendt Frank R , Pathak Gita A , Vahey Jacqueline , Qin Xuejun , Koller Dora , Cabrera-Mendoza Brenda , Haeny Angela , Harrington Kelly M , Rajeevan Nallakkandi , Duong Linh M , Levey Daniel F , De Angelis Flavio , De Lillo Antonella , Bigdeli Tim B , Pyarajan Saiju ,   VA Million Veteran Program, Gaziano J. Michael , Gelernter Joel , Aslan Mihaela , Provenzale Dawn , Helmer Drew A. , Hauser Elizabeth R. , Polimanti Renato ,   Department of Veteran Affairs Cooperative Study Program (#2006)
Published: January 2022

The Million Veteran Program (MVP) participants represent 100 years of US history, including significant social and demographic change over time. Our study assessed two aspects of the MVP: (i) longitudinal changes in population diversity and (ii) how these changes can be accounted for in genome-wide association studies (GWAS). The MVP was divided into five birth cohorts (N-range=123,888 [born from 1943-1947] to 136,699 [born from 1948-1953]). Groups of participants were defined by (i) HARE (harmonized ancestry and race/ethnicity) and (ii) a random-forest clustering approach using the 1000 Genomes Project and the Human Genome Diversity Project (1kGP+HGDP) reference panels (77 world populations representing six continental groups). In these groups, we performed GWASs of height, a trait potentially affected by population stratification. Birth cohorts demonstrate important trends in ancestry diversity over time. More recent HARE-assigned Europeans, Africans, and Hispanics had lower European ancestry proportions than older birth cohorts (0.010<Cohen’s d<0.259, p<7.80×10−4). Conversely, HARE-assigned East Asians showed an increase in European ancestry proportion over time. In GWAS of height using HARE assignments, genomic inflation due to population stratification was prevalent across all birth cohorts (linkage disequilibrium score regression intercept=1.08±0.042). The 1kGP+HGDP-based ancestry assignment significantly reduced the population stratification (mean intercept reduction=0.045±0.007, p<0.05) confounding in the GWAS statistics. This study provides a comprehensive characterization of ancestry diversity of the MVP cohort over time and highlights that more refined modeling of genetic diversity (e.g., the 1kGP+HGDP-based ancestry assignment) can more accurately capture the polygenic architecture of traits and diseases that could be affected by population stratification.
Rhythm of The Night (and Day): Predictive metabolic modeling of circadian growth in Chlamydomonas
Authors: Metcalf Alex J. , Boyle Nanette R.
Published: January 2022

Algal cells experience strong circadian rhythms under diurnal light, with regular changes in both biomass composition and transcriptomic environment. However, most metabolic models – critical tools for bioengineering organisms – assume a steady state. The conflict between these assumptions and the reality of the cellular environment make such models inappropriate for algal cells, creating a significant obstacle in engineering cells that are viable under natural light. By transforming a set of discreet transcriptomic measurements from synchronized Chlamydomonas cells grown in a 12/12 diel light regime (1) into continuous curves, we produced a complete representation of the cell’s transcriptome that can be interrogated at any arbitrary timepoint. We clustered these curves, in order to find genes that were expressed in similar patterns, and then also used it to build a metabolic model that can accumulate and catabolize different biomass components over the course of a day. This model predicts qualitative phenotypical outcomes for the sta6 mutant, including excess lipid accumulation (2) and a failure to thrive when grown diurnally in minimal media (3), representing a qualitative prediction of phenotype from genotype even under dynamic conditions. We also extended this approach to simulate all single-knockout mutants with genes represented in the model and identified potential targets for rational engineering efforts.

SIGNIFICANCE STATEMENT

We have developed the first transient metabolic model for diurnal growth of algae based on experimental data and capable of predicting phenotype from genotype. This model enables us to evaluate the impact of genetic and environmental changes on the growth, biomass composition and intracellular fluxes of the model green alga, Chlamydomonas reinhardtii. The availability of this model will enable faster and more efficient design of cells for production of fuels, chemicals and pharmaceuticals.
Exploring repeats in rice genomes: Identification, Characterization and its Applications
Authors: Das Gourab , Ghosh Indira
Published: January 2022

Biodiversity is a fundamental property of all natural systems existing in the field biology. It refers to the underlying heterogeneity at different levels of ecology, genetics and evolution. In case of plant systems, dramatic variability has been observed during the Anthropocene at different spatial scales. Environmental stress is one of the major influencing factors behind this plant biodiversity. Huge genetic diversity has been also demonstrated across varieties of important crop species like rice. Repetitive sequences which are a major contributor of genomic diversity in polyploidy plants have been found to occur ubiquitously in their genomes. To date diverse repeat types have been characterized in the plant genomes performing various functions starting from qualitative trait markers to genome evolution and stress management. With an objective to identify of plant stress associated genes using DNA repeat probes, a robust method has been developed. The method has been modularized into three distinct sections. First part is dedicated for identification of different types of repeats. Earlier review has suggested building a pipeline of multiples tools for capturing different types of repeats from the genome sequences. Specialized tools like TROLL, Tandem repeat finder (TRF), PHOBOS and database like REPBASE have been selected for performing this job. Second module is intended for screening of stress related genes from the published articles and databases and the last module has been designed for the association mining between genomic repetitive patterns with stress phenotypes. The method has been used to explore stress associated repeats from 9 Oryza species from different continents and other plants like Arabidopsis and Brachypodium. In case of Oryza species distribution repeats has been found to be significantly different between stress associated and housekeeping genes. More than 55% of the repeats are found to be in positive association (nPMI > 0) whereas 26% of the repeats are false-positives. These repetitive probes have been utilized in several applications. Firstly, using as molecular markers to identify stress related genes in different Oryza species where availability is limited. Secondly, using as a probe to reanalyzing the evolutionary lineage of Oryza species etc.